From 5817974f6548451b9b6b78efd8234f920a37cf34 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Tue, 13 Dec 2022 12:24:50 +0100 Subject: [PATCH 001/162] BAOA integrator for extended lagrangian According to Kieninger and Keller, JCTC 2022 https://doi.org/10.1021/acs.jctc.2c00585 Add comments on reflective BC implementation explain why current implementation is OK. --- src/colvar.cpp | 51 +++++++++++++++++++++++++++++++++----------------- 1 file changed, 34 insertions(+), 17 deletions(-) diff --git a/src/colvar.cpp b/src/colvar.cpp index fd5d73ee7..87a247955 100644 --- a/src/colvar.cpp +++ b/src/colvar.cpp @@ -693,7 +693,9 @@ int colvar::init_extended_Lagrangian(std::string const &conf) enable(f_cv_Langevin); ext_gamma *= 1.0e-3; // correct as long as input is required in ps-1 and cvm::dt() is in fs // Adjust Langevin sigma for slow time step if time_step_factor != 1 - ext_sigma = cvm::sqrt(2.0 * proxy->boltzmann() * temp * ext_gamma * ext_mass / (cvm::dt() * cvm::real(time_step_factor))); + // Eq. (6a) in https://doi.org/10.1021/acs.jctc.2c00585 + ext_sigma = cvm::sqrt((1.0 - cvm::exp(-2.0 * ext_gamma * cvm::dt() * cvm::real(time_step_factor))) + * ext_mass * proxy->boltzmann() * temp); } get_keyval_feature(this, conf, "reflectingLowerBoundary", f_cv_reflecting_lower_boundary, false); @@ -1820,9 +1822,11 @@ void colvar::update_extended_Lagrangian() f += fb_actual; } - fr = f; - // External force has been scaled for a 1-timestep impulse, scale it back because we will - // integrate it with the colvar's own timestep factor + // fr: bias force on extended variable (without harmonic spring), for output in trajectory + fr = f; + + // External force has been scaled for an inner-timestep impulse (for the back-end integrator) + // here we scale it back because this integrator uses only the outer (long) timestep f_ext = f / cvm::real(time_step_factor); colvarvalue f_system(fr.type()); // force exterted by the system on the extended DOF @@ -1835,15 +1839,14 @@ void colvar::update_extended_Lagrangian() } else { // the total force is applied to the fictitious mass, while the // atoms only feel the harmonic force + wall force - // fr: bias force on extended variable (without harmonic spring), for output in trajectory // f_ext: total force on extended variable (including harmonic spring) // f: - initially, external biasing force // - after this code block, colvar force to be applied to atomic coordinates // ie. spring force (fb_actual will be added just below) f_system = (-0.5 * ext_force_k) * this->dist2_lgrad(x_ext, x); f = -1.0 * f_system; - // Coupling force is a slow force, to be applied to atomic coords impulse-style - // over a single MD timestep + // Coupling force will be applied to atomic coords impulse-style + // over an inner timestep of the back-end integrator f *= cvm::real(time_step_factor); } f_ext += f_system; @@ -1863,26 +1866,34 @@ void colvar::update_extended_Lagrangian() prev_x_ext = x_ext; prev_v_ext = v_ext; - // leapfrog: starting from x_i, f_i, v_(i-1/2) - v_ext += (0.5 * dt) * f_ext / ext_mass; - // Because of leapfrog, kinetic energy at time i is approximate - kinetic_energy = 0.5 * ext_mass * v_ext * v_ext; - potential_energy = 0.5 * ext_force_k * this->dist2(x_ext, x); - // leap to v_(i+1/2) + // BAOA (GSD) integrator https://doi.org/10.1021/acs.jctc.2c00585 + // variant that reduces to leapfrog when gamma = 0 + + // starting from x_t, f_t, v_(t-1/2) + // Eq. (10a) + v_ext += dt * f_ext / ext_mass; + + // Half step in position (10b) + x_ext += dt * v_ext / 2.0; + + // leap to v_(i+1/2) (10c) if (is_enabled(f_cv_Langevin)) { - v_ext -= dt * ext_gamma * v_ext; + v_ext -= (1.0 - cvm::exp(- 1.0 * dt * ext_gamma)) * v_ext; colvarvalue rnd(x); rnd.set_random(); + // ext_sigma has been computed at init time according to (10c) v_ext += dt * ext_sigma * rnd / ext_mass; } - v_ext += (0.5 * dt) * f_ext / ext_mass; - x_ext += dt * v_ext; + // Second half step in position (10d) + x_ext += dt * v_ext / 2.0; cvm::real delta = 0; // Length of overshoot past either reflecting boundary if ((is_enabled(f_cv_reflecting_lower_boundary) && (delta = x_ext - lower_boundary) < 0) || (is_enabled(f_cv_reflecting_upper_boundary) && (delta = x_ext - upper_boundary) > 0)) { + // Reflect arrival position x_ext -= 2.0 * delta; - v_ext *= -1.0; + // Bounce happened on average at t+1/2 -> reflect velocity at t+1/2 + v_ext = -0.5 * (prev_v_ext + v_ext); if ((is_enabled(f_cv_reflecting_lower_boundary) && (x_ext - lower_boundary) < 0.0) || (is_enabled(f_cv_reflecting_upper_boundary) && (x_ext - upper_boundary) > 0.0)) { cvm::error("Error: extended coordinate value " + cvm::to_str(x_ext) + " is still outside boundaries after reflection.\n"); @@ -1891,11 +1902,17 @@ void colvar::update_extended_Lagrangian() x_ext.apply_constraints(); this->wrap(x_ext); + if (is_enabled(f_cv_external)) { // Colvar value is constrained to the extended value x = x_ext; cvcs[0]->set_value(x_ext); } + + // Final v_ext lags behind x_ext by half a timestep + // so kinetic energy is slightly off + kinetic_energy = 0.5 * ext_mass * v_ext * v_ext; + potential_energy = 0.5 * ext_force_k * this->dist2(x_ext, x); } From 78649795f5d3a4a5b37379f53655fced552ef65b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Fri, 16 Dec 2022 18:23:04 +0100 Subject: [PATCH 002/162] Refine BAOA integrator --- doc/colvars-code-refs.bib | 34 ++++++++++++++++-------- src/colvar.cpp | 25 ++++++++++-------- src/colvarmodule_refs.h | 54 +++++++++++++++++++++++++-------------- 3 files changed, 72 insertions(+), 41 deletions(-) diff --git a/doc/colvars-code-refs.bib b/doc/colvars-code-refs.bib index 4c5595c86..6aa885010 100644 --- a/doc/colvars-code-refs.bib +++ b/doc/colvars-code-refs.bib @@ -11,6 +11,19 @@ @article{Abraham2015 url = {https://doi.org/10.1016/j.softx.2015.06.001} } +% BAOA integrator +@article{BouRabee2010, + doi = {10.1137/090758842}, + url = {https://doi.org/10.1137/090758842}, + year = {2010}, + volume = {48}, + number = {1}, + pages = {278--297}, + author = {Nawaf Bou-Rabee and Houman Owhadi}, + title = {Long-Run Accuracy of Variational Integrators in the Stochastic Context}, + journal = {{SIAM} Journal on Numerical Analysis} +} + % reweightaMD colvar bias implementation (NAMD) @article{Chen2021, author = {Chen, Haochuan and Fu, Haohao and Chipot, Christophe and Shao, Xueguang and Cai, Wensheng}, @@ -194,6 +207,16 @@ @article{Henin2010 url = {https://doi.org/10.1021/ct9004432} } +% Poisson integration of 2D/3D free energy surfaces +@Article{Henin2021, + author = {H\'enin, J.}, + journal = {J. Chem. Theory Comput.}, + title = {Fast and accurate multidimensional free energy integration}, + year = {2021}, + doi = {10.1021/acs.jctc.1c00593}, + url = {https://doi.org/10.1021/acs.jctc.1c00593}, +} + % VMD engine @article{Humphrey1996, title = {{VMD}: visual molecular dynamics}, @@ -222,16 +245,6 @@ @article{Lesage2017 url = {https://doi.org/10.1021/acs.jpcb.6b10055} } -% Poisson integration of 2D/3D free energy surfaces -@Article{Henin2021, - author = {H\'enin, J.}, - journal = {J. Chem. Theory Comput.}, - title = {Fast and accurate multidimensional free energy integration}, - year = {2021}, - doi = {10.1021/acs.jctc.1c00593}, - url = {https://doi.org/10.1021/acs.jctc.1c00593}, -} - % Ensemble-biased metadynamics (ebMetaD) @article{Marinelli2015, author = {Marinelli, Fabrizio and Faraldo-G\'omez, Jos\'e D.}, @@ -319,7 +332,6 @@ @article{White2014 % --- NO CITATIONS AVAILABLE YET FOR THESE FEATURES --- % Colvars-GROMACS interface -% Colvars Dashboard (Colvars-VMD graphical user interface) % gspath colvar component % gzpath colvar component % linearCombination colvar component diff --git a/src/colvar.cpp b/src/colvar.cpp index 87a247955..e50c3ba34 100644 --- a/src/colvar.cpp +++ b/src/colvar.cpp @@ -691,6 +691,7 @@ int colvar::init_extended_Lagrangian(std::string const &conf) } if (ext_gamma != 0.0) { enable(f_cv_Langevin); + cvm::main()->cite_feature("BAOA integrator"); ext_gamma *= 1.0e-3; // correct as long as input is required in ps-1 and cvm::dt() is in fs // Adjust Langevin sigma for slow time step if time_step_factor != 1 // Eq. (6a) in https://doi.org/10.1021/acs.jctc.2c00585 @@ -1866,17 +1867,21 @@ void colvar::update_extended_Lagrangian() prev_x_ext = x_ext; prev_v_ext = v_ext; - // BAOA (GSD) integrator https://doi.org/10.1021/acs.jctc.2c00585 - // variant that reduces to leapfrog when gamma = 0 - + // BAOA (GSD) integrator as formulated in https://doi.org/10.1021/acs.jctc.2c00585 // starting from x_t, f_t, v_(t-1/2) - // Eq. (10a) - v_ext += dt * f_ext / ext_mass; - // Half step in position (10b) + // [B] Eq. (10a) split into two half-steps + // This reduces to leapfrog when gamma = 0 + v_ext += 0.5 * dt * f_ext / ext_mass; + // Kinetic energy at t + kinetic_energy = 0.5 * ext_mass * v_ext * v_ext; + v_ext += 0.5 * dt * f_ext / ext_mass; + // Final v_ext lags behind x_ext by half a timestep + + // [A] Half step in position (10b) x_ext += dt * v_ext / 2.0; - // leap to v_(i+1/2) (10c) + // [O] leap to v_(i+1/2) (10c) if (is_enabled(f_cv_Langevin)) { v_ext -= (1.0 - cvm::exp(- 1.0 * dt * ext_gamma)) * v_ext; colvarvalue rnd(x); @@ -1884,7 +1889,7 @@ void colvar::update_extended_Lagrangian() // ext_sigma has been computed at init time according to (10c) v_ext += dt * ext_sigma * rnd / ext_mass; } - // Second half step in position (10d) + // [A] Second half step in position (10d) x_ext += dt * v_ext / 2.0; cvm::real delta = 0; // Length of overshoot past either reflecting boundary @@ -1909,9 +1914,7 @@ void colvar::update_extended_Lagrangian() cvcs[0]->set_value(x_ext); } - // Final v_ext lags behind x_ext by half a timestep - // so kinetic energy is slightly off - kinetic_energy = 0.5 * ext_mass * v_ext * v_ext; + // Only compute potential energy once BC and constraints have been applied potential_energy = 0.5 * ext_force_k * this->dist2(x_ext, x); } diff --git a/src/colvarmodule_refs.h b/src/colvarmodule_refs.h index c3fccf297..b3f584242 100644 --- a/src/colvarmodule_refs.h +++ b/src/colvarmodule_refs.h @@ -14,6 +14,22 @@ " url = {https://doi.org/10.1016/j.softx.2015.06.001}\n" "}\n"; + paper_count_[std::string("BouRabee2010")] = 0; + paper_url_[std::string("BouRabee2010")] = "https://doi.org/10.1137/090758842"; + paper_bibtex_[std::string("BouRabee2010")] = + "\n" + "@article{BouRabee2010,\n" + " doi = {10.1137/090758842},\n" + " url = {https://doi.org/10.1137/090758842},\n" + " year = {2010},\n" + " volume = {48},\n" + " number = {1},\n" + " pages = {278--297},\n" + " author = {Nawaf Bou-Rabee and Houman Owhadi},\n" + " title = {Long-Run Accuracy of Variational Integrators in the Stochastic Context},\n" + " journal = {{SIAM} Journal on Numerical Analysis}\n" + "}\n"; + paper_count_[std::string("Chen2021")] = 0; paper_url_[std::string("Chen2021")] = "https://doi.org/10.1021/acs.jctc.1c00103"; paper_bibtex_[std::string("Chen2021")] = @@ -182,6 +198,19 @@ " url = {https://doi.org/10.1021/ct9004432}\n" "}\n"; + paper_count_[std::string("Henin2021")] = 0; + paper_url_[std::string("Henin2021")] = "https://doi.org/10.1021/acs.jctc.1c00593"; + paper_bibtex_[std::string("Henin2021")] = + "\n" + "@Article{Henin2021,\n" + " author = {H\\'enin, J.},\n" + " journal = {J. Chem. Theory Comput.},\n" + " title = {Fast and accurate multidimensional free energy integration},\n" + " year = {2021},\n" + " doi = {10.1021/acs.jctc.1c00593},\n" + " url = {https://doi.org/10.1021/acs.jctc.1c00593},\n" + "}\n"; + paper_count_[std::string("Humphrey1996")] = 0; paper_url_[std::string("Humphrey1996")] = "https://doi.org/10.1016/0263-7855(96)00018-5"; paper_bibtex_[std::string("Humphrey1996")] = @@ -215,19 +244,6 @@ " url = {https://doi.org/10.1021/acs.jpcb.6b10055}\n" "}\n"; - paper_count_[std::string("Henin2021")] = 0; - paper_url_[std::string("Henin2021")] = "https://doi.org/10.1021/acs.jctc.1c00593"; - paper_bibtex_[std::string("Henin2021")] = - "\n" - "@Article{Henin2021,\n" - " author = {H\\'enin, J.},\n" - " journal = {J. Chem. Theory Comput.},\n" - " title = {Fast and accurate multidimensional free energy integration},\n" - " year = {2021},\n" - " doi = {10.1021/acs.jctc.1c00593},\n" - " url = {https://doi.org/10.1021/acs.jctc.1c00593},\n" - "}\n"; - paper_count_[std::string("Marinelli2015")] = 0; paper_url_[std::string("Marinelli2015")] = "https://doi.org/10.1016/j.bpj.2015.05.024"; paper_bibtex_[std::string("Marinelli2015")] = @@ -335,6 +351,9 @@ feature_count_[std::string("GROMACS engine")] = 0; feature_paper_map_[std::string("GROMACS engine")] = "Abraham2015"; + feature_count_[std::string("BAOA integrator")] = 0; + feature_paper_map_[std::string("BAOA integrator")] = "BouRabee2010"; + feature_count_[std::string("reweightaMD colvar bias implementation (NAMD)")] = 0; feature_paper_map_[std::string("reweightaMD colvar bias implementation (NAMD)")] = "Chen2021"; @@ -500,6 +519,9 @@ feature_count_[std::string("Internal-forces free energy estimator")] = 0; feature_paper_map_[std::string("Internal-forces free energy estimator")] = "Henin2010"; + feature_count_[std::string("Poisson integration of 2D/3D free energy surfaces")] = 0; + feature_paper_map_[std::string("Poisson integration of 2D/3D free energy surfaces")] = "Henin2021"; + feature_count_[std::string("VMD engine")] = 0; feature_paper_map_[std::string("VMD engine")] = "Humphrey1996"; @@ -509,9 +531,6 @@ feature_count_[std::string("CZAR eABF estimator")] = 0; feature_paper_map_[std::string("CZAR eABF estimator")] = "Lesage2017"; - feature_count_[std::string("Poisson integration of 2D/3D free energy surfaces")] = 0; - feature_paper_map_[std::string("Poisson integration of 2D/3D free energy surfaces")] = "Henin2021"; - feature_count_[std::string("Ensemble-biased metadynamics (ebMetaD)")] = 0; feature_paper_map_[std::string("Ensemble-biased metadynamics (ebMetaD)")] = "Marinelli2015"; @@ -539,9 +558,6 @@ feature_count_[std::string("Colvars-GROMACS interface")] = 0; feature_paper_map_[std::string("Colvars-GROMACS interface")] = "n/a"; - feature_count_[std::string("Colvars Dashboard (Colvars-VMD graphical user interface)")] = 0; - feature_paper_map_[std::string("Colvars Dashboard (Colvars-VMD graphical user interface)")] = "n/a"; - feature_count_[std::string("gspath colvar component")] = 0; feature_paper_map_[std::string("gspath colvar component")] = "n/a"; From ad5459b82db8b0263dae9d1fbff963023ec28b41 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Tue, 4 Apr 2023 17:36:30 +0200 Subject: [PATCH 003/162] Fix extra factor of dt in BAOA update --- src/colvar.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/colvar.cpp b/src/colvar.cpp index e50c3ba34..3dd9989bc 100644 --- a/src/colvar.cpp +++ b/src/colvar.cpp @@ -697,6 +697,8 @@ int colvar::init_extended_Lagrangian(std::string const &conf) // Eq. (6a) in https://doi.org/10.1021/acs.jctc.2c00585 ext_sigma = cvm::sqrt((1.0 - cvm::exp(-2.0 * ext_gamma * cvm::dt() * cvm::real(time_step_factor))) * ext_mass * proxy->boltzmann() * temp); + } else { + ext_sigma = 0.0; } get_keyval_feature(this, conf, "reflectingLowerBoundary", f_cv_reflecting_lower_boundary, false); @@ -1883,11 +1885,10 @@ void colvar::update_extended_Lagrangian() // [O] leap to v_(i+1/2) (10c) if (is_enabled(f_cv_Langevin)) { - v_ext -= (1.0 - cvm::exp(- 1.0 * dt * ext_gamma)) * v_ext; colvarvalue rnd(x); rnd.set_random(); // ext_sigma has been computed at init time according to (10c) - v_ext += dt * ext_sigma * rnd / ext_mass; + v_ext = cvm::exp(- 1.0 * dt * ext_gamma) * v_ext + ext_sigma * rnd / ext_mass; } // [A] Second half step in position (10d) x_ext += dt * v_ext / 2.0; From d1be814ceb85584cd6c9a389d3d17c0c9384e7d1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Wed, 5 Apr 2023 22:58:51 +0200 Subject: [PATCH 004/162] Fix colvar energy computation --- src/colvar.cpp | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/colvar.cpp b/src/colvar.cpp index 3dd9989bc..af101ca51 100644 --- a/src/colvar.cpp +++ b/src/colvar.cpp @@ -1877,6 +1877,10 @@ void colvar::update_extended_Lagrangian() v_ext += 0.5 * dt * f_ext / ext_mass; // Kinetic energy at t kinetic_energy = 0.5 * ext_mass * v_ext * v_ext; + + // Potential energy at t + potential_energy = 0.5 * ext_force_k * this->dist2(x_ext, x); + v_ext += 0.5 * dt * f_ext / ext_mass; // Final v_ext lags behind x_ext by half a timestep @@ -1914,9 +1918,6 @@ void colvar::update_extended_Lagrangian() x = x_ext; cvcs[0]->set_value(x_ext); } - - // Only compute potential energy once BC and constraints have been applied - potential_energy = 0.5 * ext_force_k * this->dist2(x_ext, x); } From 331d7f86770c54d6cae0c3bdb657ed869968d288 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Wed, 26 Jul 2023 11:44:39 +0200 Subject: [PATCH 005/162] Update NAMD regression test results --- .../AutoDiff/test.colvars.out | 64 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 66 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../000_alpha_harmonic-fixed/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 52 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 54 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../000_angle_harmonic-fixed/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 46 +- 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.../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 6 +- .../AutoDiff/test.colvars.traj | 2 +- .../AutoDiff/test.histogram1.dat | 146 +- .../AutoDiff/test.restart.colvars.out | 6 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 18 +- .../AutoDiff/test.restart.histogram1.dat | 146 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 67 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 44 +- .../AutoDiff/test.restart.colvars.out | 69 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 44 +- .../000_dihedralwalls/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 53 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 55 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 41 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 43 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.one.corrfunc.dat | 10 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.one.corrfunc.dat | 10 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 62 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 64 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 61 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 63 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.two.corrfunc.dat | 10 +- .../AutoDiff/test.two.corrfunc.dat | 10 +- .../000_distance-corrfunc/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 3 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 6004 +++---- .../AutoDiff/test.restart.colvars.out | 3 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 6004 +++---- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 3 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 14404 ++++++++-------- .../AutoDiff/test.restart.colvars.out | 3 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 14404 ++++++++-------- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 8 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 42 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../test.restart.colvars.state.stripped | 8 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 8 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 42 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../test.restart.colvars.state.stripped | 8 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 36 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../000_distance-extended/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 14 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 72 +- .../AutoDiff/test.restart.colvars.out | 50 +- .../test.restart.colvars.state.stripped | 14 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 72 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../000_distance-grid_abf/AutoDiff/test.grad | 2 +- .../000_distance-grid_abf/AutoDiff/test.pmf | 14 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.grad | 2 +- .../AutoDiff/test.restart.pmf | 14 +- .../000_distance-grid_abf/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 48 +- .../AutoDiff/test.colvars.state.stripped | 6 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.harmonic1.ti.force | 2 +- .../AutoDiff/test.harmonic1.ti.pmf | 28 +- .../AutoDiff/test.restart.colvars.out | 50 +- .../test.restart.colvars.state.stripped | 6 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.harmonic1.ti.force | 2 +- .../AutoDiff/test.restart.harmonic1.ti.pmf | 14 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 48 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.harmonic1.ti.force | 2 +- .../AutoDiff/test.harmonic1.ti.pmf | 28 +- .../AutoDiff/test.restart.colvars.out | 50 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.harmonic1.ti.force | 2 +- .../AutoDiff/test.restart.harmonic1.ti.pmf | 14 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 50 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 50 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 42 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 42 +- .../namd-version.txt | 6 +- .../test.colvars.metadynamics1.hills.traj | 4 +- .../AutoDiff/test.colvars.out | 24 +- .../AutoDiff/test.colvars.state.stripped | 26 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 38 +- ...t.restart.colvars.metadynamics1.hills.traj | 4 +- .../AutoDiff/test.restart.colvars.out | 27 +- .../test.restart.colvars.state.stripped | 86 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 108 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 24 +- .../AutoDiff/test.colvars.state.stripped | 30 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 38 +- .../AutoDiff/test.restart.colvars.out | 27 +- .../test.restart.colvars.state.stripped | 78 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 106 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 10 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 38 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 10 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 38 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 12 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 38 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 12 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 38 +- .../namd-version.txt | 6 +- .../test.colvars.metadynamics1.hills.traj | 2 +- .../AutoDiff/test.colvars.out | 42 +- .../AutoDiff/test.colvars.state.stripped | 16 +- .../AutoDiff/test.colvars.traj | 32 +- .../AutoDiff/test.pmf | 38 +- .../AutoDiff/test.restart.colvars.out | 44 +- .../test.restart.colvars.state.stripped | 16 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 38 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 10 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 38 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 10 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 38 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.one.runave.traj | 14 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../000_distance-runave/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 25 +- .../AutoDiff/test.colvars.state.stripped | 8 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 25 +- .../test.restart.colvars.state.stripped | 8 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../000_distance/AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../000_distance/AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../library/000_distance/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 186 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 192 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 49 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 49 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 49 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 3 +- .../AutoDiff/test.restart.colvars.out | 3 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 49 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 6 +- .../AutoDiff/test.histogram1.dat | 50 +- .../AutoDiff/test.restart.colvars.out | 6 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 49 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 58 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 60 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 38 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 32 +- .../AutoDiff/test.restart.colvars.out | 38 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 38 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.hr.hist.dat | 12 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.hr.hist.dat | 12 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 58 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 60 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 48 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 44 +- .../AutoDiff/test.restart.colvars.out | 50 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 44 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 44 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 44 +- .../000_distancewalls/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 48 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 50 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 59 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 61 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 72 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 74 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 142 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 146 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 4 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 4 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 81 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 32 +- .../AutoDiff/test.restart.colvars.out | 81 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 39 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 41 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 31 +- .../AutoDiff/test.restart.colvars.out | 33 +- .../000_hbond_harmonic-fixed/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 40 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 42 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 41 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 43 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 39 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 41 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 39 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 41 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 40 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 42 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 40 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 42 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 41 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 43 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../000_rmsd_harmonic-fixed/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 37 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 39 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 37 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 39 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 55 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 57 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 48 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 50 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 40 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 42 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../000_tilt_harmonic-fixed/namd-version.txt | 4 +- .../001_10ala_RMSD/AutoDiff/test.colvars.out | 66 +- .../001_10ala_RMSD/AutoDiff/test.colvars.traj | 4 +- .../AutoDiff/test.colvars.out | 41 +- .../AutoDiff/test.colvars.traj | 2 +- .../AutoDiff/test.colvars.out | 37 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 20 +- .../AutoDiff/testres.colvars.out | 39 +- .../AutoDiff/testres.colvars.state.stripped | 4 +- .../AutoDiff/testres.colvars.traj | 22 +- .../003_10ala_SMD_restart/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 62 +- .../AutoDiff/test.colvars.traj | 20 +- .../005_Tcl_script/AutoDiff/test.Tcl.out | 6 +- .../005_Tcl_script/AutoDiff/test.colvars.out | 586 +- .../005_Tcl_script/AutoDiff/test.colvars.traj | 68 +- .../library/005_Tcl_script/AutoDiff/test.grad | 24 +- .../library/005_Tcl_script/AutoDiff/test.pmf | 24 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.traj | 44 +- .../AutoDiff/test.Tcl.out | 2 +- .../AutoDiff/test.colvars.out | 110 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 48 +- .../007_scripted_cv_biases/namd-version.txt | 8 +- .../AutoDiff/test.colvars.out | 40 +- .../AutoDiff/test.colvars.traj | 20 +- .../009_mtd_expand/AutoDiff/test.colvars.out | 38 +- .../AutoDiff/test.colvars.state.stripped | 14 +- .../009_mtd_expand/AutoDiff/test.colvars.traj | 38 +- .../library/009_mtd_expand/AutoDiff/test.pmf | 150 +- .../AutoDiff/test.colvars.out | 80 +- .../AutoDiff/test.colvars.state.stripped | 8 +- .../AutoDiff/test.colvars.traj | 20 +- .../AutoDiff/test.hist.grad | 6 +- .../010_angle_dihedral/AutoDiff/test.pmf | 1920 +- ...test.rep1.colvars.metadynamics1.rep1.state | 12 +- .../AutoDiff/test.rep1.colvars.out | 42 +- .../AutoDiff/test.rep1.colvars.state.stripped | 14 +- .../AutoDiff/test.rep1.colvars.traj | 196 +- .../AutoDiff/test.rep1.pmf | 98 +- ...test.rep2.colvars.metadynamics1.rep2.state | 12 +- .../AutoDiff/test.rep2.colvars.out | 48 +- .../AutoDiff/test.rep2.colvars.state.stripped | 14 +- .../AutoDiff/test.rep2.colvars.traj | 200 +- .../AutoDiff/test.rep2.pmf | 98 +- ...tres.rep1.colvars.metadynamics1.rep1.state | 12 +- .../AutoDiff/testres.rep1.colvars.out | 52 +- .../testres.rep1.colvars.state.stripped | 14 +- .../AutoDiff/testres.rep1.colvars.traj | 202 +- .../AutoDiff/testres.rep1.pmf | 98 +- ...tres.rep2.colvars.metadynamics1.rep2.state | 12 +- .../AutoDiff/testres.rep2.colvars.out | 52 +- .../testres.rep2.colvars.state.stripped | 14 +- .../AutoDiff/testres.rep2.colvars.traj | 202 +- .../AutoDiff/testres.rep2.pmf | 98 +- .../011_multiple_walker_mtd/namd-version.txt | 6 +- .../012_cvc_loop/AutoDiff/test.colvars.out | 164 +- .../012_cvc_loop/AutoDiff/test.colvars.traj | 40 +- .../014_refposgroup/AutoDiff/test.Tcl.out | 140 +- .../014_refposgroup/AutoDiff/test.colvars.out | 275 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../015_dummy_atom/AutoDiff/test.colvars.traj | 20 +- .../016_mts_bias/AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../016_mts_bias/AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../library/016_mts_bias/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 94 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 4 +- .../test.restart.colvars.state.stripped | 2 +- .../017_custom_function/namd-version.txt | 4 +- .../018_pathCV/AutoDiff/test.colvars.out | 84 +- .../AutoDiff/test.colvars.state.stripped | 20 +- .../018_pathCV/AutoDiff/test.colvars.traj | 20 +- .../library/018_pathCV/AutoDiff/test.pmf | 2376 +-- .../tests/library/018_pathCV/namd-version.txt | 6 +- .../019_gpathCV/AutoDiff/test.colvars.out | 177 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../019_gpathCV/AutoDiff/test.colvars.traj | 26 +- .../AutoDiff/test.restart.colvars.out | 179 +- .../AutoDiff/test.restart.colvars.traj | 22 +- .../library/019_gpathCV/namd-version.txt | 6 +- .../020_gpath/AutoDiff/test.colvars.traj | 28 +- .../AutoDiff/test.restart.colvars.traj | 6 +- namd/tests/library/020_gpath/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 476 +- .../AutoDiff/test.colvars.traj | 10 +- .../AutoDiff/test.restart.colvars.out | 478 +- .../AutoDiff/test.restart.colvars.traj | 4 +- .../021_gpathCV_distanceVec/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 532 +- .../AutoDiff/test.colvars.traj | 6 +- .../AutoDiff/test.restart.colvars.out | 534 +- .../AutoDiff/test.restart.colvars.traj | 4 +- .../022_apathCV_distanceVec/namd-version.txt | 6 +- .../023_apathCV/AutoDiff/test.colvars.out | 239 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../023_apathCV/AutoDiff/test.colvars.traj | 14 +- .../AutoDiff/test.restart.colvars.out | 241 +- .../AutoDiff/test.restart.colvars.traj | 24 +- .../library/023_apathCV/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 55 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 43 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../024_flexible_restart/namd-version.txt | 6 +- .../025_sym_rmsd/AutoDiff/test.colvars.out | 109 +- .../AutoDiff/test.colvars.state.stripped | 6 +- .../025_sym_rmsd/AutoDiff/test.colvars.traj | 22 +- .../AutoDiff/test.restart.colvars.out | 111 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../026_ABF_energy/AutoDiff/test.colvars.out | 45 +- .../library/026_ABF_energy/AutoDiff/test.grad | 2 +- .../library/026_ABF_energy/AutoDiff/test.pmf | 14 +- .../AutoDiff/test.restart.colvars.out | 45 +- .../026_ABF_energy/AutoDiff/test.restart.grad | 2 +- .../026_ABF_energy/AutoDiff/test.restart.pmf | 14 +- .../library/026_ABF_energy/namd-version.txt | 6 +- .../AutoDiff/mtd-0.colvars.state | 16 +- .../AutoDiff/mtd-1.colvars.state | 16 +- .../AutoDiff/mtd-2.colvars.state | 16 +- .../AutoDiff/test.colvars.out | 72 +- .../AutoDiff/test.colvars.state.stripped | 18 +- .../AutoDiff/test.colvars.traj | 84 +- .../027_multiple_runs/AutoDiff/test.pmf | 38 +- .../027_multiple_runs/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../namd-version.txt | 6 +- .../029_reweightamd/AutoDiff/test.colvars.out | 73 +- .../AutoDiff/test.colvars.state.stripped | 6 +- .../AutoDiff/test.colvars.traj | 40 +- .../library/029_reweightamd/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 10 +- .../AutoDiff/test.colvars.state.stripped | 62 +- .../AutoDiff/test.colvars.traj | 16 +- .../030_scaledBiasingForce/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 113 +- .../AutoDiff/test.colvars.state.stripped | 10 +- .../AutoDiff/test.colvars.traj | 40 +- .../031_neuralnetwork/AutoDiff/test.grad | 2 +- .../031_neuralnetwork/AutoDiff/test.pmf | 116 +- .../031_neuralnetwork/namd-version.txt | 6 +- 854 files changed, 41393 insertions(+), 37704 deletions(-) diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out index 8b9e9c148..208b0e2dd 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -64,7 +68,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -92,6 +96,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.1 according to the specified width (0.1). colvars: ---------------------------------------------------------------------- @@ -102,43 +107,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. -colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/3. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/4. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/5. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/6. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/7. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/8. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/9. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/10. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/11. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/12. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/13. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/14. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/15. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/16. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/17. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/18. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/19. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/20. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/21. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/22. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/23. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/24. 2 atoms: total mass = 30.006, total charge = -0.98. -colvars: Re-initialized atom group for variable "one":0/25. 2 atoms: total mass = 30.006, total charge = -0.98. -colvars: Re-initialized atom group for variable "one":0/26. 2 atoms: total mass = 30.006, total charge = -0.98. -colvars: Re-initialized atom group for variable "one":0/27. 2 atoms: total mass = 30.006, total charge = -0.98. -colvars: Re-initialized atom group for variable "one":0/28. 2 atoms: total mass = 30.006, total charge = -0.98. -colvars: Re-initialized atom group for variable "one":0/29. 2 atoms: total mass = 30.006, total charge = -0.98. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - alpha colvar component: +colvars: - angle colvar component: +colvars: - hBond colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 759c485d6..2c3923d92 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 8.42013109784351e-01 + x 8.42013109670389e-01 } restraint { diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj index 59a13c0cf..1d9d7dbb8 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 8.44342403972268e-01 -7.44342403972268e-02 - 1 8.44098854642590e-01 -7.44098854642590e-02 - 2 8.43793147698295e-01 -7.43793147698295e-02 - 3 8.43428641477914e-01 -7.43428641477913e-02 - 4 8.43016163376308e-01 -7.43016163376308e-02 - 5 8.42574360346050e-01 -7.42574360346050e-02 - 6 8.42128240619594e-01 -7.42128240619594e-02 - 7 8.41706134441275e-01 -7.41706134441275e-02 - 8 8.41335763262530e-01 -7.41335763262530e-02 - 9 8.41040339242422e-01 -7.41040339242422e-02 - 10 8.40835525453342e-01 -7.40835525453342e-02 - 11 8.40727764254687e-01 -7.40727764254687e-02 - 12 8.40714100983289e-01 -7.40714100983289e-02 - 13 8.40783339024046e-01 -7.40783339024046e-02 - 14 8.40918192530856e-01 -7.40918192530856e-02 - 15 8.41098021877668e-01 -7.41098021877668e-02 - 16 8.41301655357182e-01 -7.41301655357182e-02 - 17 8.41509730022086e-01 -7.41509730022086e-02 - 18 8.41706023231625e-01 -7.41706023231625e-02 - 19 8.41877486515835e-01 -7.41877486515835e-02 - 20 8.42013109784351e-01 -7.42013109784350e-02 + 0 8.44342403972232e-01 -7.44342403972232e-02 + 1 8.44098854642285e-01 -7.44098854642285e-02 + 2 8.43793147696887e-01 -7.43793147696886e-02 + 3 8.43428641474561e-01 -7.43428641474561e-02 + 4 8.43016163379186e-01 -7.43016163379186e-02 + 5 8.42574360353300e-01 -7.42574360353300e-02 + 6 8.42128240610470e-01 -7.42128240610470e-02 + 7 8.41706134434711e-01 -7.41706134434711e-02 + 8 8.41335763240474e-01 -7.41335763240474e-02 + 9 8.41040339208587e-01 -7.41040339208587e-02 + 10 8.40835525411341e-01 -7.40835525411341e-02 + 11 8.40727764204272e-01 -7.40727764204272e-02 + 12 8.40714100924275e-01 -7.40714100924275e-02 + 13 8.40783338958624e-01 -7.40783338958624e-02 + 14 8.40918192455347e-01 -7.40918192455347e-02 + 15 8.41098021792410e-01 -7.41098021792409e-02 + 16 8.41301655271500e-01 -7.41301655271500e-02 + 17 8.41509729929472e-01 -7.41509729929472e-02 + 18 8.41706023128253e-01 -7.41706023128253e-02 + 19 8.41877486404754e-01 -7.41877486404754e-02 + 20 8.42013109670389e-01 -7.42013109670389e-02 diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out index 09ba41c2e..e2f8eb508 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -64,7 +68,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -92,6 +96,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.1 according to the specified width (0.1). colvars: ---------------------------------------------------------------------- @@ -102,48 +107,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. -colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/3. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/4. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/5. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/6. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/7. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/8. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/9. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/10. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/11. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/12. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/13. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/14. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/15. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/16. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/17. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/18. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/19. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/20. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/21. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/22. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/23. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/24. 2 atoms: total mass = 30.006, total charge = -0.98. -colvars: Re-initialized atom group for variable "one":0/25. 2 atoms: total mass = 30.006, total charge = -0.98. -colvars: Re-initialized atom group for variable "one":0/26. 2 atoms: total mass = 30.006, total charge = -0.98. -colvars: Re-initialized atom group for variable "one":0/27. 2 atoms: total mass = 30.006, total charge = -0.98. -colvars: Re-initialized atom group for variable "one":0/28. 2 atoms: total mass = 30.006, total charge = -0.98. -colvars: Re-initialized atom group for variable "one":0/29. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - alpha colvar component: +colvars: - angle colvar component: +colvars: - hBond colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.842013 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index e09e94eee..7359bbe19 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 8.32317621580914e-01 + x 8.32317621377386e-01 } restraint { diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj index f161a80a9..5d21a33d1 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 8.42013109784351e-01 -7.42013109784350e-02 - 21 8.42102179978755e-01 -7.42102179978755e-02 - 22 8.42132754021507e-01 -7.42132754021507e-02 - 23 8.42091111321136e-01 -7.42091111321136e-02 - 24 8.41962602356096e-01 -7.41962602356095e-02 - 25 8.41733788301857e-01 -7.41733788301857e-02 - 26 8.41395277661295e-01 -7.41395277661295e-02 - 27 8.40944388762035e-01 -7.40944388762035e-02 - 28 8.40386797451279e-01 -7.40386797451279e-02 - 29 8.39736648652815e-01 -7.39736648652815e-02 - 30 8.39015059877273e-01 -7.39015059877273e-02 - 31 8.38247391341335e-01 -7.38247391341335e-02 - 32 8.37459941212710e-01 -7.37459941212710e-02 - 33 8.36676804493709e-01 -7.36676804493709e-02 - 34 8.35917530561721e-01 -7.35917530561721e-02 - 35 8.35195977325575e-01 -7.35195977325575e-02 - 36 8.34520437356997e-01 -7.34520437356996e-02 - 37 8.33894756096833e-01 -7.33894756096832e-02 - 38 8.33319850486250e-01 -7.33319850486250e-02 - 39 8.32794900028858e-01 -7.32794900028857e-02 - 40 8.32317621580914e-01 -7.32317621580914e-02 + 20 8.42013109670389e-01 -7.42013109670389e-02 + 21 8.42102179859247e-01 -7.42102179859247e-02 + 22 8.42132753897807e-01 -7.42132753897807e-02 + 23 8.42091111194279e-01 -7.42091111194279e-02 + 24 8.41962602226785e-01 -7.41962602226785e-02 + 25 8.41733788173401e-01 -7.41733788173401e-02 + 26 8.41395277535143e-01 -7.41395277535143e-02 + 27 8.40944388629140e-01 -7.40944388629140e-02 + 28 8.40386797315513e-01 -7.40386797315513e-02 + 29 8.39736648516850e-01 -7.39736648516849e-02 + 30 8.39015059742126e-01 -7.39015059742125e-02 + 31 8.38247391201732e-01 -7.38247391201732e-02 + 32 8.37459941069716e-01 -7.37459941069716e-02 + 33 8.36676804346260e-01 -7.36676804346260e-02 + 34 8.35917530408746e-01 -7.35917530408746e-02 + 35 8.35195977166090e-01 -7.35195977166090e-02 + 36 8.34520437212929e-01 -7.34520437212929e-02 + 37 8.33894755921237e-01 -7.33894755921237e-02 + 38 8.33319850305569e-01 -7.33319850305569e-02 + 39 8.32794899843751e-01 -7.32794899843751e-02 + 40 8.32317621377386e-01 -7.32317621377385e-02 diff --git a/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt b/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out index 4a19c8550..efee19466 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,42 +59,42 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] @@ -129,6 +133,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -139,16 +144,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - angle colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 43525b56b..d398132a2 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.00164524892654e+02 + x 1.00164524891460e+02 } restraint { diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj index 2c8f412a0..259181bc9 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.03254732139588e+02 -4.12618928558351e-01 - 1 1.03132366162315e+02 -4.12129464649258e-01 - 2 1.03006339773950e+02 -4.11625359095801e-01 - 3 1.02876690770137e+02 -4.11106763080547e-01 - 4 1.02743412368775e+02 -4.10573649475101e-01 - 5 1.02606460567804e+02 -4.10025842271217e-01 - 6 1.02465768469158e+02 -4.09463073876632e-01 - 7 1.02321276095597e+02 -4.08885104382386e-01 - 8 1.02172974776925e+02 -4.08291899107700e-01 - 9 1.02020953811854e+02 -4.07683815247416e-01 - 10 1.01865429972567e+02 -4.07061719890269e-01 - 11 1.01706742242773e+02 -4.06426968971090e-01 - 12 1.01545305106549e+02 -4.05781220426196e-01 - 13 1.01381527031724e+02 -4.05126108126898e-01 - 14 1.01215712239996e+02 -4.04462848959984e-01 - 15 1.01047968160132e+02 -4.03791872640529e-01 - 16 1.00878136638138e+02 -4.03112546552552e-01 - 17 1.00705758990434e+02 -4.02423035961734e-01 - 18 1.00530077456623e+02 -4.01720309826491e-01 - 19 1.00350071437758e+02 -4.01000285751032e-01 - 20 1.00164524892654e+02 -4.00258099570617e-01 + 1 1.03132366162310e+02 -4.12129464649240e-01 + 2 1.03006339773933e+02 -4.11625359095731e-01 + 3 1.02876690769855e+02 -4.11106763079420e-01 + 4 1.02743412368037e+02 -4.10573649472149e-01 + 5 1.02606460567606e+02 -4.10025842270424e-01 + 6 1.02465768469001e+02 -4.09463073876003e-01 + 7 1.02321276095485e+02 -4.08885104381940e-01 + 8 1.02172974776860e+02 -4.08291899107440e-01 + 9 1.02020953811828e+02 -4.07683815247310e-01 + 10 1.01865429972566e+02 -4.07061719890263e-01 + 11 1.01706742242777e+02 -4.06426968971107e-01 + 12 1.01545305106535e+02 -4.05781220426139e-01 + 13 1.01381527031664e+02 -4.05126108126656e-01 + 14 1.01215712239860e+02 -4.04462848959438e-01 + 15 1.01047968158544e+02 -4.03791872634177e-01 + 16 1.00878136637506e+02 -4.03112546550023e-01 + 17 1.00705758988893e+02 -4.02423035955572e-01 + 18 1.00530077455794e+02 -4.01720309823177e-01 + 19 1.00350071436460e+02 -4.01000285745841e-01 + 20 1.00164524891460e+02 -4.00258099565841e-01 diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 7b64bde0e..3752c7683 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,42 +59,42 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] @@ -129,6 +133,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -139,21 +144,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - angle colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 100.165 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 186ad215e..19ffa9256 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.50832224199785e+01 + x 9.50832224152502e+01 } restraint { diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 1173041f5..f3070f2f5 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.00164524892654e+02 -4.00258099570617e-01 - 21 9.99721208604643e+01 -3.99488483441857e-01 - 22 9.97715541539098e+01 -3.98686216615639e-01 - 23 9.95616505554525e+01 -3.97846602221810e-01 - 24 9.93414788155942e+01 -3.96965915262377e-01 - 25 9.91104429920789e+01 -3.96041771968316e-01 - 26 9.88683487929842e+01 -3.95073395171937e-01 - 27 9.86154431854530e+01 -3.94061772741812e-01 - 28 9.83524306257732e+01 -3.93009722503093e-01 - 29 9.80804706481534e+01 -3.91921882592614e-01 - 30 9.78011567175226e+01 -3.90804626870090e-01 - 31 9.75164711021598e+01 -3.89665884408639e-01 - 32 9.72287072016144e+01 -3.88514828806458e-01 - 33 9.69403528506243e+01 -3.87361411402497e-01 - 34 9.66539367622950e+01 -3.86215747049180e-01 - 35 9.63718539681591e+01 -3.85087415872637e-01 - 36 9.60961965697586e+01 -3.83984786279034e-01 - 37 9.58286196894440e+01 -3.82914478757776e-01 - 38 9.55702653365613e+01 -3.81881061346245e-01 - 39 9.53217521034107e+01 -3.80887008413643e-01 - 40 9.50832224199785e+01 -3.79932889679914e-01 + 20 1.00164524891460e+02 -4.00258099565841e-01 + 21 9.99721208590562e+01 -3.99488483436225e-01 + 22 9.97715541522898e+01 -3.98686216609159e-01 + 23 9.95616505536277e+01 -3.97846602214511e-01 + 24 9.93414788135756e+01 -3.96965915254302e-01 + 25 9.91104429898799e+01 -3.96041771959520e-01 + 26 9.88683487906183e+01 -3.95073395162473e-01 + 27 9.86154431829325e+01 -3.94061772731730e-01 + 28 9.83524306231076e+01 -3.93009722492431e-01 + 29 9.80804706453528e+01 -3.91921882581411e-01 + 30 9.78011567145892e+01 -3.90804626858357e-01 + 31 9.75164710990926e+01 -3.89665884396371e-01 + 32 9.72287071984055e+01 -3.88514828793622e-01 + 33 9.69403528472622e+01 -3.87361411389049e-01 + 34 9.66539367587656e+01 -3.86215747035062e-01 + 35 9.63718539644472e+01 -3.85087415857789e-01 + 36 9.60961965658487e+01 -3.83984786263395e-01 + 37 9.58286196853218e+01 -3.82914478741287e-01 + 38 9.55702653322208e+01 -3.81881061328883e-01 + 39 9.53217520988444e+01 -3.80887008395378e-01 + 40 9.50832224152502e+01 -3.79932889661001e-01 diff --git a/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out index 23b8999d1..d1e4a4135 100644 --- a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -118,6 +122,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,15 +133,29 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - coordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - coordNum pairlist: +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out index 49e0fbd49..43e5df3df 100644 --- a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -118,6 +122,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,20 +133,34 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - coordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - coordNum pairlist: +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt index b7bf5455c..157cac038 100644 --- a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-10-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out index 6e7b06fa6..6b75c3857 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -117,6 +121,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,15 +132,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - coordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 309db4bf6..952b2b371 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.50382512360039e-04 + x 4.50382512265436e-04 } restraint { diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj index 112ced7b7..9c31c9ffe 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 4.88336530020493e-04 3.98046653879918e-04 - 1 5.03969504626528e-04 3.97984121981494e-04 - 2 5.19354539504346e-04 3.97922581841983e-04 - 3 5.32983502659005e-04 3.97868065989364e-04 - 4 5.43368523967091e-04 3.97826525904132e-04 - 5 5.49278854680875e-04 3.97802884581276e-04 - 6 5.49958947491071e-04 3.97800164210036e-04 - 7 5.45267296469905e-04 3.97818930814120e-04 - 8 5.35697517245723e-04 3.97857209931017e-04 - 9 5.22279865782907e-04 3.97910880536868e-04 - 10 5.06396380351657e-04 3.97974414478593e-04 - 11 4.89562686981327e-04 3.98041749252075e-04 - 12 4.73229283944885e-04 3.98107082864221e-04 - 13 4.58638307482096e-04 3.98165446770072e-04 - 14 4.46747589793320e-04 3.98213009640827e-04 - 15 4.38212375509248e-04 3.98247150497963e-04 - 16 4.33402944488714e-04 3.98266388222045e-04 - 17 4.32434897055776e-04 3.98270260411777e-04 - 18 4.35195093400421e-04 3.98259219626398e-04 - 19 4.41356151408746e-04 3.98234575394365e-04 - 20 4.50382512360039e-04 3.98198469950560e-04 + 1 5.03969504628764e-04 3.97984121981485e-04 + 2 5.19354539513055e-04 3.97922581841948e-04 + 3 5.32983502677849e-04 3.97868065989289e-04 + 4 5.43368523998496e-04 3.97826525904006e-04 + 5 5.49278854725414e-04 3.97802884581098e-04 + 6 5.49958947547140e-04 3.97800164209811e-04 + 7 5.45267296533856e-04 3.97818930813865e-04 + 8 5.35697517312449e-04 3.97857209930750e-04 + 9 5.22279865846730e-04 3.97910880536613e-04 + 10 5.06396380407222e-04 3.97974414478371e-04 + 11 4.89562687024283e-04 3.98041749251903e-04 + 12 4.73229283972216e-04 3.98107082864111e-04 + 13 4.58638307492123e-04 3.98165446770032e-04 + 14 4.46747589785476e-04 3.98213009640858e-04 + 15 4.38212375483778e-04 3.98247150498065e-04 + 16 4.33402944446411e-04 3.98266388222214e-04 + 17 4.32434896997806e-04 3.98270260412009e-04 + 18 4.35195093328268e-04 3.98259219626687e-04 + 19 4.41356151324242e-04 3.98234575394703e-04 + 20 4.50382512265436e-04 3.98198469950938e-04 diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out index 27e93bffc..cd3aa273f 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -117,6 +121,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,20 +132,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - coordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.000450383 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index f07d92582..673940f1b 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.07333860152640e-04 + x 5.07333860034785e-04 } restraint { diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 7cece45e3..69dbc17d4 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 4.50382512360039e-04 3.98198469950560e-04 - 21 4.61538871322809e-04 3.98153844514709e-04 - 22 4.73915291393088e-04 3.98104338834428e-04 - 23 4.86481082447120e-04 3.98054075670212e-04 - 24 4.98171600228783e-04 3.98007313599085e-04 - 25 5.08000918865736e-04 3.97967996324537e-04 - 26 5.15183038956578e-04 3.97939267844174e-04 - 27 5.19238455014736e-04 3.97923046179941e-04 - 28 5.20063102897763e-04 3.97919747588409e-04 - 29 5.17943198990256e-04 3.97928227204039e-04 - 30 5.13510005781771e-04 3.97945959976873e-04 - 31 5.07642202491579e-04 3.97969431190034e-04 - 32 5.01335749171320e-04 3.97994657003315e-04 - 33 4.95567637267788e-04 3.98017729450929e-04 - 34 4.91176737736178e-04 3.98035293049055e-04 - 35 4.88775079125039e-04 3.98044899683500e-04 - 36 4.88691485077369e-04 3.98045234059691e-04 - 37 4.90943355434415e-04 3.98036226578262e-04 - 38 4.95233101618235e-04 3.98019067593527e-04 - 39 5.00971349500124e-04 3.97996114602000e-04 - 40 5.07333860152640e-04 3.97970664559389e-04 + 20 4.50382512265436e-04 3.98198469950938e-04 + 21 4.61538871220812e-04 3.98153844515117e-04 + 22 4.73915291286790e-04 3.98104338834853e-04 + 23 4.86481082339776e-04 3.98054075670641e-04 + 24 4.98171600123441e-04 3.98007313599506e-04 + 25 5.08000918764789e-04 3.97967996324941e-04 + 26 5.15183038861356e-04 3.97939267844555e-04 + 27 5.19238454925296e-04 3.97923046180299e-04 + 28 5.20063102812949e-04 3.97919747588748e-04 + 29 5.17943198908027e-04 3.97928227204368e-04 + 30 5.13510005699675e-04 3.97945959977201e-04 + 31 5.07642202407253e-04 3.97969431190371e-04 + 32 5.01335749082877e-04 3.97994657003669e-04 + 33 4.95567637174033e-04 3.98017729451304e-04 + 34 4.91176737636651e-04 3.98035293049453e-04 + 35 4.88775079019952e-04 3.98044899683920e-04 + 36 4.88691484967476e-04 3.98045234060130e-04 + 37 4.90943355320849e-04 3.98036226578717e-04 + 38 4.95233101502291e-04 3.98019067593991e-04 + 39 5.00971349382943e-04 3.97996114602468e-04 + 40 5.07333860034785e-04 3.97970664559861e-04 diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt index 9e5d53306..157cac038 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-12-21. -colvars: Using NAMD interface, version 2018-12-20. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out index 58f41ca99..9c06635fa 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -117,6 +121,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,15 +132,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - coordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 3f8e0f234..91bd082de 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.66463134738076e+00 + x 2.66463134760762e+00 } restraint { diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj index 7cf1cd53e..d266cabe9 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 2.67119635178005e+00 -1.02847854071202e-02 - 1 2.67227384619251e+00 -1.02890953847700e-02 - 2 2.67273226510223e+00 -1.02909290604089e-02 - 3 2.67255372186561e+00 -1.02902148874625e-02 - 4 2.67175941875083e+00 -1.02870376750033e-02 - 5 2.67040901313963e+00 -1.02816360525585e-02 - 6 2.66859725097598e+00 -1.02743890039039e-02 - 7 2.66644846888120e+00 -1.02657938755248e-02 - 8 2.66410945073814e+00 -1.02564378029526e-02 - 9 2.66174084172640e+00 -1.02469633669056e-02 - 10 2.65950718923457e+00 -1.02380287569383e-02 - 11 2.65756592966473e+00 -1.02302637186589e-02 - 12 2.65605614341187e+00 -1.02242245736475e-02 - 13 2.65508832508033e+00 -1.02203533003213e-02 - 14 2.65473648498004e+00 -1.02189459399202e-02 - 15 2.65503349617912e+00 -1.02201339847165e-02 - 16 2.65596999004862e+00 -1.02238799601945e-02 - 17 2.65749649079691e+00 -1.02299859631876e-02 - 18 2.65952812740781e+00 -1.02381125096312e-02 - 19 2.66195123554084e+00 -1.02478049421634e-02 - 20 2.66463134738076e+00 -1.02585253895231e-02 + 1 2.67227384619314e+00 -1.02890953847726e-02 + 2 2.67273226510484e+00 -1.02909290604194e-02 + 3 2.67255372187147e+00 -1.02902148874859e-02 + 4 2.67175941876139e+00 -1.02870376750455e-02 + 5 2.67040901315621e+00 -1.02816360526248e-02 + 6 2.66859725099990e+00 -1.02743890039996e-02 + 7 2.66644846891371e+00 -1.02657938756549e-02 + 8 2.66410945078046e+00 -1.02564378031219e-02 + 9 2.66174084177962e+00 -1.02469633671185e-02 + 10 2.65950718929972e+00 -1.02380287571989e-02 + 11 2.65756592974274e+00 -1.02302637189710e-02 + 12 2.65605614350359e+00 -1.02242245740144e-02 + 13 2.65508832518654e+00 -1.02203533007461e-02 + 14 2.65473648510148e+00 -1.02189459404059e-02 + 15 2.65503349631646e+00 -1.02201339852658e-02 + 16 2.65596999020253e+00 -1.02238799608101e-02 + 17 2.65749649096805e+00 -1.02299859638722e-02 + 18 2.65952812759685e+00 -1.02381125103874e-02 + 19 2.66195123574845e+00 -1.02478049429938e-02 + 20 2.66463134760762e+00 -1.02585253904305e-02 diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out index deed28969..c20b26d4f 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -117,6 +121,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,20 +132,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - coordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 2.66463 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 59a098582..4c8e4e3f2 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.67525299195737e+00 + x 2.67525299255671e+00 } restraint { diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj index bf12f4d2d..63f1a55dd 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.66463134738076e+00 -1.02585253895231e-02 - 21 2.66742226029295e+00 -1.02696890411718e-02 - 22 2.67017590921653e+00 -1.02807036368661e-02 - 23 2.67275254957261e+00 -1.02910101982905e-02 - 24 2.67503043638932e+00 -1.03001217455573e-02 - 25 2.67691398841351e+00 -1.03076559536541e-02 - 26 2.67833957637177e+00 -1.03133583054871e-02 - 27 2.67927850916844e+00 -1.03171140366738e-02 - 28 2.67973729580054e+00 -1.03189491832022e-02 - 29 2.67975557080403e+00 -1.03190222832161e-02 - 30 2.67940194130612e+00 -1.03176077652245e-02 - 31 2.67876786445484e+00 -1.03150714578194e-02 - 32 2.67795953888813e+00 -1.03118381555525e-02 - 33 2.67708810569326e+00 -1.03083524227731e-02 - 34 2.67625892895020e+00 -1.03050357158008e-02 - 35 2.67556129237875e+00 -1.03022451695150e-02 - 36 2.67505997687781e+00 -1.03002399075112e-02 - 37 2.67478990157628e+00 -1.02991596063051e-02 - 38 2.67475432151807e+00 -1.02990172860723e-02 - 39 2.67492634494164e+00 -1.02997053797666e-02 - 40 2.67525299195737e+00 -1.03010119678295e-02 + 20 2.66463134760762e+00 -1.02585253904305e-02 + 21 2.66742226053972e+00 -1.02696890421589e-02 + 22 2.67017590948386e+00 -1.02807036379355e-02 + 23 2.67275254986108e+00 -1.02910101994443e-02 + 24 2.67503043669944e+00 -1.03001217467977e-02 + 25 2.67691398874566e+00 -1.03076559549827e-02 + 26 2.67833957672623e+00 -1.03133583069049e-02 + 27 2.67927850954533e+00 -1.03171140381813e-02 + 28 2.67973729619981e+00 -1.03189491847993e-02 + 29 2.67975557122547e+00 -1.03190222849019e-02 + 30 2.67940194174935e+00 -1.03176077669974e-02 + 31 2.67876786491929e+00 -1.03150714596772e-02 + 32 2.67795953937304e+00 -1.03118381574922e-02 + 33 2.67708810619769e+00 -1.03083524247908e-02 + 34 2.67625892947302e+00 -1.03050357178921e-02 + 35 2.67556129291865e+00 -1.03022451716746e-02 + 36 2.67505997743329e+00 -1.03002399097332e-02 + 37 2.67478990214567e+00 -1.02991596085827e-02 + 38 2.67475432209952e+00 -1.02990172883981e-02 + 39 2.67492634553313e+00 -1.02997053821325e-02 + 40 2.67525299255671e+00 -1.03010119702268e-02 diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt index 4d05e12c8..157cac038 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2019-08-05". -colvars: Using NAMD interface, version "2019-08-01". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out index ec53ee630..d0660361f 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -118,6 +122,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,15 +133,29 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - coordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - coordNum pairlist: +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped index b646c70df..3ff2bc585 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01411698403566e+01 + x 1.01411698412338e+01 } restraint { diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj index 8c250f8de..c8adc634d 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.01481368521529e+01 -4.01925474086114e-02 - 1 1.01543539600385e+01 -4.02174158401538e-02 - 2 1.01579705670262e+01 -4.02318822681049e-02 - 3 1.01589102870716e+01 -4.02356411482866e-02 - 4 1.01572731010286e+01 -4.02290924041145e-02 - 5 1.01533217576159e+01 -4.02132870304636e-02 - 6 1.01474576214938e+01 -4.01898304859752e-02 - 7 1.01401899752170e+01 -4.01607599008680e-02 - 8 1.01321020976811e+01 -4.01284083907245e-02 - 9 1.01238159999362e+01 -4.00952639997449e-02 - 10 1.01159565518573e+01 -4.00638262074292e-02 - 11 1.01091157347845e+01 -4.00364629391381e-02 - 12 1.01038185754805e+01 -4.00152743019222e-02 - 13 1.01004931562647e+01 -4.00019726250588e-02 - 14 1.00994472482940e+01 -3.99977889931759e-02 - 15 1.01008533185352e+01 -4.00034132741409e-02 - 16 1.01047425594636e+01 -4.00189702378545e-02 - 17 1.01110075577148e+01 -4.00440302308591e-02 - 18 1.01194127093045e+01 -4.00776508372182e-02 - 19 1.01296114933081e+01 -4.01184459732322e-02 - 20 1.01411698403566e+01 -4.01646793614266e-02 + 1 1.01543539600401e+01 -4.02174158401602e-02 + 2 1.01579705670330e+01 -4.02318822681319e-02 + 3 1.01589102870876e+01 -4.02356411483502e-02 + 4 1.01572731010582e+01 -4.02290924042330e-02 + 5 1.01533217576642e+01 -4.02132870306567e-02 + 6 1.01474576215661e+01 -4.01898304862643e-02 + 7 1.01401899753189e+01 -4.01607599012755e-02 + 8 1.01321020978184e+01 -4.01284083912734e-02 + 9 1.01238160001145e+01 -4.00952640004581e-02 + 10 1.01159565520821e+01 -4.00638262083286e-02 + 11 1.01091157350611e+01 -4.00364629402443e-02 + 12 1.01038185758135e+01 -4.00152743032539e-02 + 13 1.01004931566581e+01 -4.00019726266324e-02 + 14 1.00994472487512e+01 -3.99977889950050e-02 + 15 1.01008533190591e+01 -4.00034132762363e-02 + 16 1.01047425600561e+01 -4.00189702402245e-02 + 17 1.01110075583774e+01 -4.00440302335097e-02 + 18 1.01194127100383e+01 -4.00776508401532e-02 + 19 1.01296114941134e+01 -4.01184459764537e-02 + 20 1.01411698412338e+01 -4.01646793649352e-02 diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out index 25d4265e0..cec376268 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -118,6 +122,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,20 +133,34 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - coordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - coordNum pairlist: +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 10.1412 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index a5a2b6938..8264680de 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01841922784258e+01 + x 1.01841922804199e+01 } restraint { diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj index c07a48c82..3d6793224 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.01411698403566e+01 -4.01646793614266e-02 - 21 1.01535946542976e+01 -4.02143786171906e-02 - 22 1.01663658694150e+01 -4.02654634776601e-02 - 23 1.01789693397072e+01 -4.03158773588289e-02 - 24 1.01909269850700e+01 -4.03637079402800e-02 - 25 1.02018206324370e+01 -4.04072825297481e-02 - 26 1.02113074874510e+01 -4.04452299498039e-02 - 27 1.02191274692122e+01 -4.04765098768487e-02 - 28 1.02251046838367e+01 -4.05004187353467e-02 - 29 1.02291462120943e+01 -4.05165848483772e-02 - 30 1.02312399806787e+01 -4.05249599227147e-02 - 31 1.02314518085137e+01 -4.05258072340550e-02 - 32 1.02299198117186e+01 -4.05196792468743e-02 - 33 1.02268443901165e+01 -4.05073775604658e-02 - 34 1.02224730705855e+01 -4.04898922823419e-02 - 35 1.02170817744726e+01 -4.04683270978904e-02 - 36 1.02109552433282e+01 -4.04438209733127e-02 - 37 1.02043693133334e+01 -4.04174772533334e-02 - 38 1.01975763279845e+01 -4.03903053119382e-02 - 39 1.01907933844900e+01 -4.03631735379599e-02 - 40 1.01841922784258e+01 -4.03367691137030e-02 + 20 1.01411698412338e+01 -4.01646793649352e-02 + 21 1.01535946552464e+01 -4.02143786209857e-02 + 22 1.01663658704350e+01 -4.02654634817400e-02 + 23 1.01789693407977e+01 -4.03158773631909e-02 + 24 1.01909269862300e+01 -4.03637079449202e-02 + 25 1.02018206336654e+01 -4.04072825346614e-02 + 26 1.02113074887461e+01 -4.04452299549842e-02 + 27 1.02191274705721e+01 -4.04765098822886e-02 + 28 1.02251046852595e+01 -4.05004187410379e-02 + 29 1.02291462135776e+01 -4.05165848543106e-02 + 30 1.02312399822203e+01 -4.05249599288811e-02 + 31 1.02314518101113e+01 -4.05258072404452e-02 + 32 1.02299198133700e+01 -4.05196792534798e-02 + 33 1.02268443918197e+01 -4.05073775672787e-02 + 34 1.02224730723386e+01 -4.04898922893544e-02 + 35 1.02170817762737e+01 -4.04683271050948e-02 + 36 1.02109552451751e+01 -4.04438209807005e-02 + 37 1.02043693152234e+01 -4.04174772608938e-02 + 38 1.01975763299143e+01 -4.03903053196573e-02 + 39 1.01907933864549e+01 -4.03631735458195e-02 + 40 1.01841922804199e+01 -4.03367691216797e-02 diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt index b2949c9aa..157cac038 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-05-08. -colvars: Using NAMD interface, version 2018-04-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out index 5f1b09b7b..28e8e90b2 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -117,6 +121,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,15 +132,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - coordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 4b97c242b..bf985d8ad 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01997380106663e+01 + x 1.01997380115249e+01 } restraint { diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj index 8cadeb993..35e491d82 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.02066554836313e+01 -4.04266219345253e-02 - 1 1.02128103525226e+01 -4.04512414100905e-02 - 2 1.02163905908367e+01 -4.04655623633469e-02 - 3 1.02173205792556e+01 -4.04692823170224e-02 - 4 1.02156993029853e+01 -4.04627972119410e-02 - 5 1.02117868889625e+01 -4.04471475558502e-02 - 6 1.02059806948824e+01 -4.04239227795298e-02 - 7 1.01987849182097e+01 -4.03951396728390e-02 - 8 1.01907770133593e+01 -4.03631080534371e-02 - 9 1.01825727798096e+01 -4.03302911192384e-02 - 10 1.01747908471046e+01 -4.02991633884182e-02 - 11 1.01680172845955e+01 -4.02720691383820e-02 - 12 1.01627718757998e+01 -4.02510875031993e-02 - 13 1.01594784282758e+01 -4.02379137131030e-02 - 14 1.01584416406077e+01 -4.02337665624308e-02 - 15 1.01598322594592e+01 -4.02393290378370e-02 - 16 1.01636811691959e+01 -4.02547246767837e-02 - 17 1.01698820340975e+01 -4.02795281363899e-02 - 18 1.01782016096006e+01 -4.03128064384024e-02 - 19 1.01882968434774e+01 -4.03531873739095e-02 - 20 1.01997380106663e+01 -4.03989520426651e-02 + 1 1.02128103525242e+01 -4.04512414100967e-02 + 2 1.02163905908650e+01 -4.04655623634601e-02 + 3 1.02173205792671e+01 -4.04692823170684e-02 + 4 1.02156993030364e+01 -4.04627972121458e-02 + 5 1.02117868890088e+01 -4.04471475560353e-02 + 6 1.02059806949699e+01 -4.04239227798795e-02 + 7 1.01987849183460e+01 -4.03951396733840e-02 + 8 1.01907770135508e+01 -4.03631080542033e-02 + 9 1.01825727800619e+01 -4.03302911202475e-02 + 10 1.01747908474213e+01 -4.02991633896850e-02 + 11 1.01680172849785e+01 -4.02720691399141e-02 + 12 1.01627718762492e+01 -4.02510875049969e-02 + 13 1.01594784287899e+01 -4.02379137151595e-02 + 14 1.01584416411835e+01 -4.02337665647338e-02 + 15 1.01598322600926e+01 -4.02393290403704e-02 + 16 1.01636811698822e+01 -4.02547246795287e-02 + 17 1.01698820348244e+01 -4.02795281392977e-02 + 18 1.01782016103793e+01 -4.03128064415171e-02 + 19 1.01882968442993e+01 -4.03531873771971e-02 + 20 1.01997380115249e+01 -4.03989520460994e-02 diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out index b16bdc9b4..56dfff67d 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -117,6 +121,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,20 +132,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - coordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 10.1997 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 845030b9e..047e1a4b2 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.02422968511954e+01 + x 1.02422968531579e+01 } restraint { diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj index d5957567b..5d7023dd8 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.01997380106663e+01 -4.03989520426651e-02 - 21 1.02120369497625e+01 -4.04481477990502e-02 - 22 1.02246787996745e+01 -4.04987151986978e-02 - 23 1.02371545599893e+01 -4.05486182399573e-02 - 24 1.02489909356603e+01 -4.05959637426412e-02 - 25 1.02597739397322e+01 -4.06390957589289e-02 - 26 1.02691642101966e+01 -4.06766568407865e-02 - 27 1.02769042713270e+01 -4.07076170853082e-02 - 28 1.02828199923736e+01 -4.07312799694943e-02 - 29 1.02868193871873e+01 -4.07472775487492e-02 - 30 1.02888905066404e+01 -4.07555620265616e-02 - 31 1.02890985142689e+01 -4.07563940570755e-02 - 32 1.02875801470742e+01 -4.07503205882967e-02 - 33 1.02845338021721e+01 -4.07381352086885e-02 - 34 1.02802045318133e+01 -4.07208181272531e-02 - 35 1.02748654982405e+01 -4.06994619929619e-02 - 36 1.02687985955587e+01 -4.06751943822348e-02 - 37 1.02622769015451e+01 -4.06491076061802e-02 - 38 1.02555502364106e+01 -4.06222009456423e-02 - 39 1.02488335268439e+01 -4.05953341073754e-02 - 40 1.02422968511954e+01 -4.05691874047814e-02 + 20 1.01997380115249e+01 -4.03989520460994e-02 + 21 1.02120369506585e+01 -4.04481478026342e-02 + 22 1.02246788006083e+01 -4.04987152024332e-02 + 23 1.02371545609629e+01 -4.05486182438517e-02 + 24 1.02489909366769e+01 -4.05959637467076e-02 + 25 1.02597739407961e+01 -4.06390957631846e-02 + 26 1.02691642113129e+01 -4.06766568452516e-02 + 27 1.02769042725010e+01 -4.07076170900039e-02 + 28 1.02828199936102e+01 -4.07312799744409e-02 + 29 1.02868193884911e+01 -4.07472775539644e-02 + 30 1.02888905080147e+01 -4.07555620320589e-02 + 31 1.02890985157159e+01 -4.07563940628635e-02 + 32 1.02875801485946e+01 -4.07503205943785e-02 + 33 1.02845338037653e+01 -4.07381352150613e-02 + 34 1.02802045334771e+01 -4.07208181339083e-02 + 35 1.02748654999713e+01 -4.06994619998850e-02 + 36 1.02687985973514e+01 -4.06751943894056e-02 + 37 1.02622769033932e+01 -4.06491076135727e-02 + 38 1.02555502383063e+01 -4.06222009532253e-02 + 39 1.02488335287781e+01 -4.05953341151125e-02 + 40 1.02422968531579e+01 -4.05691874126314e-02 diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out index 66c642d91..0267e6c70 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,48 +1,51 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: http://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is available. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. +colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Writing to colvar trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: The following index groups were read from the index file "index.ndx": -colvars: Protein (104 atoms). -colvars: Protein_noH (51 atoms). -colvars: Protein_Backbone (40 atoms). -colvars: Protein_C-alpha (10 atoms). -colvars: RMSD_atoms (10 atoms). -colvars: Protein_C-alpha_1_2 (2 atoms). -colvars: Protein_C-alpha_9_10 (2 atoms). -colvars: Protein_C-alpha_1 (1 atoms). -colvars: group1 (4 atoms). -colvars: Protein_C-alpha_2 (1 atoms). -colvars: group2 (4 atoms). -colvars: Protein_C-alpha_3 (1 atoms). -colvars: group3 (4 atoms). -colvars: Protein_C-alpha_4 (1 atoms). -colvars: group4 (4 atoms). -colvars: Protein_C-alpha_5 (1 atoms). -colvars: group5 (4 atoms). -colvars: Protein_C-alpha_6 (1 atoms). -colvars: group6 (4 atoms). -colvars: Protein_C-alpha_7 (1 atoms). -colvars: group7 (4 atoms). -colvars: Protein_C-alpha_8 (1 atoms). -colvars: group8 (4 atoms). -colvars: Protein_C-alpha_9 (1 atoms). -colvars: group9 (4 atoms). -colvars: Protein_C-alpha_10 (1 atoms). -colvars: group10 (4 atoms). -colvars: heavy_atoms (51 atoms). +colvars: # units = "" [default] +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) colvars: # smp = on [default] -colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -56,32 +59,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.72. +colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: Initializing a new "distanceVec" component. @@ -94,39 +97,45 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. +colvars: Warning: Variable r1 is absent from expression "x". +colvars: Warning: Variable r2 is absent from expression "x". +colvars: Warning: Variable r3 is absent from expression "x". +colvars: Warning: Variable r2 is absent from expression "cos(x) + r1 + r3". colvars: Expecting colvar value of type n-dimensional vector of size 2. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -134,13 +143,17 @@ colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } +colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] +colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] @@ -148,7 +161,9 @@ colvars: # centers = { ( 20 , -5 ) } colvars: # targetCenters = { ( 20 , -5 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 1 according to the specified width (1). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -157,16 +172,39 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceVec colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - Custom functions (Lepton): +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 54.028. -colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 54.028. -colvars: Re-initialized atom group one:1/0. 4 atoms: total mass = 54.028. -colvars: Re-initialized atom group one:1/1. 4 atoms: total mass = 54.028. +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 0383e1a55..318d67a54 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.25547985288590e+00 , -5.47738843832200e+00 ) + x ( 3.25547985268017e+00 , -5.47738843838940e+00 ) } restraint { diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj index 4339c71c0..1e5db1022 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one 0 ( 3.20554673468334e+00 , -5.48239480832893e+00 ) - 1 ( 3.20450053401237e+00 , -5.47990257545915e+00 ) - 2 ( 3.20435467486442e+00 , -5.47779766549509e+00 ) - 3 ( 3.20511804594931e+00 , -5.47623313988732e+00 ) - 4 ( 3.20675835826968e+00 , -5.47530637697787e+00 ) - 5 ( 3.20920474892822e+00 , -5.47505494785474e+00 ) - 6 ( 3.21235235537689e+00 , -5.47545779404524e+00 ) - 7 ( 3.21606826731175e+00 , -5.47644105785165e+00 ) - 8 ( 3.22019856592551e+00 , -5.47788745971902e+00 ) - 9 ( 3.22457647537524e+00 , -5.47964779043249e+00 ) - 10 ( 3.22903172000991e+00 , -5.48155318035021e+00 ) - 11 ( 3.23340084481198e+00 , -5.48342703484273e+00 ) - 12 ( 3.23753771533118e+00 , -5.48509601106745e+00 ) - 13 ( 3.24132302084013e+00 , -5.48639968496354e+00 ) - 14 ( 3.24467151159499e+00 , -5.48719873294262e+00 ) - 15 ( 3.24753606978343e+00 , -5.48738134514202e+00 ) - 16 ( 3.24990839073177e+00 , -5.48686751974010e+00 ) - 17 ( 3.25181665228529e+00 , -5.48561085836232e+00 ) - 18 ( 3.25332092201882e+00 , -5.48359768712336e+00 ) - 19 ( 3.25450708242444e+00 , -5.48084366843255e+00 ) - 20 ( 3.25547985288590e+00 , -5.47738843832200e+00 ) + 1 ( 3.20450053401175e+00 , -5.47990257545904e+00 ) + 2 ( 3.20435467486190e+00 , -5.47779766549469e+00 ) + 3 ( 3.20511804594360e+00 , -5.47623313988655e+00 ) + 4 ( 3.20675835825949e+00 , -5.47530637697672e+00 ) + 5 ( 3.20920474891228e+00 , -5.47505494785335e+00 ) + 6 ( 3.21235235535399e+00 , -5.47545779404383e+00 ) + 7 ( 3.21606826728072e+00 , -5.47644105785056e+00 ) + 8 ( 3.22019856588528e+00 , -5.47788745971868e+00 ) + 9 ( 3.22457647532480e+00 , -5.47964779043341e+00 ) + 10 ( 3.22903171994837e+00 , -5.48155318035299e+00 ) + 11 ( 3.23340084473853e+00 , -5.48342703484804e+00 ) + 12 ( 3.23753771524510e+00 , -5.48509601107600e+00 ) + 13 ( 3.24132302074078e+00 , -5.48639968497611e+00 ) + 14 ( 3.24467151148181e+00 , -5.48719873296004e+00 ) + 15 ( 3.24753606965591e+00 , -5.48738134516515e+00 ) + 16 ( 3.24990839058944e+00 , -5.48686751976987e+00 ) + 17 ( 3.25181665212772e+00 , -5.48561085839974e+00 ) + 18 ( 3.25332092184557e+00 , -5.48359768716950e+00 ) + 19 ( 3.25450708223514e+00 , -5.48084366848863e+00 ) + 20 ( 3.25547985268017e+00 , -5.47738843838940e+00 ) diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out index f79039b3e..c1e36fd05 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,48 +1,51 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: http://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is available. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. +colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Writing to colvar trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: The following index groups were read from the index file "index.ndx": -colvars: Protein (104 atoms). -colvars: Protein_noH (51 atoms). -colvars: Protein_Backbone (40 atoms). -colvars: Protein_C-alpha (10 atoms). -colvars: RMSD_atoms (10 atoms). -colvars: Protein_C-alpha_1_2 (2 atoms). -colvars: Protein_C-alpha_9_10 (2 atoms). -colvars: Protein_C-alpha_1 (1 atoms). -colvars: group1 (4 atoms). -colvars: Protein_C-alpha_2 (1 atoms). -colvars: group2 (4 atoms). -colvars: Protein_C-alpha_3 (1 atoms). -colvars: group3 (4 atoms). -colvars: Protein_C-alpha_4 (1 atoms). -colvars: group4 (4 atoms). -colvars: Protein_C-alpha_5 (1 atoms). -colvars: group5 (4 atoms). -colvars: Protein_C-alpha_6 (1 atoms). -colvars: group6 (4 atoms). -colvars: Protein_C-alpha_7 (1 atoms). -colvars: group7 (4 atoms). -colvars: Protein_C-alpha_8 (1 atoms). -colvars: group8 (4 atoms). -colvars: Protein_C-alpha_9 (1 atoms). -colvars: group9 (4 atoms). -colvars: Protein_C-alpha_10 (1 atoms). -colvars: group10 (4 atoms). -colvars: heavy_atoms (51 atoms). +colvars: # units = "" [default] +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) colvars: # smp = on [default] -colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -56,32 +59,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.72. +colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: Initializing a new "distanceVec" component. @@ -94,39 +97,45 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. +colvars: Warning: Variable r1 is absent from expression "x". +colvars: Warning: Variable r2 is absent from expression "x". +colvars: Warning: Variable r3 is absent from expression "x". +colvars: Warning: Variable r2 is absent from expression "cos(x) + r1 + r3". colvars: Expecting colvar value of type n-dimensional vector of size 2. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -134,13 +143,17 @@ colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } +colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] +colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] @@ -148,7 +161,9 @@ colvars: # centers = { ( 20 , -5 ) } colvars: # targetCenters = { ( 20 , -5 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 1 according to the specified width (1). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -157,20 +172,44 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceVec colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - Custom functions (Lepton): +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 3.25548 , -5.47739 ) +colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 54.028. -colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 54.028. -colvars: Re-initialized atom group one:1/0. 4 atoms: total mass = 54.028. -colvars: Re-initialized atom group one:1/1. 4 atoms: total mass = 54.028. +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Saving collective variables state to "test.restart.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Saving collective variables state to "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index a96c3f221..c9ce1cfcf 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.32026945594503e+00 , -5.34818539676131e+00 ) + x ( 3.32026945546912e+00 , -5.34818539717392e+00 ) } restraint { diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 5de5660db..fd675d4fa 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one - 20 ( 3.25547985288590e+00 , -5.47738843832200e+00 ) - 21 ( 3.25635522916335e+00 , -5.47328901186553e+00 ) - 22 ( 3.25725254129003e+00 , -5.46861283241705e+00 ) - 23 ( 3.25828644130248e+00 , -5.46343113068098e+00 ) - 24 ( 3.25955938762362e+00 , -5.45781309210418e+00 ) - 25 ( 3.26115536856813e+00 , -5.45182122562873e+00 ) - 26 ( 3.26313553215147e+00 , -5.44550828295996e+00 ) - 27 ( 3.26553608614507e+00 , -5.43891612718894e+00 ) - 28 ( 3.26836835336136e+00 , -5.43207683668482e+00 ) - 29 ( 3.27162052096783e+00 , -5.42501611649609e+00 ) - 30 ( 3.27526059101041e+00 , -5.41775865685059e+00 ) - 31 ( 3.27924018722449e+00 , -5.41033456540318e+00 ) - 32 ( 3.28349904535004e+00 , -5.40278559099195e+00 ) - 33 ( 3.28797000683518e+00 , -5.39516984621977e+00 ) - 34 ( 3.29258420395217e+00 , -5.38756403097662e+00 ) - 35 ( 3.29727601965859e+00 , -5.38006282876905e+00 ) - 36 ( 3.30198732335696e+00 , -5.37277582333816e+00 ) - 37 ( 3.30667059744180e+00 , -5.36582266862542e+00 ) - 38 ( 3.31129085438830e+00 , -5.35932721088458e+00 ) - 39 ( 3.31582650783507e+00 , -5.35341088133938e+00 ) - 40 ( 3.32026945594503e+00 , -5.34818539676131e+00 ) + 20 ( 3.25547985268017e+00 , -5.47738843838940e+00 ) + 21 ( 3.25635522894088e+00 , -5.47328901194575e+00 ) + 22 ( 3.25725254105058e+00 , -5.46861283251178e+00 ) + 23 ( 3.25828644104589e+00 , -5.46343113079200e+00 ) + 24 ( 3.25955938734984e+00 , -5.45781309223334e+00 ) + 25 ( 3.26115536827722e+00 , -5.45182122577788e+00 ) + 26 ( 3.26313553184362e+00 , -5.44550828313081e+00 ) + 27 ( 3.26553608582059e+00 , -5.43891612738297e+00 ) + 28 ( 3.26836835302064e+00 , -5.43207683690314e+00 ) + 29 ( 3.27162052061137e+00 , -5.42501611673935e+00 ) + 30 ( 3.27526059063876e+00 , -5.41775865711888e+00 ) + 31 ( 3.27924018683827e+00 , -5.41033456569601e+00 ) + 32 ( 3.28349904494989e+00 , -5.40278559130820e+00 ) + 33 ( 3.28797000642183e+00 , -5.39516984655777e+00 ) + 34 ( 3.29258420352640e+00 , -5.38756403133415e+00 ) + 35 ( 3.29727601922130e+00 , -5.38006282914348e+00 ) + 36 ( 3.30198732290916e+00 , -5.37277582372652e+00 ) + 37 ( 3.30667059698468e+00 , -5.36582266902454e+00 ) + 38 ( 3.31129085392325e+00 , -5.35932721129127e+00 ) + 39 ( 3.31582650736369e+00 , -5.35341088175048e+00 ) + 40 ( 3.32026945546912e+00 , -5.34818539717392e+00 ) diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt b/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt index b7bf5455c..157cac038 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-10-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_dihedralPC_abf2d/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dihedralPC_abf2d/AutoDiff/test.colvars.state.stripped index e7e077dc2..63ece5809 100644 --- a/namd/tests/library/000_dihedralPC_abf2d/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dihedralPC_abf2d/AutoDiff/test.colvars.state.stripped @@ -5,16 +5,16 @@ configuration { colvar { name one - x -1.07125200380591e+00 - extended_x -1.14502810666269e+00 - extended_v 4.95564329068073e-03 + x -1.07138955585665e+00 + extended_x -1.14562476858342e+00 + extended_v 4.99210251616576e-03 } colvar { name two - x -2.08003771427216e+00 - extended_x -2.11383784748319e+00 - extended_v -1.36281501667060e-03 + x -2.07996825855988e+00 + extended_x -2.11359237961121e+00 + extended_v -1.38673870606335e-03 } abf { @@ -72,8 +72,8 @@ samples 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 7 - 13 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 6 + 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 @@ -277,8 +277,8 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -4.44217917439085e+00 -5.98164763101832e-02 - -1.27364364576590e+00 5.92207052437209e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -4.58813053768885e+00 -2.04203085025158e-01 + -1.47974303036444e+00 6.34264008246081e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -742,8 +742,8 @@ z_gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -1.99167734468048e+00 8.18204122082025e-01 - -1.10446519237127e-01 1.29634199488531e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -2.02437284919381e+00 8.31267182057937e-01 + -1.18168483290997e-01 1.41756073716440e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -751,7 +751,7 @@ z_gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -4.41379423028293e+00 4.48413868549199e-01 -4.68422646703017e+00 -9.21947758969847e-01 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -4.45119053138215e+00 4.87710364809453e-01 -4.72507054399555e+00 -8.96116534859770e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_dihedralPC_abf2d/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dihedralPC_abf2d/AutoDiff/test.restart.colvars.state.stripped index 79c22e76f..80a29c2d0 100644 --- a/namd/tests/library/000_dihedralPC_abf2d/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dihedralPC_abf2d/AutoDiff/test.restart.colvars.state.stripped @@ -5,16 +5,16 @@ configuration { colvar { name one - x -1.13179064675608e+00 - extended_x -1.00821119176407e+00 - extended_v 5.18736771376423e-03 + x -1.13197161390512e+00 + extended_x -1.00850210662739e+00 + extended_v 5.26399951143340e-03 } colvar { name two - x -2.08292882801807e+00 - extended_x -2.10748583893117e+00 - extended_v 2.29199416893047e-03 + x -2.08284255790243e+00 + extended_x -2.10748148531090e+00 + extended_v 2.24780631834573e-03 } abf { @@ -73,11 +73,11 @@ samples 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 - 13 0 0 0 0 0 0 0 + 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 0 0 13 0 0 0 0 0 + 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 @@ -277,8 +277,8 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -3.73396120561055e+00 -1.75628766709736e+00 - -1.27364364576590e+00 5.92207052437209e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -3.54536635159579e+00 -2.13141186228562e+00 + -1.47974303036444e+00 6.34264008246081e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -286,7 +286,7 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 3.34288912937489e+00 -3.44051808013774e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 3.64648384718580e+00 -3.33271622311002e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -538,11 +538,11 @@ z_samples 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 - 14 0 0 0 0 0 0 0 + 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 0 0 3 13 0 0 0 0 + 0 0 3 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 @@ -742,8 +742,8 @@ z_gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -1.99167734468048e+00 8.18204122082025e-01 - 3.06576718993810e+00 -2.18500214664296e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -2.02437284919381e+00 8.31267182057937e-01 + 2.88659177839596e+00 -2.32398202632015e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -751,7 +751,7 @@ z_gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -4.41379423028293e+00 4.48413868549199e-01 -2.70291154716236e+00 -3.11948642099510e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -4.45119053138215e+00 4.87710364809453e-01 -3.02460848092237e+00 -2.98906142950661e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt b/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt index 8b2783508..157cac038 100644 --- a/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt +++ b/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2019-08-17". -colvars: Using NAMD interface, version "2019-08-17". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.out b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.out index afc18582f..44ca3d5aa 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -53,9 +57,12 @@ colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] +colvars: Warning: cannot cite unknown feature "dihedPC colvar component" colvars: # psfSegID = "BH" colvars: # vectorFile = "../Common/eigenvectors-localmin" colvars: # vectorNumber = 1 +colvars: Warning: cannot cite unknown feature "dihedralPC colvar component (derived from dihedPC)" +colvars: Warning: cannot cite unknown feature "dihedPC colvar component" colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.2 @@ -93,9 +100,12 @@ colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] +colvars: Warning: cannot cite unknown feature "dihedPC colvar component" colvars: # psfSegID = "BH" colvars: # vectorFile = "../Common/eigenvectors-localmin" colvars: # vectorNumber = 2 +colvars: Warning: cannot cite unknown feature "dihedralPC colvar component (derived from dihedPC)" +colvars: Warning: cannot cite unknown feature "dihedPC colvar component" colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.2 @@ -160,157 +170,29 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (30 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. -colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. -colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/3. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/4. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/5. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/6. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/7. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/8. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/9. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/10. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/11. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/12. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/13. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/14. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/15. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/16. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/17. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/18. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/19. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/20. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/21. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/22. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/23. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/24. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/25. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/26. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/27. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/28. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/29. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/30. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/31. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/32. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/33. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/34. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/35. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/36. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/37. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/38. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/39. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/40. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/41. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/42. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/43. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/44. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/45. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/46. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/47. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/48. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/49. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/50. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/51. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/52. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/53. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/54. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/55. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/56. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/57. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/58. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/59. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/60. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/61. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/62. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/63. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/64. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/65. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/66. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/67. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/68. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/69. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/70. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/71. 1 atoms: total mass = 12.011, total charge = 0.55. -colvars: Re-initialized atom group for variable "two":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. -colvars: Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. -colvars: Re-initialized atom group for variable "two":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/3. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/4. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/5. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/6. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/7. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/8. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/9. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/10. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/11. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/12. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/13. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/14. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/15. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/16. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/17. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/18. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/19. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/20. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/21. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/22. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/23. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/24. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/25. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/26. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/27. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/28. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/29. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/30. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/31. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/32. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/33. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/34. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/35. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/36. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/37. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/38. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/39. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/40. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/41. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/42. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/43. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/44. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/45. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/46. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/47. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/48. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/49. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/50. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/51. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/52. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/53. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/54. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/55. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/56. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/57. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/58. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/59. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/60. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/61. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/62. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/63. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/64. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/65. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/66. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/67. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/68. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/69. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/70. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/71. 1 atoms: total mass = 12.011, total charge = 0.55. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - BAOA integrator: +colvars: BouRabee2010 https://doi.org/10.1137/090758842 +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - dihedral colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (30 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.state.stripped index 6e70950e5..52f25a95a 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.state.stripped @@ -5,16 +5,16 @@ configuration { colvar { name one - x -1.07125254953554e+00 - extended_x -1.14504260899319e+00 - extended_v 4.95309531977019e-03 + x -1.07139020852240e+00 + extended_x -1.14563889103481e+00 + extended_v 4.98962426723432e-03 } colvar { name two - x -2.08003709484154e+00 - extended_x -2.11384256732221e+00 - extended_v -1.36924161929424e-03 + x -2.07996734380763e+00 + extended_x -2.11357763689771e+00 + extended_v -1.39054429900791e-03 } metadynamics { @@ -113,8 +113,8 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.11272221887018e-06 2.98620452056995e-06 - 2.95292942514468e-06 1.07588595058025e-06 1.04746276876539e-07 + 0.00000000000000e+00 1.12314993914291e-06 3.01875063256813e-06 + 2.98967234334661e-06 1.09095163400181e-06 1.06350524430211e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -124,9 +124,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 3.02837109654147e-07 5.96326142927254e-06 - 4.32739423279661e-05 1.15724155940458e-04 1.14041074951682e-04 - 4.14114998361346e-05 5.54094393591201e-06 1.92821479119623e-07 + 0.00000000000000e+00 3.03946727865229e-07 5.99392481473353e-06 + 4.35611652049253e-05 1.16667276734088e-04 1.15144883787325e-04 + 4.18763407579725e-05 5.61179567242265e-06 1.95573050903909e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -136,9 +136,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 4.39937759918221e-06 8.63016936797653e-05 6.23927594389754e-04 - 1.66237273653295e-03 1.63226945208545e-03 5.90625112625675e-04 - 7.87541801100468e-05 3.86954470159011e-06 0.00000000000000e+00 + 4.40353925722969e-06 8.65096296384818e-05 6.26354678394888e-04 + 1.67132922370537e-03 1.64353635129118e-03 5.95606609525681e-04 + 7.95403451484122e-05 3.91422606348301e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 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2.72982655182499e-06 -8.62124484546621e-05 1.66836673591529e-04 - -1.66926513480357e-03 2.29386778046841e-03 -1.19107010519156e-02 - 9.71164584166047e-03 -3.13197723555859e-02 8.10620467413459e-03 - -3.03514357039363e-02 -8.96668849993800e-03 -1.08399354903456e-02 - -9.18519145818739e-03 -1.42680840627485e-03 -1.99314028183449e-03 - -6.92146433369001e-05 -1.34564127221374e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 -1.05308070205675e-06 + 2.70072121126136e-06 -8.54761997756620e-05 1.65218374170491e-04 + -1.65737303516390e-03 2.27524888165342e-03 -1.18428950494345e-02 + 9.65060461944134e-03 -3.11868017323176e-02 8.08427276598510e-03 + -3.02670010114878e-02 -8.90285590129101e-03 -1.08258271173117e-02 + -9.14976736682080e-03 -1.42708773862744e-03 -1.98917857637688e-03 + -6.93330057577516e-05 -1.34521797906847e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -775,12 +775,12 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 -1.36513057193848e-05 - 1.69701008487424e-05 -2.63207116163892e-04 2.32422057577011e-04 - -1.86997470368458e-03 9.79540784972136e-04 -4.89560825894587e-03 - 8.10258909875143e-04 -4.72309338236105e-03 -9.06301161337512e-04 - -1.67922634165552e-03 -9.20777103118081e-04 -2.20022066157373e-04 - -1.98859451902330e-04 -1.06244489234353e-05 -1.33689752024101e-05 + 0.00000000000000e+00 0.00000000000000e+00 -1.34888303712637e-05 + 1.67577772772305e-05 -2.60443974015987e-04 2.29879107029597e-04 + -1.85299637318233e-03 9.70603546217200e-04 -4.85817829940636e-03 + 8.05758430618162e-04 -4.69382922174756e-03 -8.97298852534430e-04 + -1.67128351252832e-03 -9.14591855365312e-04 -2.19307545664087e-04 + -1.97891517730209e-04 -1.06058770455875e-05 -1.33260544108719e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -799,11 +799,11 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 -1.34249503290855e-05 - 8.72657592688637e-06 -9.50251734349522e-05 3.66197644800541e-05 - -2.47829339986562e-04 3.00298656968067e-05 -2.38163556810107e-04 - -3.39492139153494e-05 -8.43383654480558e-05 -3.42215774411738e-05 - -1.10057368970433e-05 -7.35702561533471e-06 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 -1.32424095282496e-05 + 8.60631551197807e-06 -9.38667242189058e-05 3.61811420924296e-05 + -2.45160147457255e-04 2.97770421127166e-05 -2.35940433026644e-04 + -3.35158984837922e-05 -8.36735365256005e-05 -3.38932818931820e-05 + -1.09351340344721e-05 -7.29991879265744e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -824,8 +824,8 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 -3.05287259864765e-06 2.78323604553755e-07 - -2.84872107053183e-06 -3.43165183419302e-07 0.00000000000000e+00 + 0.00000000000000e+00 -3.01033081659652e-06 2.75115485791023e-07 + -2.81274758556462e-06 -3.37830039549844e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -1267,7 +1267,7 @@ grid_parameters { hill { step 20 weight 1.00000000000000e-02 - centers -1.14504260899319e+00 -2.11384256732221e+00 + centers -1.14563889103481e+00 -2.11357763689771e+00 widths 4.00000000000000e-01 4.00000000000000e-01 } } diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.traj b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.traj index f81c1c442..d9eb4de40 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one r_one two r_two 0 -1.19120112453471e+00 -1.19120112453471e+00 -2.09082981124238e+00 -2.09082981124238e+00 - 1 -1.19027227984283e+00 -1.19124908071137e+00 -2.09272452828860e+00 -2.09131020072356e+00 - 2 -1.18860275847737e+00 -1.19086689001131e+00 -2.09473851565547e+00 -2.09183146277416e+00 - 3 -1.18597722231747e+00 -1.19014685214326e+00 -2.09686481359922e+00 -2.09248820782692e+00 - 4 -1.18224857030905e+00 -1.18928506434606e+00 -2.09912110640348e+00 -2.09336207910669e+00 - 5 -1.17735136609492e+00 -1.18855275634259e+00 -2.10153230998990e+00 -2.09402942053557e+00 - 6 -1.17130603191809e+00 -1.18747237788461e+00 -2.10410658903753e+00 -2.09454320173110e+00 - 7 -1.16420908070740e+00 -1.18639347095792e+00 -2.10681301108330e+00 -2.09483211417828e+00 - 8 -1.15621579326938e+00 -1.18469189867095e+00 -2.10956424855819e+00 -2.09525358847313e+00 - 9 -1.14751719163916e+00 -1.18283117790964e+00 -2.11220923830592e+00 -2.09575640198447e+00 - 10 -1.13832391425078e+00 -1.18115243403772e+00 -2.11453576969846e+00 -2.09680281256878e+00 - 11 -1.12885821355440e+00 -1.17896424379998e+00 -2.11628609148056e+00 -2.09772192445714e+00 - 12 -1.11935210305029e+00 -1.17636425683617e+00 -2.11718283826894e+00 -2.09860338562464e+00 - 13 -1.11005124649393e+00 -1.17381445295915e+00 -2.11696507708109e+00 -2.10015087471355e+00 - 14 -1.10121713693430e+00 -1.17107437388848e+00 -2.11542832708559e+00 -2.10209549655041e+00 - 15 -1.09312013054900e+00 -1.16760587753595e+00 -2.11245850155019e+00 -2.10449110700785e+00 - 16 -1.08602180598940e+00 -1.16380338986179e+00 -2.10805487668867e+00 -2.10675465879423e+00 - 17 -1.08015289148595e+00 -1.15940799224662e+00 -2.10233613753236e+00 -2.10897120789576e+00 - 18 -1.07568672699449e+00 -1.15490408207339e+00 -2.09553343073553e+00 -2.11077273010373e+00 - 19 -1.07271887790079e+00 -1.14999570431296e+00 -2.08797050187549e+00 -2.11247332570291e+00 - 20 -1.07125254953554e+00 -1.14504260899319e+00 -2.08003709484154e+00 -2.11384256732221e+00 + 1 -1.19027227984131e+00 -1.19122509063899e+00 -2.09272452828756e+00 -2.09106988593563e+00 + 2 -1.18860279572505e+00 -1.19105622344705e+00 -2.09473807622652e+00 -2.09157420153440e+00 + 3 -1.18597782336080e+00 -1.19050026294611e+00 -2.09686341317830e+00 -2.09217061005793e+00 + 4 -1.18225064361509e+00 -1.18969947067829e+00 -2.09911811660717e+00 -2.09294738186964e+00 + 5 -1.17735595274439e+00 -1.18888526208100e+00 -2.10152699097941e+00 -2.09373379973339e+00 + 6 -1.17131388098621e+00 -1.18795230094496e+00 -2.10409853321966e+00 -2.09434484583846e+00 + 7 -1.16422120861076e+00 -1.18683446829184e+00 -2.10680202332709e+00 -2.09477158450896e+00 + 8 -1.15623299784273e+00 -1.18539262882474e+00 -2.10955045442136e+00 -2.09515715374536e+00 + 9 -1.14754082207020e+00 -1.18354496916368e+00 -2.11219266615327e+00 -2.09565453819700e+00 + 10 -1.13835521812589e+00 -1.18169250757862e+00 -2.11451646147957e+00 -2.09646879267398e+00 + 11 -1.12889790952415e+00 -1.17965969598956e+00 -2.11626378075907e+00 -2.09749414764173e+00 + 12 -1.11940107658313e+00 -1.17714954760921e+00 -2.11715740039687e+00 -2.09843951571168e+00 + 13 -1.11011037398052e+00 -1.17444215486761e+00 -2.11693647157491e+00 -2.09969948601932e+00 + 14 -1.10128678465993e+00 -1.17164919615408e+00 -2.11539611430731e+00 -2.10148749607165e+00 + 15 -1.09320038702157e+00 -1.16838311261147e+00 -2.11242202032470e+00 -2.10369475078562e+00 + 16 -1.08611325009073e+00 -1.16457421982529e+00 -2.10801302635965e+00 -2.10605379202963e+00 + 17 -1.08025584704120e+00 -1.16029294007998e+00 -2.10228802270478e+00 -2.10831277817717e+00 + 18 -1.07580163447542e+00 -1.15565515108412e+00 -2.09547821716303e+00 -2.11032759787176e+00 + 19 -1.07284542049665e+00 -1.15075858835322e+00 -2.08790799432598e+00 -2.11206911002397e+00 + 20 -1.07139020852240e+00 -1.14563889103481e+00 -2.07996734380763e+00 -2.11357763689771e+00 diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.pmf b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.pmf index 867d3bb98..4fa817b6a 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.pmf +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.pmf @@ -2,1262 +2,1262 @@ # -3.50000000000000e+00 2.00000000000000e-01 35 0 # -3.50000000000000e+00 2.00000000000000e-01 35 0 - -3.40000000000000e+00 -3.40000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -3.20000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -3.00000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -2.80000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -2.60000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -2.40000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -2.20000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -2.00000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -1.80000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -1.60000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -1.40000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -1.20000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -1.00000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 -8.00000000000000e-01 1.74910007203883e-02 - -3.40000000000000e+00 -6.00000000000000e-01 1.74910007203883e-02 - -3.40000000000000e+00 -4.00000000000000e-01 1.74910007203883e-02 - -3.40000000000000e+00 -2.00000000000000e-01 1.74910007203883e-02 - -3.40000000000000e+00 0.00000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 2.00000000000000e-01 1.74910007203883e-02 - -3.40000000000000e+00 4.00000000000000e-01 1.74910007203883e-02 - -3.40000000000000e+00 6.00000000000001e-01 1.74910007203883e-02 - -3.40000000000000e+00 8.00000000000000e-01 1.74910007203883e-02 - -3.40000000000000e+00 1.00000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 1.20000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 1.40000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 1.60000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 1.80000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 2.00000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 2.20000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 2.40000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 2.60000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 2.80000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 3.00000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 3.20000000000000e+00 1.74910007203883e-02 - -3.40000000000000e+00 3.40000000000000e+00 1.74910007203883e-02 + -3.40000000000000e+00 -3.40000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -3.20000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -3.00000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -2.80000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -2.60000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -2.40000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -2.20000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -2.00000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -1.80000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -1.60000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -1.40000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -1.20000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -1.00000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 -8.00000000000000e-01 1.74878015727524e-02 + -3.40000000000000e+00 -6.00000000000000e-01 1.74878015727524e-02 + -3.40000000000000e+00 -4.00000000000000e-01 1.74878015727524e-02 + -3.40000000000000e+00 -2.00000000000000e-01 1.74878015727524e-02 + -3.40000000000000e+00 0.00000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 2.00000000000000e-01 1.74878015727524e-02 + -3.40000000000000e+00 4.00000000000000e-01 1.74878015727524e-02 + -3.40000000000000e+00 6.00000000000001e-01 1.74878015727524e-02 + -3.40000000000000e+00 8.00000000000000e-01 1.74878015727524e-02 + -3.40000000000000e+00 1.00000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 1.20000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 1.40000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 1.60000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 1.80000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 2.00000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 2.20000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 2.40000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 2.60000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 2.80000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 3.00000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 3.20000000000000e+00 1.74878015727524e-02 + -3.40000000000000e+00 3.40000000000000e+00 1.74878015727524e-02 - -3.20000000000000e+00 -3.40000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -3.20000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -3.00000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -2.80000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -2.60000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -2.40000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -2.20000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -2.00000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -1.80000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -1.60000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -1.40000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -1.20000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -1.00000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 -8.00000000000000e-01 1.74910007203883e-02 - -3.20000000000000e+00 -6.00000000000000e-01 1.74910007203883e-02 - -3.20000000000000e+00 -4.00000000000000e-01 1.74910007203883e-02 - -3.20000000000000e+00 -2.00000000000000e-01 1.74910007203883e-02 - -3.20000000000000e+00 0.00000000000000e+00 1.74910007203883e-02 - -3.20000000000000e+00 2.00000000000000e-01 1.74910007203883e-02 - 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1.74878015727524e-02 + 3.20000000000000e+00 -2.00000000000000e-01 1.74878015727524e-02 + 3.20000000000000e+00 0.00000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 2.00000000000000e-01 1.74878015727524e-02 + 3.20000000000000e+00 4.00000000000000e-01 1.74878015727524e-02 + 3.20000000000000e+00 6.00000000000001e-01 1.74878015727524e-02 + 3.20000000000000e+00 8.00000000000000e-01 1.74878015727524e-02 + 3.20000000000000e+00 1.00000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 1.20000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 1.40000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 1.60000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 1.80000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 2.00000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 2.20000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 2.40000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 2.60000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 2.80000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 3.00000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 3.20000000000000e+00 1.74878015727524e-02 + 3.20000000000000e+00 3.40000000000000e+00 1.74878015727524e-02 - 3.40000000000000e+00 -3.40000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -3.20000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -3.00000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -2.80000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -2.60000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -2.40000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -2.20000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -2.00000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -1.80000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -1.60000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -1.40000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -1.20000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -1.00000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 -8.00000000000000e-01 1.74910007203883e-02 - 3.40000000000000e+00 -6.00000000000000e-01 1.74910007203883e-02 - 3.40000000000000e+00 -4.00000000000000e-01 1.74910007203883e-02 - 3.40000000000000e+00 -2.00000000000000e-01 1.74910007203883e-02 - 3.40000000000000e+00 0.00000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 2.00000000000000e-01 1.74910007203883e-02 - 3.40000000000000e+00 4.00000000000000e-01 1.74910007203883e-02 - 3.40000000000000e+00 6.00000000000001e-01 1.74910007203883e-02 - 3.40000000000000e+00 8.00000000000000e-01 1.74910007203883e-02 - 3.40000000000000e+00 1.00000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 1.20000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 1.40000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 1.60000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 1.80000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 2.00000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 2.20000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 2.40000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 2.60000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 2.80000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 3.00000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 3.20000000000000e+00 1.74910007203883e-02 - 3.40000000000000e+00 3.40000000000000e+00 1.74910007203883e-02 + 3.40000000000000e+00 -3.40000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -3.20000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -3.00000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -2.80000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -2.60000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -2.40000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -2.20000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -2.00000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -1.80000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -1.60000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -1.40000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -1.20000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -1.00000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 -8.00000000000000e-01 1.74878015727524e-02 + 3.40000000000000e+00 -6.00000000000000e-01 1.74878015727524e-02 + 3.40000000000000e+00 -4.00000000000000e-01 1.74878015727524e-02 + 3.40000000000000e+00 -2.00000000000000e-01 1.74878015727524e-02 + 3.40000000000000e+00 0.00000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 2.00000000000000e-01 1.74878015727524e-02 + 3.40000000000000e+00 4.00000000000000e-01 1.74878015727524e-02 + 3.40000000000000e+00 6.00000000000001e-01 1.74878015727524e-02 + 3.40000000000000e+00 8.00000000000000e-01 1.74878015727524e-02 + 3.40000000000000e+00 1.00000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 1.20000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 1.40000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 1.60000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 1.80000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 2.00000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 2.20000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 2.40000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 2.60000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 2.80000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 3.00000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 3.20000000000000e+00 1.74878015727524e-02 + 3.40000000000000e+00 3.40000000000000e+00 1.74878015727524e-02 diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out index 61704a1b8..2695e4d53 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -53,9 +57,12 @@ colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] +colvars: Warning: cannot cite unknown feature "dihedPC colvar component" colvars: # psfSegID = "BH" colvars: # vectorFile = "../Common/eigenvectors-localmin" colvars: # vectorNumber = 1 +colvars: Warning: cannot cite unknown feature "dihedralPC colvar component (derived from dihedPC)" +colvars: Warning: cannot cite unknown feature "dihedPC colvar component" colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.2 @@ -93,9 +100,12 @@ colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] +colvars: Warning: cannot cite unknown feature "dihedPC colvar component" colvars: # psfSegID = "BH" colvars: # vectorFile = "../Common/eigenvectors-localmin" colvars: # vectorNumber = 2 +colvars: Warning: cannot cite unknown feature "dihedralPC colvar component (derived from dihedPC)" +colvars: Warning: cannot cite unknown feature "dihedPC colvar component" colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.2 @@ -160,163 +170,37 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (30 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. -colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. -colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/3. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/4. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/5. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/6. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/7. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/8. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/9. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/10. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/11. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/12. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/13. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/14. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/15. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/16. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/17. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/18. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/19. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/20. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/21. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/22. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/23. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/24. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/25. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/26. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/27. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/28. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/29. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/30. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/31. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/32. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/33. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/34. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/35. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/36. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/37. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/38. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/39. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/40. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/41. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/42. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/43. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/44. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/45. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/46. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/47. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/48. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/49. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/50. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/51. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/52. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/53. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/54. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/55. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/56. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/57. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/58. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/59. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/60. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/61. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/62. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/63. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/64. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/65. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/66. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/67. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/68. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "one":0/69. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "one":0/70. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "one":0/71. 1 atoms: total mass = 12.011, total charge = 0.55. -colvars: Re-initialized atom group for variable "two":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. -colvars: Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. -colvars: Re-initialized atom group for variable "two":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/3. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/4. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/5. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/6. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/7. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/8. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/9. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/10. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/11. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/12. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/13. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/14. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/15. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/16. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/17. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/18. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/19. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/20. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/21. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/22. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/23. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/24. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/25. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/26. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/27. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/28. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/29. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/30. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/31. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/32. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/33. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/34. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/35. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/36. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/37. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/38. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/39. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/40. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/41. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/42. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/43. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/44. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/45. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/46. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/47. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/48. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/49. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/50. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/51. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/52. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/53. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/54. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/55. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/56. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/57. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/58. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/59. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/60. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/61. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/62. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/63. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/64. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/65. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/66. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/67. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/68. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "two":0/69. 1 atoms: total mass = 14.007, total charge = -0.47. -colvars: Re-initialized atom group for variable "two":0/70. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "two":0/71. 1 atoms: total mass = 12.011, total charge = 0.55. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - BAOA integrator: +colvars: BouRabee2010 https://doi.org/10.1137/090758842 +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - dihedral colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". -colvars: Restarting collective variable "one" from value: -1.07125 -colvars: Restarting collective variable "two" from value: -2.08004 +colvars: Loading state from file "test.colvars.state". +colvars: Restarting collective variable "one" from value: -1.07139 +colvars: Restarting collective variable "two" from value: -2.07997 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (30 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.state.stripped index 5d6526f3b..d09e6d782 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.state.stripped @@ -5,16 +5,16 @@ configuration { colvar { name one - x -1.13178988227807e+00 - extended_x -1.00800789919324e+00 - extended_v 5.23317358324059e-03 + x -1.13197437578394e+00 + extended_x -1.00834779777182e+00 + extended_v 5.30672069616506e-03 } colvar { name two - x -2.08296172274834e+00 - extended_x -2.10807875324241e+00 - extended_v 2.24662046396417e-03 + x -2.08286935214585e+00 + extended_x -2.10803774920239e+00 + extended_v 2.20179026067253e-03 } metadynamics { @@ -113,8 +113,8 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.11272221887018e-06 3.20247560132600e-06 - 3.14826775463842e-06 1.07588595058025e-06 1.04746276876539e-07 + 0.00000000000000e+00 1.12314993914291e-06 3.23835864283634e-06 + 3.18837574379657e-06 1.09095163400181e-06 1.06350524430211e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -124,9 +124,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 3.02837109654147e-07 6.96509766396487e-06 - 5.00408266117772e-05 1.32548907739626e-04 1.29439849105306e-04 - 4.65996300549532e-05 6.18442008747974e-06 1.92821479119623e-07 + 0.00000000000000e+00 3.03946727865229e-07 7.00371500812350e-06 + 5.03915754857089e-05 1.33673841558955e-04 1.30731416533348e-04 + 4.71347513413164e-05 6.26483667841322e-06 1.95573050903909e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -136,9 +136,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 5.72443446435168e-06 1.10702223097227e-04 7.89342949487738e-04 - 2.07520496075793e-03 2.01158594132007e-03 7.18937668622134e-04 - 9.47344660701261e-05 4.60229536357798e-06 0.00000000000000e+00 + 5.73306143241110e-06 1.11026517791148e-04 7.92784634891750e-04 + 2.08724242890717e-03 2.02617379828929e-03 7.25203347235883e-04 + 9.56999428328911e-05 4.65605648658524e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -147,10 +147,10 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 6.17283376926752e-07 3.57872560425740e-05 - 6.86658690634754e-04 4.85737685088278e-03 1.26684089516479e-02 - 1.21817456117681e-02 4.31885400361286e-03 5.64546780344434e-04 - 2.72082801176802e-05 3.66457595467656e-07 0.00000000000000e+00 + 0.00000000000000e+00 6.15473526526448e-07 3.57511371174026e-05 + 6.86910807524001e-04 4.86585949309658e-03 1.27080612572104e-02 + 1.22368061716961e-02 4.34441200475281e-03 5.68682201257651e-04 + 2.74461829454408e-05 3.70225422023879e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -159,10 +159,10 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1.72022127856507e-06 8.89224919517835e-05 1.69421293266856e-03 - 1.18979579718996e-02 3.07993876881154e-02 2.93894864791798e-02 - 1.03379617394403e-02 1.34054409437686e-03 6.40823087507254e-05 - 1.12930405068074e-06 0.00000000000000e+00 0.00000000000000e+00 + 1.71216163292921e-06 8.86226992378869e-05 1.69071477701497e-03 + 1.18888741601188e-02 3.08158497484176e-02 2.94433063569133e-02 + 1.03703095780873e-02 1.34648278346832e-03 6.44499235670144e-05 + 1.13726668389421e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -170,10 +170,10 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 1.73246135496388e-06 - 8.91423138330038e-05 1.69003866391095e-03 1.18064204015409e-02 - 3.03923554909611e-02 2.88303341389261e-02 1.00783114334844e-02 - 1.29834768467880e-03 6.16410978888387e-05 1.07853776015495e-06 + 0.00000000000000e+00 0.00000000000000e+00 1.72085789219159e-06 + 8.86546275675720e-05 1.68283704924228e-03 1.17702109928311e-02 + 3.03350346780391e-02 2.88096819057150e-02 1.00827913572633e-02 + 1.30042380111360e-03 6.18106065187528e-05 1.08274398801814e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -182,10 +182,10 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 6.45241406399235e-07 3.62581009655544e-05 - 6.86019423477795e-04 4.78122270850261e-03 1.22749965204361e-02 - 1.16089217624534e-02 4.04443948613133e-03 5.19072660864983e-04 - 2.45419041654891e-05 1.94351193496667e-07 0.00000000000000e+00 + 0.00000000000000e+00 6.40110451046741e-07 3.59957736136374e-05 + 6.81804356561631e-04 4.75694060096285e-03 1.22254492771890e-02 + 1.15739134150090e-02 4.03629375611645e-03 5.18538388577290e-04 + 2.45404627487981e-05 1.94188369698545e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -194,9 +194,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 5.94481770003537e-06 1.12553950524831e-04 - 7.84769788052063e-04 2.01504145944096e-03 1.90540164901014e-03 - 6.63514516510673e-04 8.50895118700598e-05 4.01849665239562e-06 + 0.00000000000000e+00 5.89321809187914e-06 1.11685155926194e-04 + 7.79441216284340e-04 2.00317016878846e-03 1.89583425089636e-03 + 6.60742618703458e-04 8.48037451826453e-05 4.00820366205230e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -206,9 +206,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.49806207958978e-07 7.34153117884373e-06 5.13002091042089e-05 - 1.31983317458996e-04 1.25020600426375e-04 4.36015519863556e-05 - 5.59854730476825e-06 1.86789361432100e-07 0.00000000000000e+00 + 2.46376451325848e-07 7.27495363428157e-06 5.08758698598880e-05 + 1.30992467689441e-04 1.24173710437319e-04 4.33369024818516e-05 + 5.56835625492613e-06 1.85961457424101e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -218,8 +218,8 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1.38698799766107e-07 1.23870531087997e-06 3.32350511267815e-06 - 3.15267519710571e-06 1.05941557843544e-06 1.13333618234241e-07 + 1.37680105931028e-07 1.22721624940429e-06 3.29393301416170e-06 + 3.12653235837878e-06 1.05141496482870e-06 1.12616606970089e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -613,10 +613,10 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 2.31278278352251e-05 - 8.26962949863584e-06 6.70101426836238e-05 7.71696384912329e-06 - 6.57864286672178e-05 -8.12395837749149e-06 2.23082932078077e-05 - -8.11698994547979e-06 2.14428084659913e-06 -1.30095612395932e-06 + 0.00000000000000e+00 0.00000000000000e+00 2.33293879058975e-05 + 8.35557849923944e-06 6.77183243752410e-05 7.82789396827317e-06 + 6.65824042666908e-05 -8.20318087986522e-06 2.26057618893020e-05 + -8.22221720635756e-06 2.17568577410462e-06 -1.31999291160277e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -635,12 +635,12 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 4.80299459692474e-06 - 5.26829305336511e-06 1.12914860981479e-04 8.60477281590471e-05 - 8.09442442815930e-04 3.68556903550862e-04 2.13938766228929e-03 - 3.14932664685857e-04 2.08473288097900e-03 -3.38273059244740e-04 - 7.48952093259965e-04 -3.54293043117682e-04 9.91933029491725e-05 - -7.78786897365226e-05 2.98317757546063e-06 -3.35896372435564e-06 + 0.00000000000000e+00 0.00000000000000e+00 4.81648910241581e-06 + 5.28982127756346e-06 1.13449453651543e-04 8.65756114647140e-05 + 8.14451880259520e-04 3.71508297407394e-04 2.15576489085002e-03 + 3.18589212263868e-04 2.10377558592384e-03 -3.40678793254122e-04 + 7.56911382756425e-04 -3.58009132265948e-04 1.00396942036513e-04 + -7.88441342498812e-05 3.02310706723988e-06 -3.40526316606529e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -659,12 +659,12 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 6.58378255243521e-05 9.90605970627213e-05 1.26885118524095e-03 - 1.36342394062139e-03 9.01620898582968e-03 5.78385629547920e-03 - 2.36222121999800e-02 4.85329215057413e-03 2.28192865540429e-02 - -5.33087139540405e-03 8.12767483154479e-03 -5.49194881035683e-03 - 1.06735157679088e-03 -1.19630852446980e-03 5.16792384229682e-05 - -8.10797574396904e-05 0.00000000000000e+00 0.00000000000000e+00 + 6.58637370230391e-05 9.92504907157671e-05 1.27113019737368e-03 + 1.36820749971712e-03 9.04510521961482e-03 5.81474005382660e-03 + 2.37313814577560e-02 4.89644456244732e-03 2.29572794235440e-02 + -5.35487488253978e-03 8.18849820322356e-03 -5.53452946914962e-03 + 1.07688470754396e-03 -1.20779814270557e-03 5.22163191894865e-05 + -8.19924299027048e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -681,14 +681,14 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 4.04162331229628e-06 - 1.37347876892220e-05 2.44882862400609e-04 6.17897446287810e-04 - 4.67233127021253e-03 8.42985517776889e-03 3.28618195800552e-02 - 3.53984019772030e-02 8.52018810361822e-02 2.91194572315694e-02 - 8.14368098888324e-02 -3.27726519651500e-02 2.86957806768867e-02 - -3.31652347035553e-02 3.72777703829194e-03 -7.15170771187374e-03 - 1.78534548944028e-04 -4.80416042362040e-04 2.12221807320614e-06 - -8.27133816749347e-06 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 4.02099776209912e-06 + 1.36991585099172e-05 2.44196102513867e-04 6.17519974219686e-04 + 4.66541723464651e-03 8.43767973348783e-03 3.28566199828025e-02 + 3.54937631183707e-02 8.53009002960734e-02 2.92984254683264e-02 + 8.16390529787792e-02 -3.28358994481630e-02 2.88050438539838e-02 + -3.33312158151046e-02 3.74692616895343e-03 -7.20010762897811e-03 + 1.79690244219923e-04 -4.84422881236418e-04 2.13880997815971e-06 + -8.35349572180457e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -705,13 +705,13 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.95914299263381e-06 3.82265818115122e-05 2.02037086714065e-04 - 1.53224688502224e-03 3.79693357510979e-03 2.07386192563353e-02 - 2.62793535788264e-02 8.62680519579717e-02 6.69859513210589e-02 - 6.96265991634228e-02 6.28850705079488e-02 -8.02098552660051e-02 - 2.17426933295632e-02 -7.97979076366115e-02 2.76877762172194e-03 - -1.70363530838813e-02 1.29860934060231e-04 -1.13413381211102e-03 - 2.24331993112255e-06 -2.56211807198152e-05 0.00000000000000e+00 + 3.92189414473847e-06 3.80588178247303e-05 2.00356320367603e-04 + 1.52766349047296e-03 3.76934074153100e-03 2.07068419908081e-02 + 2.61150485914872e-02 8.62794825027918e-02 6.66326637405550e-02 + 6.98635494439653e-02 6.26126531044651e-02 -8.01661646857379e-02 + 2.16682187931839e-02 -7.99804519353648e-02 2.76170920595249e-03 + -1.71030887565164e-02 1.29638392929760e-04 -1.14022013045465e-03 + 2.24128700614383e-06 -2.57943861992276e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -728,13 +728,13 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 -3.85692736858852e-06 3.84598905854972e-05 - -1.99889491075751e-04 1.53390535822502e-03 -3.81958508600884e-03 - 2.06444657246771e-02 -2.69117781956383e-02 8.52845055246836e-02 - -6.99177537611560e-02 6.78337427002428e-02 -6.69833084145879e-02 - -7.95584137167197e-02 -2.36641539096223e-02 -7.81155969285727e-02 - -3.08295817706694e-03 -1.65436113535291e-02 -1.48115055179706e-04 - -1.09308902085485e-03 -2.62412142627646e-06 -2.45087896271388e-05 + 0.00000000000000e+00 -3.84701790232031e-06 3.82130045596661e-05 + -1.99659473549772e-04 1.52605641327668e-03 -3.82060603334556e-03 + 2.05666495255184e-02 -2.69571529835613e-02 8.50930299065967e-02 + -7.01349803347731e-02 6.78843485105251e-02 -6.72868182850159e-02 + -7.93335064530012e-02 -2.38051951428986e-02 -7.80920041945267e-02 + -3.10575725653726e-03 -1.65625851980554e-02 -1.49424041298915e-04 + -1.09574050902469e-03 -2.65112006548936e-06 -2.45981679677064e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -751,14 +751,14 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 -4.19226242555207e-06 - 1.42954145039803e-05 -2.45072273022842e-04 6.23566580580924e-04 - -4.63879709725517e-03 8.37249316288454e-03 -3.23505057136338e-02 - 3.44774834632457e-02 -8.31257823346198e-02 2.72219965730463e-02 - -7.87015273646957e-02 -3.22213540117781e-02 -2.74559374639244e-02 - -3.14201465431150e-02 -3.52945080889722e-03 -6.62430323413701e-03 - -1.67188632757061e-04 -4.35736667346323e-04 -1.01066458662350e-06 - -4.41215473704067e-06 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 -4.16410899915809e-06 + 1.41853399537393e-05 -2.43588094311579e-04 6.19255198664553e-04 + -4.61619528552726e-03 8.32474788440458e-03 -3.22305588696707e-02 + 3.43275719390633e-02 -8.29129467210221e-02 2.71754035232290e-02 + -7.85891161952420e-02 -3.20655140963277e-02 -2.74474475059759e-02 + -3.13367887252739e-02 -3.53227208378628e-03 -6.61494872536247e-03 + -1.67506294950176e-04 -4.35592741300181e-04 -1.01146797948982e-06 + -4.40825925355873e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -775,12 +775,12 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 -6.73897475514336e-05 - 1.02262489546657e-04 -1.27492868464018e-03 1.37396571968713e-03 - -8.88342250162743e-03 5.66007716605609e-03 -2.27971787961938e-02 - 4.46864284603031e-03 -2.15472577516050e-02 -5.29151305869696e-03 - -7.50095458721570e-03 -5.15674286025331e-03 -9.61740662559205e-04 - -1.08630440780360e-03 -4.54170998866411e-05 -7.13739305008083e-05 + 0.00000000000000e+00 0.00000000000000e+00 -6.68438407314432e-05 + 1.01403924566886e-04 -1.26590039666148e-03 1.36389180532399e-03 + -8.82930526309527e-03 5.62522980734564e-03 -2.26802133032326e-02 + 4.45122383641948e-03 -2.14568482218361e-02 -5.25678316534657e-03 + -7.47631074454558e-03 -5.13244308359127e-03 -9.59435216283728e-04 + -1.08231249932260e-03 -4.53476713817755e-05 -7.11753056023775e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -799,12 +799,12 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -5.49155994289569e-06 6.01964865805263e-06 -1.17377894846997e-04 - 8.97034938878903e-05 -8.19507621917738e-04 3.70532657888432e-04 - -2.10674791883695e-03 2.93922685619022e-04 -1.99416723447505e-03 - -3.46175509065280e-04 -6.95018666345888e-04 -3.38562531455186e-04 - -8.91894914274312e-05 -7.14427583618481e-05 -2.83923518089943e-06 - -3.30653945404465e-06 0.00000000000000e+00 0.00000000000000e+00 + -3.74706428967292e-06 4.26208009507402e-06 -1.16360201643970e-04 + 8.89198795930162e-05 -8.13088135795563e-04 3.67667885594643e-04 + -2.09193957310727e-03 2.92210073233015e-04 -1.98169272965543e-03 + -3.43381365631709e-04 -6.91188435665462e-04 -3.36357047829999e-04 + -8.87619617025164e-05 -7.10389015412434e-05 -2.82823107735977e-06 + -3.29169329382394e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -823,10 +823,10 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -2.80174314549090e-06 1.70572216261814e-06 -2.54572956347690e-05 - 8.96199419526157e-06 -6.86466414453448e-05 7.42711051687085e-06 - -6.50628208131938e-05 -8.70902973668050e-06 -2.17210748865457e-05 - -8.21714377678674e-06 -2.28936146943544e-06 -1.43956008632260e-06 + -2.78233526065845e-06 1.69333537009704e-06 -2.52302258708530e-05 + 8.88272832596476e-06 -6.80602104811845e-05 7.37134848776804e-06 + -6.45479525225560e-05 -8.62750870311771e-06 -2.15660888307118e-05 + -8.15228971678873e-06 -2.27583465592016e-06 -1.43033718819736e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -1267,13 +1267,13 @@ grid_parameters { hill { step 30 weight 1.00000000000000e-02 - centers -1.07642948397421e+00 -2.12035990922620e+00 + centers -1.07712346073985e+00 -2.12000618454050e+00 widths 4.00000000000000e-01 4.00000000000000e-01 } hill { step 40 weight 1.00000000000000e-02 - centers -1.00800789919324e+00 -2.10807875324241e+00 + centers -1.00834779777182e+00 -2.10803774920239e+00 widths 4.00000000000000e-01 4.00000000000000e-01 } } diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.traj index d3a2457e5..815ac8fac 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one r_one two r_two - 20 -1.07125254953554e+00 -1.14504260899319e+00 -2.08003709484154e+00 -2.11384256732221e+00 - 21 -1.07119796918443e+00 -1.13985232700735e+00 -2.07215411011455e+00 -2.11556017658898e+00 - 22 -1.07238196627094e+00 -1.13397115957196e+00 -2.06473689576996e+00 -2.11714330518857e+00 - 23 -1.07456972666948e+00 -1.12752462497645e+00 -2.05815626048283e+00 -2.11864533464635e+00 - 24 -1.07749714966584e+00 -1.12075063661102e+00 -2.05270572735711e+00 -2.12011043298098e+00 - 25 -1.08090758091289e+00 -1.11397020265678e+00 -2.04857951018513e+00 -2.12108245515148e+00 - 26 -1.08458581444980e+00 -1.10676255472813e+00 -2.04586296155451e+00 -2.12158765929346e+00 - 27 -1.08837791545571e+00 -1.09953985926307e+00 -2.04453898245717e+00 -2.12153420708683e+00 - 28 -1.09219757379667e+00 -1.09174071275577e+00 -2.04450492888607e+00 -2.12126456175939e+00 - 29 -1.09601333021551e+00 -1.08389925842272e+00 -2.04559895948568e+00 -2.12071958611127e+00 - 30 -1.09982950294195e+00 -1.07642948397421e+00 -2.04762611374193e+00 -2.12035990922620e+00 - 31 -1.10366323002404e+00 -1.06871259846932e+00 -2.05038319291416e+00 -2.11952191064911e+00 - 32 -1.10752237362737e+00 -1.06092028249770e+00 -2.05367662138831e+00 -2.11830649523538e+00 - 33 -1.11139120516980e+00 -1.05358740527634e+00 -2.05733502902402e+00 -2.11743541238045e+00 - 34 -1.11522392549938e+00 -1.04654394287290e+00 -2.06121589004280e+00 -2.11666202023110e+00 - 35 -1.11894408707070e+00 -1.03931823572774e+00 -2.06520278625068e+00 -2.11607257620306e+00 - 36 -1.12244849901315e+00 -1.03236561806878e+00 -2.06919597301143e+00 -2.11512352898028e+00 - 37 -1.12561697198072e+00 -1.02548083118939e+00 -2.07309550431626e+00 -2.11394597129353e+00 - 38 -1.12831919699839e+00 -1.01919309486942e+00 -2.07678632360923e+00 -2.11222340556280e+00 - 39 -1.13042155168616e+00 -1.01324107277648e+00 -2.08012863616435e+00 -2.11032537370637e+00 - 40 -1.13178988227807e+00 -1.00800789919324e+00 -2.08296172274834e+00 -2.10807875324241e+00 + 20 -1.07139020852240e+00 -1.14563889103481e+00 -2.07996734380763e+00 -2.11357763689771e+00 + 21 -1.07134541827650e+00 -1.14038380434313e+00 -2.07207780857289e+00 -2.11507768654840e+00 + 22 -1.07253775201003e+00 -1.13467355748825e+00 -2.06465449633230e+00 -2.11666726427053e+00 + 23 -1.07473285920836e+00 -1.12834731056824e+00 -2.05806819168533e+00 -2.11813287779448e+00 + 24 -1.07766703492786e+00 -1.12158934211256e+00 -2.05261228995111e+00 -2.11952520866886e+00 + 25 -1.08108375161885e+00 -1.11468104542564e+00 -2.04848085769139e+00 -2.12064093922482e+00 + 26 -1.08476725468940e+00 -1.10757406333789e+00 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-1.02622424241271e+00 -2.07299922375146e+00 -2.11344349267500e+00 + 38 -1.12850747463206e+00 -1.01976327197941e+00 -2.07669134474466e+00 -2.11195779261659e+00 + 39 -1.13060801591005e+00 -1.01378475014668e+00 -2.08003497306252e+00 -2.11012335395400e+00 + 40 -1.13197437578394e+00 -1.00834779777182e+00 -2.08286935214585e+00 -2.10803774920239e+00 diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.pmf b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.pmf index 5f4a7648b..003c811d3 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.pmf @@ -2,1262 +2,1262 @@ # -3.50000000000000e+00 2.00000000000000e-01 35 0 # -3.50000000000000e+00 2.00000000000000e-01 35 0 - -3.40000000000000e+00 -3.40000000000000e+00 3.07993876881154e-02 - -3.40000000000000e+00 -3.20000000000000e+00 3.07993876881154e-02 - -3.40000000000000e+00 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3.40000000000000e+00 1.20000000000000e+00 3.08158497484176e-02 + 3.40000000000000e+00 1.40000000000000e+00 3.08158497484176e-02 + 3.40000000000000e+00 1.60000000000000e+00 3.08158497484176e-02 + 3.40000000000000e+00 1.80000000000000e+00 3.08158497484176e-02 + 3.40000000000000e+00 2.00000000000000e+00 3.08158497484176e-02 + 3.40000000000000e+00 2.20000000000000e+00 3.08158497484176e-02 + 3.40000000000000e+00 2.40000000000000e+00 3.08158497484176e-02 + 3.40000000000000e+00 2.60000000000000e+00 3.08158497484176e-02 + 3.40000000000000e+00 2.80000000000000e+00 3.08158497484176e-02 + 3.40000000000000e+00 3.00000000000000e+00 3.08158497484176e-02 + 3.40000000000000e+00 3.20000000000000e+00 3.08158497484176e-02 + 3.40000000000000e+00 3.40000000000000e+00 3.08158497484176e-02 diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt b/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt index e2b19c981..157cac038 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out index e7f89a4ff..9ad41eda8 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,56 +59,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -114,10 +118,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -143,6 +147,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -153,17 +158,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - dihedral colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 66b27ad46..3d5bd5995 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.98300515592260e+01 + x 5.98300515486710e+01 } restraint { diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj index b78cecb35..1c292a5fb 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 6.31129478791929e+01 -2.52051791516771e-01 - 1 6.30779645383520e+01 -2.51911858153408e-01 - 2 6.30166636722659e+01 -2.51666654689064e-01 - 3 6.29277968222057e+01 -2.51311187288823e-01 - 4 6.28110919641768e+01 -2.50844367856707e-01 - 5 6.26673366028881e+01 -2.50269346411552e-01 - 6 6.24983825393602e+01 -2.49593530157441e-01 - 7 6.23070775481485e+01 -2.48828310192594e-01 - 8 6.20971375584149e+01 -2.47988550233660e-01 - 9 6.18729765882759e+01 -2.47091906353104e-01 - 10 6.16395107192542e+01 -2.46158042877017e-01 - 11 6.14019498492506e+01 -2.45207799397002e-01 - 12 6.11655875941102e+01 -2.44262350376441e-01 - 13 6.09355955400464e+01 -2.43342382160186e-01 - 14 6.07168266200639e+01 -2.42467306480256e-01 - 15 6.05136310274090e+01 -2.41654524109636e-01 - 16 6.03296902229661e+01 -2.40918760891865e-01 - 17 6.01678777239959e+01 -2.40271510895984e-01 - 18 6.00301578248419e+01 -2.39720631299368e-01 - 19 5.99175335802490e+01 -2.39270134320996e-01 - 20 5.98300515592260e+01 -2.38920206236904e-01 + 0 6.31129478791928e+01 -2.52051791516771e-01 + 1 6.30779645383122e+01 -2.51911858153249e-01 + 2 6.30166636721089e+01 -2.51666654688436e-01 + 3 6.29277968203376e+01 -2.51311187281350e-01 + 4 6.28110919635306e+01 -2.50844367854122e-01 + 5 6.26673366019378e+01 -2.50269346407751e-01 + 6 6.24983825380393e+01 -2.49593530152157e-01 + 7 6.23070775463950e+01 -2.48828310185580e-01 + 8 6.20971375561705e+01 -2.47988550224682e-01 + 9 6.18729765854906e+01 -2.47091906341962e-01 + 10 6.16395107158807e+01 -2.46158042863523e-01 + 11 6.14019498452446e+01 -2.45207799380978e-01 + 12 6.11655875894309e+01 -2.44262350357724e-01 + 13 6.09355955346581e+01 -2.43342382138632e-01 + 14 6.07168266139377e+01 -2.42467306455751e-01 + 15 6.05136310205547e+01 -2.41654524082219e-01 + 16 6.03296902153746e+01 -2.40918760861498e-01 + 17 6.01678777158193e+01 -2.40271510863277e-01 + 18 6.00301578158095e+01 -2.39720631263238e-01 + 19 5.99175335696155e+01 -2.39270134278462e-01 + 20 5.98300515486710e+01 -2.38920206194684e-01 diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out index 237f53c44..9ce9a9ef3 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,56 +59,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -114,10 +118,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -143,6 +147,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -153,22 +158,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - dihedral colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 59.8301 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 44e24f2b2..108bc4cd0 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.97551054664761e+01 + x 5.97551054473693e+01 } restraint { diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 71d70ae0b..3cf42a7dc 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.98300515592260e+01 -2.38920206236904e-01 - 21 5.97668650506981e+01 -2.38667460202792e-01 - 22 5.97263508310798e+01 -2.38505403324319e-01 - 23 5.97062661660438e+01 -2.38425064664175e-01 - 24 5.97039266476832e+01 -2.38415706590733e-01 - 25 5.97163828026047e+01 -2.38465531210419e-01 - 26 5.97405738751603e+01 -2.38562295500641e-01 - 27 5.97734430509102e+01 -2.38693772203641e-01 - 28 5.98120053098547e+01 -2.38848021239419e-01 - 29 5.98533709694021e+01 -2.39013483877608e-01 - 30 5.98947361725041e+01 -2.39178944690016e-01 - 31 5.99333583559336e+01 -2.39333433423734e-01 - 32 5.99665374039350e+01 -2.39466149615740e-01 - 33 5.99916207683209e+01 -2.39566483073283e-01 - 34 6.00060427089216e+01 -2.39624170835686e-01 - 35 6.00073965504200e+01 -2.39629586201680e-01 - 36 5.99935249121635e+01 -2.39574099648654e-01 - 37 5.99626029708492e+01 -2.39450411883397e-01 - 38 5.99131916964115e+01 -2.39252766785646e-01 - 39 5.98442490868439e+01 -2.38976996347376e-01 - 40 5.97551054664761e+01 -2.38620421865904e-01 + 20 5.98300515486710e+01 -2.38920206194684e-01 + 21 5.97668650394525e+01 -2.38667460157810e-01 + 22 5.97263508192266e+01 -2.38505403276906e-01 + 23 5.97062661536266e+01 -2.38425064614506e-01 + 24 5.97039266347449e+01 -2.38415706538980e-01 + 25 5.97163827891862e+01 -2.38465531156745e-01 + 26 5.97405738612989e+01 -2.38562295445196e-01 + 27 5.97734430366384e+01 -2.38693772146554e-01 + 28 5.98120052955854e+01 -2.38848021182342e-01 + 29 5.98533709544186e+01 -2.39013483817674e-01 + 30 5.98947361572460e+01 -2.39178944628984e-01 + 31 5.99333583402208e+01 -2.39333433360883e-01 + 32 5.99665373878884e+01 -2.39466149551554e-01 + 33 5.99916207519385e+01 -2.39566483007754e-01 + 34 6.00060426921965e+01 -2.39624170768786e-01 + 35 6.00073965333411e+01 -2.39629586133365e-01 + 36 5.99935248947171e+01 -2.39574099578868e-01 + 37 5.99626029530151e+01 -2.39450411812060e-01 + 38 5.99131916781728e+01 -2.39252766712691e-01 + 39 5.98442490681818e+01 -2.38976996272727e-01 + 40 5.97551054473693e+01 -2.38620421789477e-01 diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt b/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out index da0de3420..f460ff36e 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out @@ -4,10 +4,9 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -170,10 +170,12 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj index e603d2abe..222745310 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj @@ -16,7 +16,7 @@ 14 6.09757828886766e+01 0.00000000000000e+00 15 6.08031168275266e+01 0.00000000000000e+00 16 6.06502098430779e+01 0.00000000000000e+00 - 17 6.05198025267681e+01 0.00000000000000e+00 + 17 6.05198025267682e+01 0.00000000000000e+00 18 6.04137510819450e+01 0.00000000000000e+00 19 6.03329740983039e+01 0.00000000000000e+00 20 6.02774557419409e+01 0.00000000000000e+00 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat index add429103..29c2e88d8 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat @@ -1,75 +1,75 @@ # 1 -# -60 5 72 1 +# -6.00000000000000e+01 5.00000000000000e+00 72 1 - -57.5 0 - -52.5 0 - -47.5 0 - -42.5 0 - -37.5 0 - -32.5 0 - -27.5 0 - -22.5 0 - -17.5 0 - -12.5 0 - -7.5 0 - -2.5 0 - 2.5 0 - 7.5 0 - 12.5 0 - 17.5 0 - 22.5 0 - 27.5 0 - 32.5 0 - 37.5 0 - 42.5 0 - 47.5 0 - 52.5 0 - 57.5 0 - 62.5 20 - 67.5 0 - 72.5 0 - 77.5 0 - 82.5 0 - 87.5 0 - 92.5 0 - 97.5 0 - 102.5 0 - 107.5 0 - 112.5 0 - 117.5 0 - 122.5 0 - 127.5 0 - 132.5 0 - 137.5 0 - 142.5 0 - 147.5 0 - 152.5 0 - 157.5 0 - 162.5 0 - 167.5 0 - 172.5 0 - 177.5 0 - 182.5 0 - 187.5 0 - 192.5 0 - 197.5 0 - 202.5 0 - 207.5 0 - 212.5 0 - 217.5 0 - 222.5 0 - 227.5 0 - 232.5 0 - 237.5 0 - 242.5 0 - 247.5 0 - 252.5 0 - 257.5 0 - 262.5 0 - 267.5 0 - 272.5 0 - 277.5 0 - 282.5 0 - 287.5 0 - 292.5 0 - 297.5 0 + -5.75000000000000e+01 0.00000000000000e+00 + -5.25000000000000e+01 0.00000000000000e+00 + -4.75000000000000e+01 0.00000000000000e+00 + -4.25000000000000e+01 0.00000000000000e+00 + -3.75000000000000e+01 0.00000000000000e+00 + -3.25000000000000e+01 0.00000000000000e+00 + -2.75000000000000e+01 0.00000000000000e+00 + -2.25000000000000e+01 0.00000000000000e+00 + -1.75000000000000e+01 0.00000000000000e+00 + -1.25000000000000e+01 0.00000000000000e+00 + -7.50000000000000e+00 0.00000000000000e+00 + -2.50000000000000e+00 0.00000000000000e+00 + 2.50000000000000e+00 0.00000000000000e+00 + 7.50000000000000e+00 0.00000000000000e+00 + 1.25000000000000e+01 0.00000000000000e+00 + 1.75000000000000e+01 0.00000000000000e+00 + 2.25000000000000e+01 0.00000000000000e+00 + 2.75000000000000e+01 0.00000000000000e+00 + 3.25000000000000e+01 0.00000000000000e+00 + 3.75000000000000e+01 0.00000000000000e+00 + 4.25000000000000e+01 0.00000000000000e+00 + 4.75000000000000e+01 0.00000000000000e+00 + 5.25000000000000e+01 0.00000000000000e+00 + 5.75000000000000e+01 0.00000000000000e+00 + 6.25000000000000e+01 2.00000000000000e+01 + 6.75000000000000e+01 0.00000000000000e+00 + 7.25000000000000e+01 0.00000000000000e+00 + 7.75000000000000e+01 0.00000000000000e+00 + 8.25000000000000e+01 0.00000000000000e+00 + 8.75000000000000e+01 0.00000000000000e+00 + 9.25000000000000e+01 0.00000000000000e+00 + 9.75000000000000e+01 0.00000000000000e+00 + 1.02500000000000e+02 0.00000000000000e+00 + 1.07500000000000e+02 0.00000000000000e+00 + 1.12500000000000e+02 0.00000000000000e+00 + 1.17500000000000e+02 0.00000000000000e+00 + 1.22500000000000e+02 0.00000000000000e+00 + 1.27500000000000e+02 0.00000000000000e+00 + 1.32500000000000e+02 0.00000000000000e+00 + 1.37500000000000e+02 0.00000000000000e+00 + 1.42500000000000e+02 0.00000000000000e+00 + 1.47500000000000e+02 0.00000000000000e+00 + 1.52500000000000e+02 0.00000000000000e+00 + 1.57500000000000e+02 0.00000000000000e+00 + 1.62500000000000e+02 0.00000000000000e+00 + 1.67500000000000e+02 0.00000000000000e+00 + 1.72500000000000e+02 0.00000000000000e+00 + 1.77500000000000e+02 0.00000000000000e+00 + 1.82500000000000e+02 0.00000000000000e+00 + 1.87500000000000e+02 0.00000000000000e+00 + 1.92500000000000e+02 0.00000000000000e+00 + 1.97500000000000e+02 0.00000000000000e+00 + 2.02500000000000e+02 0.00000000000000e+00 + 2.07500000000000e+02 0.00000000000000e+00 + 2.12500000000000e+02 0.00000000000000e+00 + 2.17500000000000e+02 0.00000000000000e+00 + 2.22500000000000e+02 0.00000000000000e+00 + 2.27500000000000e+02 0.00000000000000e+00 + 2.32500000000000e+02 0.00000000000000e+00 + 2.37500000000000e+02 0.00000000000000e+00 + 2.42500000000000e+02 0.00000000000000e+00 + 2.47500000000000e+02 0.00000000000000e+00 + 2.52500000000000e+02 0.00000000000000e+00 + 2.57500000000000e+02 0.00000000000000e+00 + 2.62500000000000e+02 0.00000000000000e+00 + 2.67500000000000e+02 0.00000000000000e+00 + 2.72500000000000e+02 0.00000000000000e+00 + 2.77500000000000e+02 0.00000000000000e+00 + 2.82500000000000e+02 0.00000000000000e+00 + 2.87500000000000e+02 0.00000000000000e+00 + 2.92500000000000e+02 0.00000000000000e+00 + 2.97500000000000e+02 0.00000000000000e+00 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out index 6b4f434fe..b917756f8 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out @@ -4,10 +4,9 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -170,6 +170,7 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 60.2775 @@ -179,6 +180,7 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped index 801e6d28b..0871d37c1 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.08972121817133e+01 + x 6.08972121817132e+01 } histogram { diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj index 26132495a..309eb03b3 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj @@ -10,13 +10,13 @@ 28 6.05174152507232e+01 0.00000000000000e+00 29 6.05916134367745e+01 0.00000000000000e+00 30 6.06661106175895e+01 0.00000000000000e+00 - 31 6.07382493916988e+01 0.00000000000000e+00 + 31 6.07382493916987e+01 0.00000000000000e+00 32 6.08054278361141e+01 0.00000000000000e+00 - 33 6.08651028913519e+01 0.00000000000000e+00 - 34 6.09148265769852e+01 0.00000000000000e+00 - 35 6.09523144047668e+01 0.00000000000000e+00 - 36 6.09755306486177e+01 0.00000000000000e+00 - 37 6.09827676263966e+01 0.00000000000000e+00 - 38 6.09726956103268e+01 0.00000000000000e+00 - 39 6.09443715231752e+01 0.00000000000000e+00 - 40 6.08972121817133e+01 0.00000000000000e+00 + 33 6.08651028913518e+01 0.00000000000000e+00 + 34 6.09148265769850e+01 0.00000000000000e+00 + 35 6.09523144047667e+01 0.00000000000000e+00 + 36 6.09755306486176e+01 0.00000000000000e+00 + 37 6.09827676263964e+01 0.00000000000000e+00 + 38 6.09726956103267e+01 0.00000000000000e+00 + 39 6.09443715231751e+01 0.00000000000000e+00 + 40 6.08972121817132e+01 0.00000000000000e+00 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat index 44f8e383f..7d3ef8bb5 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat @@ -1,75 +1,75 @@ # 1 -# -60 5 72 1 +# -6.00000000000000e+01 5.00000000000000e+00 72 1 - -57.5 0 - -52.5 0 - -47.5 0 - -42.5 0 - -37.5 0 - -32.5 0 - -27.5 0 - -22.5 0 - -17.5 0 - -12.5 0 - -7.5 0 - -2.5 0 - 2.5 0 - 7.5 0 - 12.5 0 - 17.5 0 - 22.5 0 - 27.5 0 - 32.5 0 - 37.5 0 - 42.5 0 - 47.5 0 - 52.5 0 - 57.5 0 - 62.5 40 - 67.5 0 - 72.5 0 - 77.5 0 - 82.5 0 - 87.5 0 - 92.5 0 - 97.5 0 - 102.5 0 - 107.5 0 - 112.5 0 - 117.5 0 - 122.5 0 - 127.5 0 - 132.5 0 - 137.5 0 - 142.5 0 - 147.5 0 - 152.5 0 - 157.5 0 - 162.5 0 - 167.5 0 - 172.5 0 - 177.5 0 - 182.5 0 - 187.5 0 - 192.5 0 - 197.5 0 - 202.5 0 - 207.5 0 - 212.5 0 - 217.5 0 - 222.5 0 - 227.5 0 - 232.5 0 - 237.5 0 - 242.5 0 - 247.5 0 - 252.5 0 - 257.5 0 - 262.5 0 - 267.5 0 - 272.5 0 - 277.5 0 - 282.5 0 - 287.5 0 - 292.5 0 - 297.5 0 + -5.75000000000000e+01 0.00000000000000e+00 + -5.25000000000000e+01 0.00000000000000e+00 + -4.75000000000000e+01 0.00000000000000e+00 + -4.25000000000000e+01 0.00000000000000e+00 + -3.75000000000000e+01 0.00000000000000e+00 + -3.25000000000000e+01 0.00000000000000e+00 + -2.75000000000000e+01 0.00000000000000e+00 + -2.25000000000000e+01 0.00000000000000e+00 + -1.75000000000000e+01 0.00000000000000e+00 + -1.25000000000000e+01 0.00000000000000e+00 + -7.50000000000000e+00 0.00000000000000e+00 + -2.50000000000000e+00 0.00000000000000e+00 + 2.50000000000000e+00 0.00000000000000e+00 + 7.50000000000000e+00 0.00000000000000e+00 + 1.25000000000000e+01 0.00000000000000e+00 + 1.75000000000000e+01 0.00000000000000e+00 + 2.25000000000000e+01 0.00000000000000e+00 + 2.75000000000000e+01 0.00000000000000e+00 + 3.25000000000000e+01 0.00000000000000e+00 + 3.75000000000000e+01 0.00000000000000e+00 + 4.25000000000000e+01 0.00000000000000e+00 + 4.75000000000000e+01 0.00000000000000e+00 + 5.25000000000000e+01 0.00000000000000e+00 + 5.75000000000000e+01 0.00000000000000e+00 + 6.25000000000000e+01 4.00000000000000e+01 + 6.75000000000000e+01 0.00000000000000e+00 + 7.25000000000000e+01 0.00000000000000e+00 + 7.75000000000000e+01 0.00000000000000e+00 + 8.25000000000000e+01 0.00000000000000e+00 + 8.75000000000000e+01 0.00000000000000e+00 + 9.25000000000000e+01 0.00000000000000e+00 + 9.75000000000000e+01 0.00000000000000e+00 + 1.02500000000000e+02 0.00000000000000e+00 + 1.07500000000000e+02 0.00000000000000e+00 + 1.12500000000000e+02 0.00000000000000e+00 + 1.17500000000000e+02 0.00000000000000e+00 + 1.22500000000000e+02 0.00000000000000e+00 + 1.27500000000000e+02 0.00000000000000e+00 + 1.32500000000000e+02 0.00000000000000e+00 + 1.37500000000000e+02 0.00000000000000e+00 + 1.42500000000000e+02 0.00000000000000e+00 + 1.47500000000000e+02 0.00000000000000e+00 + 1.52500000000000e+02 0.00000000000000e+00 + 1.57500000000000e+02 0.00000000000000e+00 + 1.62500000000000e+02 0.00000000000000e+00 + 1.67500000000000e+02 0.00000000000000e+00 + 1.72500000000000e+02 0.00000000000000e+00 + 1.77500000000000e+02 0.00000000000000e+00 + 1.82500000000000e+02 0.00000000000000e+00 + 1.87500000000000e+02 0.00000000000000e+00 + 1.92500000000000e+02 0.00000000000000e+00 + 1.97500000000000e+02 0.00000000000000e+00 + 2.02500000000000e+02 0.00000000000000e+00 + 2.07500000000000e+02 0.00000000000000e+00 + 2.12500000000000e+02 0.00000000000000e+00 + 2.17500000000000e+02 0.00000000000000e+00 + 2.22500000000000e+02 0.00000000000000e+00 + 2.27500000000000e+02 0.00000000000000e+00 + 2.32500000000000e+02 0.00000000000000e+00 + 2.37500000000000e+02 0.00000000000000e+00 + 2.42500000000000e+02 0.00000000000000e+00 + 2.47500000000000e+02 0.00000000000000e+00 + 2.52500000000000e+02 0.00000000000000e+00 + 2.57500000000000e+02 0.00000000000000e+00 + 2.62500000000000e+02 0.00000000000000e+00 + 2.67500000000000e+02 0.00000000000000e+00 + 2.72500000000000e+02 0.00000000000000e+00 + 2.77500000000000e+02 0.00000000000000e+00 + 2.82500000000000e+02 0.00000000000000e+00 + 2.87500000000000e+02 0.00000000000000e+00 + 2.92500000000000e+02 0.00000000000000e+00 + 2.97500000000000e+02 0.00000000000000e+00 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt index 2c2fdb849..157cac038 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2021-10-13. -colvars: Using NAMD interface, version "2021-10-13". +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out index 1218eda97..50378ec14 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,56 +59,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -114,10 +118,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -140,6 +144,7 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { -10 } colvars: # upperWalls = { 10 } @@ -155,17 +160,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - dihedral colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped index e98cccfbb..84a539af0 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.99015240169243e+01 + x 5.99015240062048e+01 } restraint { diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj index f83c37fda..bf8a645ef 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 0 6.31129478791929e+01 -2.12451791516771e-01 - 1 6.30782207430626e+01 -2.12312882972251e-01 - 2 6.30176844598780e+01 -2.12070737839512e-01 - 3 6.29300795621464e+01 -2.11720318248586e-01 - 4 6.28151165882276e+01 -2.11260466352910e-01 - 5 6.26735597690779e+01 -2.10694239076312e-01 - 6 6.25072326037074e+01 -2.10028930414830e-01 - 7 6.23189505070414e+01 -2.09275802028166e-01 - 8 6.21123940698095e+01 -2.08449576279238e-01 - 9 6.18919401229661e+01 -2.07567760491865e-01 - 10 6.16624668357318e+01 -2.06649867342927e-01 - 11 6.14291465368246e+01 -2.05716586147298e-01 - 12 6.11972365876074e+01 -2.04788946350430e-01 - 13 6.09718744761807e+01 -2.03887497904723e-01 - 14 6.07578818543115e+01 -2.03031527417246e-01 - 15 6.05595809338303e+01 -2.02238323735321e-01 - 16 6.03806287808051e+01 -2.01522515123221e-01 - 17 6.02238782208511e+01 -2.00895512883405e-01 - 18 6.00912764895398e+01 -2.00365105958159e-01 - 19 5.99838130302367e+01 -1.99935252120947e-01 - 20 5.99015240167765e+01 -1.99606096067106e-01 +# step one fa_one + 0 6.31129478791928e+01 -2.12451791516771e-01 + 1 6.30782207430228e+01 -2.12312882972091e-01 + 2 6.30176844597210e+01 -2.12070737838884e-01 + 3 6.29300795604372e+01 -2.11720318241749e-01 + 4 6.28151165875842e+01 -2.11260466350337e-01 + 5 6.26735597681268e+01 -2.10694239072507e-01 + 6 6.25072326023818e+01 -2.10028930409527e-01 + 7 6.23189505052794e+01 -2.09275802021118e-01 + 8 6.21123940675534e+01 -2.08449576270213e-01 + 9 6.18919401201661e+01 -2.07567760480665e-01 + 10 6.16624668323414e+01 -2.06649867329365e-01 + 11 6.14291465328002e+01 -2.05716586131201e-01 + 12 6.11972365829090e+01 -2.04788946331636e-01 + 13 6.09718744707731e+01 -2.03887497883092e-01 + 14 6.07578818481667e+01 -2.03031527392667e-01 + 15 6.05595809269580e+01 -2.02238323707832e-01 + 16 6.03806287731779e+01 -2.01522515092712e-01 + 17 6.02238782127047e+01 -2.00895512850819e-01 + 18 6.00912764804658e+01 -2.00365105921863e-01 + 19 5.99838130196557e+01 -1.99935252078623e-01 + 20 5.99015240062048e+01 -1.99606096024819e-01 diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out index 2b1dab030..03cf0c9a7 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,56 +59,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -114,10 +118,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -140,6 +144,7 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { -10 } colvars: # upperWalls = { 10 } @@ -155,22 +160,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - dihedral colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 59.9015 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped index 203f4469d..77bac4e9f 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 5.99403692730741e+01 + x 5.99403692539448e+01 } diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj index 9c2977f98..5b3f70be7 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 20 5.99015240167765e+01 -1.99606096067106e-01 - 21 5.98435552301064e+01 -1.99374220920425e-01 - 22 5.98082785300632e+01 -1.99233114120253e-01 - 23 5.97934485072713e+01 -1.99173794029085e-01 - 24 5.97963800479404e+01 -1.99185520191762e-01 - 25 5.98141247224277e+01 -1.99256498889711e-01 - 26 5.98436244315244e+01 -1.99374497726098e-01 - 27 5.98818266497052e+01 -1.99527306598821e-01 - 28 5.99257523617425e+01 -1.99703009446970e-01 - 29 5.99725198560893e+01 -1.99890079424357e-01 - 30 6.00193353776544e+01 -2.00077341510617e-01 - 31 6.00634687369522e+01 -2.00253874947809e-01 - 32 6.01022344261894e+01 -2.00408937704758e-01 - 33 6.01329965086264e+01 -2.00531986034505e-01 - 34 6.01532074105757e+01 -2.00612829642303e-01 - 35 6.01604795521431e+01 -2.00641918208573e-01 - 36 6.01526748917010e+01 -2.00610699566804e-01 - 37 6.01279874293707e+01 -2.00511949717483e-01 - 38 6.00849959571649e+01 -2.00339983828660e-01 - 39 6.00226748938869e+01 -2.00090699575548e-01 - 40 5.99403692730741e+01 -1.99761477092296e-01 +# step one fa_one + 20 5.99015240062048e+01 -1.99606096024819e-01 + 21 5.98435552188444e+01 -1.99374220875378e-01 + 22 5.98082785181930e+01 -1.99233114072772e-01 + 23 5.97934484948365e+01 -1.99173793979346e-01 + 24 5.97963800349839e+01 -1.99185520139936e-01 + 25 5.98141247089905e+01 -1.99256498835962e-01 + 26 5.98436244176440e+01 -1.99374497670576e-01 + 27 5.98818266354142e+01 -1.99527306541657e-01 + 28 5.99257523474475e+01 -1.99703009389790e-01 + 29 5.99725198410855e+01 -1.99890079364342e-01 + 30 6.00193353623784e+01 -2.00077341449514e-01 + 31 6.00634687212219e+01 -2.00253874884888e-01 + 32 6.01022344101259e+01 -2.00408937640504e-01 + 33 6.01329964922276e+01 -2.00531985968910e-01 + 34 6.01532073938345e+01 -2.00612829575338e-01 + 35 6.01604795350481e+01 -2.00641918140193e-01 + 36 6.01526748742382e+01 -2.00610699496953e-01 + 37 6.01279874115193e+01 -2.00511949646077e-01 + 38 6.00849959389077e+01 -2.00339983755631e-01 + 39 6.00226748752046e+01 -2.00090699500818e-01 + 40 5.99403692539448e+01 -1.99761477015779e-01 diff --git a/namd/tests/library/000_dihedralwalls/namd-version.txt b/namd/tests/library/000_dihedralwalls/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_dihedralwalls/namd-version.txt +++ b/namd/tests/library/000_dihedralwalls/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out index c0fccf38e..c512baba0 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,40 +59,40 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -126,6 +130,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -136,16 +141,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - dipoleAngle colvar component: +colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 291b73e90..9f4d54156 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.36349055337838e+01 + x 9.36349055389455e+01 } restraint { diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj index 336b7c00f..44c231c6c 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 8.97962480697652e+01 -3.58784992279061e-01 - 1 9.00687365880860e+01 -3.59874946352344e-01 - 2 9.03696531713662e+01 -3.61078612685465e-01 - 3 9.06810803332082e+01 -3.62324321332833e-01 - 4 9.09847043026283e+01 -3.63538817210513e-01 - 5 9.12638043490304e+01 -3.64655217396121e-01 - 6 9.15051697805885e+01 -3.65620679122354e-01 - 7 9.17006524132711e+01 -3.66402609653084e-01 - 8 9.18480994648365e+01 -3.66992397859346e-01 - 9 9.19515174481835e+01 -3.67406069792734e-01 - 10 9.20204550815615e+01 -3.67681820326246e-01 - 11 9.20687188076611e+01 -3.67874875230645e-01 - 12 9.21126240084645e+01 -3.68050496033858e-01 - 13 9.21690190278993e+01 -3.68276076111597e-01 - 14 9.22533018460045e+01 -3.68613207384018e-01 - 15 9.23775997077804e+01 -3.69110398831122e-01 - 16 9.25492271261785e+01 -3.69796908504714e-01 - 17 9.27695098354046e+01 -3.70678039341619e-01 - 18 9.30330692722776e+01 -3.71732277089110e-01 - 19 9.33276898480665e+01 -3.72910759392266e-01 - 20 9.36349055337838e+01 -3.74139622135135e-01 + 1 9.00687365881581e+01 -3.59874946352633e-01 + 2 9.03696531716400e+01 -3.61078612686560e-01 + 3 9.06810803337954e+01 -3.62324321335182e-01 + 4 9.09847043036197e+01 -3.63538817214479e-01 + 5 9.12638043504929e+01 -3.64655217401972e-01 + 6 9.15051697825636e+01 -3.65620679130254e-01 + 7 9.17006524157741e+01 -3.66402609663097e-01 + 8 9.18480994678579e+01 -3.66992397871432e-01 + 9 9.19515174516923e+01 -3.67406069806769e-01 + 10 9.20204550855094e+01 -3.67681820342038e-01 + 11 9.20687188119887e+01 -3.67874875247955e-01 + 12 9.21126240131068e+01 -3.68050496052427e-01 + 13 9.21690190327914e+01 -3.68276076131166e-01 + 14 9.22533018510856e+01 -3.68613207404342e-01 + 15 9.23775997129957e+01 -3.69110398851983e-01 + 16 9.25492271314794e+01 -3.69796908525918e-01 + 17 9.27695098407462e+01 -3.70678039362985e-01 + 18 9.30330692776144e+01 -3.71732277110457e-01 + 19 9.33276898533472e+01 -3.72910759413389e-01 + 20 9.36349055389455e+01 -3.74139622155782e-01 diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 99d488573..48c3860e5 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,40 +59,40 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -126,6 +130,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -136,21 +141,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - dipoleAngle colvar component: +colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 93.6349 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 4da36d6f0..651e66dc5 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.01098742103920e+01 + x 9.01098741923154e+01 } restraint { diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 7e403dd06..ee86202c8 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.36349055337838e+01 -3.74139622135135e-01 - 21 9.39314096558801e+01 -3.75325638623520e-01 - 22 9.41912842222173e+01 -3.76365136888869e-01 - 23 9.43888705849112e+01 -3.77155482339645e-01 - 24 9.45019115100439e+01 -3.77607646040175e-01 - 25 9.45144559351512e+01 -3.77657823740605e-01 - 26 9.44189957490813e+01 -3.77275982996325e-01 - 27 9.42174306906690e+01 -3.76469722762676e-01 - 28 9.39206949362101e+01 -3.75282779744841e-01 - 29 9.35471730256220e+01 -3.73788692102488e-01 - 30 9.31202694774434e+01 -3.72081077909774e-01 - 31 9.26656093133783e+01 -3.70262437253513e-01 - 32 9.22083464080232e+01 -3.68433385632093e-01 - 33 9.17709340635645e+01 -3.66683736254258e-01 - 34 9.13715370513921e+01 -3.65086148205568e-01 - 35 9.10230941369154e+01 -3.63692376547662e-01 - 36 9.07329203802995e+01 -3.62531681521198e-01 - 37 9.05026913550711e+01 -3.61610765420284e-01 - 38 9.03286700407576e+01 -3.60914680163030e-01 - 39 9.02021116972737e+01 -3.60408446789095e-01 - 40 9.01098742103920e+01 -3.60039496841568e-01 + 20 9.36349055389455e+01 -3.74139622155782e-01 + 21 9.39314096608430e+01 -3.75325638643372e-01 + 22 9.41912842268812e+01 -3.76365136907525e-01 + 23 9.43888705891540e+01 -3.77155482356616e-01 + 24 9.45019115137236e+01 -3.77607646054895e-01 + 25 9.45144559381111e+01 -3.77657823752444e-01 + 26 9.44189957511575e+01 -3.77275983004630e-01 + 27 9.42174306917003e+01 -3.76469722766801e-01 + 28 9.39206949360476e+01 -3.75282779744190e-01 + 29 9.35471730241369e+01 -3.73788692096548e-01 + 30 9.31202694745324e+01 -3.72081077898130e-01 + 31 9.26656093089659e+01 -3.70262437235864e-01 + 32 9.22083464020604e+01 -3.68433385608242e-01 + 33 9.17709340560258e+01 -3.66683736224103e-01 + 34 9.13715370422709e+01 -3.65086148169084e-01 + 35 9.10230941262197e+01 -3.63692376504879e-01 + 36 9.07329203680483e+01 -3.62531681472193e-01 + 37 9.05026913412928e+01 -3.61610765365171e-01 + 38 9.03286700254905e+01 -3.60914680101962e-01 + 39 9.02021116805683e+01 -3.60408446722273e-01 + 40 9.01098741923154e+01 -3.60039496769262e-01 diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt index 9e5d53306..157cac038 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-12-21. -colvars: Using NAMD interface, version 2018-12-20. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out index eb22b6e44..20f72749d 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,7 +76,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -100,6 +104,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -110,14 +115,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - dipoleMagnitude colvar component: +colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped index e17335d86..9fd17e29c 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.25718680414711e+00 + x 1.25718680414489e+00 } restraint { diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj index 897dd65db..8a5faec6e 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.27248491620818e+00 -4.68993966483274e-03 - 1 1.27180733121971e+00 -4.68722932487885e-03 - 2 1.27112801338806e+00 -4.68451205355224e-03 - 3 1.27047853507430e+00 -4.68191414029720e-03 - 4 1.26988621687686e+00 -4.67954486750746e-03 - 5 1.26936978124426e+00 -4.67747912497706e-03 - 6 1.26893615427789e+00 -4.67574461711154e-03 - 7 1.26857880873190e+00 -4.67431523492760e-03 - 8 1.26827782880573e+00 -4.67311131522291e-03 - 9 1.26800167046013e+00 -4.67200668184053e-03 - 10 1.26771038149865e+00 -4.67084152599461e-03 - 11 1.26735983260005e+00 -4.66943933040020e-03 - 12 1.26690635772161e+00 -4.66762543088644e-03 - 13 1.26631116925277e+00 -4.66524467701107e-03 - 14 1.26554403808362e+00 -4.66217615233448e-03 - 15 1.26458596330773e+00 -4.65834385323092e-03 - 16 1.26343080408792e+00 -4.65372321635169e-03 - 17 1.26208600681664e+00 -4.64834402726657e-03 - 18 1.26057258582039e+00 -4.64229034328157e-03 - 19 1.25892442270322e+00 -4.63569769081287e-03 - 20 1.25718680414711e+00 -4.62874721658843e-03 + 1 1.27180733121966e+00 -4.68722932487864e-03 + 2 1.27112801338785e+00 -4.68451205355138e-03 + 3 1.27047853507381e+00 -4.68191414029525e-03 + 4 1.26988621687599e+00 -4.67954486750395e-03 + 5 1.26936978124289e+00 -4.67747912497155e-03 + 6 1.26893615427592e+00 -4.67574461710367e-03 + 7 1.26857880872927e+00 -4.67431523491708e-03 + 8 1.26827782880240e+00 -4.67311131520959e-03 + 9 1.26800167045610e+00 -4.67200668182440e-03 + 10 1.26771038149395e+00 -4.67084152597581e-03 + 11 1.26735983259476e+00 -4.66943933037905e-03 + 12 1.26690635771585e+00 -4.66762543086338e-03 + 13 1.26631116924668e+00 -4.66524467698671e-03 + 14 1.26554403807739e+00 -4.66217615230955e-03 + 15 1.26458596330156e+00 -4.65834385320625e-03 + 16 1.26343080408206e+00 -4.65372321632822e-03 + 17 1.26208600681132e+00 -4.64834402724529e-03 + 18 1.26057258581588e+00 -4.64229034326350e-03 + 19 1.25892442269974e+00 -4.63569769079898e-03 + 20 1.25718680414489e+00 -4.62874721657957e-03 diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out index c8da2f965..4e9d16093 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,7 +76,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -100,6 +104,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -110,19 +115,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - dipoleMagnitude colvar component: +colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 1.25719 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 51fc5108c..3e1eeb606 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.23965387204761e+00 + x 1.23965387203052e+00 } restraint { diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj index b874d05f4..f3b3820c2 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.25718680414711e+00 -4.62874721658843e-03 - 21 1.25541401041707e+00 -4.62165604166829e-03 - 22 1.25366577392626e+00 -4.61466309570505e-03 - 23 1.25200261425396e+00 -4.60801045701586e-03 - 24 1.25048035907975e+00 -4.60192143631898e-03 - 25 1.24914448988648e+00 -4.59657795954592e-03 - 26 1.24802517146302e+00 -4.59210068585208e-03 - 27 1.24713379712889e+00 -4.58853518851555e-03 - 28 1.24646162388128e+00 -4.58584649552511e-03 - 29 1.24598068901487e+00 -4.58392275605946e-03 - 30 1.24564683482598e+00 -4.58258733930391e-03 - 31 1.24540441092625e+00 -4.58161764370501e-03 - 32 1.24519207689444e+00 -4.58076830757776e-03 - 33 1.24494905239767e+00 -4.57979620959067e-03 - 34 1.24462113711636e+00 -4.57848454846545e-03 - 35 1.24416586581212e+00 -4.57666346324848e-03 - 36 1.24355630166006e+00 -4.57422520664022e-03 - 37 1.24278318452544e+00 -4.57113273810176e-03 - 38 1.24185538440224e+00 -4.56742153760896e-03 - 39 1.24079879241559e+00 -4.56319516966238e-03 - 40 1.23965387204761e+00 -4.55861548819043e-03 + 20 1.25718680414489e+00 -4.62874721657957e-03 + 21 1.25541401041628e+00 -4.62165604166510e-03 + 22 1.25366577392698e+00 -4.61466309570791e-03 + 23 1.25200261425621e+00 -4.60801045702483e-03 + 24 1.25048035908344e+00 -4.60192143633375e-03 + 25 1.24914448989145e+00 -4.59657795956581e-03 + 26 1.24802517146902e+00 -4.59210068587607e-03 + 27 1.24713379713557e+00 -4.58853518854227e-03 + 28 1.24646162388823e+00 -4.58584649555294e-03 + 29 1.24598068902163e+00 -4.58392275608653e-03 + 30 1.24564683483206e+00 -4.58258733932823e-03 + 31 1.24540441093114e+00 -4.58161764372455e-03 + 32 1.24519207689764e+00 -4.58076830759057e-03 + 33 1.24494905239874e+00 -4.57979620959498e-03 + 34 1.24462113711495e+00 -4.57848454845980e-03 + 35 1.24416586580795e+00 -4.57666346323180e-03 + 36 1.24355630165299e+00 -4.57422520661195e-03 + 37 1.24278318451547e+00 -4.57113273806189e-03 + 38 1.24185538438953e+00 -4.56742153755813e-03 + 39 1.24079879240046e+00 -4.56319516960184e-03 + 40 1.23965387203052e+00 -4.55861548812208e-03 diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt index 9e5d53306..157cac038 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-12-21. -colvars: Using NAMD interface, version 2018-12-20. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out index 0c998afc9..6de123229 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,15 +120,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped index c1e336541..5268daf85 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21688253464583e+00 + x 3.21688253444007e+00 } diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj index 787f78aa5..9f55268e7 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 0.00000000000000e+00 - 11 3.21950367383415e+00 0.00000000000000e+00 - 12 3.22130499858006e+00 0.00000000000000e+00 - 13 3.22263479496347e+00 0.00000000000000e+00 - 14 3.22341769665784e+00 0.00000000000000e+00 - 15 3.22361473677138e+00 0.00000000000000e+00 - 16 3.22322417514557e+00 0.00000000000000e+00 - 17 3.22227942564879e+00 0.00000000000000e+00 - 18 3.22084479803044e+00 0.00000000000000e+00 - 19 3.21900979846930e+00 0.00000000000000e+00 - 20 3.21688253464583e+00 0.00000000000000e+00 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 0.00000000000000e+00 + 11 3.21950367376059e+00 0.00000000000000e+00 + 12 3.22130499849384e+00 0.00000000000000e+00 + 13 3.22263479486396e+00 0.00000000000000e+00 + 14 3.22341769654449e+00 0.00000000000000e+00 + 15 3.22361473664369e+00 0.00000000000000e+00 + 16 3.22322417500307e+00 0.00000000000000e+00 + 17 3.22227942549106e+00 0.00000000000000e+00 + 18 3.22084479785707e+00 0.00000000000000e+00 + 19 3.21900979827991e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat index 54058e8f8..23457f54b 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.94036335239450e-01 - 4 5.63764182658574e-01 - 6 8.25197229800656e-02 - 8 -4.33277910141469e-01 - 10 -8.58922876516564e-01 + 2 8.94036329632288e-01 + 4 5.63764173125217e-01 + 6 8.25197122357662e-02 + 8 -4.33277918980290e-01 + 10 -8.58922880671951e-01 diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out index 923c7f755..effa805d2 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,19 +120,30 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped index 139366ade..b307ede0d 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21404878547144e+00 + x 3.21404878499019e+00 } diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj index 3b596ebde..177b1bbb8 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253464583e+00 0.00000000000000e+00 - 21 3.21458253157603e+00 0.00000000000000e+00 - 22 3.21223315254029e+00 0.00000000000000e+00 - 23 3.20995392032979e+00 0.00000000000000e+00 - 24 3.20785326966943e+00 0.00000000000000e+00 - 25 3.20602244845117e+00 0.00000000000000e+00 - 26 3.20453120146139e+00 0.00000000000000e+00 - 27 3.20342556480347e+00 0.00000000000000e+00 - 28 3.20272769852622e+00 0.00000000000000e+00 - 29 3.20243730776714e+00 0.00000000000000e+00 - 30 3.20253423308456e+00 0.00000000000000e+00 - 31 3.20298183362156e+00 0.00000000000000e+00 - 32 3.20373100914607e+00 0.00000000000000e+00 - 33 3.20472468746373e+00 0.00000000000000e+00 - 34 3.20590256221113e+00 0.00000000000000e+00 - 35 3.20720566184671e+00 0.00000000000000e+00 - 36 3.20858030459458e+00 0.00000000000000e+00 - 37 3.20998111854285e+00 0.00000000000000e+00 - 38 3.21137308334419e+00 0.00000000000000e+00 - 39 3.21273274315657e+00 0.00000000000000e+00 - 40 3.21404878547144e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 + 21 3.21458253135360e+00 0.00000000000000e+00 + 22 3.21223315230095e+00 0.00000000000000e+00 + 23 3.20995392007338e+00 0.00000000000000e+00 + 24 3.20785326939589e+00 0.00000000000000e+00 + 25 3.20602244816055e+00 0.00000000000000e+00 + 26 3.20453120115385e+00 0.00000000000000e+00 + 27 3.20342556447929e+00 0.00000000000000e+00 + 28 3.20272769818575e+00 0.00000000000000e+00 + 29 3.20243730741081e+00 0.00000000000000e+00 + 30 3.20253423271288e+00 0.00000000000000e+00 + 31 3.20298183323508e+00 0.00000000000000e+00 + 32 3.20373100874536e+00 0.00000000000000e+00 + 33 3.20472468704943e+00 0.00000000000000e+00 + 34 3.20590256178394e+00 0.00000000000000e+00 + 35 3.20720566140745e+00 0.00000000000000e+00 + 36 3.20858030414420e+00 0.00000000000000e+00 + 37 3.20998111808250e+00 0.00000000000000e+00 + 38 3.21137308287521e+00 0.00000000000000e+00 + 39 3.21273274268056e+00 0.00000000000000e+00 + 40 3.21404878499019e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat index b55885c02..702a517c3 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.20806874278982e-01 - 4 4.95149538768788e-01 - 6 3.29843664998698e-02 - 8 -5.10193943420893e-01 - 10 -1.03852680015666e+00 + 2 8.20806872403133e-01 + 4 4.95149534314936e-01 + 6 3.29843583885573e-02 + 8 -5.10193956226866e-01 + 10 -1.03852681816246e+00 diff --git a/namd/tests/library/000_distance-autocorrfunc/namd-version.txt b/namd/tests/library/000_distance-autocorrfunc/namd-version.txt index b7bf5455c..157cac038 100644 --- a/namd/tests/library/000_distance-autocorrfunc/namd-version.txt +++ b/namd/tests/library/000_distance-autocorrfunc/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-10-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out index c89a0b8e7..9a7a8d5d0 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -93,28 +97,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -125,7 +129,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -153,6 +157,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -163,17 +168,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Linear and polynomial combination of colvar components: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped index eb4ad3fa9..ae9aba124 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.04350737609886e+01 + x 1.04350737604756e+01 } restraint { diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj index 31f5eef44..d89de7465 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.04177432613594e+01 -4.12709730454376e-02 - 1 1.04084193931741e+01 -4.12336775726963e-02 - 2 1.04020579749880e+01 -4.12082318999518e-02 - 3 1.03989629511090e+01 -4.11958518044361e-02 - 4 1.03992141620145e+01 -4.11968566480581e-02 - 5 1.04026682615430e+01 -4.12106730461720e-02 - 6 1.04089744652310e+01 -4.12358978609239e-02 - 7 1.04176020661138e+01 -4.12704082644551e-02 - 8 1.04278769154677e+01 -4.13115076618707e-02 - 9 1.04390245453922e+01 -4.13560981815686e-02 - 10 1.04502182764206e+01 -4.14008731056823e-02 - 11 1.04606302348533e+01 -4.14425209394133e-02 - 12 1.04694824776150e+01 -4.14779299104599e-02 - 13 1.04760942604439e+01 -4.15043770417758e-02 - 14 1.04799211560697e+01 -4.15196846242787e-02 - 15 1.04805822769989e+01 -4.15223291079955e-02 - 16 1.04778735083513e+01 -4.15114940334051e-02 - 17 1.04717666630482e+01 -4.14870666521928e-02 - 18 1.04623962956600e+01 -4.14495851826398e-02 - 19 1.04500369412003e+01 -4.14001477648012e-02 - 20 1.04350737609886e+01 -4.13402950439545e-02 + 1 1.04084193931719e+01 -4.12336775726876e-02 + 2 1.04020579749793e+01 -4.12082318999174e-02 + 3 1.03989629510900e+01 -4.11958518043599e-02 + 4 1.03992141619813e+01 -4.11968566479251e-02 + 5 1.04026682614922e+01 -4.12106730459687e-02 + 6 1.04089744651595e+01 -4.12358978606380e-02 + 7 1.04176020660190e+01 -4.12704082640760e-02 + 8 1.04278769153472e+01 -4.13115076613887e-02 + 9 1.04390245452438e+01 -4.13560981809752e-02 + 10 1.04502182762425e+01 -4.14008731049699e-02 + 11 1.04606302346439e+01 -4.14425209385756e-02 + 12 1.04694824773729e+01 -4.14779299094914e-02 + 13 1.04760942601681e+01 -4.15043770406723e-02 + 14 1.04799211557593e+01 -4.15196846230373e-02 + 15 1.04805822766537e+01 -4.15223291066147e-02 + 16 1.04778735079711e+01 -4.15114940318845e-02 + 17 1.04717666626334e+01 -4.14870666505335e-02 + 18 1.04623962952111e+01 -4.14495851808446e-02 + 19 1.04500369407186e+01 -4.14001477628744e-02 + 20 1.04350737604756e+01 -4.13402950419026e-02 diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out index 1bd56dbf9..e7657a286 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -93,28 +97,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -125,7 +129,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -153,6 +157,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -163,22 +168,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Linear and polynomial combination of colvar components: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 10.4351 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index b8451d7e6..11055164f 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01168439975032e+01 + x 1.01168439967474e+01 } restraint { diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 94f67cf85..ee78c4b0f 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.04350737609886e+01 -4.13402950439545e-02 - 21 1.04179692243383e+01 -4.12718768973531e-02 - 22 1.03992281891713e+01 -4.11969127566851e-02 - 23 1.03793633980993e+01 -4.11174535923974e-02 - 24 1.03588635770104e+01 -4.10354543080416e-02 - 25 1.03381666087226e+01 -4.09526664348903e-02 - 26 1.03176399252079e+01 -4.08705597008314e-02 - 27 1.02975696745142e+01 -4.07902786980569e-02 - 28 1.02781591065183e+01 -4.07126364260730e-02 - 29 1.02595353413618e+01 -4.06381413654473e-02 - 30 1.02417631919532e+01 -4.05670527678126e-02 - 31 1.02248638717473e+01 -4.04994554869891e-02 - 32 1.02088361345094e+01 -4.04353445380376e-02 - 33 1.01936770395323e+01 -4.03747081581293e-02 - 34 1.01793996409827e+01 -4.03175985639309e-02 - 35 1.01660453826794e+01 -4.02641815307176e-02 - 36 1.01536901430796e+01 -4.02147605723186e-02 - 37 1.01424440841347e+01 -4.01697763365387e-02 - 38 1.01324465166516e+01 -4.01297860666066e-02 - 39 1.01238570544997e+01 -4.00954282179988e-02 - 40 1.01168439975032e+01 -4.00673759900128e-02 + 20 1.04350737604756e+01 -4.13402950419026e-02 + 21 1.04179692237962e+01 -4.12718768951847e-02 + 22 1.03992281886028e+01 -4.11969127544111e-02 + 23 1.03793633975077e+01 -4.11174535900307e-02 + 24 1.03588635763992e+01 -4.10354543055969e-02 + 25 1.03381666080959e+01 -4.09526664323835e-02 + 26 1.03176399245696e+01 -4.08705596982785e-02 + 27 1.02975696738682e+01 -4.07902786954729e-02 + 28 1.02781591058678e+01 -4.07126364234711e-02 + 29 1.02595353407094e+01 -4.06381413628374e-02 + 30 1.02417631913002e+01 -4.05670527652007e-02 + 31 1.02248638710941e+01 -4.04994554843765e-02 + 32 1.02088361338553e+01 -4.04353445354210e-02 + 33 1.01936770388753e+01 -4.03747081555012e-02 + 34 1.01793996403201e+01 -4.03175985612803e-02 + 35 1.01660453820078e+01 -4.02641815280313e-02 + 36 1.01536901423957e+01 -4.02147605695830e-02 + 37 1.01424440834353e+01 -4.01697763337413e-02 + 38 1.01324465159344e+01 -4.01297860637376e-02 + 39 1.01238570537632e+01 -4.00954282150527e-02 + 40 1.01168439967474e+01 -4.00673759869896e-02 diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt index fc4f9e327..157cac038 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. -colvars: Using NAMD interface, version 2016-11-23. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out index a8e792240..139d30fdd 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,28 +116,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -144,7 +148,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -173,17 +177,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped index 7aec83be0..b28d17171 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped @@ -5,11 +5,11 @@ configuration { colvar { name one - x 3.21688253464583e+00 + x 3.21688253444007e+00 } colvar { name two - x 3.24433794490785e+00 + x 3.24433794495372e+00 } diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj index 5633fa456..0cd566be4 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one two fa_two 0 3.20554673468334e+00 0.00000000000000e+00 3.24960869251665e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 3.24790015328139e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 3.24647131781376e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 3.24540254817816e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 3.24474238725816e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 3.24450566303520e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 3.24467445105498e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 3.24520145991536e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 3.24601517427313e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 3.24702592907053e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 0.00000000000000e+00 3.24813222715817e+00 0.00000000000000e+00 - 11 3.21950367383415e+00 0.00000000000000e+00 3.24922681805023e+00 0.00000000000000e+00 - 12 3.22130499858006e+00 0.00000000000000e+00 3.25020238550581e+00 0.00000000000000e+00 - 13 3.22263479496347e+00 0.00000000000000e+00 3.25095679938081e+00 0.00000000000000e+00 - 14 3.22341769665784e+00 0.00000000000000e+00 3.25139788923999e+00 0.00000000000000e+00 - 15 3.22361473677138e+00 0.00000000000000e+00 3.25144751333927e+00 0.00000000000000e+00 - 16 3.22322417514557e+00 0.00000000000000e+00 3.25104460690651e+00 0.00000000000000e+00 - 17 3.22227942564879e+00 0.00000000000000e+00 3.25014688211417e+00 0.00000000000000e+00 - 18 3.22084479803044e+00 0.00000000000000e+00 3.24873101648273e+00 0.00000000000000e+00 - 19 3.21900979846930e+00 0.00000000000000e+00 3.24679142389449e+00 0.00000000000000e+00 - 20 3.21688253464583e+00 0.00000000000000e+00 3.24433794490785e+00 0.00000000000000e+00 + 1 3.20437148316484e+00 0.00000000000000e+00 3.24790015328133e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 3.24647131781360e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 3.24540254817793e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 3.24474238725799e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 3.24450566303529e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 3.24467445105563e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 3.24520145991688e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 3.24601517427588e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 3.24702592907485e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 0.00000000000000e+00 3.24813222716439e+00 0.00000000000000e+00 + 11 3.21950367376059e+00 0.00000000000000e+00 3.24922681805867e+00 0.00000000000000e+00 + 12 3.22130499849384e+00 0.00000000000000e+00 3.25020238551676e+00 0.00000000000000e+00 + 13 3.22263479486396e+00 0.00000000000000e+00 3.25095679939459e+00 0.00000000000000e+00 + 14 3.22341769654449e+00 0.00000000000000e+00 3.25139788925691e+00 0.00000000000000e+00 + 15 3.22361473664369e+00 0.00000000000000e+00 3.25144751335969e+00 0.00000000000000e+00 + 16 3.22322417500307e+00 0.00000000000000e+00 3.25104460693083e+00 0.00000000000000e+00 + 17 3.22227942549106e+00 0.00000000000000e+00 3.25014688214290e+00 0.00000000000000e+00 + 18 3.22084479785707e+00 0.00000000000000e+00 3.24873101651643e+00 0.00000000000000e+00 + 19 3.21900979827991e+00 0.00000000000000e+00 3.24679142393386e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 3.24433794495372e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out index 0fdca4e94..ce5cb44d2 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,28 +116,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -144,7 +148,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -173,22 +177,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting collective variable "two" from value: 3.24434 colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped index d4fe5f034..68f23fd0a 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped @@ -5,11 +5,11 @@ configuration { colvar { name one - x 3.21404878547144e+00 + x 3.21404878499019e+00 } colvar { name two - x 3.14863335158646e+00 + x 3.14863335183754e+00 } diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj index a61269b0f..af3ea4517 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one two fa_two - 20 3.21688253464583e+00 0.00000000000000e+00 3.24433794490785e+00 0.00000000000000e+00 - 21 3.21458253157603e+00 0.00000000000000e+00 3.24139291291795e+00 0.00000000000000e+00 - 22 3.21223315254029e+00 0.00000000000000e+00 3.23798808480870e+00 0.00000000000000e+00 - 23 3.20995392032979e+00 0.00000000000000e+00 3.23416173168426e+00 0.00000000000000e+00 - 24 3.20785326966943e+00 0.00000000000000e+00 3.22995602388112e+00 0.00000000000000e+00 - 25 3.20602244845117e+00 0.00000000000000e+00 3.22541476802931e+00 0.00000000000000e+00 - 26 3.20453120146139e+00 0.00000000000000e+00 3.22058155446344e+00 0.00000000000000e+00 - 27 3.20342556480347e+00 0.00000000000000e+00 3.21549850207982e+00 0.00000000000000e+00 - 28 3.20272769852622e+00 0.00000000000000e+00 3.21020584522746e+00 0.00000000000000e+00 - 29 3.20243730776714e+00 0.00000000000000e+00 3.20474257673639e+00 0.00000000000000e+00 - 30 3.20253423308456e+00 0.00000000000000e+00 3.19914817062614e+00 0.00000000000000e+00 - 31 3.20298183362156e+00 0.00000000000000e+00 3.19346509284150e+00 0.00000000000000e+00 - 32 3.20373100914607e+00 0.00000000000000e+00 3.18774148364007e+00 0.00000000000000e+00 - 33 3.20472468746373e+00 0.00000000000000e+00 3.18203328855458e+00 0.00000000000000e+00 - 34 3.20590256221113e+00 0.00000000000000e+00 3.17640518170088e+00 0.00000000000000e+00 - 35 3.20720566184671e+00 0.00000000000000e+00 3.17092997359260e+00 0.00000000000000e+00 - 36 3.20858030459458e+00 0.00000000000000e+00 3.16568658615923e+00 0.00000000000000e+00 - 37 3.20998111854285e+00 0.00000000000000e+00 3.16075695158616e+00 0.00000000000000e+00 - 38 3.21137308334419e+00 0.00000000000000e+00 3.15622225111600e+00 0.00000000000000e+00 - 39 3.21273274315657e+00 0.00000000000000e+00 3.15215875128202e+00 0.00000000000000e+00 - 40 3.21404878547144e+00 0.00000000000000e+00 3.14863335158646e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 3.24433794495372e+00 0.00000000000000e+00 + 21 3.21458253135360e+00 0.00000000000000e+00 3.24139291297126e+00 0.00000000000000e+00 + 22 3.21223315230095e+00 0.00000000000000e+00 3.23798808487052e+00 0.00000000000000e+00 + 23 3.20995392007338e+00 0.00000000000000e+00 3.23416173175576e+00 0.00000000000000e+00 + 24 3.20785326939589e+00 0.00000000000000e+00 3.22995602396352e+00 0.00000000000000e+00 + 25 3.20602244816055e+00 0.00000000000000e+00 3.22541476812382e+00 0.00000000000000e+00 + 26 3.20453120115385e+00 0.00000000000000e+00 3.22058155457121e+00 0.00000000000000e+00 + 27 3.20342556447929e+00 0.00000000000000e+00 3.21549850220181e+00 0.00000000000000e+00 + 28 3.20272769818575e+00 0.00000000000000e+00 3.21020584536443e+00 0.00000000000000e+00 + 29 3.20243730741081e+00 0.00000000000000e+00 3.20474257688878e+00 0.00000000000000e+00 + 30 3.20253423271288e+00 0.00000000000000e+00 3.19914817079401e+00 0.00000000000000e+00 + 31 3.20298183323508e+00 0.00000000000000e+00 3.19346509302453e+00 0.00000000000000e+00 + 32 3.20373100874536e+00 0.00000000000000e+00 3.18774148383751e+00 0.00000000000000e+00 + 33 3.20472468704943e+00 0.00000000000000e+00 3.18203328876528e+00 0.00000000000000e+00 + 34 3.20590256178394e+00 0.00000000000000e+00 3.17640518192333e+00 0.00000000000000e+00 + 35 3.20720566140745e+00 0.00000000000000e+00 3.17092997382502e+00 0.00000000000000e+00 + 36 3.20858030414420e+00 0.00000000000000e+00 3.16568658639959e+00 0.00000000000000e+00 + 37 3.20998111808250e+00 0.00000000000000e+00 3.16075695183232e+00 0.00000000000000e+00 + 38 3.21137308287521e+00 0.00000000000000e+00 3.15622225136581e+00 0.00000000000000e+00 + 39 3.21273274268056e+00 0.00000000000000e+00 3.15215875153341e+00 0.00000000000000e+00 + 40 3.21404878499019e+00 0.00000000000000e+00 3.14863335183754e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat index 82ce99983..c212baec7 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.20806874278982e-01 - 4 4.95149538768788e-01 - 6 3.29843664998698e-02 - 8 -5.10193943420893e-01 - 10 -1.03852680015666e+00 + 2 8.20806872403133e-01 + 4 4.95149534314936e-01 + 6 3.29843583885573e-02 + 8 -5.10193956226866e-01 + 10 -1.03852681816246e+00 diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat index d0534bfc8..aafb87afd 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.94036335239450e-01 - 4 5.63764182658574e-01 - 6 8.25197229800656e-02 - 8 -4.33277910141469e-01 - 10 -8.58922876516564e-01 + 2 8.94036329632288e-01 + 4 5.63764173125217e-01 + 6 8.25197122357662e-02 + 8 -4.33277918980290e-01 + 10 -8.58922880671951e-01 diff --git a/namd/tests/library/000_distance-corrfunc/namd-version.txt b/namd/tests/library/000_distance-corrfunc/namd-version.txt index b7bf5455c..157cac038 100644 --- a/namd/tests/library/000_distance-corrfunc/namd-version.txt +++ b/namd/tests/library/000_distance-corrfunc/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-10-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out index b48697538..8acf9d14a 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out @@ -7,7 +7,6 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -229,10 +228,12 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped index 39cdbdd58..41807dd58 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21688253464583e+00 + x 3.21688253444007e+00 } colvar { name phi - x 6.02774557527018e+01 + x 6.02774557419409e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj index 0d258d955..19662210d 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step r phi 0 3.20554673468334e+00 6.31129478791928e+01 - 1 3.20437148316546e+00 6.30795952609024e+01 - 2 3.20384028589204e+00 6.30231590817356e+01 - 3 3.20396721187433e+00 6.29423176380356e+01 - 4 3.20472817287036e+00 6.28366833861828e+01 - 5 3.20606308066645e+00 6.27068898721072e+01 - 6 3.20787989003051e+00 6.25546017866590e+01 - 7 3.21005997943917e+00 6.23824530261739e+01 - 8 3.21246460655188e+00 6.21939260051983e+01 - 9 3.21494247388772e+00 6.19931890919450e+01 - 10 3.21733851236362e+00 6.17849080688927e+01 - 11 3.21950367383415e+00 6.15740450245643e+01 - 12 3.22130499858006e+00 6.13656547661594e+01 - 13 3.22263479496346e+00 6.11646847438178e+01 - 14 3.22341769665784e+00 6.09757828950022e+01 - 15 3.22361473677138e+00 6.08031168346083e+01 - 16 3.22322417514557e+00 6.06502098509209e+01 - 17 3.22227942564879e+00 6.05198025353684e+01 - 18 3.22084479803044e+00 6.04137510912894e+01 - 19 3.21900979846930e+00 6.03329741083708e+01 - 20 3.21688253464583e+00 6.02774557527018e+01 + 1 3.20437148316484e+00 6.30795952608635e+01 + 2 3.20384028588952e+00 6.30231590815800e+01 + 3 3.20396721186862e+00 6.29423176376863e+01 + 4 3.20472817286016e+00 6.28366833855655e+01 + 5 3.20606308065050e+00 6.27068898711517e+01 + 6 3.20787989000757e+00 6.25546017852999e+01 + 7 3.21005997940810e+00 6.23824530243513e+01 + 8 3.21246460651160e+00 6.21939260028577e+01 + 9 3.21494247383722e+00 6.19931890890363e+01 + 10 3.21733851230199e+00 6.17849080653709e+01 + 11 3.21950367376059e+00 6.15740450203887e+01 + 12 3.22130499849384e+00 6.13656547612945e+01 + 13 3.22263479486396e+00 6.11646847382338e+01 + 14 3.22341769654449e+00 6.09757828886766e+01 + 15 3.22361473664369e+00 6.08031168275266e+01 + 16 3.22322417500307e+00 6.06502098430779e+01 + 17 3.22227942549106e+00 6.05198025267682e+01 + 18 3.22084479785707e+00 6.04137510819450e+01 + 19 3.21900979827991e+00 6.03329740983039e+01 + 20 3.21688253444007e+00 6.02774557419409e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat index 4ca2d87c5..337d77a7b 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat @@ -1,3053 +1,3053 @@ # 2 -# 0 0.2 50 0 -# 0 6 60 1 +# 0.00000000000000e+00 2.00000000000000e-01 50 0 +# 0.00000000000000e+00 6.00000000000000e+00 60 1 - 0.1 3 0 - 0.1 9 0 - 0.1 15 0 - 0.1 21 0 - 0.1 27 0 - 0.1 33 0 - 0.1 39 0 - 0.1 45 0 - 0.1 51 0 - 0.1 57 0 - 0.1 63 0 - 0.1 69 0 - 0.1 75 0 - 0.1 81 0 - 0.1 87 0 - 0.1 93 0 - 0.1 99 0 - 0.1 105 0 - 0.1 111 0 - 0.1 117 0 - 0.1 123 0 - 0.1 129 0 - 0.1 135 0 - 0.1 141 0 - 0.1 147 0 - 0.1 153 0 - 0.1 159 0 - 0.1 165 0 - 0.1 171 0 - 0.1 177 0 - 0.1 183 0 - 0.1 189 0 - 0.1 195 0 - 0.1 201 0 - 0.1 207 0 - 0.1 213 0 - 0.1 219 0 - 0.1 225 0 - 0.1 231 0 - 0.1 237 0 - 0.1 243 0 - 0.1 249 0 - 0.1 255 0 - 0.1 261 0 - 0.1 267 0 - 0.1 273 0 - 0.1 279 0 - 0.1 285 0 - 0.1 291 0 - 0.1 297 0 - 0.1 303 0 - 0.1 309 0 - 0.1 315 0 - 0.1 321 0 - 0.1 327 0 - 0.1 333 0 - 0.1 339 0 - 0.1 345 0 - 0.1 351 0 - 0.1 357 0 + 1.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 + 1.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 + 1.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 3.30000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 3.90000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 4.50000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 5.10000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 5.70000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 6.30000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 6.90000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 7.50000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 8.10000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 8.70000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 9.30000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 9.90000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 1.05000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.11000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.17000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.23000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.29000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.35000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.41000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.47000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.53000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.59000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.65000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.71000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.77000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.83000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.89000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.95000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.01000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.07000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.13000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.19000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.25000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.31000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.37000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.43000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.49000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.55000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.61000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.67000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.73000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.79000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.85000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.91000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 2.97000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 3.03000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 3.09000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 3.15000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 3.21000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 3.27000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 3.33000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 3.39000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 3.45000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 3.51000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 3.57000000000000e+02 0.00000000000000e+00 - 0.3 3 0 - 0.3 9 0 - 0.3 15 0 - 0.3 21 0 - 0.3 27 0 - 0.3 33 0 - 0.3 39 0 - 0.3 45 0 - 0.3 51 0 - 0.3 57 0 - 0.3 63 0 - 0.3 69 0 - 0.3 75 0 - 0.3 81 0 - 0.3 87 0 - 0.3 93 0 - 0.3 99 0 - 0.3 105 0 - 0.3 111 0 - 0.3 117 0 - 0.3 123 0 - 0.3 129 0 - 0.3 135 0 - 0.3 141 0 - 0.3 147 0 - 0.3 153 0 - 0.3 159 0 - 0.3 165 0 - 0.3 171 0 - 0.3 177 0 - 0.3 183 0 - 0.3 189 0 - 0.3 195 0 - 0.3 201 0 - 0.3 207 0 - 0.3 213 0 - 0.3 219 0 - 0.3 225 0 - 0.3 231 0 - 0.3 237 0 - 0.3 243 0 - 0.3 249 0 - 0.3 255 0 - 0.3 261 0 - 0.3 267 0 - 0.3 273 0 - 0.3 279 0 - 0.3 285 0 - 0.3 291 0 - 0.3 297 0 - 0.3 303 0 - 0.3 309 0 - 0.3 315 0 - 0.3 321 0 - 0.3 327 0 - 0.3 333 0 - 0.3 339 0 - 0.3 345 0 - 0.3 351 0 - 0.3 357 0 + 3.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 + 3.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 + 3.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 3.30000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 3.90000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 4.50000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 5.10000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 5.70000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 6.30000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 6.90000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 7.50000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 8.10000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 8.70000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 9.30000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 9.90000000000000e+01 0.00000000000000e+00 + 3.00000000000000e-01 1.05000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.11000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.17000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.23000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.29000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.35000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.41000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.47000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.53000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.59000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.65000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.71000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.77000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.83000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.89000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 1.95000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.01000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.07000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.13000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.19000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.25000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.31000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.37000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.43000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.49000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.55000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.61000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.67000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.73000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.79000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.85000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.91000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 2.97000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 3.03000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 3.09000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 3.15000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 3.21000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 3.27000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 3.33000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 3.39000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 3.45000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 3.51000000000000e+02 0.00000000000000e+00 + 3.00000000000000e-01 3.57000000000000e+02 0.00000000000000e+00 - 0.5 3 0 - 0.5 9 0 - 0.5 15 0 - 0.5 21 0 - 0.5 27 0 - 0.5 33 0 - 0.5 39 0 - 0.5 45 0 - 0.5 51 0 - 0.5 57 0 - 0.5 63 0 - 0.5 69 0 - 0.5 75 0 - 0.5 81 0 - 0.5 87 0 - 0.5 93 0 - 0.5 99 0 - 0.5 105 0 - 0.5 111 0 - 0.5 117 0 - 0.5 123 0 - 0.5 129 0 - 0.5 135 0 - 0.5 141 0 - 0.5 147 0 - 0.5 153 0 - 0.5 159 0 - 0.5 165 0 - 0.5 171 0 - 0.5 177 0 - 0.5 183 0 - 0.5 189 0 - 0.5 195 0 - 0.5 201 0 - 0.5 207 0 - 0.5 213 0 - 0.5 219 0 - 0.5 225 0 - 0.5 231 0 - 0.5 237 0 - 0.5 243 0 - 0.5 249 0 - 0.5 255 0 - 0.5 261 0 - 0.5 267 0 - 0.5 273 0 - 0.5 279 0 - 0.5 285 0 - 0.5 291 0 - 0.5 297 0 - 0.5 303 0 - 0.5 309 0 - 0.5 315 0 - 0.5 321 0 - 0.5 327 0 - 0.5 333 0 - 0.5 339 0 - 0.5 345 0 - 0.5 351 0 - 0.5 357 0 + 5.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 + 5.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 + 5.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 3.30000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 3.90000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 4.50000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 5.10000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 5.70000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 6.30000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 6.90000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 7.50000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 8.10000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 8.70000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 9.30000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 9.90000000000000e+01 0.00000000000000e+00 + 5.00000000000000e-01 1.05000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.11000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.17000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.23000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.29000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.35000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.41000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.47000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.53000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.59000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.65000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.71000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.77000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.83000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.89000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 1.95000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.01000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.07000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.13000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.19000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.25000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.31000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.37000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.43000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.49000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.55000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.61000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.67000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.73000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.79000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.85000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.91000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 2.97000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 3.03000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 3.09000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 3.15000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 3.21000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 3.27000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 3.33000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 3.39000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 3.45000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 3.51000000000000e+02 0.00000000000000e+00 + 5.00000000000000e-01 3.57000000000000e+02 0.00000000000000e+00 - 0.7 3 0 - 0.7 9 0 - 0.7 15 0 - 0.7 21 0 - 0.7 27 0 - 0.7 33 0 - 0.7 39 0 - 0.7 45 0 - 0.7 51 0 - 0.7 57 0 - 0.7 63 0 - 0.7 69 0 - 0.7 75 0 - 0.7 81 0 - 0.7 87 0 - 0.7 93 0 - 0.7 99 0 - 0.7 105 0 - 0.7 111 0 - 0.7 117 0 - 0.7 123 0 - 0.7 129 0 - 0.7 135 0 - 0.7 141 0 - 0.7 147 0 - 0.7 153 0 - 0.7 159 0 - 0.7 165 0 - 0.7 171 0 - 0.7 177 0 - 0.7 183 0 - 0.7 189 0 - 0.7 195 0 - 0.7 201 0 - 0.7 207 0 - 0.7 213 0 - 0.7 219 0 - 0.7 225 0 - 0.7 231 0 - 0.7 237 0 - 0.7 243 0 - 0.7 249 0 - 0.7 255 0 - 0.7 261 0 - 0.7 267 0 - 0.7 273 0 - 0.7 279 0 - 0.7 285 0 - 0.7 291 0 - 0.7 297 0 - 0.7 303 0 - 0.7 309 0 - 0.7 315 0 - 0.7 321 0 - 0.7 327 0 - 0.7 333 0 - 0.7 339 0 - 0.7 345 0 - 0.7 351 0 - 0.7 357 0 + 7.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 + 7.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 + 7.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 + 7.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 + 7.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 + 7.00000000000000e-01 3.30000000000000e+01 0.00000000000000e+00 + 7.00000000000000e-01 3.90000000000000e+01 0.00000000000000e+00 + 7.00000000000000e-01 4.50000000000000e+01 0.00000000000000e+00 + 7.00000000000000e-01 5.10000000000000e+01 0.00000000000000e+00 + 7.00000000000000e-01 5.70000000000000e+01 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0.00000000000000e+00 + 9.50000000000000e+00 2.97000000000000e+02 0.00000000000000e+00 + 9.50000000000000e+00 3.03000000000000e+02 0.00000000000000e+00 + 9.50000000000000e+00 3.09000000000000e+02 0.00000000000000e+00 + 9.50000000000000e+00 3.15000000000000e+02 0.00000000000000e+00 + 9.50000000000000e+00 3.21000000000000e+02 0.00000000000000e+00 + 9.50000000000000e+00 3.27000000000000e+02 0.00000000000000e+00 + 9.50000000000000e+00 3.33000000000000e+02 0.00000000000000e+00 + 9.50000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 + 9.50000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 + 9.50000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 + 9.50000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 - 9.7 3 0 - 9.7 9 0 - 9.7 15 0 - 9.7 21 0 - 9.7 27 0 - 9.7 33 0 - 9.7 39 0 - 9.7 45 0 - 9.7 51 0 - 9.7 57 0 - 9.7 63 0 - 9.7 69 0 - 9.7 75 0 - 9.7 81 0 - 9.7 87 0 - 9.7 93 0 - 9.7 99 0 - 9.7 105 0 - 9.7 111 0 - 9.7 117 0 - 9.7 123 0 - 9.7 129 0 - 9.7 135 0 - 9.7 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5.10000000000000e+01 0.00000000000000e+00 + 9.70000000000000e+00 5.70000000000000e+01 0.00000000000000e+00 + 9.70000000000000e+00 6.30000000000000e+01 0.00000000000000e+00 + 9.70000000000000e+00 6.90000000000000e+01 0.00000000000000e+00 + 9.70000000000000e+00 7.50000000000000e+01 0.00000000000000e+00 + 9.70000000000000e+00 8.10000000000000e+01 0.00000000000000e+00 + 9.70000000000000e+00 8.70000000000000e+01 0.00000000000000e+00 + 9.70000000000000e+00 9.30000000000000e+01 0.00000000000000e+00 + 9.70000000000000e+00 9.90000000000000e+01 0.00000000000000e+00 + 9.70000000000000e+00 1.05000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.11000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.17000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.23000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.29000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.35000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.41000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.47000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.53000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.59000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.65000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.71000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.77000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.83000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.89000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 1.95000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.01000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.07000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.13000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.19000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.25000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.31000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.37000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.43000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.49000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.55000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.61000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.67000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.73000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.79000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.85000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.91000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 2.97000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.03000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.09000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.15000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.21000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.27000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.33000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 - 9.9 3 0 - 9.9 9 0 - 9.9 15 0 - 9.9 21 0 - 9.9 27 0 - 9.9 33 0 - 9.9 39 0 - 9.9 45 0 - 9.9 51 0 - 9.9 57 0 - 9.9 63 0 - 9.9 69 0 - 9.9 75 0 - 9.9 81 0 - 9.9 87 0 - 9.9 93 0 - 9.9 99 0 - 9.9 105 0 - 9.9 111 0 - 9.9 117 0 - 9.9 123 0 - 9.9 129 0 - 9.9 135 0 - 9.9 141 0 - 9.9 147 0 - 9.9 153 0 - 9.9 159 0 - 9.9 165 0 - 9.9 171 0 - 9.9 177 0 - 9.9 183 0 - 9.9 189 0 - 9.9 195 0 - 9.9 201 0 - 9.9 207 0 - 9.9 213 0 - 9.9 219 0 - 9.9 225 0 - 9.9 231 0 - 9.9 237 0 - 9.9 243 0 - 9.9 249 0 - 9.9 255 0 - 9.9 261 0 - 9.9 267 0 - 9.9 273 0 - 9.9 279 0 - 9.9 285 0 - 9.9 291 0 - 9.9 297 0 - 9.9 303 0 - 9.9 309 0 - 9.9 315 0 - 9.9 321 0 - 9.9 327 0 - 9.9 333 0 - 9.9 339 0 - 9.9 345 0 - 9.9 351 0 - 9.9 357 0 + 9.90000000000000e+00 3.00000000000000e+00 0.00000000000000e+00 + 9.90000000000000e+00 9.00000000000000e+00 0.00000000000000e+00 + 9.90000000000000e+00 1.50000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 2.10000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 2.70000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 3.30000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 3.90000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 4.50000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 5.10000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 5.70000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 6.30000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 6.90000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 7.50000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 8.10000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 8.70000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 9.30000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 9.90000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 1.05000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.11000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.17000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.23000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.29000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.35000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.41000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.47000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.53000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.59000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.65000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.71000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.77000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.83000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.89000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.95000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.01000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.07000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.13000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.19000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.25000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.31000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.37000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.43000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.49000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.55000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.61000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.67000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.73000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.79000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.85000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.91000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.97000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.03000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.09000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.15000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.21000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.27000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.33000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out index 5c3fb9114..7e5cda273 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out @@ -7,7 +7,6 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -229,6 +228,7 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "r" from value: 3.21688 @@ -239,6 +239,7 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped index 16d91a903..ff6d40c16 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21404878547144e+00 + x 3.21404878499019e+00 } colvar { name phi - x 6.08972122017851e+01 + x 6.08972121817132e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj index 6e6a9d108..00a61ca9a 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step r phi - 20 3.21688253464583e+00 6.02774557527018e+01 - 21 3.21458253157603e+00 6.02463068700288e+01 - 22 3.21223315254029e+00 6.02378794668108e+01 - 23 3.20995392032979e+00 6.02499213792704e+01 - 24 3.20785326966943e+00 6.02797520575071e+01 - 25 3.20602244845117e+00 6.03244375021622e+01 - 26 3.20453120146139e+00 6.03809430522940e+01 - 27 3.20342556480347e+00 6.04462482372788e+01 - 28 3.20272769852622e+00 6.05174152657937e+01 - 29 3.20243730776714e+00 6.05916134522643e+01 - 30 3.20253423308456e+00 6.06661106334871e+01 - 31 3.20298183362156e+00 6.07382494079973e+01 - 32 3.20373100914607e+00 6.08054278528112e+01 - 33 3.20472468746373e+00 6.08651029084488e+01 - 34 3.20590256221113e+00 6.09148265944857e+01 - 35 3.20720566184671e+00 6.09523144226767e+01 - 36 3.20858030459458e+00 6.09755306669437e+01 - 37 3.20998111854285e+00 6.09827676451462e+01 - 38 3.21137308334418e+00 6.09726956295080e+01 - 39 3.21273274315657e+00 6.09443715427968e+01 - 40 3.21404878547144e+00 6.08972122017851e+01 + 20 3.21688253444007e+00 6.02774557419409e+01 + 21 3.21458253135360e+00 6.02463068586077e+01 + 22 3.21223315230095e+00 6.02378794547663e+01 + 23 3.20995392007338e+00 6.02499213666401e+01 + 24 3.20785326939589e+00 6.02797520443280e+01 + 25 3.20602244816055e+00 6.03244374884686e+01 + 26 3.20453120115385e+00 6.03809430381167e+01 + 27 3.20342556447929e+00 6.04462482226441e+01 + 28 3.20272769818575e+00 6.05174152507232e+01 + 29 3.20243730741081e+00 6.05916134367745e+01 + 30 3.20253423271288e+00 6.06661106175895e+01 + 31 3.20298183323508e+00 6.07382493916987e+01 + 32 3.20373100874536e+00 6.08054278361141e+01 + 33 3.20472468704943e+00 6.08651028913518e+01 + 34 3.20590256178394e+00 6.09148265769850e+01 + 35 3.20720566140745e+00 6.09523144047667e+01 + 36 3.20858030414420e+00 6.09755306486176e+01 + 37 3.20998111808250e+00 6.09827676263964e+01 + 38 3.21137308287521e+00 6.09726956103267e+01 + 39 3.21273274268056e+00 6.09443715231751e+01 + 40 3.21404878499019e+00 6.08972121817132e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat index bcd93aff0..60d272104 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat @@ -1,3053 +1,3053 @@ # 2 -# 0 0.2 50 0 -# 0 6 60 1 +# 0.00000000000000e+00 2.00000000000000e-01 50 0 +# 0.00000000000000e+00 6.00000000000000e+00 60 1 - 0.1 3 0 - 0.1 9 0 - 0.1 15 0 - 0.1 21 0 - 0.1 27 0 - 0.1 33 0 - 0.1 39 0 - 0.1 45 0 - 0.1 51 0 - 0.1 57 0 - 0.1 63 0 - 0.1 69 0 - 0.1 75 0 - 0.1 81 0 - 0.1 87 0 - 0.1 93 0 - 0.1 99 0 - 0.1 105 0 - 0.1 111 0 - 0.1 117 0 - 0.1 123 0 - 0.1 129 0 - 0.1 135 0 - 0.1 141 0 - 0.1 147 0 - 0.1 153 0 - 0.1 159 0 - 0.1 165 0 - 0.1 171 0 - 0.1 177 0 - 0.1 183 0 - 0.1 189 0 - 0.1 195 0 - 0.1 201 0 - 0.1 207 0 - 0.1 213 0 - 0.1 219 0 - 0.1 225 0 - 0.1 231 0 - 0.1 237 0 - 0.1 243 0 - 0.1 249 0 - 0.1 255 0 - 0.1 261 0 - 0.1 267 0 - 0.1 273 0 - 0.1 279 0 - 0.1 285 0 - 0.1 291 0 - 0.1 297 0 - 0.1 303 0 - 0.1 309 0 - 0.1 315 0 - 0.1 321 0 - 0.1 327 0 - 0.1 333 0 - 0.1 339 0 - 0.1 345 0 - 0.1 351 0 - 0.1 357 0 + 1.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 + 1.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 + 1.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 3.30000000000000e+01 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0.00000000000000e+00 + 9.90000000000000e+00 1.71000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.77000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.83000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.89000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.95000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.01000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.07000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.13000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.19000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.25000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.31000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.37000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.43000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.49000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.55000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.61000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.67000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.73000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.79000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.85000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.91000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.97000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.03000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.09000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.15000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.21000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.27000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.33000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt index 017b69b3a..157cac038 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2022-04-14. -colvars: Using NAMD interface, version "2022-04-06". +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out index 0254b6e28..a28b5f43d 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out @@ -7,7 +7,6 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -226,10 +225,12 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped index b2dc7dab5..3008cc63c 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21688253464583e+00 + x 3.21688253444007e+00 } colvar { name phi - x 6.02774557527018e+01 + x 6.02774557419409e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj index 0d258d955..19662210d 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step r phi 0 3.20554673468334e+00 6.31129478791928e+01 - 1 3.20437148316546e+00 6.30795952609024e+01 - 2 3.20384028589204e+00 6.30231590817356e+01 - 3 3.20396721187433e+00 6.29423176380356e+01 - 4 3.20472817287036e+00 6.28366833861828e+01 - 5 3.20606308066645e+00 6.27068898721072e+01 - 6 3.20787989003051e+00 6.25546017866590e+01 - 7 3.21005997943917e+00 6.23824530261739e+01 - 8 3.21246460655188e+00 6.21939260051983e+01 - 9 3.21494247388772e+00 6.19931890919450e+01 - 10 3.21733851236362e+00 6.17849080688927e+01 - 11 3.21950367383415e+00 6.15740450245643e+01 - 12 3.22130499858006e+00 6.13656547661594e+01 - 13 3.22263479496346e+00 6.11646847438178e+01 - 14 3.22341769665784e+00 6.09757828950022e+01 - 15 3.22361473677138e+00 6.08031168346083e+01 - 16 3.22322417514557e+00 6.06502098509209e+01 - 17 3.22227942564879e+00 6.05198025353684e+01 - 18 3.22084479803044e+00 6.04137510912894e+01 - 19 3.21900979846930e+00 6.03329741083708e+01 - 20 3.21688253464583e+00 6.02774557527018e+01 + 1 3.20437148316484e+00 6.30795952608635e+01 + 2 3.20384028588952e+00 6.30231590815800e+01 + 3 3.20396721186862e+00 6.29423176376863e+01 + 4 3.20472817286016e+00 6.28366833855655e+01 + 5 3.20606308065050e+00 6.27068898711517e+01 + 6 3.20787989000757e+00 6.25546017852999e+01 + 7 3.21005997940810e+00 6.23824530243513e+01 + 8 3.21246460651160e+00 6.21939260028577e+01 + 9 3.21494247383722e+00 6.19931890890363e+01 + 10 3.21733851230199e+00 6.17849080653709e+01 + 11 3.21950367376059e+00 6.15740450203887e+01 + 12 3.22130499849384e+00 6.13656547612945e+01 + 13 3.22263479486396e+00 6.11646847382338e+01 + 14 3.22341769654449e+00 6.09757828886766e+01 + 15 3.22361473664369e+00 6.08031168275266e+01 + 16 3.22322417500307e+00 6.06502098430779e+01 + 17 3.22227942549106e+00 6.05198025267682e+01 + 18 3.22084479785707e+00 6.04137510819450e+01 + 19 3.21900979827991e+00 6.03329740983039e+01 + 20 3.21688253444007e+00 6.02774557419409e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat index d42b8f708..560cfda3e 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat @@ -1,7223 +1,7223 @@ # 2 -# 0 1 20 0 -# -180 1 360 1 +# 0.00000000000000e+00 1.00000000000000e+00 20 0 +# -1.80000000000000e+02 1.00000000000000e+00 360 1 - 0.5 -179.5 0 - 0.5 -178.5 0 - 0.5 -177.5 0 - 0.5 -176.5 0 - 0.5 -175.5 0 - 0.5 -174.5 0 - 0.5 -173.5 0 - 0.5 -172.5 0 - 0.5 -171.5 0 - 0.5 -170.5 0 - 0.5 -169.5 0 - 0.5 -168.5 0 - 0.5 -167.5 0 - 0.5 -166.5 0 - 0.5 -165.5 0 - 0.5 -164.5 0 - 0.5 -163.5 0 - 0.5 -162.5 0 - 0.5 -161.5 0 - 0.5 -160.5 0 - 0.5 -159.5 0 - 0.5 -158.5 0 - 0.5 -157.5 0 - 0.5 -156.5 0 - 0.5 -155.5 0 - 0.5 -154.5 0 - 0.5 -153.5 0 - 0.5 -152.5 0 - 0.5 -151.5 0 - 0.5 -150.5 0 - 0.5 -149.5 0 - 0.5 -148.5 0 - 0.5 -147.5 0 - 0.5 -146.5 0 - 0.5 -145.5 0 - 0.5 -144.5 0 - 0.5 -143.5 0 - 0.5 -142.5 0 - 0.5 -141.5 0 - 0.5 -140.5 0 - 0.5 -139.5 0 - 0.5 -138.5 0 - 0.5 -137.5 0 - 0.5 -136.5 0 - 0.5 -135.5 0 - 0.5 -134.5 0 - 0.5 -133.5 0 - 0.5 -132.5 0 - 0.5 -131.5 0 - 0.5 -130.5 0 - 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1.53500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.54500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.55500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.56500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.57500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.58500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.59500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.60500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.61500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.62500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.63500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.64500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.65500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.66500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.67500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.68500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.69500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.70500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.71500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.72500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.73500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.74500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.75500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.76500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.77500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.78500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.79500000000000e+02 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.out index 43174e795..74614ceb4 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.out @@ -7,7 +7,6 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -226,6 +225,7 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "r" from value: 3.21688 @@ -236,6 +236,7 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped index 1d0bd953f..51260c395 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21404878547144e+00 + x 3.21404878499019e+00 } colvar { name phi - x 6.08972122017851e+01 + x 6.08972121817132e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj index 6e6a9d108..00a61ca9a 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step r phi - 20 3.21688253464583e+00 6.02774557527018e+01 - 21 3.21458253157603e+00 6.02463068700288e+01 - 22 3.21223315254029e+00 6.02378794668108e+01 - 23 3.20995392032979e+00 6.02499213792704e+01 - 24 3.20785326966943e+00 6.02797520575071e+01 - 25 3.20602244845117e+00 6.03244375021622e+01 - 26 3.20453120146139e+00 6.03809430522940e+01 - 27 3.20342556480347e+00 6.04462482372788e+01 - 28 3.20272769852622e+00 6.05174152657937e+01 - 29 3.20243730776714e+00 6.05916134522643e+01 - 30 3.20253423308456e+00 6.06661106334871e+01 - 31 3.20298183362156e+00 6.07382494079973e+01 - 32 3.20373100914607e+00 6.08054278528112e+01 - 33 3.20472468746373e+00 6.08651029084488e+01 - 34 3.20590256221113e+00 6.09148265944857e+01 - 35 3.20720566184671e+00 6.09523144226767e+01 - 36 3.20858030459458e+00 6.09755306669437e+01 - 37 3.20998111854285e+00 6.09827676451462e+01 - 38 3.21137308334418e+00 6.09726956295080e+01 - 39 3.21273274315657e+00 6.09443715427968e+01 - 40 3.21404878547144e+00 6.08972122017851e+01 + 20 3.21688253444007e+00 6.02774557419409e+01 + 21 3.21458253135360e+00 6.02463068586077e+01 + 22 3.21223315230095e+00 6.02378794547663e+01 + 23 3.20995392007338e+00 6.02499213666401e+01 + 24 3.20785326939589e+00 6.02797520443280e+01 + 25 3.20602244816055e+00 6.03244374884686e+01 + 26 3.20453120115385e+00 6.03809430381167e+01 + 27 3.20342556447929e+00 6.04462482226441e+01 + 28 3.20272769818575e+00 6.05174152507232e+01 + 29 3.20243730741081e+00 6.05916134367745e+01 + 30 3.20253423271288e+00 6.06661106175895e+01 + 31 3.20298183323508e+00 6.07382493916987e+01 + 32 3.20373100874536e+00 6.08054278361141e+01 + 33 3.20472468704943e+00 6.08651028913518e+01 + 34 3.20590256178394e+00 6.09148265769850e+01 + 35 3.20720566140745e+00 6.09523144047667e+01 + 36 3.20858030414420e+00 6.09755306486176e+01 + 37 3.20998111808250e+00 6.09827676263964e+01 + 38 3.21137308287521e+00 6.09726956103267e+01 + 39 3.21273274268056e+00 6.09443715231751e+01 + 40 3.21404878499019e+00 6.08972121817132e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat index 3099652d8..4d18e65a0 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat @@ -1,7223 +1,7223 @@ # 2 -# 0 1 20 0 -# -180 1 360 1 +# 0.00000000000000e+00 1.00000000000000e+00 20 0 +# -1.80000000000000e+02 1.00000000000000e+00 360 1 - 0.5 -179.5 0 - 0.5 -178.5 0 - 0.5 -177.5 0 - 0.5 -176.5 0 - 0.5 -175.5 0 - 0.5 -174.5 0 - 0.5 -173.5 0 - 0.5 -172.5 0 - 0.5 -171.5 0 - 0.5 -170.5 0 - 0.5 -169.5 0 - 0.5 -168.5 0 - 0.5 -167.5 0 - 0.5 -166.5 0 - 0.5 -165.5 0 - 0.5 -164.5 0 - 0.5 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1.95000000000000e+01 1.60500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.61500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.62500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.63500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.64500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.65500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.66500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.67500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.68500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.69500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.70500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.71500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.72500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.73500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.74500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.75500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.76500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.77500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.78500000000000e+02 0.00000000000000e+00 + 1.95000000000000e+01 1.79500000000000e+02 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt index 017b69b3a..157cac038 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2022-04-14. -colvars: Using NAMD interface, version "2022-04-06". +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.out index 8f7f16dfc..29efeb040 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -131,15 +135,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.state.stripped index 1496b7b42..80db08403 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21549729243177e+00 - v 1.66004320267550e-04 - extended_x 3.20655438768302e+00 - extended_v 1.66004320267550e-04 + x 3.21549729223606e+00 + v 1.66004318946232e-04 + extended_x 3.20655438767549e+00 + extended_v 1.66004318946232e-04 } histogram { diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.traj index 806e5b8bd..fd37c0df1 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 3.20554673468334e+00 -1.17525151787978e-03 0.00000000000000e+00 0.00000000000000e+00 - 2 3.20384207676648e+00 3.20554557475659e+00 -5.29406398987575e-04 -1.15992675532533e-06 0.00000000000000e+00 - 3 3.20397336463584e+00 3.20554273354471e+00 1.31287869361341e-04 -2.84121188137078e-06 0.00000000000000e+00 - 4 3.20474099644192e+00 3.20553834342780e+00 7.67631806078306e-04 -4.39011691036157e-06 0.00000000000000e+00 - 5 3.20608362355857e+00 3.20553316636095e+00 1.34262711665745e-03 -5.17706684246563e-06 0.00000000000000e+00 - 6 3.20790705618803e+00 3.20552853257359e+00 1.82343262945217e-03 -4.63378736444209e-06 0.00000000000000e+00 - 7 3.21008981945490e+00 3.20552624629494e+00 2.18276326687761e-03 -2.28627865112881e-06 0.00000000000000e+00 - 8 3.21248983390024e+00 3.20552846408246e+00 2.40001444533844e-03 2.21778752329949e-06 0.00000000000000e+00 - 9 3.21495224228226e+00 3.20553755246660e+00 2.46240838201839e-03 9.08838414241666e-06 0.00000000000000e+00 - 10 3.21731847446546e+00 3.20555593277715e+00 2.36623218319787e-03 1.83803105463654e-05 0.00000000000000e+00 - 11 3.21943632296051e+00 3.20558592225102e+00 2.11784849505436e-03 2.99894738678567e-05 0.00000000000000e+00 - 12 3.22117027447190e+00 3.20562958152247e+00 1.73395151138855e-03 4.36592714477837e-05 0.00000000000000e+00 - 13 3.22241091368139e+00 3.20568857884307e+00 1.24063920948991e-03 5.89973206007553e-05 0.00000000000000e+00 - 14 3.22308214692374e+00 3.20576408044662e+00 6.71233242349967e-04 7.55016035524360e-05 0.00000000000000e+00 - 15 3.22314537206879e+00 3.20585667429668e+00 6.32251450487509e-05 9.25938500645313e-05 0.00000000000000e+00 - 16 3.22260032437968e+00 3.20596633140751e+00 -5.45047689109790e-04 1.09657110826599e-04 0.00000000000000e+00 - 17 3.22148294583595e+00 3.20609240561136e+00 -1.11737854372507e-03 1.26074203851179e-04 0.00000000000000e+00 - 18 3.21986099902724e+00 3.20623366966957e+00 -1.62194680871552e-03 1.41264058204757e-04 0.00000000000000e+00 - 19 3.21782818036332e+00 3.20638838336275e+00 -2.03281866392047e-03 1.54713693185114e-04 0.00000000000000e+00 - 20 3.21549729243177e+00 3.20655438768302e+00 -2.33088793154801e-03 1.66004320267550e-04 0.00000000000000e+00 + 1 3.20437148316484e+00 3.20554673468334e+00 -1.17525151850328e-03 0.00000000000000e+00 0.00000000000000e+00 + 2 3.20384207676395e+00 3.20554557475659e+00 -5.29406400886501e-04 -1.15992675594070e-06 0.00000000000000e+00 + 3 3.20397336463013e+00 3.20554273354470e+00 1.31287866173224e-04 -2.84121188447568e-06 0.00000000000000e+00 + 4 3.20474099643173e+00 3.20553834342779e+00 7.67631801607216e-04 -4.39011691909949e-06 0.00000000000000e+00 + 5 3.20608362354267e+00 3.20553316636092e+00 1.34262711093314e-03 -5.17706686124102e-06 0.00000000000000e+00 + 6 3.20790705616520e+00 3.20552853257352e+00 1.82343262252793e-03 -4.63378739888577e-06 0.00000000000000e+00 + 7 3.21008981942402e+00 3.20552624629482e+00 2.18276325882849e-03 -2.28627870804055e-06 0.00000000000000e+00 + 8 3.21248983386027e+00 3.20552846408225e+00 2.40001443624793e-03 2.21778743603120e-06 0.00000000000000e+00 + 9 3.21495224223226e+00 3.20553755246627e+00 2.46240837198597e-03 9.08838401590574e-06 0.00000000000000e+00 + 10 3.21731847440459e+00 3.20555593277664e+00 2.36623217233012e-03 1.83803103708351e-05 0.00000000000000e+00 + 11 3.21943632288805e+00 3.20558592225027e+00 2.11784848345964e-03 2.99894736327547e-05 0.00000000000000e+00 + 12 3.22117027438722e+00 3.20562958152141e+00 1.73395149917299e-03 4.36592711418987e-05 0.00000000000000e+00 + 13 3.22241091358397e+00 3.20568857884163e+00 1.24063919675121e-03 5.89973202123335e-05 0.00000000000000e+00 + 14 3.22308214681315e+00 3.20576408044470e+00 6.71233229177393e-04 7.55016030692882e-05 0.00000000000000e+00 + 15 3.22314537194466e+00 3.20585667429417e+00 6.32251315102472e-05 9.25938494741335e-05 0.00000000000000e+00 + 16 3.22260032424170e+00 3.20596633140428e+00 -5.45047702959156e-04 1.09657110116172e-04 0.00000000000000e+00 + 17 3.22148294568386e+00 3.20609240560729e+00 -1.11737855784311e-03 1.26074203007756e-04 0.00000000000000e+00 + 18 3.21986099886079e+00 3.20623366966451e+00 -1.62194682306716e-03 1.41264057215237e-04 0.00000000000000e+00 + 19 3.21782818018232e+00 3.20638838335654e+00 -2.03281867847016e-03 1.54713692036308e-04 0.00000000000000e+00 + 20 3.21549729223606e+00 3.20655438767549e+00 -2.33088794625580e-03 1.66004318946232e-04 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.histogram1.dat index 09d19a2d1..69e912676 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.histogram1.dat @@ -1,23 +1,23 @@ # 1 -# 0 0.5 20 0 +# 0.00000000000000e+00 5.00000000000000e-01 20 0 - 0.25 0 - 0.75 0 - 1.25 0 - 1.75 0 - 2.25 0 - 2.75 0 - 3.25 20 - 3.75 0 - 4.25 0 - 4.75 0 - 5.25 0 - 5.75 0 - 6.25 0 - 6.75 0 - 7.25 0 - 7.75 0 - 8.25 0 - 8.75 0 - 9.25 0 - 9.75 0 + 2.50000000000000e-01 0.00000000000000e+00 + 7.50000000000000e-01 0.00000000000000e+00 + 1.25000000000000e+00 0.00000000000000e+00 + 1.75000000000000e+00 0.00000000000000e+00 + 2.25000000000000e+00 0.00000000000000e+00 + 2.75000000000000e+00 0.00000000000000e+00 + 3.25000000000000e+00 2.00000000000000e+01 + 3.75000000000000e+00 0.00000000000000e+00 + 4.25000000000000e+00 0.00000000000000e+00 + 4.75000000000000e+00 0.00000000000000e+00 + 5.25000000000000e+00 0.00000000000000e+00 + 5.75000000000000e+00 0.00000000000000e+00 + 6.25000000000000e+00 0.00000000000000e+00 + 6.75000000000000e+00 0.00000000000000e+00 + 7.25000000000000e+00 0.00000000000000e+00 + 7.75000000000000e+00 0.00000000000000e+00 + 8.25000000000000e+00 0.00000000000000e+00 + 8.75000000000000e+00 0.00000000000000e+00 + 9.25000000000000e+00 0.00000000000000e+00 + 9.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out index e576ed733..fd1bac75c 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -131,20 +135,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.2155 colvars: Restarting histogram bias "histogram1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.state.stripped index 3110bf4ce..beb2691ef 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21132143720911e+00 - v 1.04669174158030e-04 - extended_x 3.20946748687297e+00 - extended_v 1.04669174158030e-04 + x 3.21132143681526e+00 + v 1.04669167318816e-04 + extended_x 3.20946748678570e+00 + extended_v 1.04669167318816e-04 } histogram { diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.traj index 1791c31a3..2713c291f 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 20 3.21549729243177e+00 3.20655438768302e+00 0.00000000000000e+00 1.66004320267550e-04 0.00000000000000e+00 - 21 3.21299279860961e+00 3.20672921829649e+00 -2.50449382215923e-03 1.74830613474229e-04 0.00000000000000e+00 - 22 3.21044297404629e+00 3.20691023081595e+00 -2.54982456331954e-03 1.81012519456721e-04 0.00000000000000e+00 - 23 3.20797196956081e+00 3.20709473001322e+00 -2.47100448548521e-03 1.84499197270131e-04 0.00000000000000e+00 - 24 3.20569233667745e+00 3.20728009501122e+00 -2.27963288336186e-03 1.85364998000097e-04 0.00000000000000e+00 - 25 3.20369874909954e+00 3.20746389295456e+00 -1.99358757790735e-03 1.83797943336207e-04 0.00000000000000e+00 - 26 3.20206356012972e+00 3.20764397484986e+00 -1.63518896981651e-03 1.80081895299983e-04 0.00000000000000e+00 - 27 3.20083453399825e+00 3.20781854909659e+00 -1.22902613147335e-03 1.74574246731807e-04 0.00000000000000e+00 - 28 3.20003466940781e+00 3.20798623039671e+00 -7.99864590434129e-04 1.67681300116621e-04 0.00000000000000e+00 - 29 3.19966366617398e+00 3.20814606382069e+00 -3.71003233836653e-04 1.59833423983471e-04 0.00000000000000e+00 - 30 3.19970060593396e+00 3.20829752545376e+00 3.69397599828680e-05 1.51461633068893e-04 0.00000000000000e+00 - 31 3.20010746077786e+00 3.20844050226735e+00 4.06854843902238e-04 1.42976813596051e-04 0.00000000000000e+00 - 32 3.20083326294086e+00 3.20857525469865e+00 7.25802162999667e-04 1.34752431300136e-04 0.00000000000000e+00 - 33 3.20181875720671e+00 3.20870236609036e+00 9.85494265844711e-04 1.27111391707545e-04 0.00000000000000e+00 - 34 3.20300129361245e+00 3.20882268363242e+00 1.18253640574428e-03 1.20317542054195e-04 0.00000000000000e+00 - 35 3.20431952758785e+00 3.20893725569281e+00 1.31823397539854e-03 1.14572060398045e-04 0.00000000000000e+00 - 36 3.20571748562482e+00 3.20904727023825e+00 1.39795803697362e-03 1.10014545435265e-04 0.00000000000000e+00 - 37 3.20714765705722e+00 3.20915399841800e+00 1.43017143239943e-03 1.06728179747730e-04 0.00000000000000e+00 - 38 3.20857308613613e+00 3.20925874641819e+00 1.42542907890419e-03 1.04748000195290e-04 0.00000000000000e+00 - 39 3.20996861050691e+00 3.20936281769881e+00 1.39552437078372e-03 1.04071280621537e-04 0.00000000000000e+00 - 40 3.21132143720911e+00 3.20946748687297e+00 1.35282670220427e-03 1.04669174158030e-04 0.00000000000000e+00 + 20 3.21549729223606e+00 3.20655438767549e+00 0.00000000000000e+00 1.66004318946232e-04 0.00000000000000e+00 + 21 3.21299279839909e+00 3.20672921828746e+00 -2.50449383696960e-03 1.74830611967189e-04 0.00000000000000e+00 + 22 3.21044297382093e+00 3.20691023080521e+00 -2.54982457816277e-03 1.81012517750828e-04 0.00000000000000e+00 + 23 3.20797196932066e+00 3.20709473000056e+00 -2.47100450027160e-03 1.84499195352419e-04 0.00000000000000e+00 + 24 3.20569233642268e+00 3.20728009499642e+00 -2.27963289798438e-03 1.85364995857865e-04 0.00000000000000e+00 + 25 3.20369874883042e+00 3.20746389293738e+00 -1.99358759225499e-03 1.83797940957138e-04 0.00000000000000e+00 + 26 3.20206355984665e+00 3.20764397483005e+00 -1.63518898377291e-03 1.80081892672264e-04 0.00000000000000e+00 + 27 3.20083453370172e+00 3.20781854907389e+00 -1.22902614493015e-03 1.74574243844257e-04 0.00000000000000e+00 + 28 3.20003466909842e+00 3.20798623037085e+00 -7.99864603297173e-04 1.67681296958808e-04 0.00000000000000e+00 + 29 3.19966366585238e+00 3.20814606379140e+00 -3.71003246035784e-04 1.59833420545817e-04 0.00000000000000e+00 + 30 3.19970060560089e+00 3.20829752542074e+00 3.69397485058265e-05 1.51461629342751e-04 0.00000000000000e+00 + 31 3.20010746043407e+00 3.20844050223031e+00 4.06854833183257e-04 1.42976809573772e-04 0.00000000000000e+00 + 32 3.20083326258715e+00 3.20857525465729e+00 7.25802153073385e-04 1.34752426975110e-04 0.00000000000000e+00 + 33 3.20181875684390e+00 3.20870236604436e+00 9.85494256751096e-04 1.27111387074243e-04 0.00000000000000e+00 + 34 3.20300129324144e+00 3.20882268358147e+00 1.18253639754595e-03 1.20317537108215e-04 0.00000000000000e+00 + 35 3.20431952720963e+00 3.20893725563661e+00 1.31823396818787e-03 1.14572055136176e-04 0.00000000000000e+00 + 36 3.20571748524051e+00 3.20904727017646e+00 1.39795803087983e-03 1.10014539855585e-04 0.00000000000000e+00 + 37 3.20714765666810e+00 3.20915399835031e+00 1.43017142759172e-03 1.06728173849729e-04 0.00000000000000e+00 + 38 3.20857308574368e+00 3.20925874634429e+00 1.42542907557441e-03 1.04747993980047e-04 0.00000000000000e+00 + 39 3.20996861011282e+00 3.20936281761839e+00 1.39552436913792e-03 1.04071274091898e-04 0.00000000000000e+00 + 40 3.21132143681526e+00 3.20946748678570e+00 1.35282670244763e-03 1.04669167318816e-04 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.histogram1.dat index 544c0ba33..fe4ddc2fd 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.histogram1.dat @@ -1,23 +1,23 @@ # 1 -# 0 0.5 20 0 +# 0.00000000000000e+00 5.00000000000000e-01 20 0 - 0.25 0 - 0.75 0 - 1.25 0 - 1.75 0 - 2.25 0 - 2.75 0 - 3.25 40 - 3.75 0 - 4.25 0 - 4.75 0 - 5.25 0 - 5.75 0 - 6.25 0 - 6.75 0 - 7.25 0 - 7.75 0 - 8.25 0 - 8.75 0 - 9.25 0 - 9.75 0 + 2.50000000000000e-01 0.00000000000000e+00 + 7.50000000000000e-01 0.00000000000000e+00 + 1.25000000000000e+00 0.00000000000000e+00 + 1.75000000000000e+00 0.00000000000000e+00 + 2.25000000000000e+00 0.00000000000000e+00 + 2.75000000000000e+00 0.00000000000000e+00 + 3.25000000000000e+00 4.00000000000000e+01 + 3.75000000000000e+00 0.00000000000000e+00 + 4.25000000000000e+00 0.00000000000000e+00 + 4.75000000000000e+00 0.00000000000000e+00 + 5.25000000000000e+00 0.00000000000000e+00 + 5.75000000000000e+00 0.00000000000000e+00 + 6.25000000000000e+00 0.00000000000000e+00 + 6.75000000000000e+00 0.00000000000000e+00 + 7.25000000000000e+00 0.00000000000000e+00 + 7.75000000000000e+00 0.00000000000000e+00 + 8.25000000000000e+00 0.00000000000000e+00 + 8.75000000000000e+00 0.00000000000000e+00 + 9.25000000000000e+00 0.00000000000000e+00 + 9.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt index e2b19c981..157cac038 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.out index 8cc6fdd1e..3a60d5ed3 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -130,15 +134,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.state.stripped index 1496b7b42..80db08403 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21549729243177e+00 - v 1.66004320267550e-04 - extended_x 3.20655438768302e+00 - extended_v 1.66004320267550e-04 + x 3.21549729223606e+00 + v 1.66004318946232e-04 + extended_x 3.20655438767549e+00 + extended_v 1.66004318946232e-04 } histogram { diff --git a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.traj index 806e5b8bd..fd37c0df1 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 3.20554673468334e+00 -1.17525151787978e-03 0.00000000000000e+00 0.00000000000000e+00 - 2 3.20384207676648e+00 3.20554557475659e+00 -5.29406398987575e-04 -1.15992675532533e-06 0.00000000000000e+00 - 3 3.20397336463584e+00 3.20554273354471e+00 1.31287869361341e-04 -2.84121188137078e-06 0.00000000000000e+00 - 4 3.20474099644192e+00 3.20553834342780e+00 7.67631806078306e-04 -4.39011691036157e-06 0.00000000000000e+00 - 5 3.20608362355857e+00 3.20553316636095e+00 1.34262711665745e-03 -5.17706684246563e-06 0.00000000000000e+00 - 6 3.20790705618803e+00 3.20552853257359e+00 1.82343262945217e-03 -4.63378736444209e-06 0.00000000000000e+00 - 7 3.21008981945490e+00 3.20552624629494e+00 2.18276326687761e-03 -2.28627865112881e-06 0.00000000000000e+00 - 8 3.21248983390024e+00 3.20552846408246e+00 2.40001444533844e-03 2.21778752329949e-06 0.00000000000000e+00 - 9 3.21495224228226e+00 3.20553755246660e+00 2.46240838201839e-03 9.08838414241666e-06 0.00000000000000e+00 - 10 3.21731847446546e+00 3.20555593277715e+00 2.36623218319787e-03 1.83803105463654e-05 0.00000000000000e+00 - 11 3.21943632296051e+00 3.20558592225102e+00 2.11784849505436e-03 2.99894738678567e-05 0.00000000000000e+00 - 12 3.22117027447190e+00 3.20562958152247e+00 1.73395151138855e-03 4.36592714477837e-05 0.00000000000000e+00 - 13 3.22241091368139e+00 3.20568857884307e+00 1.24063920948991e-03 5.89973206007553e-05 0.00000000000000e+00 - 14 3.22308214692374e+00 3.20576408044662e+00 6.71233242349967e-04 7.55016035524360e-05 0.00000000000000e+00 - 15 3.22314537206879e+00 3.20585667429668e+00 6.32251450487509e-05 9.25938500645313e-05 0.00000000000000e+00 - 16 3.22260032437968e+00 3.20596633140751e+00 -5.45047689109790e-04 1.09657110826599e-04 0.00000000000000e+00 - 17 3.22148294583595e+00 3.20609240561136e+00 -1.11737854372507e-03 1.26074203851179e-04 0.00000000000000e+00 - 18 3.21986099902724e+00 3.20623366966957e+00 -1.62194680871552e-03 1.41264058204757e-04 0.00000000000000e+00 - 19 3.21782818036332e+00 3.20638838336275e+00 -2.03281866392047e-03 1.54713693185114e-04 0.00000000000000e+00 - 20 3.21549729243177e+00 3.20655438768302e+00 -2.33088793154801e-03 1.66004320267550e-04 0.00000000000000e+00 + 1 3.20437148316484e+00 3.20554673468334e+00 -1.17525151850328e-03 0.00000000000000e+00 0.00000000000000e+00 + 2 3.20384207676395e+00 3.20554557475659e+00 -5.29406400886501e-04 -1.15992675594070e-06 0.00000000000000e+00 + 3 3.20397336463013e+00 3.20554273354470e+00 1.31287866173224e-04 -2.84121188447568e-06 0.00000000000000e+00 + 4 3.20474099643173e+00 3.20553834342779e+00 7.67631801607216e-04 -4.39011691909949e-06 0.00000000000000e+00 + 5 3.20608362354267e+00 3.20553316636092e+00 1.34262711093314e-03 -5.17706686124102e-06 0.00000000000000e+00 + 6 3.20790705616520e+00 3.20552853257352e+00 1.82343262252793e-03 -4.63378739888577e-06 0.00000000000000e+00 + 7 3.21008981942402e+00 3.20552624629482e+00 2.18276325882849e-03 -2.28627870804055e-06 0.00000000000000e+00 + 8 3.21248983386027e+00 3.20552846408225e+00 2.40001443624793e-03 2.21778743603120e-06 0.00000000000000e+00 + 9 3.21495224223226e+00 3.20553755246627e+00 2.46240837198597e-03 9.08838401590574e-06 0.00000000000000e+00 + 10 3.21731847440459e+00 3.20555593277664e+00 2.36623217233012e-03 1.83803103708351e-05 0.00000000000000e+00 + 11 3.21943632288805e+00 3.20558592225027e+00 2.11784848345964e-03 2.99894736327547e-05 0.00000000000000e+00 + 12 3.22117027438722e+00 3.20562958152141e+00 1.73395149917299e-03 4.36592711418987e-05 0.00000000000000e+00 + 13 3.22241091358397e+00 3.20568857884163e+00 1.24063919675121e-03 5.89973202123335e-05 0.00000000000000e+00 + 14 3.22308214681315e+00 3.20576408044470e+00 6.71233229177393e-04 7.55016030692882e-05 0.00000000000000e+00 + 15 3.22314537194466e+00 3.20585667429417e+00 6.32251315102472e-05 9.25938494741335e-05 0.00000000000000e+00 + 16 3.22260032424170e+00 3.20596633140428e+00 -5.45047702959156e-04 1.09657110116172e-04 0.00000000000000e+00 + 17 3.22148294568386e+00 3.20609240560729e+00 -1.11737855784311e-03 1.26074203007756e-04 0.00000000000000e+00 + 18 3.21986099886079e+00 3.20623366966451e+00 -1.62194682306716e-03 1.41264057215237e-04 0.00000000000000e+00 + 19 3.21782818018232e+00 3.20638838335654e+00 -2.03281867847016e-03 1.54713692036308e-04 0.00000000000000e+00 + 20 3.21549729223606e+00 3.20655438767549e+00 -2.33088794625580e-03 1.66004318946232e-04 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.histogram1.dat index 09d19a2d1..69e912676 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.histogram1.dat @@ -1,23 +1,23 @@ # 1 -# 0 0.5 20 0 +# 0.00000000000000e+00 5.00000000000000e-01 20 0 - 0.25 0 - 0.75 0 - 1.25 0 - 1.75 0 - 2.25 0 - 2.75 0 - 3.25 20 - 3.75 0 - 4.25 0 - 4.75 0 - 5.25 0 - 5.75 0 - 6.25 0 - 6.75 0 - 7.25 0 - 7.75 0 - 8.25 0 - 8.75 0 - 9.25 0 - 9.75 0 + 2.50000000000000e-01 0.00000000000000e+00 + 7.50000000000000e-01 0.00000000000000e+00 + 1.25000000000000e+00 0.00000000000000e+00 + 1.75000000000000e+00 0.00000000000000e+00 + 2.25000000000000e+00 0.00000000000000e+00 + 2.75000000000000e+00 0.00000000000000e+00 + 3.25000000000000e+00 2.00000000000000e+01 + 3.75000000000000e+00 0.00000000000000e+00 + 4.25000000000000e+00 0.00000000000000e+00 + 4.75000000000000e+00 0.00000000000000e+00 + 5.25000000000000e+00 0.00000000000000e+00 + 5.75000000000000e+00 0.00000000000000e+00 + 6.25000000000000e+00 0.00000000000000e+00 + 6.75000000000000e+00 0.00000000000000e+00 + 7.25000000000000e+00 0.00000000000000e+00 + 7.75000000000000e+00 0.00000000000000e+00 + 8.25000000000000e+00 0.00000000000000e+00 + 8.75000000000000e+00 0.00000000000000e+00 + 9.25000000000000e+00 0.00000000000000e+00 + 9.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out index f67286f65..b5dee23d8 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -130,20 +134,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.2155 colvars: Restarting histogram bias "histogram1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.state.stripped index 3110bf4ce..beb2691ef 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21132143720911e+00 - v 1.04669174158030e-04 - extended_x 3.20946748687297e+00 - extended_v 1.04669174158030e-04 + x 3.21132143681526e+00 + v 1.04669167318816e-04 + extended_x 3.20946748678570e+00 + extended_v 1.04669167318816e-04 } histogram { diff --git a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.traj index 1791c31a3..2713c291f 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 20 3.21549729243177e+00 3.20655438768302e+00 0.00000000000000e+00 1.66004320267550e-04 0.00000000000000e+00 - 21 3.21299279860961e+00 3.20672921829649e+00 -2.50449382215923e-03 1.74830613474229e-04 0.00000000000000e+00 - 22 3.21044297404629e+00 3.20691023081595e+00 -2.54982456331954e-03 1.81012519456721e-04 0.00000000000000e+00 - 23 3.20797196956081e+00 3.20709473001322e+00 -2.47100448548521e-03 1.84499197270131e-04 0.00000000000000e+00 - 24 3.20569233667745e+00 3.20728009501122e+00 -2.27963288336186e-03 1.85364998000097e-04 0.00000000000000e+00 - 25 3.20369874909954e+00 3.20746389295456e+00 -1.99358757790735e-03 1.83797943336207e-04 0.00000000000000e+00 - 26 3.20206356012972e+00 3.20764397484986e+00 -1.63518896981651e-03 1.80081895299983e-04 0.00000000000000e+00 - 27 3.20083453399825e+00 3.20781854909659e+00 -1.22902613147335e-03 1.74574246731807e-04 0.00000000000000e+00 - 28 3.20003466940781e+00 3.20798623039671e+00 -7.99864590434129e-04 1.67681300116621e-04 0.00000000000000e+00 - 29 3.19966366617398e+00 3.20814606382069e+00 -3.71003233836653e-04 1.59833423983471e-04 0.00000000000000e+00 - 30 3.19970060593396e+00 3.20829752545376e+00 3.69397599828680e-05 1.51461633068893e-04 0.00000000000000e+00 - 31 3.20010746077786e+00 3.20844050226735e+00 4.06854843902238e-04 1.42976813596051e-04 0.00000000000000e+00 - 32 3.20083326294086e+00 3.20857525469865e+00 7.25802162999667e-04 1.34752431300136e-04 0.00000000000000e+00 - 33 3.20181875720671e+00 3.20870236609036e+00 9.85494265844711e-04 1.27111391707545e-04 0.00000000000000e+00 - 34 3.20300129361245e+00 3.20882268363242e+00 1.18253640574428e-03 1.20317542054195e-04 0.00000000000000e+00 - 35 3.20431952758785e+00 3.20893725569281e+00 1.31823397539854e-03 1.14572060398045e-04 0.00000000000000e+00 - 36 3.20571748562482e+00 3.20904727023825e+00 1.39795803697362e-03 1.10014545435265e-04 0.00000000000000e+00 - 37 3.20714765705722e+00 3.20915399841800e+00 1.43017143239943e-03 1.06728179747730e-04 0.00000000000000e+00 - 38 3.20857308613613e+00 3.20925874641819e+00 1.42542907890419e-03 1.04748000195290e-04 0.00000000000000e+00 - 39 3.20996861050691e+00 3.20936281769881e+00 1.39552437078372e-03 1.04071280621537e-04 0.00000000000000e+00 - 40 3.21132143720911e+00 3.20946748687297e+00 1.35282670220427e-03 1.04669174158030e-04 0.00000000000000e+00 + 20 3.21549729223606e+00 3.20655438767549e+00 0.00000000000000e+00 1.66004318946232e-04 0.00000000000000e+00 + 21 3.21299279839909e+00 3.20672921828746e+00 -2.50449383696960e-03 1.74830611967189e-04 0.00000000000000e+00 + 22 3.21044297382093e+00 3.20691023080521e+00 -2.54982457816277e-03 1.81012517750828e-04 0.00000000000000e+00 + 23 3.20797196932066e+00 3.20709473000056e+00 -2.47100450027160e-03 1.84499195352419e-04 0.00000000000000e+00 + 24 3.20569233642268e+00 3.20728009499642e+00 -2.27963289798438e-03 1.85364995857865e-04 0.00000000000000e+00 + 25 3.20369874883042e+00 3.20746389293738e+00 -1.99358759225499e-03 1.83797940957138e-04 0.00000000000000e+00 + 26 3.20206355984665e+00 3.20764397483005e+00 -1.63518898377291e-03 1.80081892672264e-04 0.00000000000000e+00 + 27 3.20083453370172e+00 3.20781854907389e+00 -1.22902614493015e-03 1.74574243844257e-04 0.00000000000000e+00 + 28 3.20003466909842e+00 3.20798623037085e+00 -7.99864603297173e-04 1.67681296958808e-04 0.00000000000000e+00 + 29 3.19966366585238e+00 3.20814606379140e+00 -3.71003246035784e-04 1.59833420545817e-04 0.00000000000000e+00 + 30 3.19970060560089e+00 3.20829752542074e+00 3.69397485058265e-05 1.51461629342751e-04 0.00000000000000e+00 + 31 3.20010746043407e+00 3.20844050223031e+00 4.06854833183257e-04 1.42976809573772e-04 0.00000000000000e+00 + 32 3.20083326258715e+00 3.20857525465729e+00 7.25802153073385e-04 1.34752426975110e-04 0.00000000000000e+00 + 33 3.20181875684390e+00 3.20870236604436e+00 9.85494256751096e-04 1.27111387074243e-04 0.00000000000000e+00 + 34 3.20300129324144e+00 3.20882268358147e+00 1.18253639754595e-03 1.20317537108215e-04 0.00000000000000e+00 + 35 3.20431952720963e+00 3.20893725563661e+00 1.31823396818787e-03 1.14572055136176e-04 0.00000000000000e+00 + 36 3.20571748524051e+00 3.20904727017646e+00 1.39795803087983e-03 1.10014539855585e-04 0.00000000000000e+00 + 37 3.20714765666810e+00 3.20915399835031e+00 1.43017142759172e-03 1.06728173849729e-04 0.00000000000000e+00 + 38 3.20857308574368e+00 3.20925874634429e+00 1.42542907557441e-03 1.04747993980047e-04 0.00000000000000e+00 + 39 3.20996861011282e+00 3.20936281761839e+00 1.39552436913792e-03 1.04071274091898e-04 0.00000000000000e+00 + 40 3.21132143681526e+00 3.20946748678570e+00 1.35282670244763e-03 1.04669167318816e-04 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.histogram1.dat index 544c0ba33..fe4ddc2fd 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.histogram1.dat @@ -1,23 +1,23 @@ # 1 -# 0 0.5 20 0 +# 0.00000000000000e+00 5.00000000000000e-01 20 0 - 0.25 0 - 0.75 0 - 1.25 0 - 1.75 0 - 2.25 0 - 2.75 0 - 3.25 40 - 3.75 0 - 4.25 0 - 4.75 0 - 5.25 0 - 5.75 0 - 6.25 0 - 6.75 0 - 7.25 0 - 7.75 0 - 8.25 0 - 8.75 0 - 9.25 0 - 9.75 0 + 2.50000000000000e-01 0.00000000000000e+00 + 7.50000000000000e-01 0.00000000000000e+00 + 1.25000000000000e+00 0.00000000000000e+00 + 1.75000000000000e+00 0.00000000000000e+00 + 2.25000000000000e+00 0.00000000000000e+00 + 2.75000000000000e+00 0.00000000000000e+00 + 3.25000000000000e+00 4.00000000000000e+01 + 3.75000000000000e+00 0.00000000000000e+00 + 4.25000000000000e+00 0.00000000000000e+00 + 4.75000000000000e+00 0.00000000000000e+00 + 5.25000000000000e+00 0.00000000000000e+00 + 5.75000000000000e+00 0.00000000000000e+00 + 6.25000000000000e+00 0.00000000000000e+00 + 6.75000000000000e+00 0.00000000000000e+00 + 7.25000000000000e+00 0.00000000000000e+00 + 7.75000000000000e+00 0.00000000000000e+00 + 8.25000000000000e+00 0.00000000000000e+00 + 8.75000000000000e+00 0.00000000000000e+00 + 9.25000000000000e+00 0.00000000000000e+00 + 9.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt b/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt index e2b19c981..157cac038 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt +++ b/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.out index 01c072afe..7fd16b5d8 100644 --- a/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -118,15 +122,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.state.stripped index f51aa3936..27b752242 100644 --- a/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.state.stripped @@ -6,8 +6,8 @@ configuration { colvar { name one x 3.21549729223606e+00 - v 1.66004318946233e-04 + v 1.66004318946232e-04 extended_x 3.20655438767549e+00 - extended_v 1.66004318946233e-04 + extended_v 1.66004318946232e-04 } diff --git a/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.traj index 2dae7b9d3..732bd415c 100644 --- a/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-extended/AutoDiff/test.colvars.traj @@ -2,21 +2,21 @@ 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 1 3.20437148316484e+00 3.20554673468334e+00 -1.17525151850328e-03 0.00000000000000e+00 0.00000000000000e+00 2 3.20384207676395e+00 3.20554557475659e+00 -5.29406400886501e-04 -1.15992675594070e-06 0.00000000000000e+00 - 3 3.20397336463013e+00 3.20554273354470e+00 1.31287866173224e-04 -2.84121188447525e-06 0.00000000000000e+00 - 4 3.20474099643173e+00 3.20553834342778e+00 7.67631801607216e-04 -4.39011691909861e-06 0.00000000000000e+00 - 5 3.20608362354267e+00 3.20553316636092e+00 1.34262711093314e-03 -5.17706686123971e-06 0.00000000000000e+00 - 6 3.20790705616520e+00 3.20552853257352e+00 1.82343262252793e-03 -4.63378739888402e-06 0.00000000000000e+00 - 7 3.21008981942402e+00 3.20552624629482e+00 2.18276325882849e-03 -2.28627870803880e-06 0.00000000000000e+00 - 8 3.21248983386027e+00 3.20552846408225e+00 2.40001443624793e-03 2.21778743603339e-06 0.00000000000000e+00 - 9 3.21495224223226e+00 3.20553755246627e+00 2.46240837198597e-03 9.08838401590881e-06 0.00000000000000e+00 - 10 3.21731847440459e+00 3.20555593277664e+00 2.36623217233012e-03 1.83803103708391e-05 0.00000000000000e+00 - 11 3.21943632288805e+00 3.20558592225027e+00 2.11784848345964e-03 2.99894736327591e-05 0.00000000000000e+00 - 12 3.22117027438722e+00 3.20562958152141e+00 1.73395149917299e-03 4.36592711419031e-05 0.00000000000000e+00 - 13 3.22241091358397e+00 3.20568857884163e+00 1.24063919675121e-03 5.89973202123374e-05 0.00000000000000e+00 - 14 3.22308214681315e+00 3.20576408044470e+00 6.71233229177837e-04 7.55016030692917e-05 0.00000000000000e+00 - 15 3.22314537194466e+00 3.20585667429417e+00 6.32251315098031e-05 9.25938494741371e-05 0.00000000000000e+00 - 16 3.22260032424170e+00 3.20596633140429e+00 -5.45047702959156e-04 1.09657110116175e-04 0.00000000000000e+00 - 17 3.22148294568386e+00 3.20609240560729e+00 -1.11737855784311e-03 1.26074203007759e-04 0.00000000000000e+00 - 18 3.21986099886079e+00 3.20623366966451e+00 -1.62194682306760e-03 1.41264057215238e-04 0.00000000000000e+00 - 19 3.21782818018232e+00 3.20638838335655e+00 -2.03281867846972e-03 1.54713692036309e-04 0.00000000000000e+00 - 20 3.21549729223606e+00 3.20655438767549e+00 -2.33088794625580e-03 1.66004318946233e-04 0.00000000000000e+00 + 3 3.20397336463013e+00 3.20554273354470e+00 1.31287866173224e-04 -2.84121188447568e-06 0.00000000000000e+00 + 4 3.20474099643173e+00 3.20553834342779e+00 7.67631801607216e-04 -4.39011691909949e-06 0.00000000000000e+00 + 5 3.20608362354267e+00 3.20553316636092e+00 1.34262711093314e-03 -5.17706686124102e-06 0.00000000000000e+00 + 6 3.20790705616520e+00 3.20552853257352e+00 1.82343262252793e-03 -4.63378739888577e-06 0.00000000000000e+00 + 7 3.21008981942402e+00 3.20552624629482e+00 2.18276325882849e-03 -2.28627870804055e-06 0.00000000000000e+00 + 8 3.21248983386027e+00 3.20552846408225e+00 2.40001443624793e-03 2.21778743603120e-06 0.00000000000000e+00 + 9 3.21495224223226e+00 3.20553755246627e+00 2.46240837198597e-03 9.08838401590574e-06 0.00000000000000e+00 + 10 3.21731847440459e+00 3.20555593277664e+00 2.36623217233012e-03 1.83803103708351e-05 0.00000000000000e+00 + 11 3.21943632288805e+00 3.20558592225027e+00 2.11784848345964e-03 2.99894736327547e-05 0.00000000000000e+00 + 12 3.22117027438722e+00 3.20562958152141e+00 1.73395149917299e-03 4.36592711418987e-05 0.00000000000000e+00 + 13 3.22241091358397e+00 3.20568857884163e+00 1.24063919675121e-03 5.89973202123335e-05 0.00000000000000e+00 + 14 3.22308214681315e+00 3.20576408044470e+00 6.71233229177393e-04 7.55016030692882e-05 0.00000000000000e+00 + 15 3.22314537194466e+00 3.20585667429417e+00 6.32251315102472e-05 9.25938494741335e-05 0.00000000000000e+00 + 16 3.22260032424170e+00 3.20596633140428e+00 -5.45047702959156e-04 1.09657110116172e-04 0.00000000000000e+00 + 17 3.22148294568386e+00 3.20609240560729e+00 -1.11737855784311e-03 1.26074203007756e-04 0.00000000000000e+00 + 18 3.21986099886079e+00 3.20623366966451e+00 -1.62194682306716e-03 1.41264057215237e-04 0.00000000000000e+00 + 19 3.21782818018232e+00 3.20638838335654e+00 -2.03281867847016e-03 1.54713692036308e-04 0.00000000000000e+00 + 20 3.21549729223606e+00 3.20655438767549e+00 -2.33088794625580e-03 1.66004318946232e-04 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.out index 008768aaf..26ea35d7c 100644 --- a/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -118,19 +122,30 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.2155 colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.state.stripped index d0ac119c8..658a18125 100644 --- a/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.state.stripped @@ -6,8 +6,8 @@ configuration { colvar { name one x 3.21132143681526e+00 - v 1.04669167318825e-04 + v 1.04669167318816e-04 extended_x 3.20946748678570e+00 - extended_v 1.04669167318825e-04 + extended_v 1.04669167318816e-04 } diff --git a/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.traj index c86f1abc7..220a5517c 100644 --- a/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-extended/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 20 3.21549729223606e+00 3.20655438767549e+00 0.00000000000000e+00 1.66004318946233e-04 0.00000000000000e+00 - 21 3.21299279839909e+00 3.20672921828746e+00 -2.50449383697005e-03 1.74830611967190e-04 0.00000000000000e+00 - 22 3.21044297382093e+00 3.20691023080521e+00 -2.54982457816233e-03 1.81012517750828e-04 0.00000000000000e+00 - 23 3.20797196932066e+00 3.20709473000056e+00 -2.47100450027116e-03 1.84499195352419e-04 0.00000000000000e+00 - 24 3.20569233642268e+00 3.20728009499642e+00 -2.27963289798483e-03 1.85364995857866e-04 0.00000000000000e+00 - 25 3.20369874883042e+00 3.20746389293738e+00 -1.99358759225454e-03 1.83797940957138e-04 0.00000000000000e+00 - 26 3.20206355984665e+00 3.20764397483005e+00 -1.63518898377335e-03 1.80081892672265e-04 0.00000000000000e+00 - 27 3.20083453370172e+00 3.20781854907389e+00 -1.22902614492970e-03 1.74574243844258e-04 0.00000000000000e+00 - 28 3.20003466909842e+00 3.20798623037085e+00 -7.99864603297173e-04 1.67681296958810e-04 0.00000000000000e+00 - 29 3.19966366585239e+00 3.20814606379140e+00 -3.71003246035340e-04 1.59833420545819e-04 0.00000000000000e+00 - 30 3.19970060560089e+00 3.20829752542074e+00 3.69397485053824e-05 1.51461629342754e-04 0.00000000000000e+00 - 31 3.20010746043407e+00 3.20844050223031e+00 4.06854833183701e-04 1.42976809573776e-04 0.00000000000000e+00 - 32 3.20083326258715e+00 3.20857525465729e+00 7.25802153071609e-04 1.34752426975114e-04 0.00000000000000e+00 - 33 3.20181875684390e+00 3.20870236604436e+00 9.85494256751984e-04 1.27111387074247e-04 0.00000000000000e+00 - 34 3.20300129324144e+00 3.20882268358147e+00 1.18253639754595e-03 1.20317537108219e-04 0.00000000000000e+00 - 35 3.20431952720963e+00 3.20893725563661e+00 1.31823396818653e-03 1.14572055136181e-04 0.00000000000000e+00 - 36 3.20571748524051e+00 3.20904727017646e+00 1.39795803088116e-03 1.10014539855589e-04 0.00000000000000e+00 - 37 3.20714765666810e+00 3.20915399835031e+00 1.43017142759083e-03 1.06728173849736e-04 0.00000000000000e+00 - 38 3.20857308574368e+00 3.20925874634429e+00 1.42542907557397e-03 1.04747993980054e-04 0.00000000000000e+00 - 39 3.20996861011282e+00 3.20936281761838e+00 1.39552436913837e-03 1.04071274091906e-04 0.00000000000000e+00 - 40 3.21132143681526e+00 3.20946748678570e+00 1.35282670244719e-03 1.04669167318825e-04 0.00000000000000e+00 + 20 3.21549729223606e+00 3.20655438767549e+00 0.00000000000000e+00 1.66004318946232e-04 0.00000000000000e+00 + 21 3.21299279839909e+00 3.20672921828746e+00 -2.50449383696960e-03 1.74830611967189e-04 0.00000000000000e+00 + 22 3.21044297382093e+00 3.20691023080521e+00 -2.54982457816277e-03 1.81012517750828e-04 0.00000000000000e+00 + 23 3.20797196932066e+00 3.20709473000056e+00 -2.47100450027160e-03 1.84499195352419e-04 0.00000000000000e+00 + 24 3.20569233642268e+00 3.20728009499642e+00 -2.27963289798438e-03 1.85364995857865e-04 0.00000000000000e+00 + 25 3.20369874883042e+00 3.20746389293738e+00 -1.99358759225499e-03 1.83797940957138e-04 0.00000000000000e+00 + 26 3.20206355984665e+00 3.20764397483005e+00 -1.63518898377291e-03 1.80081892672264e-04 0.00000000000000e+00 + 27 3.20083453370172e+00 3.20781854907389e+00 -1.22902614493015e-03 1.74574243844257e-04 0.00000000000000e+00 + 28 3.20003466909842e+00 3.20798623037085e+00 -7.99864603297173e-04 1.67681296958808e-04 0.00000000000000e+00 + 29 3.19966366585238e+00 3.20814606379140e+00 -3.71003246035784e-04 1.59833420545817e-04 0.00000000000000e+00 + 30 3.19970060560089e+00 3.20829752542074e+00 3.69397485058265e-05 1.51461629342751e-04 0.00000000000000e+00 + 31 3.20010746043407e+00 3.20844050223031e+00 4.06854833183257e-04 1.42976809573772e-04 0.00000000000000e+00 + 32 3.20083326258715e+00 3.20857525465729e+00 7.25802153073385e-04 1.34752426975110e-04 0.00000000000000e+00 + 33 3.20181875684390e+00 3.20870236604436e+00 9.85494256751096e-04 1.27111387074243e-04 0.00000000000000e+00 + 34 3.20300129324144e+00 3.20882268358147e+00 1.18253639754595e-03 1.20317537108215e-04 0.00000000000000e+00 + 35 3.20431952720963e+00 3.20893725563661e+00 1.31823396818787e-03 1.14572055136176e-04 0.00000000000000e+00 + 36 3.20571748524051e+00 3.20904727017646e+00 1.39795803087983e-03 1.10014539855585e-04 0.00000000000000e+00 + 37 3.20714765666810e+00 3.20915399835031e+00 1.43017142759172e-03 1.06728173849729e-04 0.00000000000000e+00 + 38 3.20857308574368e+00 3.20925874634429e+00 1.42542907557441e-03 1.04747993980047e-04 0.00000000000000e+00 + 39 3.20996861011282e+00 3.20936281761839e+00 1.39552436913792e-03 1.04071274091898e-04 0.00000000000000e+00 + 40 3.21132143681526e+00 3.20946748678570e+00 1.35282670244763e-03 1.04669167318816e-04 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-extended/namd-version.txt b/namd/tests/library/000_distance-extended/namd-version.txt index 6fd41ef56..157cac038 100644 --- a/namd/tests/library/000_distance-extended/namd-version.txt +++ b/namd/tests/library/000_distance-extended/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2019-06-19". -colvars: Using NAMD interface, version "2019-02-12". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out index d0cd986cf..04c1af77b 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -86,7 +90,7 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 -colvars: # lowerBoundary = 0 +colvars: # lowerBoundary = 0 [default] colvars: # upperBoundary = 0.1 colvars: # hardLowerBoundary = on colvars: # hardUpperBoundary = off [default] @@ -137,15 +141,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped index 21d01f18d..10c1037b0 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688804971810e+00 + x 3.21688804951235e+00 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 2.26845124673292e-07 - 5.71217594827238e-05 1.12710965685979e-03 1.74270242088282e-03 - 2.11141094092476e-04 2.00454019640119e-06 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 2.26845126752189e-07 + 5.71217598091379e-05 1.12710965943565e-03 1.74270241892652e-03 + 2.11141093140343e-04 2.00454018061483e-06 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients grid_parameters { @@ -51,9 +51,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 1.54297694279170e-05 - 2.43078779178197e-03 1.92623445074912e-02 -1.45941325201129e-02 - -7.14477983084629e-03 -1.18875948766480e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.54297695614713e-05 + 2.43078780370765e-03 1.92623445129830e-02 -1.45941325629368e-02 + -7.14477980575610e-03 -1.18875947897555e-04 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj index f51a5d30c..06d632fae 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 7.26085412753031e-03 - 11 3.21950378533161e+00 7.26085412753031e-03 - 12 3.22130533168958e+00 7.26085412753031e-03 - 13 3.22263545699519e+00 7.26085412753031e-03 - 14 3.22341879081745e+00 7.26085412753031e-03 - 15 3.22361636104338e+00 7.26085412753031e-03 - 16 3.22322642140893e+00 7.26085412753031e-03 - 17 3.22228237905726e+00 7.26085412753031e-03 - 18 3.22084853667244e+00 7.26085412753031e-03 - 19 3.21901439330651e+00 7.26085412753031e-03 - 20 3.21688804971810e+00 1.45941325201129e-02 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 7.26085413750919e-03 + 11 3.21950378525805e+00 7.26085413750919e-03 + 12 3.22130533160336e+00 7.26085413750919e-03 + 13 3.22263545689569e+00 7.26085413750919e-03 + 14 3.22341879070410e+00 7.26085413750919e-03 + 15 3.22361636091569e+00 7.26085413750919e-03 + 16 3.22322642126644e+00 7.26085413750919e-03 + 17 3.22228237889954e+00 7.26085413750919e-03 + 18 3.22084853649908e+00 7.26085413750919e-03 + 19 3.21901439311712e+00 7.26085413750919e-03 + 20 3.21688804951235e+00 1.45941325629368e-02 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf index dc034b29d..80c051dc8 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf @@ -1,40 +1,40 @@ # 1 # 0.00000000000000e+00 1.00000000000000e-01 37 0 - 5.00000000000000e-02 1.74270242088282e-03 - 1.50000000000000e-01 1.74270242088282e-03 - 2.50000000000000e-01 1.74270242088282e-03 - 3.50000000000000e-01 1.74270242088282e-03 - 4.50000000000000e-01 1.74270242088282e-03 - 5.50000000000000e-01 1.74270242088282e-03 - 6.50000000000000e-01 1.74270242088282e-03 - 7.50000000000000e-01 1.74270242088282e-03 - 8.50000000000000e-01 1.74270242088282e-03 - 9.50000000000000e-01 1.74270242088282e-03 - 1.05000000000000e+00 1.74270242088282e-03 - 1.15000000000000e+00 1.74270242088282e-03 - 1.25000000000000e+00 1.74270242088282e-03 - 1.35000000000000e+00 1.74270242088282e-03 - 1.45000000000000e+00 1.74270242088282e-03 - 1.55000000000000e+00 1.74270242088282e-03 - 1.65000000000000e+00 1.74270242088282e-03 - 1.75000000000000e+00 1.74270242088282e-03 - 1.85000000000000e+00 1.74270242088282e-03 - 1.95000000000000e+00 1.74270242088282e-03 - 2.05000000000000e+00 1.74270242088282e-03 - 2.15000000000000e+00 1.74270242088282e-03 - 2.25000000000000e+00 1.74270242088282e-03 - 2.35000000000000e+00 1.74270242088282e-03 - 2.45000000000000e+00 1.74270242088282e-03 - 2.55000000000000e+00 1.74270242088282e-03 - 2.65000000000000e+00 1.74270242088282e-03 - 2.75000000000000e+00 1.74270242088282e-03 - 2.85000000000000e+00 1.74270242088282e-03 - 2.95000000000000e+00 1.74247557575815e-03 - 3.05000000000000e+00 1.68558066140010e-03 - 3.15000000000000e+00 6.15592764023032e-04 + 5.00000000000000e-02 1.74270241892652e-03 + 1.50000000000000e-01 1.74270241892652e-03 + 2.50000000000000e-01 1.74270241892652e-03 + 3.50000000000000e-01 1.74270241892652e-03 + 4.50000000000000e-01 1.74270241892652e-03 + 5.50000000000000e-01 1.74270241892652e-03 + 6.50000000000000e-01 1.74270241892652e-03 + 7.50000000000000e-01 1.74270241892652e-03 + 8.50000000000000e-01 1.74270241892652e-03 + 9.50000000000000e-01 1.74270241892652e-03 + 1.05000000000000e+00 1.74270241892652e-03 + 1.15000000000000e+00 1.74270241892652e-03 + 1.25000000000000e+00 1.74270241892652e-03 + 1.35000000000000e+00 1.74270241892652e-03 + 1.45000000000000e+00 1.74270241892652e-03 + 1.55000000000000e+00 1.74270241892652e-03 + 1.65000000000000e+00 1.74270241892652e-03 + 1.75000000000000e+00 1.74270241892652e-03 + 1.85000000000000e+00 1.74270241892652e-03 + 1.95000000000000e+00 1.74270241892652e-03 + 2.05000000000000e+00 1.74270241892652e-03 + 2.15000000000000e+00 1.74270241892652e-03 + 2.25000000000000e+00 1.74270241892652e-03 + 2.35000000000000e+00 1.74270241892652e-03 + 2.45000000000000e+00 1.74270241892652e-03 + 2.55000000000000e+00 1.74270241892652e-03 + 2.65000000000000e+00 1.74270241892652e-03 + 2.75000000000000e+00 1.74270241892652e-03 + 2.85000000000000e+00 1.74270241892652e-03 + 2.95000000000000e+00 1.74247557379976e-03 + 3.05000000000000e+00 1.68558065911738e-03 + 3.15000000000000e+00 6.15592759490865e-04 3.25000000000000e+00 -0.00000000000000e+00 - 3.35000000000000e+00 1.53156132679035e-03 - 3.45000000000000e+00 1.74069788068642e-03 - 3.55000000000000e+00 1.74270242088282e-03 - 3.65000000000000e+00 1.74270242088282e-03 + 3.35000000000000e+00 1.53156132578617e-03 + 3.45000000000000e+00 1.74069787874590e-03 + 3.55000000000000e+00 1.74270241892652e-03 + 3.65000000000000e+00 1.74270241892652e-03 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out index 5813ff1d2..e41a5cf1c 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -86,7 +90,7 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 -colvars: # lowerBoundary = 0 +colvars: # lowerBoundary = 0 [default] colvars: # upperBoundary = 0.1 colvars: # hardLowerBoundary = on colvars: # hardUpperBoundary = off [default] @@ -137,20 +141,34 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21689 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped index 34fd5ad0c..16770ad61 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21410417631119e+00 + x 3.21410417583007e+00 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 6.62978143841745e-07 - 1.41194486168262e-04 2.42321239420736e-03 3.34221727286243e-03 - 3.69169357278679e-04 3.25342742518778e-06 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 6.62978157520071e-07 + 1.41194487892242e-04 2.42321240493645e-03 3.34221726380270e-03 + 3.69169353864755e-04 3.25342737556381e-06 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients grid_parameters { @@ -51,9 +51,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 4.38875861559355e-05 - 5.79221281512363e-03 3.83513133612739e-02 -3.14227498048830e-02 - -1.27980745147960e-02 -1.95106965527919e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 4.38875870035617e-05 + 5.79221287439899e-03 3.83513133503907e-02 -3.14227499478963e-02 + -1.27980744195482e-02 -1.95106962739560e-04 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj index 6941fb0a6..bc03d36a4 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688804971810e+00 1.45941325201129e-02 - 21 3.21458913721366e+00 1.45941325201129e-02 - 22 3.21224101163817e+00 1.45941325201129e-02 - 23 3.20996318761655e+00 1.45941325201129e-02 - 24 3.20786409118692e+00 1.45941325201129e-02 - 25 3.20603496122295e+00 1.45941325201129e-02 - 26 3.20454553334930e+00 1.45941325201129e-02 - 27 3.20344183450406e+00 1.45941325201129e-02 - 28 3.20274601569592e+00 1.45941325201129e-02 - 29 3.20245777323046e+00 1.45941325201129e-02 - 30 3.20255693910090e+00 2.36650233314395e-02 - 31 3.20300700352046e+00 2.36650233314395e-02 - 32 3.20375885644980e+00 2.36650233314395e-02 - 33 3.20475541437456e+00 2.36650233314395e-02 - 34 3.20593635825493e+00 2.36650233314395e-02 - 35 3.20724270282681e+00 2.36650233314395e-02 - 36 3.20862075181587e+00 2.36650233314395e-02 - 37 3.21002511848469e+00 2.36650233314395e-02 - 38 3.21142076768566e+00 2.36650233314395e-02 - 39 3.21278422910227e+00 2.36650233314395e-02 - 40 3.21410417631119e+00 3.14227498048830e-02 + 20 3.21688804951235e+00 1.45941325629368e-02 + 21 3.21458913699124e+00 1.45941325629368e-02 + 22 3.21224101139884e+00 1.45941325629368e-02 + 23 3.20996318736015e+00 1.45941325629368e-02 + 24 3.20786409091340e+00 1.45941325629368e-02 + 25 3.20603496093235e+00 1.45941325629368e-02 + 26 3.20454553304178e+00 1.45941325629368e-02 + 27 3.20344183417990e+00 1.45941325629368e-02 + 28 3.20274601535548e+00 1.45941325629368e-02 + 29 3.20245777287417e+00 1.45941325629368e-02 + 30 3.20255693872927e+00 2.36650234045914e-02 + 31 3.20300700313402e+00 2.36650234045914e-02 + 32 3.20375885604914e+00 2.36650234045914e-02 + 33 3.20475541396031e+00 2.36650234045914e-02 + 34 3.20593635782781e+00 2.36650234045914e-02 + 35 3.20724270238762e+00 2.36650234045914e-02 + 36 3.20862075136558e+00 2.36650234045914e-02 + 37 3.21002511802444e+00 2.36650234045914e-02 + 38 3.21142076721680e+00 2.36650234045914e-02 + 39 3.21278422862637e+00 2.36650234045914e-02 + 40 3.21410417583007e+00 3.14227499478963e-02 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf index dd7b19d0a..63d82cbc3 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf @@ -1,40 +1,40 @@ # 1 # 0.00000000000000e+00 1.00000000000000e-01 37 0 - 5.00000000000000e-02 3.34221727286243e-03 - 1.50000000000000e-01 3.34221727286243e-03 - 2.50000000000000e-01 3.34221727286243e-03 - 3.50000000000000e-01 3.34221727286243e-03 - 4.50000000000000e-01 3.34221727286243e-03 - 5.50000000000000e-01 3.34221727286243e-03 - 6.50000000000000e-01 3.34221727286243e-03 - 7.50000000000000e-01 3.34221727286243e-03 - 8.50000000000000e-01 3.34221727286243e-03 - 9.50000000000000e-01 3.34221727286243e-03 - 1.05000000000000e+00 3.34221727286243e-03 - 1.15000000000000e+00 3.34221727286243e-03 - 1.25000000000000e+00 3.34221727286243e-03 - 1.35000000000000e+00 3.34221727286243e-03 - 1.45000000000000e+00 3.34221727286243e-03 - 1.55000000000000e+00 3.34221727286243e-03 - 1.65000000000000e+00 3.34221727286243e-03 - 1.75000000000000e+00 3.34221727286243e-03 - 1.85000000000000e+00 3.34221727286243e-03 - 1.95000000000000e+00 3.34221727286243e-03 - 2.05000000000000e+00 3.34221727286243e-03 - 2.15000000000000e+00 3.34221727286243e-03 - 2.25000000000000e+00 3.34221727286243e-03 - 2.35000000000000e+00 3.34221727286243e-03 - 2.45000000000000e+00 3.34221727286243e-03 - 2.55000000000000e+00 3.34221727286243e-03 - 2.65000000000000e+00 3.34221727286243e-03 - 2.75000000000000e+00 3.34221727286243e-03 - 2.85000000000000e+00 3.34221727286243e-03 - 2.95000000000000e+00 3.34155429471859e-03 - 3.05000000000000e+00 3.20102278669417e-03 - 3.15000000000000e+00 9.19004878655076e-04 + 5.00000000000000e-02 3.34221726380270e-03 + 1.50000000000000e-01 3.34221726380270e-03 + 2.50000000000000e-01 3.34221726380270e-03 + 3.50000000000000e-01 3.34221726380270e-03 + 4.50000000000000e-01 3.34221726380270e-03 + 5.50000000000000e-01 3.34221726380270e-03 + 6.50000000000000e-01 3.34221726380270e-03 + 7.50000000000000e-01 3.34221726380270e-03 + 8.50000000000000e-01 3.34221726380270e-03 + 9.50000000000000e-01 3.34221726380270e-03 + 1.05000000000000e+00 3.34221726380270e-03 + 1.15000000000000e+00 3.34221726380270e-03 + 1.25000000000000e+00 3.34221726380270e-03 + 1.35000000000000e+00 3.34221726380270e-03 + 1.45000000000000e+00 3.34221726380270e-03 + 1.55000000000000e+00 3.34221726380270e-03 + 1.65000000000000e+00 3.34221726380270e-03 + 1.75000000000000e+00 3.34221726380270e-03 + 1.85000000000000e+00 3.34221726380270e-03 + 1.95000000000000e+00 3.34221726380270e-03 + 2.05000000000000e+00 3.34221726380270e-03 + 2.15000000000000e+00 3.34221726380270e-03 + 2.25000000000000e+00 3.34221726380270e-03 + 2.35000000000000e+00 3.34221726380270e-03 + 2.45000000000000e+00 3.34221726380270e-03 + 2.55000000000000e+00 3.34221726380270e-03 + 2.65000000000000e+00 3.34221726380270e-03 + 2.75000000000000e+00 3.34221726380270e-03 + 2.85000000000000e+00 3.34221726380270e-03 + 2.95000000000000e+00 3.34155428564518e-03 + 3.05000000000000e+00 3.20102277591046e-03 + 3.15000000000000e+00 9.19004858866248e-04 3.25000000000000e+00 -0.00000000000000e+00 - 3.35000000000000e+00 2.97304791558375e-03 - 3.45000000000000e+00 3.33896384543724e-03 - 3.55000000000000e+00 3.34221727286243e-03 - 3.65000000000000e+00 3.34221727286243e-03 + 3.35000000000000e+00 2.97304790993794e-03 + 3.45000000000000e+00 3.33896383642714e-03 + 3.55000000000000e+00 3.34221726380270e-03 + 3.65000000000000e+00 3.34221726380270e-03 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt b/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt index e2b19c981..157cac038 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out index 7522b04bf..49233a154 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -129,15 +133,30 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - ABF colvar bias implementation: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped index 20f2914d8..dd78a9c08 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.19500142883077e+00 + x 3.19500142870476e+00 } abf { @@ -20,7 +20,7 @@ samples 0 0 0 0 gradient - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -2.00127627059354e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -2.00127620028148e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj index c883ca64b..5cab1a630 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 -7.68950956048151e+00 - 7 3.20994206785783e+00 -1.45081022282339e+01 - 8 3.21200777966617e+00 -2.01168223516023e+01 - 9 3.21384392083996e+00 -2.42708475491531e+01 - 10 3.21523959939197e+00 -2.68357716619527e+01 - 11 3.21601851665685e+00 -2.31658531617215e+01 - 12 3.21612044374608e+00 -1.94776791332188e+01 - 13 3.21551354965183e+00 -1.59170234235171e+01 - 14 3.21419762173747e+00 -1.26130068374289e+01 - 15 3.21220454739271e+00 -9.67058892511207e+00 - 16 3.20959604460089e+00 -7.16540389913541e+00 - 17 3.20645917277260e+00 -5.14219083172278e+00 - 18 3.20290044136922e+00 -3.61665567522571e+00 - 19 3.19903928579189e+00 -2.57951944961151e+00 - 20 3.19500142883077e+00 -2.00127627059354e+00 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 -7.68950954395538e+00 + 7 3.20994206782701e+00 -1.45081021954275e+01 + 8 3.21200777962688e+00 -2.01168223029416e+01 + 9 3.21384392079195e+00 -2.42708474851834e+01 + 10 3.21523959933526e+00 -2.68357715832755e+01 + 11 3.21601851659179e+00 -2.31658530843961e+01 + 12 3.21612044367303e+00 -1.94776790572418e+01 + 13 3.21551354957116e+00 -1.59170233488103e+01 + 14 3.21419762164954e+00 -1.26130067638535e+01 + 15 3.21220454729786e+00 -9.67058885249113e+00 + 16 3.20959604449940e+00 -7.16540382727106e+00 + 17 3.20645917266472e+00 -5.14219076042560e+00 + 18 3.20290044125515e+00 -3.61665560433892e+00 + 19 3.19903928567179e+00 -2.57951937903240e+00 + 20 3.19500142870476e+00 -2.00127620028148e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad index a9d8b5547..f1d0f6536 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -2.00127627059354e+00 + 3.25000000000000e+00 -2.00127620028148e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf index a9c224cc4..46f65d7e5 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 1.00063813529677e+00 - 5.00000000000000e-01 1.00063813529677e+00 - 1.00000000000000e+00 1.00063813529677e+00 - 1.50000000000000e+00 1.00063813529677e+00 - 2.00000000000000e+00 1.00063813529677e+00 - 2.50000000000000e+00 1.00063813529677e+00 - 3.00000000000000e+00 1.00063813529677e+00 + 0.00000000000000e+00 1.00063810014074e+00 + 5.00000000000000e-01 1.00063810014074e+00 + 1.00000000000000e+00 1.00063810014074e+00 + 1.50000000000000e+00 1.00063810014074e+00 + 2.00000000000000e+00 1.00063810014074e+00 + 2.50000000000000e+00 1.00063810014074e+00 + 3.00000000000000e+00 1.00063810014074e+00 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out index 1fa514166..e69be3fb4 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -129,20 +133,35 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - ABF colvar bias implementation: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.195 colvars: Restarting abf bias "abf1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped index 5ddfe2247..cf3a7c63e 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.16157768320120e+00 + x 3.16157768304247e+00 } abf { @@ -20,7 +20,7 @@ samples 0 0 0 0 gradient - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -1.06018969033008e+01 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -1.06018968543260e+01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj index 6b2274e24..790f5da38 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.19500142883077e+00 -2.00127627059354e+00 - 21 3.19091235926421e+00 -1.83655678093969e+00 - 22 3.18689102877202e+00 -2.02779471927389e+00 - 23 3.18304398646448e+00 -2.50868601661760e+00 - 24 3.17946034172504e+00 -3.20793288196262e+00 - 25 3.17620810295805e+00 -4.05360363219171e+00 - 26 3.17333232282842e+00 -4.97767855224492e+00 - 27 3.17085517082510e+00 -5.92001161542199e+00 - 28 3.16877768272762e+00 -6.83099319137926e+00 - 29 3.16708266056064e+00 -7.67258384905857e+00 - 30 3.16573827082641e+00 -8.41821679971556e+00 - 31 3.16470189541734e+00 -9.05180805822893e+00 - 32 3.16392411295527e+00 -9.56669442294402e+00 - 33 3.16335264560683e+00 -9.96442501653096e+00 - 34 3.16293610819235e+00 -1.02534301892968e+01 - 35 3.16262726171125e+00 -1.04473359016060e+01 - 36 3.16238550246452e+00 -1.05630326492936e+01 - 37 3.16217843220556e+00 -1.06187381167053e+01 - 38 3.16198265895496e+00 -1.06325725682142e+01 - 39 3.16178405684152e+00 -1.06216993704827e+01 - 40 3.16157768320120e+00 -1.06018969033008e+01 + 20 3.19500142870476e+00 -2.00127620028148e+00 + 21 3.19091235913242e+00 -1.83655671092344e+00 + 22 3.18689102863460e+00 -2.02779464964507e+00 + 23 3.18304398632164e+00 -2.50868594751815e+00 + 24 3.17946034157703e+00 -3.20793281356371e+00 + 25 3.17620810280522e+00 -4.05360356466712e+00 + 26 3.17333232267116e+00 -4.97767848574970e+00 + 27 3.17085517066390e+00 -5.92001155007172e+00 + 28 3.16877768256299e+00 -6.83099312723649e+00 + 29 3.16708266039313e+00 -7.67258378612514e+00 + 30 3.16573827065657e+00 -8.41821673794446e+00 + 31 3.16470189524569e+00 -9.05180799754020e+00 + 32 3.16392411278234e+00 -9.56669436325192e+00 + 33 3.16335264543312e+00 -9.96442495777829e+00 + 34 3.16293610801839e+00 -1.02534301314753e+01 + 35 3.16262726153762e+00 -1.04473358447738e+01 + 36 3.16238550229189e+00 -1.05630325935795e+01 + 37 3.16217843203474e+00 -1.06187380623063e+01 + 38 3.16198265878694e+00 -1.06325725153697e+01 + 39 3.16178405667746e+00 -1.06216993194485e+01 + 40 3.16157768304247e+00 -1.06018968543260e+01 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad index 9b2cd506d..be93459e2 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.06018969033008e+01 + 3.25000000000000e+00 -1.06018968543260e+01 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf index 0ddef6258..34e7b0c50 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 5.30094845165041e+00 - 5.00000000000000e-01 5.30094845165041e+00 - 1.00000000000000e+00 5.30094845165041e+00 - 1.50000000000000e+00 5.30094845165041e+00 - 2.00000000000000e+00 5.30094845165041e+00 - 2.50000000000000e+00 5.30094845165041e+00 - 3.00000000000000e+00 5.30094845165041e+00 + 0.00000000000000e+00 5.30094842716302e+00 + 5.00000000000000e-01 5.30094842716302e+00 + 1.00000000000000e+00 5.30094842716302e+00 + 1.50000000000000e+00 5.30094842716302e+00 + 2.00000000000000e+00 5.30094842716302e+00 + 2.50000000000000e+00 5.30094842716302e+00 + 3.00000000000000e+00 5.30094842716302e+00 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/namd-version.txt b/namd/tests/library/000_distance-grid_abf/namd-version.txt index e2b19c981..157cac038 100644 --- a/namd/tests/library/000_distance-grid_abf/namd-version.txt +++ b/namd/tests/library/000_distance-grid_abf/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out index 61f53d955..143074633 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -118,6 +122,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,15 +133,30 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped index e48d1c4ec..72e414d40 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685457639221e+00 + x 3.21685457618647e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486621732e-03 + accumulatedWork -1.22142486620766e-03 } histogram @@ -29,7 +29,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -1.45777476148254e+00 0.00000000000000e+00 0.00000000000000e+00 + -1.45777482050594e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj index c0e02c1fa..5eec6dc1f 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788663e+00 -1.23774855515465e-02 1.91502685723428e-02 1.10000000000000e-01 -1.23774855515465e-04 - 2 3.20383990680667e+00 -1.23353596272267e-02 1.90201371416267e-02 1.20000000000000e-01 -2.47128451787732e-04 - 3 3.20396636491675e+00 -1.22958654596670e-02 1.88985384252790e-02 1.30000000000000e-01 -3.70087106384402e-04 - 4 3.20472668060584e+00 -1.22589067224234e-02 1.87850992536346e-02 1.40000000000000e-01 -4.92676173608635e-04 - 5 3.20606077412683e+00 -1.22242430965073e-02 1.86790149103134e-02 1.50000000000000e-01 -6.14918604573709e-04 - 6 3.20787661015870e+00 -1.21915064406348e-02 1.85791036615050e-02 1.60000000000000e-01 -7.36833668980057e-04 - 7 3.21005557811738e+00 -1.21602223124695e-02 1.84838758360852e-02 1.70000000000000e-01 -8.58435892104752e-04 - 8 3.21245894720608e+00 -1.21298357888243e-02 1.83916145329805e-02 1.80000000000000e-01 -9.79734249992995e-04 - 9 3.21493543167171e+00 -1.20997417266868e-02 1.83004687315658e-02 1.90000000000000e-01 -1.10073166725986e-03 - 10 3.21732997393638e+00 -1.20693198957455e-02 1.82085603432298e-02 2.00000000000000e-01 -1.22142486621732e-03 - 11 3.21949353676140e+00 -1.20779741470456e-02 1.82346824370878e-02 2.00000000000000e-01 -1.22142486621732e-03 - 12 3.22129316981759e+00 -1.20851726792704e-02 1.82564248359729e-02 2.00000000000000e-01 -1.22142486621732e-03 - 13 3.22262118971552e+00 -1.20904847588621e-02 1.82724777130345e-02 2.00000000000000e-01 -1.22142486621732e-03 - 14 3.22340223714544e+00 -1.20936089485818e-02 1.82819221751521e-02 2.00000000000000e-01 -1.22142486621732e-03 - 15 3.22359735101788e+00 -1.20943894040715e-02 1.82842818821647e-02 2.00000000000000e-01 -1.22142486621732e-03 - 16 3.22320479587449e+00 -1.20928191834980e-02 1.82795344755970e-02 2.00000000000000e-01 -1.22142486621732e-03 - 17 3.22225798937996e+00 -1.20890319575198e-02 1.82680867087420e-02 2.00000000000000e-01 -1.22142486621732e-03 - 18 3.22082124442969e+00 -1.20832849777187e-02 1.82507219815954e-02 2.00000000000000e-01 -1.22142486621732e-03 - 19 3.21898406998055e+00 -1.20759362799222e-02 1.82285296295926e-02 2.00000000000000e-01 -1.22142486621732e-03 - 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 + 1 3.20437138788600e+00 -1.23774855515440e-02 1.91502685723351e-02 1.10000000000000e-01 -1.23774855515440e-04 + 2 3.20383990680414e+00 -1.23353596272166e-02 1.90201371415956e-02 1.20000000000000e-01 -2.47128451787606e-04 + 3 3.20396636491103e+00 -1.22958654596441e-02 1.88985384252087e-02 1.30000000000000e-01 -3.70087106384047e-04 + 4 3.20472668059564e+00 -1.22589067223826e-02 1.87850992535096e-02 1.40000000000000e-01 -4.92676173607873e-04 + 5 3.20606077411088e+00 -1.22242430964435e-02 1.86790149101184e-02 1.50000000000000e-01 -6.14918604572308e-04 + 6 3.20787661013578e+00 -1.21915064405431e-02 1.85791036612255e-02 1.60000000000000e-01 -7.36833668977739e-04 + 7 3.21005557808631e+00 -1.21602223123453e-02 1.84838758357074e-02 1.70000000000000e-01 -8.58435892101191e-04 + 8 3.21245894716580e+00 -1.21298357886632e-02 1.83916145324919e-02 1.80000000000000e-01 -9.79734249987824e-04 + 9 3.21493543162121e+00 -1.20997417264848e-02 1.83004687309548e-02 1.90000000000000e-01 -1.10073166725267e-03 + 10 3.21732997387476e+00 -1.20693198954990e-02 1.82085603424861e-02 2.00000000000000e-01 -1.22142486620766e-03 + 11 3.21949353668785e+00 -1.20779741467514e-02 1.82346824361994e-02 2.00000000000000e-01 -1.22142486620766e-03 + 12 3.22129316973139e+00 -1.20851726789256e-02 1.82564248349311e-02 2.00000000000000e-01 -1.22142486620766e-03 + 13 3.22262118961603e+00 -1.20904847584641e-02 1.82724777118316e-02 2.00000000000000e-01 -1.22142486620766e-03 + 14 3.22340223703211e+00 -1.20936089481284e-02 1.82819221737815e-02 2.00000000000000e-01 -1.22142486620766e-03 + 15 3.22359735089020e+00 -1.20943894035608e-02 1.82842818806205e-02 2.00000000000000e-01 -1.22142486620766e-03 + 16 3.22320479573201e+00 -1.20928191829280e-02 1.82795344738740e-02 2.00000000000000e-01 -1.22142486620766e-03 + 17 3.22225798922225e+00 -1.20890319568890e-02 1.82680867068354e-02 2.00000000000000e-01 -1.22142486620766e-03 + 18 3.22082124425633e+00 -1.20832849770253e-02 1.82507219795008e-02 2.00000000000000e-01 -1.22142486620766e-03 + 19 3.21898406979118e+00 -1.20759362791647e-02 1.82285296273058e-02 2.00000000000000e-01 -1.22142486620766e-03 + 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force index 29f1a8c10..f26fbcd58 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.45777476148234e+00 + 3.25000000000000e+00 -1.45777482050594e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf index f89ed6bc3..34593c780 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf @@ -6,17 +6,17 @@ 2 0 2.5 0 3 0 - 3.5 0.72888738074127 - 4 0.72888738074127 - 4.5 0.72888738074127 - 5 0.72888738074127 - 5.5 0.72888738074127 - 6 0.72888738074127 - 6.5 0.72888738074127 - 7 0.72888738074127 - 7.5 0.72888738074127 - 8 0.72888738074127 - 8.5 0.72888738074127 - 9 0.72888738074127 - 9.5 0.72888738074127 - 10 0.72888738074127 + 3.5 0.72888741025297 + 4 0.72888741025297 + 4.5 0.72888741025297 + 5 0.72888741025297 + 5.5 0.72888741025297 + 6 0.72888741025297 + 6.5 0.72888741025297 + 7 0.72888741025297 + 7.5 0.72888741025297 + 8 0.72888741025297 + 8.5 0.72888741025297 + 9 0.72888741025297 + 9.5 0.72888741025297 + 10 0.72888741025297 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out index 2a03c4ebb..496158813 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -118,6 +122,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,20 +133,35 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped index e3d52dfab..f5fbca6c7 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397324487089e+00 + x 3.21397324438969e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486621732e-03 + accumulatedWork -1.22142486620766e-03 } histogram @@ -29,7 +29,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 4.72492119104379e+00 0.00000000000000e+00 0.00000000000000e+00 + 4.72492117878643e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj index 82871cb9e..9592912c4 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 - 21 3.21455229152270e+00 -1.20582091660908e-02 1.81750510366495e-02 2.00000000000000e-01 -1.22142486621732e-03 - 22 3.21220058191067e+00 -1.20488023276427e-02 1.81467046913260e-02 2.00000000000000e-01 -1.22142486621732e-03 - 23 3.20991897426449e+00 -1.20396758970580e-02 1.81192244632749e-02 2.00000000000000e-01 -1.22142486621732e-03 - 24 3.20781590805930e+00 -1.20312636322372e-02 1.80939130735492e-02 2.00000000000000e-01 -1.22142486621732e-03 - 25 3.20598263691365e+00 -1.20239305476546e-02 1.80718632268527e-02 2.00000000000000e-01 -1.22142486621732e-03 - 26 3.20448891230251e+00 -1.20179556492100e-02 1.80539072482974e-02 2.00000000000000e-01 -1.22142486621732e-03 - 27 3.20338077792898e+00 -1.20135231117159e-02 1.80405921944666e-02 2.00000000000000e-01 -1.22142486621732e-03 - 28 3.20268040216098e+00 -1.20107216086439e-02 1.80321791950433e-02 2.00000000000000e-01 -1.22142486621732e-03 - 29 3.20238749898247e+00 -1.20095499959299e-02 1.80286613880924e-02 2.00000000000000e-01 -1.22142486621732e-03 - 30 3.20248191805753e+00 -1.20099276722301e-02 1.80297953365248e-02 2.00000000000000e-01 -1.22142486621732e-03 - 31 3.20292702752774e+00 -1.20117081101110e-02 1.80351414653132e-02 2.00000000000000e-01 -1.22142486621732e-03 - 32 3.20367373567078e+00 -1.20146949426831e-02 1.80441118207169e-02 2.00000000000000e-01 -1.22142486621732e-03 - 33 3.20466497797716e+00 -1.20186599119087e-02 1.80560232597650e-02 2.00000000000000e-01 -1.22142486621732e-03 - 34 3.20584045462068e+00 -1.20233618184827e-02 1.80701536772685e-02 2.00000000000000e-01 -1.22142486621732e-03 - 35 3.20714119904756e+00 -1.20285647961903e-02 1.80857963820184e-02 2.00000000000000e-01 -1.22142486621732e-03 - 36 3.20851353280837e+00 -1.20340541312335e-02 1.81023073541822e-02 2.00000000000000e-01 -1.22142486621732e-03 - 37 3.20991208545797e+00 -1.20396483418319e-02 1.81191415243719e-02 2.00000000000000e-01 -1.22142486621732e-03 - 38 3.21130183636701e+00 -1.20452073454680e-02 1.81358774994146e-02 2.00000000000000e-01 -1.22142486621732e-03 - 39 3.21265932794554e+00 -1.20506373117822e-02 1.81522324525146e-02 2.00000000000000e-01 -1.22142486621732e-03 - 40 3.21397324487089e+00 -1.20558929794836e-02 1.81680694415952e-02 2.00000000000000e-01 -1.22142486621732e-03 + 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 + 21 3.21455229130029e+00 -1.20582091652012e-02 1.81750510339676e-02 2.00000000000000e-01 -1.22142486620766e-03 + 22 3.21220058167135e+00 -1.20488023266854e-02 1.81467046884425e-02 2.00000000000000e-01 -1.22142486620766e-03 + 23 3.20991897400811e+00 -1.20396758960324e-02 1.81192244601880e-02 2.00000000000000e-01 -1.22142486620766e-03 + 24 3.20781590778578e+00 -1.20312636311431e-02 1.80939130702584e-02 2.00000000000000e-01 -1.22142486620766e-03 + 25 3.20598263662306e+00 -1.20239305464922e-02 1.80718632233586e-02 2.00000000000000e-01 -1.22142486620766e-03 + 26 3.20448891199500e+00 -1.20179556479800e-02 1.80539072446018e-02 2.00000000000000e-01 -1.22142486620766e-03 + 27 3.20338077760483e+00 -1.20135231104193e-02 1.80405921905723e-02 2.00000000000000e-01 -1.22142486620766e-03 + 28 3.20268040182054e+00 -1.20107216072822e-02 1.80321791909543e-02 2.00000000000000e-01 -1.22142486620766e-03 + 29 3.20238749862618e+00 -1.20095499945047e-02 1.80286613838135e-02 2.00000000000000e-01 -1.22142486620766e-03 + 30 3.20248191768589e+00 -1.20099276707435e-02 1.80297953320614e-02 2.00000000000000e-01 -1.22142486620766e-03 + 31 3.20292702714129e+00 -1.20117081085652e-02 1.80351414606713e-02 2.00000000000000e-01 -1.22142486620766e-03 + 32 3.20367373527010e+00 -1.20146949410804e-02 1.80441118159029e-02 2.00000000000000e-01 -1.22142486620766e-03 + 33 3.20466497756289e+00 -1.20186599102516e-02 1.80560232547861e-02 2.00000000000000e-01 -1.22142486620766e-03 + 34 3.20584045419353e+00 -1.20233618167741e-02 1.80701536721327e-02 2.00000000000000e-01 -1.22142486620766e-03 + 35 3.20714119860834e+00 -1.20285647944334e-02 1.80857963767352e-02 2.00000000000000e-01 -1.22142486620766e-03 + 36 3.20851353235803e+00 -1.20340541294321e-02 1.81023073487628e-02 2.00000000000000e-01 -1.22142486620766e-03 + 37 3.20991208499767e+00 -1.20396483399907e-02 1.81191415188300e-02 2.00000000000000e-01 -1.22142486620766e-03 + 38 3.21130183589808e+00 -1.20452073435923e-02 1.81358774937663e-02 2.00000000000000e-01 -1.22142486620766e-03 + 39 3.21265932746957e+00 -1.20506373098783e-02 1.81522324467788e-02 2.00000000000000e-01 -1.22142486620766e-03 + 40 3.21397324438969e+00 -1.20558929775587e-02 1.81680694357938e-02 2.00000000000000e-01 -1.22142486620766e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force index f7701bacb..1c62523ef 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 4.72492119104315e+00 + 3.25000000000000e+00 4.72492117878643e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf index 19f56570c..d82c0a308 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf @@ -1,11 +1,11 @@ # xi A(xi) - 0 2.3624605955218 - 0.5 2.3624605955218 - 1 2.3624605955218 - 1.5 2.3624605955218 - 2 2.3624605955218 - 2.5 2.3624605955218 - 3 2.3624605955218 + 0 2.3624605893932 + 0.5 2.3624605893932 + 1 2.3624605893932 + 1.5 2.3624605893932 + 2 2.3624605893932 + 2.5 2.3624605893932 + 3 2.3624605893932 3.5 0 4 0 4.5 0 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out index 4054ca6f6..b95774d40 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -118,6 +122,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,15 +133,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped index 4109af1f5..5ef095f44 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685457639221e+00 + x 3.21685457618647e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486621732e-03 + accumulatedWork -1.22142486620766e-03 } } diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj index c0e02c1fa..5eec6dc1f 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788663e+00 -1.23774855515465e-02 1.91502685723428e-02 1.10000000000000e-01 -1.23774855515465e-04 - 2 3.20383990680667e+00 -1.23353596272267e-02 1.90201371416267e-02 1.20000000000000e-01 -2.47128451787732e-04 - 3 3.20396636491675e+00 -1.22958654596670e-02 1.88985384252790e-02 1.30000000000000e-01 -3.70087106384402e-04 - 4 3.20472668060584e+00 -1.22589067224234e-02 1.87850992536346e-02 1.40000000000000e-01 -4.92676173608635e-04 - 5 3.20606077412683e+00 -1.22242430965073e-02 1.86790149103134e-02 1.50000000000000e-01 -6.14918604573709e-04 - 6 3.20787661015870e+00 -1.21915064406348e-02 1.85791036615050e-02 1.60000000000000e-01 -7.36833668980057e-04 - 7 3.21005557811738e+00 -1.21602223124695e-02 1.84838758360852e-02 1.70000000000000e-01 -8.58435892104752e-04 - 8 3.21245894720608e+00 -1.21298357888243e-02 1.83916145329805e-02 1.80000000000000e-01 -9.79734249992995e-04 - 9 3.21493543167171e+00 -1.20997417266868e-02 1.83004687315658e-02 1.90000000000000e-01 -1.10073166725986e-03 - 10 3.21732997393638e+00 -1.20693198957455e-02 1.82085603432298e-02 2.00000000000000e-01 -1.22142486621732e-03 - 11 3.21949353676140e+00 -1.20779741470456e-02 1.82346824370878e-02 2.00000000000000e-01 -1.22142486621732e-03 - 12 3.22129316981759e+00 -1.20851726792704e-02 1.82564248359729e-02 2.00000000000000e-01 -1.22142486621732e-03 - 13 3.22262118971552e+00 -1.20904847588621e-02 1.82724777130345e-02 2.00000000000000e-01 -1.22142486621732e-03 - 14 3.22340223714544e+00 -1.20936089485818e-02 1.82819221751521e-02 2.00000000000000e-01 -1.22142486621732e-03 - 15 3.22359735101788e+00 -1.20943894040715e-02 1.82842818821647e-02 2.00000000000000e-01 -1.22142486621732e-03 - 16 3.22320479587449e+00 -1.20928191834980e-02 1.82795344755970e-02 2.00000000000000e-01 -1.22142486621732e-03 - 17 3.22225798937996e+00 -1.20890319575198e-02 1.82680867087420e-02 2.00000000000000e-01 -1.22142486621732e-03 - 18 3.22082124442969e+00 -1.20832849777187e-02 1.82507219815954e-02 2.00000000000000e-01 -1.22142486621732e-03 - 19 3.21898406998055e+00 -1.20759362799222e-02 1.82285296295926e-02 2.00000000000000e-01 -1.22142486621732e-03 - 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 + 1 3.20437138788600e+00 -1.23774855515440e-02 1.91502685723351e-02 1.10000000000000e-01 -1.23774855515440e-04 + 2 3.20383990680414e+00 -1.23353596272166e-02 1.90201371415956e-02 1.20000000000000e-01 -2.47128451787606e-04 + 3 3.20396636491103e+00 -1.22958654596441e-02 1.88985384252087e-02 1.30000000000000e-01 -3.70087106384047e-04 + 4 3.20472668059564e+00 -1.22589067223826e-02 1.87850992535096e-02 1.40000000000000e-01 -4.92676173607873e-04 + 5 3.20606077411088e+00 -1.22242430964435e-02 1.86790149101184e-02 1.50000000000000e-01 -6.14918604572308e-04 + 6 3.20787661013578e+00 -1.21915064405431e-02 1.85791036612255e-02 1.60000000000000e-01 -7.36833668977739e-04 + 7 3.21005557808631e+00 -1.21602223123453e-02 1.84838758357074e-02 1.70000000000000e-01 -8.58435892101191e-04 + 8 3.21245894716580e+00 -1.21298357886632e-02 1.83916145324919e-02 1.80000000000000e-01 -9.79734249987824e-04 + 9 3.21493543162121e+00 -1.20997417264848e-02 1.83004687309548e-02 1.90000000000000e-01 -1.10073166725267e-03 + 10 3.21732997387476e+00 -1.20693198954990e-02 1.82085603424861e-02 2.00000000000000e-01 -1.22142486620766e-03 + 11 3.21949353668785e+00 -1.20779741467514e-02 1.82346824361994e-02 2.00000000000000e-01 -1.22142486620766e-03 + 12 3.22129316973139e+00 -1.20851726789256e-02 1.82564248349311e-02 2.00000000000000e-01 -1.22142486620766e-03 + 13 3.22262118961603e+00 -1.20904847584641e-02 1.82724777118316e-02 2.00000000000000e-01 -1.22142486620766e-03 + 14 3.22340223703211e+00 -1.20936089481284e-02 1.82819221737815e-02 2.00000000000000e-01 -1.22142486620766e-03 + 15 3.22359735089020e+00 -1.20943894035608e-02 1.82842818806205e-02 2.00000000000000e-01 -1.22142486620766e-03 + 16 3.22320479573201e+00 -1.20928191829280e-02 1.82795344738740e-02 2.00000000000000e-01 -1.22142486620766e-03 + 17 3.22225798922225e+00 -1.20890319568890e-02 1.82680867068354e-02 2.00000000000000e-01 -1.22142486620766e-03 + 18 3.22082124425633e+00 -1.20832849770253e-02 1.82507219795008e-02 2.00000000000000e-01 -1.22142486620766e-03 + 19 3.21898406979118e+00 -1.20759362791647e-02 1.82285296273058e-02 2.00000000000000e-01 -1.22142486620766e-03 + 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out index 88405593c..40e76217d 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -118,6 +122,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,20 +133,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped index 100eebdff..a27db3dc3 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397324487089e+00 + x 3.21397324438969e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486621732e-03 + accumulatedWork -1.22142486620766e-03 } } diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj index 82871cb9e..9592912c4 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 - 21 3.21455229152270e+00 -1.20582091660908e-02 1.81750510366495e-02 2.00000000000000e-01 -1.22142486621732e-03 - 22 3.21220058191067e+00 -1.20488023276427e-02 1.81467046913260e-02 2.00000000000000e-01 -1.22142486621732e-03 - 23 3.20991897426449e+00 -1.20396758970580e-02 1.81192244632749e-02 2.00000000000000e-01 -1.22142486621732e-03 - 24 3.20781590805930e+00 -1.20312636322372e-02 1.80939130735492e-02 2.00000000000000e-01 -1.22142486621732e-03 - 25 3.20598263691365e+00 -1.20239305476546e-02 1.80718632268527e-02 2.00000000000000e-01 -1.22142486621732e-03 - 26 3.20448891230251e+00 -1.20179556492100e-02 1.80539072482974e-02 2.00000000000000e-01 -1.22142486621732e-03 - 27 3.20338077792898e+00 -1.20135231117159e-02 1.80405921944666e-02 2.00000000000000e-01 -1.22142486621732e-03 - 28 3.20268040216098e+00 -1.20107216086439e-02 1.80321791950433e-02 2.00000000000000e-01 -1.22142486621732e-03 - 29 3.20238749898247e+00 -1.20095499959299e-02 1.80286613880924e-02 2.00000000000000e-01 -1.22142486621732e-03 - 30 3.20248191805753e+00 -1.20099276722301e-02 1.80297953365248e-02 2.00000000000000e-01 -1.22142486621732e-03 - 31 3.20292702752774e+00 -1.20117081101110e-02 1.80351414653132e-02 2.00000000000000e-01 -1.22142486621732e-03 - 32 3.20367373567078e+00 -1.20146949426831e-02 1.80441118207169e-02 2.00000000000000e-01 -1.22142486621732e-03 - 33 3.20466497797716e+00 -1.20186599119087e-02 1.80560232597650e-02 2.00000000000000e-01 -1.22142486621732e-03 - 34 3.20584045462068e+00 -1.20233618184827e-02 1.80701536772685e-02 2.00000000000000e-01 -1.22142486621732e-03 - 35 3.20714119904756e+00 -1.20285647961903e-02 1.80857963820184e-02 2.00000000000000e-01 -1.22142486621732e-03 - 36 3.20851353280837e+00 -1.20340541312335e-02 1.81023073541822e-02 2.00000000000000e-01 -1.22142486621732e-03 - 37 3.20991208545797e+00 -1.20396483418319e-02 1.81191415243719e-02 2.00000000000000e-01 -1.22142486621732e-03 - 38 3.21130183636701e+00 -1.20452073454680e-02 1.81358774994146e-02 2.00000000000000e-01 -1.22142486621732e-03 - 39 3.21265932794554e+00 -1.20506373117822e-02 1.81522324525146e-02 2.00000000000000e-01 -1.22142486621732e-03 - 40 3.21397324487089e+00 -1.20558929794836e-02 1.81680694415952e-02 2.00000000000000e-01 -1.22142486621732e-03 + 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 + 21 3.21455229130029e+00 -1.20582091652012e-02 1.81750510339676e-02 2.00000000000000e-01 -1.22142486620766e-03 + 22 3.21220058167135e+00 -1.20488023266854e-02 1.81467046884425e-02 2.00000000000000e-01 -1.22142486620766e-03 + 23 3.20991897400811e+00 -1.20396758960324e-02 1.81192244601880e-02 2.00000000000000e-01 -1.22142486620766e-03 + 24 3.20781590778578e+00 -1.20312636311431e-02 1.80939130702584e-02 2.00000000000000e-01 -1.22142486620766e-03 + 25 3.20598263662306e+00 -1.20239305464922e-02 1.80718632233586e-02 2.00000000000000e-01 -1.22142486620766e-03 + 26 3.20448891199500e+00 -1.20179556479800e-02 1.80539072446018e-02 2.00000000000000e-01 -1.22142486620766e-03 + 27 3.20338077760483e+00 -1.20135231104193e-02 1.80405921905723e-02 2.00000000000000e-01 -1.22142486620766e-03 + 28 3.20268040182054e+00 -1.20107216072822e-02 1.80321791909543e-02 2.00000000000000e-01 -1.22142486620766e-03 + 29 3.20238749862618e+00 -1.20095499945047e-02 1.80286613838135e-02 2.00000000000000e-01 -1.22142486620766e-03 + 30 3.20248191768589e+00 -1.20099276707435e-02 1.80297953320614e-02 2.00000000000000e-01 -1.22142486620766e-03 + 31 3.20292702714129e+00 -1.20117081085652e-02 1.80351414606713e-02 2.00000000000000e-01 -1.22142486620766e-03 + 32 3.20367373527010e+00 -1.20146949410804e-02 1.80441118159029e-02 2.00000000000000e-01 -1.22142486620766e-03 + 33 3.20466497756289e+00 -1.20186599102516e-02 1.80560232547861e-02 2.00000000000000e-01 -1.22142486620766e-03 + 34 3.20584045419353e+00 -1.20233618167741e-02 1.80701536721327e-02 2.00000000000000e-01 -1.22142486620766e-03 + 35 3.20714119860834e+00 -1.20285647944334e-02 1.80857963767352e-02 2.00000000000000e-01 -1.22142486620766e-03 + 36 3.20851353235803e+00 -1.20340541294321e-02 1.81023073487628e-02 2.00000000000000e-01 -1.22142486620766e-03 + 37 3.20991208499767e+00 -1.20396483399907e-02 1.81191415188300e-02 2.00000000000000e-01 -1.22142486620766e-03 + 38 3.21130183589808e+00 -1.20452073435923e-02 1.81358774937663e-02 2.00000000000000e-01 -1.22142486620766e-03 + 39 3.21265932746957e+00 -1.20506373098783e-02 1.81522324467788e-02 2.00000000000000e-01 -1.22142486620766e-03 + 40 3.21397324438969e+00 -1.20558929775587e-02 1.81680694357938e-02 2.00000000000000e-01 -1.22142486620766e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out index 9b0d8d5c9..3d0f629a2 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -115,6 +119,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -125,15 +130,30 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped index 3f9b13bdc..301b9ace6 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685399837991e+00 + x 3.21685399817416e+00 } restraint { @@ -26,7 +26,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -1.45768702613562e+00 0.00000000000000e+00 0.00000000000000e+00 + -1.45768708516242e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj index ccbac37f2..2cd06ea2b 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.24221869387334e-02 - 1 3.20437138788663e+00 -1.24174855515465e-02 - 2 3.20383990619321e+00 -1.24153596247728e-02 - 3 3.20396636247149e+00 -1.24158654498859e-02 - 4 3.20472667452156e+00 -1.24189066980862e-02 - 5 3.20606076202988e+00 -1.24242430481195e-02 - 6 3.20787658913670e+00 -1.24315063565468e-02 - 7 3.21005554475098e+00 -1.24402221790039e-02 - 8 3.21245889760366e+00 -1.24498355904146e-02 - 9 3.21493536150581e+00 -1.24597414460232e-02 - 10 3.21732987848069e+00 -1.24693195139228e-02 - 11 3.21949341092696e+00 -1.24779736437079e-02 - 12 3.22129300880163e+00 -1.24851720352065e-02 - 13 3.22262098902515e+00 -1.24904839561006e-02 - 14 3.22340199261010e+00 -1.24936079704404e-02 - 15 3.22359705879087e+00 -1.24943882351635e-02 - 16 3.22320445242483e+00 -1.24928178096993e-02 - 17 3.22225759147620e+00 -1.24890303659048e-02 - 18 3.22082078911784e+00 -1.24832831564713e-02 - 19 3.21898355455808e+00 -1.24759342182323e-02 - 20 3.21685399837991e+00 -1.24674159935196e-02 + 1 3.20437138788600e+00 -1.24174855515440e-02 + 2 3.20383990619069e+00 -1.24153596247627e-02 + 3 3.20396636246577e+00 -1.24158654498631e-02 + 4 3.20472667451135e+00 -1.24189066980454e-02 + 5 3.20606076201392e+00 -1.24242430480557e-02 + 6 3.20787658911377e+00 -1.24315063564551e-02 + 7 3.21005554471991e+00 -1.24402221788797e-02 + 8 3.21245889756338e+00 -1.24498355902535e-02 + 9 3.21493536145531e+00 -1.24597414458212e-02 + 10 3.21732987841907e+00 -1.24693195136763e-02 + 11 3.21949341085340e+00 -1.24779736434136e-02 + 12 3.22129300871542e+00 -1.24851720348617e-02 + 13 3.22262098892565e+00 -1.24904839557026e-02 + 14 3.22340199249676e+00 -1.24936079699870e-02 + 15 3.22359705866319e+00 -1.24943882346527e-02 + 16 3.22320445228234e+00 -1.24928178091294e-02 + 17 3.22225759131848e+00 -1.24890303652739e-02 + 18 3.22082078894448e+00 -1.24832831557779e-02 + 19 3.21898355436871e+00 -1.24759342174748e-02 + 20 3.21685399817416e+00 -1.24674159926967e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force index 1b3e03edb..640855ec6 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.45768702613609e+00 + 3.25000000000000e+00 -1.45768708516242e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf index af50b46fb..270f05c0e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf @@ -6,17 +6,17 @@ 2 0 2.5 0 3 0 - 3.5 0.72884351306783 - 4 0.72884351306783 - 4.5 0.72884351306783 - 5 0.72884351306783 - 5.5 0.72884351306783 - 6 0.72884351306783 - 6.5 0.72884351306783 - 7 0.72884351306783 - 7.5 0.72884351306783 - 8 0.72884351306783 - 8.5 0.72884351306783 - 9 0.72884351306783 - 9.5 0.72884351306783 - 10 0.72884351306783 + 3.5 0.72884354258121 + 4 0.72884354258121 + 4.5 0.72884354258121 + 5 0.72884354258121 + 5.5 0.72884354258121 + 6 0.72884354258121 + 6.5 0.72884354258121 + 7 0.72884354258121 + 7.5 0.72884354258121 + 8 0.72884354258121 + 8.5 0.72884354258121 + 9 0.72884354258121 + 9.5 0.72884354258121 + 10 0.72884354258121 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out index d2b2d5ed3..618f855ff 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -115,6 +119,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -125,20 +130,35 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped index 4f7e0b7d8..17f669708 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397114765047e+00 + x 3.21397114716924e+00 } restraint { @@ -26,7 +26,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 4.72514255041894e+00 0.00000000000000e+00 0.00000000000000e+00 + 4.72514253816199e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj index 47d79951b..8924671f5 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685399837991e+00 -1.24674159935196e-02 - 21 3.21455164863636e+00 -1.24582065945454e-02 - 22 3.21219987203489e+00 -1.24487994881395e-02 - 23 3.20991819543127e+00 -1.24396727817251e-02 - 24 3.20781505843291e+00 -1.24312602337316e-02 - 25 3.20598171478412e+00 -1.24239268591365e-02 - 26 3.20448791608644e+00 -1.24179516643458e-02 - 27 3.20337970617851e+00 -1.24135188247141e-02 - 28 3.20267925357806e+00 -1.24107170143122e-02 - 29 3.20238627243809e+00 -1.24095450897524e-02 - 30 3.20248061261333e+00 -1.24099224504533e-02 - 31 3.20292564245608e+00 -1.24117025698243e-02 - 32 3.20367227047127e+00 -1.24146890818851e-02 - 33 3.20466343238851e+00 -1.24186537295541e-02 - 34 3.20583882862542e+00 -1.24233553145017e-02 - 35 3.20713949286431e+00 -1.24285579714572e-02 - 36 3.20851174687611e+00 -1.24340469875045e-02 - 37 3.20991022040763e+00 -1.24396408816305e-02 - 38 3.21129989298713e+00 -1.24451995719485e-02 - 39 3.21265730714637e+00 -1.24506292285855e-02 - 40 3.21397114765047e+00 -1.24558845906019e-02 + 20 3.21685399817416e+00 -1.24674159926967e-02 + 21 3.21455164841394e+00 -1.24582065936557e-02 + 22 3.21219987179556e+00 -1.24487994871822e-02 + 23 3.20991819517487e+00 -1.24396727806995e-02 + 24 3.20781505815938e+00 -1.24312602326375e-02 + 25 3.20598171449351e+00 -1.24239268579740e-02 + 26 3.20448791577891e+00 -1.24179516631157e-02 + 27 3.20337970585434e+00 -1.24135188234173e-02 + 28 3.20267925323760e+00 -1.24107170129504e-02 + 29 3.20238627208178e+00 -1.24095450883271e-02 + 30 3.20248061224166e+00 -1.24099224489666e-02 + 31 3.20292564206961e+00 -1.24117025682784e-02 + 32 3.20367227007056e+00 -1.24146890802823e-02 + 33 3.20466343197421e+00 -1.24186537278969e-02 + 34 3.20583882819824e+00 -1.24233553127930e-02 + 35 3.20713949242506e+00 -1.24285579697002e-02 + 36 3.20851174642574e+00 -1.24340469857030e-02 + 37 3.20991021994729e+00 -1.24396408797892e-02 + 38 3.21129989251817e+00 -1.24451995700727e-02 + 39 3.21265730667037e+00 -1.24506292266815e-02 + 40 3.21397114716924e+00 -1.24558845886769e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force index 1a0e24a9e..ac92ca14c 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 4.72514255041972e+00 + 3.25000000000000e+00 4.72514253816199e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf index 8cf383c9e..9c98fb5a6 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf @@ -1,11 +1,11 @@ # xi A(xi) - 0 2.3625712752095 - 0.5 2.3625712752095 - 1 2.3625712752095 - 1.5 2.3625712752095 - 2 2.3625712752095 - 2.5 2.3625712752095 - 3 2.3625712752095 + 0 2.362571269081 + 0.5 2.362571269081 + 1 2.362571269081 + 1.5 2.362571269081 + 2 2.362571269081 + 2.5 2.362571269081 + 3 2.362571269081 3.5 0 4 0 4.5 0 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out index 71d7e2285..001440131 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -115,6 +119,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -125,15 +130,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 9eef8b44e..fec1e803e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685399835649e+00 + x 3.21685399817416e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj index 5a6aa23cd..2cd06ea2b 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.24221869387334e-02 - 1 3.20437138788661e+00 -1.24174855515465e-02 - 2 3.20383990624489e+00 -1.24153596249795e-02 - 3 3.20396636247331e+00 -1.24158654498932e-02 - 4 3.20472667455914e+00 -1.24189066982366e-02 - 5 3.20606076201901e+00 -1.24242430480760e-02 - 6 3.20787658913293e+00 -1.24315063565317e-02 - 7 3.21005554475517e+00 -1.24402221790207e-02 - 8 3.21245889761578e+00 -1.24498355904631e-02 - 9 3.21493536152545e+00 -1.24597414461018e-02 - 10 3.21732987850678e+00 -1.24693195140271e-02 - 11 3.21949341095784e+00 -1.24779736438313e-02 - 12 3.22129300883514e+00 -1.24851720353406e-02 - 13 3.22262098905883e+00 -1.24904839562353e-02 - 14 3.22340199264132e+00 -1.24936079705653e-02 - 15 3.22359705881703e+00 -1.24943882352681e-02 - 16 3.22320445244359e+00 -1.24928178097743e-02 - 17 3.22225759148518e+00 -1.24890303659407e-02 - 18 3.22082078911634e+00 -1.24832831564654e-02 - 19 3.21898355455034e+00 -1.24759342182014e-02 - 20 3.21685399835649e+00 -1.24674159934260e-02 + 1 3.20437138788600e+00 -1.24174855515440e-02 + 2 3.20383990619069e+00 -1.24153596247627e-02 + 3 3.20396636246577e+00 -1.24158654498631e-02 + 4 3.20472667451135e+00 -1.24189066980454e-02 + 5 3.20606076201392e+00 -1.24242430480557e-02 + 6 3.20787658911377e+00 -1.24315063564551e-02 + 7 3.21005554471991e+00 -1.24402221788797e-02 + 8 3.21245889756338e+00 -1.24498355902535e-02 + 9 3.21493536145531e+00 -1.24597414458212e-02 + 10 3.21732987841907e+00 -1.24693195136763e-02 + 11 3.21949341085340e+00 -1.24779736434136e-02 + 12 3.22129300871542e+00 -1.24851720348617e-02 + 13 3.22262098892565e+00 -1.24904839557026e-02 + 14 3.22340199249676e+00 -1.24936079699870e-02 + 15 3.22359705866319e+00 -1.24943882346527e-02 + 16 3.22320445228234e+00 -1.24928178091294e-02 + 17 3.22225759131848e+00 -1.24890303652739e-02 + 18 3.22082078894448e+00 -1.24832831557779e-02 + 19 3.21898355436871e+00 -1.24759342174748e-02 + 20 3.21685399817416e+00 -1.24674159926967e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out index f795a4bf4..fcf2bfa9e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -115,6 +119,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -125,20 +130,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index ba9e5b167..086f80ad0 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397114764396e+00 + x 3.21397114716924e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj index d18eb0fa7..8924671f5 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685399835649e+00 -1.24674159934260e-02 - 21 3.21455164860269e+00 -1.24582065944107e-02 - 22 3.21219987199261e+00 -1.24487994879705e-02 - 23 3.20991819538261e+00 -1.24396727815305e-02 - 24 3.20781505838050e+00 -1.24312602335220e-02 - 25 3.20598171473079e+00 -1.24239268589232e-02 - 26 3.20448791603500e+00 -1.24179516641400e-02 - 27 3.20337970613153e+00 -1.24135188245261e-02 - 28 3.20267925353770e+00 -1.24107170141508e-02 - 29 3.20238627240592e+00 -1.24095450896237e-02 - 30 3.20248061259023e+00 -1.24099224503609e-02 - 31 3.20292564244219e+00 -1.24117025697688e-02 - 32 3.20367227046597e+00 -1.24146890818639e-02 - 33 3.20466343239054e+00 -1.24186537295621e-02 - 34 3.20583882863293e+00 -1.24233553145317e-02 - 35 3.20713949287508e+00 -1.24285579715003e-02 - 36 3.20851174688770e+00 -1.24340469875508e-02 - 37 3.20991022041763e+00 -1.24396408816705e-02 - 38 3.21129989299330e+00 -1.24451995719732e-02 - 39 3.21265730714688e+00 -1.24506292285875e-02 - 40 3.21397114764396e+00 -1.24558845905758e-02 + 20 3.21685399817416e+00 -1.24674159926967e-02 + 21 3.21455164841394e+00 -1.24582065936557e-02 + 22 3.21219987179556e+00 -1.24487994871822e-02 + 23 3.20991819517487e+00 -1.24396727806995e-02 + 24 3.20781505815938e+00 -1.24312602326375e-02 + 25 3.20598171449351e+00 -1.24239268579740e-02 + 26 3.20448791577891e+00 -1.24179516631157e-02 + 27 3.20337970585434e+00 -1.24135188234173e-02 + 28 3.20267925323760e+00 -1.24107170129504e-02 + 29 3.20238627208178e+00 -1.24095450883271e-02 + 30 3.20248061224166e+00 -1.24099224489666e-02 + 31 3.20292564206961e+00 -1.24117025682784e-02 + 32 3.20367227007056e+00 -1.24146890802823e-02 + 33 3.20466343197421e+00 -1.24186537278969e-02 + 34 3.20583882819824e+00 -1.24233553127930e-02 + 35 3.20713949242506e+00 -1.24285579697002e-02 + 36 3.20851174642574e+00 -1.24340469857030e-02 + 37 3.20991021994729e+00 -1.24396408797892e-02 + 38 3.21129989251817e+00 -1.24451995700727e-02 + 39 3.21265730667037e+00 -1.24506292266815e-02 + 40 3.21397114716924e+00 -1.24558845886769e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out index f64f6efa8..eebcebec0 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -115,13 +119,14 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -131,15 +136,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped index 4507a2d83..6d65b453d 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687020515258e+00 + x 3.21687020497026e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj index f58ff8ba4..a79591894 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 - 1 3.20437138788661e+00 -1.12999118519073e-02 1.75395615193509e-02 - 2 3.20383992338449e+00 -1.01805949487011e-02 1.57994685227925e-02 - 3 3.20396643078647e+00 -9.06358197789650e-03 1.40665271010360e-02 - 4 3.20472684453174e+00 -7.94810072200125e-03 1.23383408373197e-02 - 5 3.20606109997726e+00 -6.83333441994998e-03 1.06123771124712e-02 - 6 3.20787717649369e+00 -5.71849400474838e-03 8.88618850063674e-03 - 7 3.21005647716855e+00 -4.60288358620946e-03 7.15761395547176e-03 - 8 3.21246028402867e+00 -3.48595551811211e-03 5.42494905100725e-03 - 9 3.21493732319445e+00 -2.36735236562779e-03 3.68707712042334e-03 - 10 3.21733254799115e+00 -1.24693301919646e-03 1.94355244295300e-03 - 11 3.21949693112495e+00 -1.24779877244998e-03 1.94625222065960e-03 - 12 3.22129751465341e+00 -1.24851900586136e-03 1.94849963499631e-03 - 13 3.22262660690669e+00 -1.24905064276268e-03 1.95015938523232e-03 - 14 3.22340883992570e+00 -1.24936353597028e-03 1.95113655626521e-03 - 15 3.22360524389145e+00 -1.24944209755658e-03 1.95138194393324e-03 - 16 3.22321407479779e+00 -1.24928562991912e-03 1.95089323140301e-03 - 17 3.22226874215941e+00 -1.24890749686377e-03 1.94971241965315e-03 - 18 3.22083355128627e+00 -1.24833342051451e-03 1.94792041096681e-03 - 19 3.21899800422646e+00 -1.24759920169058e-03 1.94562971007373e-03 - 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 + 1 3.20437138788600e+00 -1.12999118519050e-02 1.75395615193440e-02 + 2 3.20383992333029e+00 -1.01805949485234e-02 1.57994685222408e-02 + 3 3.20396643077894e+00 -9.06358197787450e-03 1.40665271009677e-02 + 4 3.20472684448397e+00 -7.94810072187895e-03 1.23383408369400e-02 + 5 3.20606109997218e+00 -6.83333441993879e-03 1.06123771124364e-02 + 6 3.20787717647453e+00 -5.71849400471313e-03 8.88618850052717e-03 + 7 3.21005647713329e+00 -4.60288358615728e-03 7.15761395530948e-03 + 8 3.21246028397626e+00 -3.48595551805342e-03 5.42494905082458e-03 + 9 3.21493732312431e+00 -2.36735236557448e-03 3.68707712025729e-03 + 10 3.21733254790344e+00 -1.24693301916138e-03 1.94355244284363e-03 + 11 3.21949693102052e+00 -1.24779877240821e-03 1.94625222052929e-03 + 12 3.22129751453369e+00 -1.24851900581348e-03 1.94849963484684e-03 + 13 3.22262660677352e+00 -1.24905064270941e-03 1.95015938506598e-03 + 14 3.22340883978115e+00 -1.24936353591246e-03 1.95113655608461e-03 + 15 3.22360524373761e+00 -1.24944209749504e-03 1.95138194374102e-03 + 16 3.22321407463655e+00 -1.24928562985462e-03 1.95089323120157e-03 + 17 3.22226874199272e+00 -1.24890749679709e-03 1.94971241944496e-03 + 18 3.22083355111441e+00 -1.24833342044576e-03 1.94792041075227e-03 + 19 3.21899800404481e+00 -1.24759920161792e-03 1.94562970984710e-03 + 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out index c2057ff6d..01867c7f6 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -115,13 +119,14 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -131,20 +136,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped index 32715071f..226b212c1 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21402990715919e+00 + x 3.21402990668451e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj index 0970380b3..2753d1963 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 - 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 - 21 3.21456967651805e+00 -1.24582787060722e-03 1.94010885397715e-03 - 22 3.21221978014351e+00 -1.24488791205741e-03 1.93718239198331e-03 - 23 3.20994003861018e+00 -1.24397601544407e-03 1.93434540875013e-03 - 24 3.20783888769037e+00 -1.24313555507615e-03 1.93173251036810e-03 - 25 3.20600757749894e+00 -1.24240303099958e-03 1.92945661429617e-03 - 26 3.20451585601250e+00 -1.24180634240500e-03 1.92760374004661e-03 - 27 3.20340976322452e+00 -1.24136390528981e-03 1.92623043169546e-03 - 28 3.20271146343875e+00 -1.24108458537550e-03 1.92536368507084e-03 - 29 3.20242066608521e+00 -1.24096826643409e-03 1.92500279787052e-03 - 30 3.20251721571819e+00 -1.24100688628728e-03 1.92512261476555e-03 - 31 3.20296447484878e+00 -1.24118578993951e-03 1.92567770643472e-03 - 32 3.20371334569543e+00 -1.24148533827817e-03 1.92660730644958e-03 - 33 3.20470675738049e+00 -1.24188270295219e-03 1.92784080986481e-03 - 34 3.20588440358750e+00 -1.24235376143500e-03 1.92930358568961e-03 - 35 3.20718731148154e+00 -1.24287492459262e-03 1.93092259772638e-03 - 36 3.20856179675119e+00 -1.24342471870048e-03 1.93263128884420e-03 - 37 3.20996248385038e+00 -1.24398499354015e-03 1.93437333019136e-03 - 38 3.21135434796541e+00 -1.24454173918616e-03 1.93610517572065e-03 - 39 3.21271392828201e+00 -1.24508557131280e-03 1.93779759986417e-03 - 40 3.21402990715919e+00 -1.24561196286367e-03 1.93943645253637e-03 + 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 + 21 3.21456967632931e+00 -1.24582787053172e-03 1.94010885374201e-03 + 22 3.21221977994646e+00 -1.24488791197858e-03 1.93718239173800e-03 + 23 3.20994003840243e+00 -1.24397601536097e-03 1.93434540849171e-03 + 24 3.20783888746925e+00 -1.24313555498770e-03 1.93173251009322e-03 + 25 3.20600757726167e+00 -1.24240303090467e-03 1.92945661400138e-03 + 26 3.20451585575643e+00 -1.24180634230257e-03 1.92760373972862e-03 + 27 3.20340976294734e+00 -1.24136390517894e-03 1.92623043135138e-03 + 28 3.20271146313867e+00 -1.24108458525547e-03 1.92536368469842e-03 + 29 3.20242066576110e+00 -1.24096826630444e-03 1.92500279746831e-03 + 30 3.20251721536965e+00 -1.24100688614786e-03 1.92512261433301e-03 + 31 3.20296447447623e+00 -1.24118578979049e-03 1.92567770597231e-03 + 32 3.20371334530005e+00 -1.24148533812002e-03 1.92660730595873e-03 + 33 3.20470675696420e+00 -1.24188270278568e-03 1.92784080934784e-03 + 34 3.20588440315285e+00 -1.24235376126114e-03 1.92930358514962e-03 + 35 3.20718731103156e+00 -1.24287492441263e-03 1.93092259716711e-03 + 36 3.20856179628928e+00 -1.24342471851571e-03 1.93263128826985e-03 + 37 3.20996248338009e+00 -1.24398499335204e-03 1.93437332960633e-03 + 38 3.21135434749032e+00 -1.24454173899613e-03 1.93610517512938e-03 + 39 3.21271392780555e+00 -1.24508557112222e-03 1.93779759927093e-03 + 40 3.21402990668451e+00 -1.24561196267380e-03 1.93943645194510e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out index 2cb8b2826..151617c95 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -123,15 +127,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped index 48987f05a..f1f122306 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688253464583e+00 + x 3.21688253444007e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj index 2d1d01de3..a3529376d 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 0.00000000000000e+00 - 11 3.21950367383415e+00 0.00000000000000e+00 - 12 3.22130499858006e+00 0.00000000000000e+00 - 13 3.22263479496346e+00 0.00000000000000e+00 - 14 3.22341769665784e+00 0.00000000000000e+00 - 15 3.22361473677138e+00 0.00000000000000e+00 - 16 3.22322417514557e+00 0.00000000000000e+00 - 17 3.22227942564879e+00 0.00000000000000e+00 - 18 3.22084479803044e+00 0.00000000000000e+00 - 19 3.21900979846930e+00 0.00000000000000e+00 - 20 3.21688253464583e+00 0.00000000000000e+00 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 0.00000000000000e+00 + 11 3.21950367376059e+00 0.00000000000000e+00 + 12 3.22130499849384e+00 0.00000000000000e+00 + 13 3.22263479486396e+00 0.00000000000000e+00 + 14 3.22341769654449e+00 0.00000000000000e+00 + 15 3.22361473664369e+00 0.00000000000000e+00 + 16 3.22322417500307e+00 0.00000000000000e+00 + 17 3.22227942549106e+00 0.00000000000000e+00 + 18 3.22084479785707e+00 0.00000000000000e+00 + 19 3.21900979827991e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat index 1b0ff42d4..6ff3132f9 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 0.6 0.2 24 0 +# 6.00000000000000e-01 2.00000000000000e-01 24 0 - 0.7 0 - 0.9 0 - 1.1 0 - 1.3 0 - 1.5 0 - 1.7 0 - 1.9 0 - 2.1 0 - 2.3 0 - 2.5 0 - 2.7 0 - 2.9 0 - 3.1 0 - 3.3 20 - 3.5 0 - 3.7 0 - 3.9 0 - 4.1 0 - 4.3 0 - 4.5 0 - 4.7 0 - 4.9 0 - 5.1 0 - 5.3 0 + 7.00000000000000e-01 0.00000000000000e+00 + 9.00000000000000e-01 0.00000000000000e+00 + 1.10000000000000e+00 0.00000000000000e+00 + 1.30000000000000e+00 0.00000000000000e+00 + 1.50000000000000e+00 0.00000000000000e+00 + 1.70000000000000e+00 0.00000000000000e+00 + 1.90000000000000e+00 0.00000000000000e+00 + 2.10000000000000e+00 0.00000000000000e+00 + 2.30000000000000e+00 0.00000000000000e+00 + 2.50000000000000e+00 0.00000000000000e+00 + 2.70000000000000e+00 0.00000000000000e+00 + 2.90000000000000e+00 0.00000000000000e+00 + 3.10000000000000e+00 0.00000000000000e+00 + 3.30000000000000e+00 2.00000000000000e+01 + 3.50000000000000e+00 0.00000000000000e+00 + 3.70000000000000e+00 0.00000000000000e+00 + 3.90000000000000e+00 0.00000000000000e+00 + 4.10000000000000e+00 0.00000000000000e+00 + 4.30000000000000e+00 0.00000000000000e+00 + 4.50000000000000e+00 0.00000000000000e+00 + 4.70000000000000e+00 0.00000000000000e+00 + 4.90000000000000e+00 0.00000000000000e+00 + 5.10000000000000e+00 0.00000000000000e+00 + 5.30000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out index 231ed2e71..a72b72b3d 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -123,20 +127,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting histogram bias "histogram1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped index 35abb4af3..7ca010783 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21404878547144e+00 + x 3.21404878499019e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj index 58d908160..9c9860479 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253464583e+00 0.00000000000000e+00 - 21 3.21458253157603e+00 0.00000000000000e+00 - 22 3.21223315254029e+00 0.00000000000000e+00 - 23 3.20995392032979e+00 0.00000000000000e+00 - 24 3.20785326966943e+00 0.00000000000000e+00 - 25 3.20602244845117e+00 0.00000000000000e+00 - 26 3.20453120146139e+00 0.00000000000000e+00 - 27 3.20342556480347e+00 0.00000000000000e+00 - 28 3.20272769852622e+00 0.00000000000000e+00 - 29 3.20243730776714e+00 0.00000000000000e+00 - 30 3.20253423308456e+00 0.00000000000000e+00 - 31 3.20298183362156e+00 0.00000000000000e+00 - 32 3.20373100914607e+00 0.00000000000000e+00 - 33 3.20472468746373e+00 0.00000000000000e+00 - 34 3.20590256221113e+00 0.00000000000000e+00 - 35 3.20720566184671e+00 0.00000000000000e+00 - 36 3.20858030459458e+00 0.00000000000000e+00 - 37 3.20998111854285e+00 0.00000000000000e+00 - 38 3.21137308334418e+00 0.00000000000000e+00 - 39 3.21273274315657e+00 0.00000000000000e+00 - 40 3.21404878547144e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 + 21 3.21458253135360e+00 0.00000000000000e+00 + 22 3.21223315230095e+00 0.00000000000000e+00 + 23 3.20995392007338e+00 0.00000000000000e+00 + 24 3.20785326939589e+00 0.00000000000000e+00 + 25 3.20602244816055e+00 0.00000000000000e+00 + 26 3.20453120115385e+00 0.00000000000000e+00 + 27 3.20342556447929e+00 0.00000000000000e+00 + 28 3.20272769818575e+00 0.00000000000000e+00 + 29 3.20243730741081e+00 0.00000000000000e+00 + 30 3.20253423271288e+00 0.00000000000000e+00 + 31 3.20298183323508e+00 0.00000000000000e+00 + 32 3.20373100874536e+00 0.00000000000000e+00 + 33 3.20472468704943e+00 0.00000000000000e+00 + 34 3.20590256178394e+00 0.00000000000000e+00 + 35 3.20720566140745e+00 0.00000000000000e+00 + 36 3.20858030414420e+00 0.00000000000000e+00 + 37 3.20998111808250e+00 0.00000000000000e+00 + 38 3.21137308287521e+00 0.00000000000000e+00 + 39 3.21273274268056e+00 0.00000000000000e+00 + 40 3.21404878499019e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat index 2a16dc5f6..686fae912 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 0.6 0.2 24 0 +# 6.00000000000000e-01 2.00000000000000e-01 24 0 - 0.7 0 - 0.9 0 - 1.1 0 - 1.3 0 - 1.5 0 - 1.7 0 - 1.9 0 - 2.1 0 - 2.3 0 - 2.5 0 - 2.7 0 - 2.9 0 - 3.1 0 - 3.3 40 - 3.5 0 - 3.7 0 - 3.9 0 - 4.1 0 - 4.3 0 - 4.5 0 - 4.7 0 - 4.9 0 - 5.1 0 - 5.3 0 + 7.00000000000000e-01 0.00000000000000e+00 + 9.00000000000000e-01 0.00000000000000e+00 + 1.10000000000000e+00 0.00000000000000e+00 + 1.30000000000000e+00 0.00000000000000e+00 + 1.50000000000000e+00 0.00000000000000e+00 + 1.70000000000000e+00 0.00000000000000e+00 + 1.90000000000000e+00 0.00000000000000e+00 + 2.10000000000000e+00 0.00000000000000e+00 + 2.30000000000000e+00 0.00000000000000e+00 + 2.50000000000000e+00 0.00000000000000e+00 + 2.70000000000000e+00 0.00000000000000e+00 + 2.90000000000000e+00 0.00000000000000e+00 + 3.10000000000000e+00 0.00000000000000e+00 + 3.30000000000000e+00 4.00000000000000e+01 + 3.50000000000000e+00 0.00000000000000e+00 + 3.70000000000000e+00 0.00000000000000e+00 + 3.90000000000000e+00 0.00000000000000e+00 + 4.10000000000000e+00 0.00000000000000e+00 + 4.30000000000000e+00 0.00000000000000e+00 + 4.50000000000000e+00 0.00000000000000e+00 + 4.70000000000000e+00 0.00000000000000e+00 + 4.90000000000000e+00 0.00000000000000e+00 + 5.10000000000000e+00 0.00000000000000e+00 + 5.30000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt b/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt index e2b19c981..157cac038 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out index 5d2854533..d6add8f3d 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -120,15 +124,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped index a717bee50..ccbc01c61 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688253464583e+00 + x 3.21688253444007e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj index 2d1d01de3..a3529376d 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 0.00000000000000e+00 - 11 3.21950367383415e+00 0.00000000000000e+00 - 12 3.22130499858006e+00 0.00000000000000e+00 - 13 3.22263479496346e+00 0.00000000000000e+00 - 14 3.22341769665784e+00 0.00000000000000e+00 - 15 3.22361473677138e+00 0.00000000000000e+00 - 16 3.22322417514557e+00 0.00000000000000e+00 - 17 3.22227942564879e+00 0.00000000000000e+00 - 18 3.22084479803044e+00 0.00000000000000e+00 - 19 3.21900979846930e+00 0.00000000000000e+00 - 20 3.21688253464583e+00 0.00000000000000e+00 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 0.00000000000000e+00 + 11 3.21950367376059e+00 0.00000000000000e+00 + 12 3.22130499849384e+00 0.00000000000000e+00 + 13 3.22263479486396e+00 0.00000000000000e+00 + 14 3.22341769654449e+00 0.00000000000000e+00 + 15 3.22361473664369e+00 0.00000000000000e+00 + 16 3.22322417500307e+00 0.00000000000000e+00 + 17 3.22227942549106e+00 0.00000000000000e+00 + 18 3.22084479785707e+00 0.00000000000000e+00 + 19 3.21900979827991e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat index 09d19a2d1..69e912676 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat @@ -1,23 +1,23 @@ # 1 -# 0 0.5 20 0 +# 0.00000000000000e+00 5.00000000000000e-01 20 0 - 0.25 0 - 0.75 0 - 1.25 0 - 1.75 0 - 2.25 0 - 2.75 0 - 3.25 20 - 3.75 0 - 4.25 0 - 4.75 0 - 5.25 0 - 5.75 0 - 6.25 0 - 6.75 0 - 7.25 0 - 7.75 0 - 8.25 0 - 8.75 0 - 9.25 0 - 9.75 0 + 2.50000000000000e-01 0.00000000000000e+00 + 7.50000000000000e-01 0.00000000000000e+00 + 1.25000000000000e+00 0.00000000000000e+00 + 1.75000000000000e+00 0.00000000000000e+00 + 2.25000000000000e+00 0.00000000000000e+00 + 2.75000000000000e+00 0.00000000000000e+00 + 3.25000000000000e+00 2.00000000000000e+01 + 3.75000000000000e+00 0.00000000000000e+00 + 4.25000000000000e+00 0.00000000000000e+00 + 4.75000000000000e+00 0.00000000000000e+00 + 5.25000000000000e+00 0.00000000000000e+00 + 5.75000000000000e+00 0.00000000000000e+00 + 6.25000000000000e+00 0.00000000000000e+00 + 6.75000000000000e+00 0.00000000000000e+00 + 7.25000000000000e+00 0.00000000000000e+00 + 7.75000000000000e+00 0.00000000000000e+00 + 8.25000000000000e+00 0.00000000000000e+00 + 8.75000000000000e+00 0.00000000000000e+00 + 9.25000000000000e+00 0.00000000000000e+00 + 9.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out index 091d85f52..a9d49b469 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -120,20 +124,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting histogram bias "histogram1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped index 6df06ad1d..0a3fe4f9c 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21404878547144e+00 + x 3.21404878499019e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj index 58d908160..9c9860479 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253464583e+00 0.00000000000000e+00 - 21 3.21458253157603e+00 0.00000000000000e+00 - 22 3.21223315254029e+00 0.00000000000000e+00 - 23 3.20995392032979e+00 0.00000000000000e+00 - 24 3.20785326966943e+00 0.00000000000000e+00 - 25 3.20602244845117e+00 0.00000000000000e+00 - 26 3.20453120146139e+00 0.00000000000000e+00 - 27 3.20342556480347e+00 0.00000000000000e+00 - 28 3.20272769852622e+00 0.00000000000000e+00 - 29 3.20243730776714e+00 0.00000000000000e+00 - 30 3.20253423308456e+00 0.00000000000000e+00 - 31 3.20298183362156e+00 0.00000000000000e+00 - 32 3.20373100914607e+00 0.00000000000000e+00 - 33 3.20472468746373e+00 0.00000000000000e+00 - 34 3.20590256221113e+00 0.00000000000000e+00 - 35 3.20720566184671e+00 0.00000000000000e+00 - 36 3.20858030459458e+00 0.00000000000000e+00 - 37 3.20998111854285e+00 0.00000000000000e+00 - 38 3.21137308334418e+00 0.00000000000000e+00 - 39 3.21273274315657e+00 0.00000000000000e+00 - 40 3.21404878547144e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 + 21 3.21458253135360e+00 0.00000000000000e+00 + 22 3.21223315230095e+00 0.00000000000000e+00 + 23 3.20995392007338e+00 0.00000000000000e+00 + 24 3.20785326939589e+00 0.00000000000000e+00 + 25 3.20602244816055e+00 0.00000000000000e+00 + 26 3.20453120115385e+00 0.00000000000000e+00 + 27 3.20342556447929e+00 0.00000000000000e+00 + 28 3.20272769818575e+00 0.00000000000000e+00 + 29 3.20243730741081e+00 0.00000000000000e+00 + 30 3.20253423271288e+00 0.00000000000000e+00 + 31 3.20298183323508e+00 0.00000000000000e+00 + 32 3.20373100874536e+00 0.00000000000000e+00 + 33 3.20472468704943e+00 0.00000000000000e+00 + 34 3.20590256178394e+00 0.00000000000000e+00 + 35 3.20720566140745e+00 0.00000000000000e+00 + 36 3.20858030414420e+00 0.00000000000000e+00 + 37 3.20998111808250e+00 0.00000000000000e+00 + 38 3.21137308287521e+00 0.00000000000000e+00 + 39 3.21273274268056e+00 0.00000000000000e+00 + 40 3.21404878499019e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat index 544c0ba33..fe4ddc2fd 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat @@ -1,23 +1,23 @@ # 1 -# 0 0.5 20 0 +# 0.00000000000000e+00 5.00000000000000e-01 20 0 - 0.25 0 - 0.75 0 - 1.25 0 - 1.75 0 - 2.25 0 - 2.75 0 - 3.25 40 - 3.75 0 - 4.25 0 - 4.75 0 - 5.25 0 - 5.75 0 - 6.25 0 - 6.75 0 - 7.25 0 - 7.75 0 - 8.25 0 - 8.75 0 - 9.25 0 - 9.75 0 + 2.50000000000000e-01 0.00000000000000e+00 + 7.50000000000000e-01 0.00000000000000e+00 + 1.25000000000000e+00 0.00000000000000e+00 + 1.75000000000000e+00 0.00000000000000e+00 + 2.25000000000000e+00 0.00000000000000e+00 + 2.75000000000000e+00 0.00000000000000e+00 + 3.25000000000000e+00 4.00000000000000e+01 + 3.75000000000000e+00 0.00000000000000e+00 + 4.25000000000000e+00 0.00000000000000e+00 + 4.75000000000000e+00 0.00000000000000e+00 + 5.25000000000000e+00 0.00000000000000e+00 + 5.75000000000000e+00 0.00000000000000e+00 + 6.25000000000000e+00 0.00000000000000e+00 + 6.75000000000000e+00 0.00000000000000e+00 + 7.25000000000000e+00 0.00000000000000e+00 + 7.75000000000000e+00 0.00000000000000e+00 + 8.25000000000000e+00 0.00000000000000e+00 + 8.75000000000000e+00 0.00000000000000e+00 + 9.25000000000000e+00 0.00000000000000e+00 + 9.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram/namd-version.txt b/namd/tests/library/000_distance-grid_histogram/namd-version.txt index e2b19c981..157cac038 100644 --- a/namd/tests/library/000_distance-grid_histogram/namd-version.txt +++ b/namd/tests/library/000_distance-grid_histogram/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj index 6a779c875..dd7940783 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj @@ -1,2 +1,2 @@ - 10 3.21733851236362e+00 7.50000000000000e-01 1.00000000000000e-02 - 20 3.21688297526674e+00 7.50000000000000e-01 1.00000000000000e-02 + 10 3.21733851230199e+00 7.50000000000000e-01 1.00000000000000e-02 + 20 3.21688297506098e+00 7.50000000000000e-01 1.00000000000000e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out index 2404d2e37..2c566b0cb 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out @@ -1,13 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -141,10 +141,26 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped index 908bf7241..e88987e94 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688297526674e+00 + x 3.21688297506098e+00 } metadynamics { @@ -22,11 +22,11 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 7.98796537205394e-06 8.94022105027543e-05 6.41564889500790e-04 - 2.95197835125314e-03 8.70895398489406e-03 1.64740003795870e-02 - 1.99807780438813e-02 1.55383882008336e-02 7.74782472489960e-03 - 2.47704476592871e-03 5.07771324793184e-04 6.67394672587493e-05 - 5.62441746115269e-06 3.03915330677999e-07 0.00000000000000e+00 + 7.98796537769059e-06 8.94022105552033e-05 6.41564889800856e-04 + 2.95197835228273e-03 8.70895398689607e-03 1.64740003814156e-02 + 1.99807780437246e-02 1.55383881988653e-02 7.74782472299776e-03 + 2.47704476502647e-03 5.07771324547938e-04 6.67394672185917e-05 + 5.62441745710086e-06 3.03915330422993e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients @@ -37,23 +37,23 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 4.21354234501736e-05 3.92115793261853e-04 2.24360723661620e-03 - 7.69934000924979e-03 1.49733727811320e-02 1.36803233088098e-02 - -1.16827176399835e-03 -1.47204255412967e-02 -1.42269229850317e-02 - -6.75028437082004e-03 -1.83509826767759e-03 -3.00522069320091e-04 - -3.03257488301764e-05 -1.90879841336284e-06 0.00000000000000e+00 + 4.21354234780051e-05 3.92115793470621e-04 2.24360723751294e-03 + 7.69934001123311e-03 1.49733727825032e-02 1.36803233064121e-02 + -1.16827176873810e-03 -1.47204255431243e-02 -1.42269229833801e-02 + -6.75028436894966e-03 -1.83509826691184e-03 -3.00522069155109e-04 + -3.03257488096648e-05 -1.90879841183335e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 hill { step 10 weight 1.00000000000000e-02 - centers 3.21733851236362e+00 + centers 3.21733851230199e+00 widths 1.50000000000000e+00 } hill { step 20 weight 1.00000000000000e-02 - centers 3.21688297526674e+00 + centers 3.21688297506098e+00 widths 1.50000000000000e+00 } } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj index 5824ebe05..dedaa4935 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 5.80098334331777e-04 - 11 3.21950368274213e+00 5.80098334331777e-04 - 12 3.22130502519349e+00 5.80098334331777e-04 - 13 3.22263484785580e+00 5.80098334331777e-04 - 14 3.22341778407457e+00 5.80098334331777e-04 - 15 3.22361486654089e+00 5.80098334331777e-04 - 16 3.22322435460843e+00 5.80098334331777e-04 - 17 3.22227966160826e+00 5.80098334331777e-04 - 18 3.22084509672532e+00 5.80098334331777e-04 - 19 3.21901016556900e+00 5.80098334331777e-04 - 20 3.21688297526674e+00 1.16827176399835e-03 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 5.80098335424304e-04 + 11 3.21950368266856e+00 5.80098335424304e-04 + 12 3.22130502510728e+00 5.80098335424304e-04 + 13 3.22263484775629e+00 5.80098335424304e-04 + 14 3.22341778396123e+00 5.80098335424304e-04 + 15 3.22361486641320e+00 5.80098335424304e-04 + 16 3.22322435446593e+00 5.80098335424304e-04 + 17 3.22227966145053e+00 5.80098335424304e-04 + 18 3.22084509655195e+00 5.80098335424304e-04 + 19 3.21901016537961e+00 5.80098335424304e-04 + 20 3.21688297506098e+00 1.16827176873810e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf index 9da766ced..9d98a1715 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.99727900785093e-02 - 7.50000000000000e-01 1.98913758333786e-02 - 1.25000000000000e+00 1.93392131543806e-02 - 1.75000000000000e+00 1.70287996926282e-02 - 2.25000000000000e+00 1.12718240589873e-02 - 2.75000000000000e+00 3.50677766429439e-03 + 2.50000000000000e-01 1.99727900783469e-02 + 7.50000000000000e-01 1.98913758331694e-02 + 1.25000000000000e+00 1.93392131539237e-02 + 1.75000000000000e+00 1.70287996914418e-02 + 2.25000000000000e+00 1.12718240568285e-02 + 2.75000000000000e+00 3.50677766230894e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 4.44238984304775e-03 - 4.25000000000000e+00 1.22329533189817e-02 - 4.75000000000000e+00 1.75037332779526e-02 - 5.25000000000000e+00 1.94730067190882e-02 - 5.75000000000000e+00 1.99140385766226e-02 - 6.25000000000000e+00 1.99751536264202e-02 - 6.75000000000000e+00 1.99804741285507e-02 - 7.25000000000000e+00 1.99807780438813e-02 - 7.75000000000000e+00 1.99807780438813e-02 - 8.25000000000000e+00 1.99807780438813e-02 - 8.75000000000000e+00 1.99807780438813e-02 - 9.25000000000000e+00 1.99807780438813e-02 - 9.75000000000000e+00 1.99807780438813e-02 + 3.75000000000000e+00 4.44238984485923e-03 + 4.25000000000000e+00 1.22329533207268e-02 + 4.75000000000000e+00 1.75037332786981e-02 + 5.25000000000000e+00 1.94730067191766e-02 + 5.75000000000000e+00 1.99140385765060e-02 + 6.25000000000000e+00 1.99751536262675e-02 + 6.75000000000000e+00 1.99804741283941e-02 + 7.25000000000000e+00 1.99807780437246e-02 + 7.75000000000000e+00 1.99807780437246e-02 + 8.25000000000000e+00 1.99807780437246e-02 + 8.75000000000000e+00 1.99807780437246e-02 + 9.25000000000000e+00 1.99807780437246e-02 + 9.75000000000000e+00 1.99807780437246e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj index d357d6751..bf802816e 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj @@ -1,2 +1,2 @@ - 30 3.20253726808121e+00 2.00000000000000e+00 1.00000000000000e-14 - 40 3.21405662921571e+00 2.00000000000000e+00 1.00000000000000e-14 + 30 3.20253726770953e+00 2.00000000000000e+00 1.00000000000000e-14 + 40 3.21405662873448e+00 2.00000000000000e+00 1.00000000000000e-14 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out index 3b6b317a8..25e53b613 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out @@ -1,13 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.restart.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -139,12 +139,28 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: This state file/stream contains explicit hills. colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: Read 2 hills. +colvars: read biasing energy and forces from grids. +colvars: read 2 additional explicit hills. colvars: Rebinning the energy and forces grids from 2 hills (this may take a while)... colvars: 0.00% done. colvars: 100.00% done. @@ -154,6 +170,7 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped index 23fdc9ae2..f3ae76614 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405662921571e+00 + x 3.21405662873448e+00 } metadynamics { @@ -22,25 +22,25 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 3.72168800800684e-04 7.62454154875249e-04 1.45480353405707e-03 - 2.58530507717515e-03 4.27893895254244e-03 6.59594797527291e-03 - 9.46967757451101e-03 1.26622243109190e-02 1.57689092172573e-02 - 1.82898499591976e-02 1.97576583936095e-02 1.98782268066167e-02 - 1.86267313311331e-02 1.62559553981891e-02 1.32131141614850e-02 - 1.00026417662927e-02 7.05246732965355e-03 4.63110140187036e-03 - 2.83233316289399e-03 1.61332262432165e-03 8.55884084525168e-04 - 4.22888151001758e-04 1.94604519696452e-04 8.34059758722572e-05 - 3.32934080306407e-05 1.23775924373641e-05 4.28579055416322e-06 - 1.38210980704854e-06 4.15117455368664e-07 3.64063576811435e-15 - 3.01191095986970e-15 2.46697141460954e-15 2.00052137877865e-15 - 1.60612509458054e-15 1.27665229333083e-15 1.00466895613666e-15 - 7.82763249307229e-16 6.03802578026978e-16 4.61122793154982e-16 - 3.48654526402326e-16 2.60994356708439e-16 1.93430082660864e-16 - 1.41929936677652e-16 1.03105324114947e-16 7.41558241301806e-17 - 5.28039645693086e-17 3.72258726563668e-17 2.59824640429186e-17 - 1.79544817430310e-17 1.22835105643033e-17 8.32011300231200e-18 - 5.57947116155582e-18 3.70436643767441e-18 2.43496058423845e-18 - 1.58462689039896e-18 + 3.72168800988033e-04 7.62454155222791e-04 1.45480353465099e-03 + 2.58530507810761e-03 4.27893895388223e-03 6.59594797702447e-03 + 9.46967757657534e-03 1.26622243130771e-02 1.57689092191951e-02 + 1.82898499605756e-02 1.97576583941589e-02 1.98782268062245e-02 + 1.86267313298802e-02 1.62559553963231e-02 1.32131141593403e-02 + 1.00026417641938e-02 7.05246732783860e-03 4.63110140045852e-03 + 2.83233316189597e-03 1.61332262367653e-03 8.55884084142272e-04 + 4.22888150792485e-04 1.94604519590907e-04 8.34059758230608e-05 + 3.32934080094220e-05 1.23775924288879e-05 4.28579055102484e-06 + 1.38210980597084e-06 4.15117455025274e-07 3.64063576668077e-15 + 3.01191095861938e-15 2.46697141353276e-15 2.00052137786274e-15 + 1.60612509381090e-15 1.27665229269180e-15 1.00466895561231e-15 + 7.82763248881975e-16 6.03802577686049e-16 4.61122792884764e-16 + 3.48654526190564e-16 2.60994356544342e-16 1.93430082535114e-16 + 1.41929936582350e-16 1.03105324043511e-16 7.41558240772166e-17 + 5.28039645304659e-17 3.72258726281876e-17 2.59824640226949e-17 + 1.79544817286721e-17 1.22835105542170e-17 8.32011299530226e-18 + 5.57947115673577e-18 3.70436643439502e-18 2.43496058203075e-18 + 1.58462688892833e-18 hills_energy_gradients grid_parameters { n_colvars 1 @@ -49,47 +49,47 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 1.40075110044120e-03 2.59859363048141e-03 4.44099297432371e-03 - 6.97278888331524e-03 1.00192639052802e-02 1.30993843008538e-02 - 1.54395417654311e-02 1.61426066782075e-02 1.44964828843116e-02 - 1.03109464709461e-02 4.11348241265501e-03 -2.92922894632563e-03 - -9.36764744077205e-03 -1.39552453099017e-02 -1.60410539900880e-02 - -1.56999540167490e-02 -1.35769607049026e-02 -1.05621149951951e-02 - -7.46673071966103e-03 -4.82674321921130e-03 -2.86495075314130e-03 - -1.56591840894438e-03 -7.89796491068873e-04 -3.68156057379246e-04 - -1.58795588356400e-04 -6.34368443496714e-05 -2.34890958561326e-05 - -8.06633422826891e-06 -2.57032529596210e-06 -3.36000867736823e-15 - -2.93034146555533e-15 -2.52350768759663e-15 -2.14639312540996e-15 - -1.80354428947083e-15 -1.49740594641337e-15 -1.22862536008705e-15 - -9.96391242774491e-16 -7.98779361552378e-16 -6.33082112166259e-16 - -4.96105393565718e-16 -3.84422123803986e-16 -2.94577213164243e-16 - -2.23243402488820e-16 -1.67330899065332e-16 -1.24056159817874e-16 - -9.09765564426929e-17 -6.59981613366451e-17 -4.73637102870346e-17 - -3.36271325374767e-17 -2.36200830358874e-17 -1.64148291606559e-17 - -1.12867623526432e-17 -7.67881294206302e-18 -5.16919768691752e-18 - -3.44324803937870e-18 + 1.40075110105780e-03 2.59859363148452e-03 4.44099297579070e-03 + 6.97278888521528e-03 1.00192639073998e-02 1.30993843027639e-02 + 1.54395417665452e-02 1.61426066779483e-02 1.44964828823443e-02 + 1.03109464673752e-02 4.11348240807316e-03 -2.92922895099231e-03 + -9.36764744456861e-03 -1.39552453121627e-02 -1.60410539906239e-02 + -1.56999540158312e-02 -1.35769607030841e-02 -1.05621149930753e-02 + -7.46673071770275e-03 -4.82674321766440e-03 -2.86495075206286e-03 + -1.56591840826989e-03 -7.89796490686730e-04 -3.68156057181895e-04 + -1.58795588263100e-04 -6.34368443091680e-05 -2.34890958399494e-05 + -8.06633422230724e-06 -2.57032529393441e-06 -3.36000867643381e-15 + -2.93034146466045e-15 -2.52350768675858e-15 -2.14639312464089e-15 + -1.80354428877811e-15 -1.49740594580019e-15 -1.22862535955312e-15 + -9.96391242316789e-16 -7.98779361165857e-16 -6.33082111844533e-16 + -4.96105393301648e-16 -3.84422123590172e-16 -2.94577212993405e-16 + -2.23243402354083e-16 -1.67330898960416e-16 -1.24056159737195e-16 + -9.09765563814143e-17 -6.59981612906651e-17 -4.73637102529462e-17 + -3.36271325125033e-17 -2.36200830178057e-17 -1.64148291477159e-17 + -1.12867623434892e-17 -7.67881293566128e-18 -5.16919768249119e-18 + -3.44324803635265e-18 hill { step 10 weight 1.00000000000000e-02 - centers 3.21733851236362e+00 + centers 3.21733851230199e+00 widths 1.50000000000000e+00 } hill { step 20 weight 1.00000000000000e-02 - centers 3.21688297526674e+00 + centers 3.21688297506098e+00 widths 1.50000000000000e+00 } hill { step 30 weight 1.00000000000000e-14 - centers 3.20253726808121e+00 + centers 3.20253726770953e+00 widths 4.00000000000000e+00 } hill { step 40 weight 1.00000000000000e-14 - centers 3.21405662921571e+00 + centers 3.21405662873448e+00 widths 4.00000000000000e+00 } } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj index 05c21c5c1..b775fab7c 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688297526674e+00 2.92922894632517e-03 - 21 3.21458307290139e+00 2.92922894632517e-03 - 22 3.21223383450427e+00 2.92922894632517e-03 - 23 3.20995478164873e+00 2.92922894632517e-03 - 24 3.20785434745816e+00 2.92922894632517e-03 - 25 3.20602377789862e+00 2.92922894632517e-03 - 26 3.20453281557945e+00 2.92922894632517e-03 - 27 3.20342749425391e+00 2.92922894632517e-03 - 28 3.20272997152892e+00 2.92922894632517e-03 - 29 3.20243995008546e+00 2.92922894632517e-03 - 30 3.20253726808121e+00 2.92922894632541e-03 - 31 3.20298528238019e+00 2.92922894632541e-03 - 32 3.20373489064589e+00 2.92922894632541e-03 - 33 3.20472901878714e+00 2.92922894632541e-03 - 34 3.20590735876660e+00 2.92922894632541e-03 - 35 3.20721093759908e+00 2.92922894632541e-03 - 36 3.20858607227153e+00 2.92922894632541e-03 - 37 3.20998738982642e+00 2.92922894632541e-03 - 38 3.21137986902379e+00 2.92922894632541e-03 - 39 3.21274005323456e+00 2.92922894632541e-03 - 40 3.21405662921571e+00 2.92922894632563e-03 + 20 3.21688297506098e+00 2.92922895099185e-03 + 21 3.21458307267896e+00 2.92922895099185e-03 + 22 3.21223383426493e+00 2.92922895099185e-03 + 23 3.20995478139232e+00 2.92922895099185e-03 + 24 3.20785434718462e+00 2.92922895099185e-03 + 25 3.20602377760800e+00 2.92922895099185e-03 + 26 3.20453281527191e+00 2.92922895099185e-03 + 27 3.20342749392972e+00 2.92922895099185e-03 + 28 3.20272997118845e+00 2.92922895099185e-03 + 29 3.20243994972914e+00 2.92922895099185e-03 + 30 3.20253726770953e+00 2.92922895099210e-03 + 31 3.20298528199370e+00 2.92922895099210e-03 + 32 3.20373489024518e+00 2.92922895099210e-03 + 33 3.20472901837284e+00 2.92922895099210e-03 + 34 3.20590735833942e+00 2.92922895099210e-03 + 35 3.20721093715982e+00 2.92922895099210e-03 + 36 3.20858607182116e+00 2.92922895099210e-03 + 37 3.20998738936608e+00 2.92922895099210e-03 + 38 3.21137986855483e+00 2.92922895099210e-03 + 39 3.21274005275856e+00 2.92922895099210e-03 + 40 3.21405662873448e+00 2.92922895099231e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf index 35289f537..775f05da1 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf @@ -1,58 +1,58 @@ # 1 # 1.00000000000000e+00 2.00000000000000e-01 55 0 - 1.10000000000000e+00 1.95060580058160e-02 - 1.30000000000000e+00 1.91157726517414e-02 - 1.50000000000000e+00 1.84234232725596e-02 - 1.70000000000000e+00 1.72929217294415e-02 - 1.90000000000000e+00 1.55992878540742e-02 - 2.10000000000000e+00 1.32822788313438e-02 - 2.30000000000000e+00 1.04085492321057e-02 - 2.50000000000000e+00 7.21600249569771e-03 - 2.70000000000000e+00 4.10931758935941e-03 - 2.90000000000000e+00 1.58837684741911e-03 - 3.10000000000000e+00 1.20568413007130e-04 + 1.10000000000000e+00 1.95060580052365e-02 + 1.30000000000000e+00 1.91157726510017e-02 + 1.50000000000000e+00 1.84234232715735e-02 + 1.70000000000000e+00 1.72929217281169e-02 + 1.90000000000000e+00 1.55992878523423e-02 + 2.10000000000000e+00 1.32822788292000e-02 + 2.30000000000000e+00 1.04085492296491e-02 + 2.50000000000000e+00 7.21600249314737e-03 + 2.70000000000000e+00 4.10931758702936e-03 + 2.90000000000000e+00 1.58837684564884e-03 + 3.10000000000000e+00 1.20568412065550e-04 3.30000000000000e+00 -0.00000000000000e+00 - 3.50000000000000e+00 1.25149547548363e-03 - 3.70000000000000e+00 3.62227140842760e-03 - 3.90000000000000e+00 6.66511264513171e-03 - 4.10000000000000e+00 9.87558504032401e-03 - 4.30000000000000e+00 1.28257594769631e-02 - 4.50000000000000e+00 1.52471254047463e-02 - 4.70000000000000e+00 1.70458936437227e-02 - 4.90000000000000e+00 1.82649041822950e-02 - 5.10000000000000e+00 1.90223427220915e-02 - 5.30000000000000e+00 1.94553386556149e-02 - 5.50000000000000e+00 1.96836222869202e-02 - 5.70000000000000e+00 1.97948208307444e-02 - 5.90000000000000e+00 1.98449333985860e-02 - 6.10000000000000e+00 1.98658492141793e-02 - 6.30000000000000e+00 1.98739410160625e-02 - 6.50000000000000e+00 1.98768446968096e-02 - 6.70000000000000e+00 1.98778116891613e-02 - 6.90000000000000e+00 1.98782268066130e-02 - 7.10000000000000e+00 1.98782268066137e-02 - 7.30000000000000e+00 1.98782268066142e-02 - 7.50000000000000e+00 1.98782268066147e-02 - 7.70000000000000e+00 1.98782268066151e-02 - 7.90000000000000e+00 1.98782268066154e-02 - 8.10000000000000e+00 1.98782268066157e-02 - 8.30000000000000e+00 1.98782268066159e-02 - 8.50000000000000e+00 1.98782268066161e-02 - 8.70000000000000e+00 1.98782268066162e-02 - 8.90000000000000e+00 1.98782268066163e-02 - 9.10000000000000e+00 1.98782268066164e-02 - 9.30000000000000e+00 1.98782268066165e-02 - 9.50000000000000e+00 1.98782268066165e-02 - 9.70000000000000e+00 1.98782268066166e-02 - 9.90000000000000e+00 1.98782268066166e-02 - 1.01000000000000e+01 1.98782268066166e-02 - 1.03000000000000e+01 1.98782268066166e-02 - 1.05000000000000e+01 1.98782268066167e-02 - 1.07000000000000e+01 1.98782268066167e-02 - 1.09000000000000e+01 1.98782268066167e-02 - 1.11000000000000e+01 1.98782268066167e-02 - 1.13000000000000e+01 1.98782268066167e-02 - 1.15000000000000e+01 1.98782268066167e-02 - 1.17000000000000e+01 1.98782268066167e-02 - 1.19000000000000e+01 1.98782268066167e-02 + 3.50000000000000e+00 1.25149547634431e-03 + 3.70000000000000e+00 3.62227140990143e-03 + 3.90000000000000e+00 6.66511264688419e-03 + 4.10000000000000e+00 9.87558504203071e-03 + 4.30000000000000e+00 1.28257594783859e-02 + 4.50000000000000e+00 1.52471254057660e-02 + 4.70000000000000e+00 1.70458936443285e-02 + 4.90000000000000e+00 1.82649041825480e-02 + 5.10000000000000e+00 1.90223427220822e-02 + 5.30000000000000e+00 1.94553386554320e-02 + 5.50000000000000e+00 1.96836222866336e-02 + 5.70000000000000e+00 1.97948208304014e-02 + 5.90000000000000e+00 1.98449333982151e-02 + 6.10000000000000e+00 1.98658492137956e-02 + 6.30000000000000e+00 1.98739410156735e-02 + 6.50000000000000e+00 1.98768446964185e-02 + 6.70000000000000e+00 1.98778116887695e-02 + 6.90000000000000e+00 1.98782268062208e-02 + 7.10000000000000e+00 1.98782268062215e-02 + 7.30000000000000e+00 1.98782268062220e-02 + 7.50000000000000e+00 1.98782268062225e-02 + 7.70000000000000e+00 1.98782268062229e-02 + 7.90000000000000e+00 1.98782268062232e-02 + 8.10000000000000e+00 1.98782268062235e-02 + 8.30000000000000e+00 1.98782268062237e-02 + 8.50000000000000e+00 1.98782268062239e-02 + 8.70000000000000e+00 1.98782268062240e-02 + 8.90000000000000e+00 1.98782268062241e-02 + 9.10000000000000e+00 1.98782268062242e-02 + 9.30000000000000e+00 1.98782268062243e-02 + 9.50000000000000e+00 1.98782268062243e-02 + 9.70000000000000e+00 1.98782268062244e-02 + 9.90000000000000e+00 1.98782268062244e-02 + 1.01000000000000e+01 1.98782268062244e-02 + 1.03000000000000e+01 1.98782268062244e-02 + 1.05000000000000e+01 1.98782268062245e-02 + 1.07000000000000e+01 1.98782268062245e-02 + 1.09000000000000e+01 1.98782268062245e-02 + 1.11000000000000e+01 1.98782268062245e-02 + 1.13000000000000e+01 1.98782268062245e-02 + 1.15000000000000e+01 1.98782268062245e-02 + 1.17000000000000e+01 1.98782268062245e-02 + 1.19000000000000e+01 1.98782268062245e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt index 49dcaf892..157cac038 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2021-03-09. -colvars: Using NAMD interface, version "2021-03-02". +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out index 3b35ba0c9..25ec7c329 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out @@ -1,13 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -139,10 +139,26 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped index 24be7d8f2..a9f5cad12 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688254084712e+00 + x 3.21688254064136e+00 } metadynamics { @@ -21,13 +21,13 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 6.65430605193845e-04 9.34557512978891e-04 1.23300798762255e-03 - 1.52820755416809e-03 1.77932544544850e-03 1.94618908282799e-03 - 1.99972957592804e-03 1.93025240791188e-03 1.75030418488448e-03 - 1.49097223022159e-03 1.19311463643918e-03 8.96915206877818e-04 - 6.33398742165647e-04 4.20203437672161e-04 2.61877749887666e-04 - 1.53318370777537e-04 8.43230653380996e-05 4.35667507594360e-05 - 2.11456262493941e-05 9.64145386786002e-06 + 6.65430605259840e-04 9.34557513055957e-04 1.23300798770362e-03 + 1.52820755424302e-03 1.77932544550601e-03 1.94618908285837e-03 + 1.99972957592583e-03 1.93025240787750e-03 1.75030418482405e-03 + 1.49097223014520e-03 1.19311463635811e-03 8.96915206801889e-04 + 6.33398742101442e-04 4.20203437622546e-04 2.61877749852370e-04 + 1.53318370754311e-04 8.43230653239168e-05 4.35667507513804e-05 + 2.11456262451310e-05 9.64145386575516e-06 hills_energy_gradients grid_parameters { n_colvars 1 @@ -36,12 +36,12 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 4.93601531934965e-04 5.76414162006946e-04 6.06365740080861e-04 - 5.60512340105952e-04 4.30201086547313e-04 2.27271348885101e-04 - -1.64425129573257e-05 -2.57152793951181e-04 -4.51967686078399e-04 - -5.71373901782952e-04 -6.06367538363199e-04 -5.67946764126985e-04 - -4.80257088153256e-04 -3.71133070586411e-04 -2.64031001778642e-04 - -1.73743804986186e-04 -1.06097165597456e-04 -6.02625033836491e-05 - -3.18923060876561e-05 -1.57466379157729e-05 + 4.93601531961674e-04 5.76414162023237e-04 6.06365740079512e-04 + 5.60512340082354e-04 4.30201086501742e-04 2.27271348823597e-04 + -1.64425130241460e-05 -2.57152794011114e-04 -4.51967686121292e-04 + -5.71373901803506e-04 -6.06367538361871e-04 -5.67946764108878e-04 + -4.80257088125742e-04 -3.71133070556632e-04 -2.64031001751807e-04 + -1.73743804964989e-04 -1.06097165582428e-04 -6.02625033739621e-05 + -3.18923060819328e-05 -1.57466379126574e-05 } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj index 372662fa9..0738ec8f1 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 8.16428315713133e-06 - 11 3.21950367395952e+00 8.16428315713133e-06 - 12 3.22130499895462e+00 8.16428315713133e-06 - 13 3.22263479570787e+00 8.16428315713133e-06 - 14 3.22341769788814e+00 8.16428315713133e-06 - 15 3.22361473859775e+00 8.16428315713133e-06 - 16 3.22322417767132e+00 8.16428315713133e-06 - 17 3.22227942896967e+00 8.16428315713133e-06 - 18 3.22084480223426e+00 8.16428315713133e-06 - 19 3.21900980363585e+00 8.16428315713133e-06 - 20 3.21688254084712e+00 1.64425129573257e-05 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 8.16428317253262e-06 + 11 3.21950367388596e+00 8.16428317253262e-06 + 12 3.22130499886840e+00 8.16428317253262e-06 + 13 3.22263479560837e+00 8.16428317253262e-06 + 14 3.22341769777479e+00 8.16428317253262e-06 + 15 3.22361473847006e+00 8.16428317253262e-06 + 16 3.22322417752882e+00 8.16428317253262e-06 + 17 3.22227942881194e+00 8.16428317253262e-06 + 18 3.22084480206089e+00 8.16428317253262e-06 + 19 3.21900980344646e+00 8.16428317253262e-06 + 20 3.21688254064136e+00 1.64425130241460e-05 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf index 67c5801c2..bcac69118 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.33429897073419e-03 - 7.50000000000000e-01 1.06517206294915e-03 - 1.25000000000000e+00 7.66721588305484e-04 - 1.75000000000000e+00 4.71522021759950e-04 - 2.25000000000000e+00 2.20404130479536e-04 - 2.75000000000000e+00 5.35404931000470e-05 + 2.50000000000000e-01 1.33429897066599e-03 + 7.50000000000000e-01 1.06517206286987e-03 + 1.25000000000000e+00 7.66721588222210e-04 + 1.75000000000000e+00 4.71522021682808e-04 + 2.25000000000000e+00 2.20404130419819e-04 + 2.75000000000000e+00 5.35404930674629e-05 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 6.94771680161525e-05 - 4.25000000000000e+00 2.49425391043558e-04 - 4.75000000000000e+00 5.08757345706442e-04 - 5.25000000000000e+00 8.06614939488859e-04 - 5.75000000000000e+00 1.10281436905022e-03 - 6.25000000000000e+00 1.36633083376239e-03 - 6.75000000000000e+00 1.57952613825587e-03 - 7.25000000000000e+00 1.73785182604037e-03 - 7.75000000000000e+00 1.84641120515050e-03 - 8.25000000000000e+00 1.91540651058994e-03 - 8.75000000000000e+00 1.95616282516860e-03 - 9.25000000000000e+00 1.97858394967864e-03 - 9.75000000000000e+00 1.99008812206018e-03 + 3.75000000000000e+00 6.94771680483336e-05 + 4.25000000000000e+00 2.49425391101783e-04 + 4.75000000000000e+00 5.08757345780628e-04 + 5.25000000000000e+00 8.06614939567721e-04 + 5.75000000000000e+00 1.10281436912394e-03 + 6.25000000000000e+00 1.36633083382439e-03 + 6.75000000000000e+00 1.57952613830328e-03 + 7.25000000000000e+00 1.73785182607346e-03 + 7.75000000000000e+00 1.84641120517152e-03 + 8.25000000000000e+00 1.91540651060191e-03 + 8.75000000000000e+00 1.95616282517445e-03 + 9.25000000000000e+00 1.97858394968070e-03 + 9.75000000000000e+00 1.99008812206007e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out index 2a87d0982..f80dd081e 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out @@ -1,13 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.restart.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -139,17 +139,34 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: Read 0 hills. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: Rebinning the energy and forces grids from the grids in the restart file. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped index ce121d56f..81421cf45 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21404884013792e+00 + x 3.21404883965667e+00 } metadynamics { @@ -21,25 +21,25 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 1.23300798763402e-03 1.23300798763524e-03 1.52820755418198e-03 - 1.52820755418314e-03 1.52820755418424e-03 1.77932544546565e-03 - 1.77932544546654e-03 1.94618908284677e-03 1.94618908284735e-03 - 1.94618908284775e-03 1.99972957594801e-03 1.99972957594802e-03 - 1.93025240793167e-03 1.93025240793128e-03 1.93025240793072e-03 - 1.75030418490259e-03 1.75030418490171e-03 1.49097223023783e-03 - 1.49097223023673e-03 1.49097223023558e-03 1.19311463645197e-03 - 1.19311463645075e-03 8.96915206888191e-04 8.96915206887022e-04 - 8.96915206885903e-04 6.33398742172679e-04 6.33398742171702e-04 - 4.20203437677323e-04 4.20203437676518e-04 4.20203437675802e-04 - 2.61877749890678e-04 2.61877749890133e-04 1.53318370779538e-04 - 1.53318370779143e-04 1.53318370778814e-04 8.43230653391043e-05 - 8.43230653388823e-05 4.35667507600398e-05 4.35667507598971e-05 - 4.35667507597847e-05 2.11456262496551e-05 2.11456262495875e-05 - 9.64145386800195e-06 9.64145386796312e-06 9.64145386793418e-06 - 5.28034713900195e-17 3.72255148346162e-17 2.59822072163652e-17 - 1.79542993773489e-17 1.22833824511992e-17 8.32002395780095e-18 - 5.57940992670954e-18 3.70432477169169e-18 2.43493253191679e-18 - 1.58460820200618e-18 + 1.23300798771509e-03 1.23300798771631e-03 1.52820755425691e-03 + 1.52820755425807e-03 1.52820755425917e-03 1.77932544552316e-03 + 1.77932544552405e-03 1.94618908287715e-03 1.94618908287773e-03 + 1.94618908287813e-03 1.99972957594580e-03 1.99972957594581e-03 + 1.93025240789729e-03 1.93025240789690e-03 1.93025240789634e-03 + 1.75030418484216e-03 1.75030418484128e-03 1.49097223016143e-03 + 1.49097223016034e-03 1.49097223015919e-03 1.19311463637090e-03 + 1.19311463636968e-03 8.96915206812262e-04 8.96915206811093e-04 + 8.96915206809974e-04 6.33398742108474e-04 6.33398742107497e-04 + 4.20203437627708e-04 4.20203437626903e-04 4.20203437626187e-04 + 2.61877749855382e-04 2.61877749854837e-04 1.53318370756312e-04 + 1.53318370755917e-04 1.53318370755588e-04 8.43230653249215e-05 + 8.43230653246995e-05 4.35667507519842e-05 4.35667507518415e-05 + 4.35667507517290e-05 2.11456262453920e-05 2.11456262453244e-05 + 9.64145386589709e-06 9.64145386585826e-06 9.64145386582932e-06 + 5.28034713511762e-17 3.72255148064365e-17 2.59822071961412e-17 + 1.79542993629898e-17 1.22833824411128e-17 8.32002395079111e-18 + 5.57940992188942e-18 3.70432476841225e-18 2.43493252970905e-18 + 1.58460820053553e-18 hills_energy_gradients grid_parameters { n_colvars 1 @@ -48,24 +48,24 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 6.06365740086909e-04 6.06365740086913e-04 5.60512340111883e-04 - 5.60512340111627e-04 5.60512340111233e-04 4.30201086552066e-04 - 4.30201086551409e-04 2.27271348888427e-04 2.27271348887562e-04 - 2.27271348886624e-04 -1.64425129567850e-05 -1.64425129577838e-05 - -2.57152793952624e-04 -2.57152793953566e-04 -2.57152793954439e-04 - -4.51967686082436e-04 -4.51967686083102e-04 -5.71373901788195e-04 - -5.71373901788600e-04 -5.71373901788867e-04 -6.06367538369246e-04 - -6.06367538369252e-04 -5.67946764132928e-04 -5.67946764132719e-04 - -5.67946764132426e-04 -4.80257088158340e-04 -4.80257088157936e-04 - -3.71133070590659e-04 -3.71133070590214e-04 -3.71133070589771e-04 - -2.64031001781572e-04 -2.64031001781165e-04 -1.73743804988332e-04 - -1.73743804987990e-04 -1.73743804987683e-04 -1.06097165598685e-04 - -1.06097165598452e-04 -6.02625033844479e-05 -6.02625033842822e-05 - -6.02625033841452e-05 -3.18923060880405e-05 -3.18923060879507e-05 - -1.57466379159961e-05 -1.57466379159402e-05 -1.57466379158970e-05 - -9.09757786387114e-17 -6.59975776517344e-17 -4.73632775119337e-17 - -3.36268154490693e-17 -2.36198534286094e-17 -1.64146648272399e-17 - -1.12866460888857e-17 -7.67873162523311e-18 -5.16914145666077e-18 - -3.44320959382525e-18 + 6.06365740085560e-04 6.06365740085564e-04 5.60512340088285e-04 + 5.60512340088029e-04 5.60512340087635e-04 4.30201086506495e-04 + 4.30201086505838e-04 2.27271348826923e-04 2.27271348826058e-04 + 2.27271348825120e-04 -1.64425130236053e-05 -1.64425130246041e-05 + -2.57152794012557e-04 -2.57152794013499e-04 -2.57152794014372e-04 + -4.51967686125329e-04 -4.51967686125995e-04 -5.71373901808749e-04 + -5.71373901809154e-04 -5.71373901809421e-04 -6.06367538367918e-04 + -6.06367538367924e-04 -5.67946764114821e-04 -5.67946764114611e-04 + -5.67946764114319e-04 -4.80257088130826e-04 -4.80257088130422e-04 + -3.71133070560880e-04 -3.71133070560435e-04 -3.71133070559992e-04 + -2.64031001754737e-04 -2.64031001754330e-04 -1.73743804967135e-04 + -1.73743804966793e-04 -1.73743804966486e-04 -1.06097165583657e-04 + -1.06097165583424e-04 -6.02625033747609e-05 -6.02625033745952e-05 + -6.02625033744582e-05 -3.18923060823172e-05 -3.18923060822274e-05 + -1.57466379128806e-05 -1.57466379128247e-05 -1.57466379127815e-05 + -9.09757785774318e-17 -6.59975776057536e-17 -4.73632774778447e-17 + -3.36268154240955e-17 -2.36198534105275e-17 -1.64146648142998e-17 + -1.12866460797317e-17 -7.67873161883127e-18 -5.16914145223437e-18 + -3.44320959079916e-18 } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj index fb142e4f6..509a07520 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688254084712e+00 1.64425129573257e-05 - 21 3.21458253900407e+00 1.64425129573257e-05 - 22 3.21223316137874e+00 1.64425129573257e-05 - 23 3.20995393075312e+00 1.64425129573257e-05 - 24 3.20785328184230e+00 1.64425129573257e-05 - 25 3.20602246252810e+00 1.64425129573257e-05 - 26 3.20453121758655e+00 1.64425129573257e-05 - 27 3.20342558311071e+00 1.64425129573257e-05 - 28 3.20272771913917e+00 1.64425129573257e-05 - 29 3.20243733079947e+00 1.64425129573257e-05 - 30 3.20253425864031e+00 1.64425129575691e-05 - 31 3.20298186179545e+00 1.64425129575691e-05 - 32 3.20373104002396e+00 1.64425129575691e-05 - 33 3.20472472112302e+00 1.64425129575691e-05 - 34 3.20590259872112e+00 1.64425129575691e-05 - 35 3.20720570126905e+00 1.64425129575691e-05 - 36 3.20858034698356e+00 1.64425129575691e-05 - 37 3.20998116394591e+00 1.64425129575691e-05 - 38 3.21137313180225e+00 1.64425129575691e-05 - 39 3.21273279470442e+00 1.64425129575691e-05 - 40 3.21404884013792e+00 1.64425129577838e-05 + 20 3.21688254064136e+00 1.64425130241460e-05 + 21 3.21458253878164e+00 1.64425130241460e-05 + 22 3.21223316113940e+00 1.64425130241460e-05 + 23 3.20995393049671e+00 1.64425130241460e-05 + 24 3.20785328156876e+00 1.64425130241460e-05 + 25 3.20602246223748e+00 1.64425130241460e-05 + 26 3.20453121727901e+00 1.64425130241460e-05 + 27 3.20342558278651e+00 1.64425130241460e-05 + 28 3.20272771879869e+00 1.64425130241460e-05 + 29 3.20243733044315e+00 1.64425130241460e-05 + 30 3.20253425826863e+00 1.64425130243894e-05 + 31 3.20298186140896e+00 1.64425130243894e-05 + 32 3.20373103962324e+00 1.64425130243894e-05 + 33 3.20472472070871e+00 1.64425130243894e-05 + 34 3.20590259829393e+00 1.64425130243894e-05 + 35 3.20720570082978e+00 1.64425130243894e-05 + 36 3.20858034653318e+00 1.64425130243894e-05 + 37 3.20998116348556e+00 1.64425130243894e-05 + 38 3.21137313133328e+00 1.64425130243894e-05 + 39 3.21273279422841e+00 1.64425130243894e-05 + 40 3.21404883965667e+00 1.64425130246041e-05 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf index 225f83d93..9054286e1 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf @@ -1,58 +1,58 @@ # 1 # 1.00000000000000e+00 2.00000000000000e-01 55 0 - 1.10000000000000e+00 7.66721588313994e-04 - 1.30000000000000e+00 7.66721588312782e-04 - 1.50000000000000e+00 4.71522021766042e-04 - 1.70000000000000e+00 4.71522021764879e-04 - 1.90000000000000e+00 4.71522021763781e-04 - 2.10000000000000e+00 2.20404130482366e-04 - 2.30000000000000e+00 2.20404130481479e-04 - 2.50000000000000e+00 5.35404931012447e-05 - 2.70000000000000e+00 5.35404931006646e-05 - 2.90000000000000e+00 5.35404931002652e-05 + 1.10000000000000e+00 7.66721588230714e-04 + 1.30000000000000e+00 7.66721588229502e-04 + 1.50000000000000e+00 4.71522021688902e-04 + 1.70000000000000e+00 4.71522021687739e-04 + 1.90000000000000e+00 4.71522021686641e-04 + 2.10000000000000e+00 2.20404130422646e-04 + 2.30000000000000e+00 2.20404130421759e-04 + 2.50000000000000e+00 5.35404930686546e-05 + 2.70000000000000e+00 5.35404930680746e-05 + 2.90000000000000e+00 5.35404930676752e-05 3.10000000000000e+00 8.23993651088983e-18 3.30000000000000e+00 -0.00000000000000e+00 - 3.50000000000000e+00 6.94771680163505e-05 - 3.70000000000000e+00 6.94771680167345e-05 - 3.90000000000000e+00 6.94771680173000e-05 - 4.10000000000000e+00 2.49425391045431e-04 - 4.30000000000000e+00 2.49425391046307e-04 - 4.50000000000000e+00 5.08757345710194e-04 - 4.70000000000000e+00 5.08757345711285e-04 - 4.90000000000000e+00 5.08757345712444e-04 - 5.10000000000000e+00 8.06614939496052e-04 - 5.30000000000000e+00 8.06614939497264e-04 - 5.50000000000000e+00 1.10281436905983e-03 - 5.70000000000000e+00 1.10281436906100e-03 - 5.90000000000000e+00 1.10281436906212e-03 - 6.10000000000000e+00 1.36633083377534e-03 - 6.30000000000000e+00 1.36633083377632e-03 - 6.50000000000000e+00 1.57952613827070e-03 - 6.70000000000000e+00 1.57952613827150e-03 - 6.90000000000000e+00 1.57952613827222e-03 - 7.10000000000000e+00 1.73785182605734e-03 - 7.30000000000000e+00 1.73785182605789e-03 - 7.50000000000000e+00 1.84641120516848e-03 - 7.70000000000000e+00 1.84641120516888e-03 - 7.90000000000000e+00 1.84641120516921e-03 - 8.10000000000000e+00 1.91540651060891e-03 - 8.30000000000000e+00 1.91540651060914e-03 - 8.50000000000000e+00 1.95616282518798e-03 - 8.70000000000000e+00 1.95616282518812e-03 - 8.90000000000000e+00 1.95616282518823e-03 - 9.10000000000000e+00 1.97858394969836e-03 - 9.30000000000000e+00 1.97858394969843e-03 - 9.50000000000000e+00 1.99008812208002e-03 - 9.70000000000000e+00 1.99008812208006e-03 - 9.90000000000000e+00 1.99008812208008e-03 - 1.01000000000000e+01 1.99972957594797e-03 - 1.03000000000000e+01 1.99972957594798e-03 - 1.05000000000000e+01 1.99972957594799e-03 - 1.07000000000000e+01 1.99972957594800e-03 - 1.09000000000000e+01 1.99972957594801e-03 - 1.11000000000000e+01 1.99972957594801e-03 - 1.13000000000000e+01 1.99972957594801e-03 - 1.15000000000000e+01 1.99972957594801e-03 - 1.17000000000000e+01 1.99972957594802e-03 - 1.19000000000000e+01 1.99972957594802e-03 + 3.50000000000000e+00 6.94771680485205e-05 + 3.70000000000000e+00 6.94771680489045e-05 + 3.90000000000000e+00 6.94771680494700e-05 + 4.10000000000000e+00 2.49425391103651e-04 + 4.30000000000000e+00 2.49425391104527e-04 + 4.50000000000000e+00 5.08757345784374e-04 + 4.70000000000000e+00 5.08757345785465e-04 + 4.90000000000000e+00 5.08757345786624e-04 + 5.10000000000000e+00 8.06614939574912e-04 + 5.30000000000000e+00 8.06614939576124e-04 + 5.50000000000000e+00 1.10281436913355e-03 + 5.70000000000000e+00 1.10281436913472e-03 + 5.90000000000000e+00 1.10281436913583e-03 + 6.10000000000000e+00 1.36633083383733e-03 + 6.30000000000000e+00 1.36633083383831e-03 + 6.50000000000000e+00 1.57952613831810e-03 + 6.70000000000000e+00 1.57952613831891e-03 + 6.90000000000000e+00 1.57952613831962e-03 + 7.10000000000000e+00 1.73785182609043e-03 + 7.30000000000000e+00 1.73785182609097e-03 + 7.50000000000000e+00 1.84641120518950e-03 + 7.70000000000000e+00 1.84641120518989e-03 + 7.90000000000000e+00 1.84641120519022e-03 + 8.10000000000000e+00 1.91540651062089e-03 + 8.30000000000000e+00 1.91540651062111e-03 + 8.50000000000000e+00 1.95616282519382e-03 + 8.70000000000000e+00 1.95616282519397e-03 + 8.90000000000000e+00 1.95616282519408e-03 + 9.10000000000000e+00 1.97858394970042e-03 + 9.30000000000000e+00 1.97858394970048e-03 + 9.50000000000000e+00 1.99008812207991e-03 + 9.70000000000000e+00 1.99008812207995e-03 + 9.90000000000000e+00 1.99008812207998e-03 + 1.01000000000000e+01 1.99972957594576e-03 + 1.03000000000000e+01 1.99972957594577e-03 + 1.05000000000000e+01 1.99972957594578e-03 + 1.07000000000000e+01 1.99972957594579e-03 + 1.09000000000000e+01 1.99972957594580e-03 + 1.11000000000000e+01 1.99972957594580e-03 + 1.13000000000000e+01 1.99972957594580e-03 + 1.15000000000000e+01 1.99972957594580e-03 + 1.17000000000000e+01 1.99972957594581e-03 + 1.19000000000000e+01 1.99972957594581e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt index 49dcaf892..157cac038 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2021-03-09. -colvars: Using NAMD interface, version "2021-03-02". +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out index a5e27860c..caed7f14e 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -134,15 +138,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped index 6de09bffd..ab45cb882 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688278597333e+00 + x 3.21688278576757e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.46920492770083e-08 1.70721010112539e-05 6.58298335288197e-04 - 1.98901157291202e-03 4.70902104436801e-04 8.73580076380761e-06 + 3.46920493464415e-08 1.70721010337625e-05 6.58298335707084e-04 + 1.98901157282260e-03 4.70902104095221e-04 8.73580075153432e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 5.18433073974142e-07 1.68175610579987e-04 3.13214890940428e-03 - -6.66334787942696e-04 -2.55603942784152e-03 -9.19086519769792e-05 + 5.18433074964325e-07 1.68175610778412e-04 3.13214891049980e-03 + -6.66334790621162e-04 -2.55603942662786e-03 -9.19086518597186e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj index 3ac32bb03..56616ce4c 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 3.30884583259955e-04 - 11 3.21950367891521e+00 3.30884583259955e-04 - 12 3.22130501376020e+00 3.30884583259955e-04 - 13 3.22263482513293e+00 3.30884583259955e-04 - 14 3.22341774651982e+00 3.30884583259955e-04 - 15 3.22361481079113e+00 3.30884583259955e-04 - 16 3.22322427751010e+00 3.30884583259955e-04 - 17 3.22227956023865e+00 3.30884583259955e-04 - 18 3.22084496840419e+00 3.30884583259955e-04 - 19 3.21901000786075e+00 3.30884583259955e-04 - 20 3.21688278597333e+00 6.66334787942696e-04 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 3.30884583877525e-04 + 11 3.21950367884164e+00 3.30884583877525e-04 + 12 3.22130501367398e+00 3.30884583877525e-04 + 13 3.22263482503343e+00 3.30884583877525e-04 + 14 3.22341774640647e+00 3.30884583877525e-04 + 15 3.22361481066343e+00 3.30884583877525e-04 + 16 3.22322427736760e+00 3.30884583877525e-04 + 17 3.22227956008091e+00 3.30884583877525e-04 + 18 3.22084496823082e+00 3.30884583877525e-04 + 19 3.21901000767136e+00 3.30884583877525e-04 + 20 3.21688278576757e+00 6.66334790621162e-04 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf index 3a05a7c71..7a24c6664 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.98901157291202e-03 - 7.50000000000000e-01 1.98901157291202e-03 - 1.25000000000000e+00 1.98901157291202e-03 - 1.75000000000000e+00 1.98897688086274e-03 - 2.25000000000000e+00 1.97193947190077e-03 - 2.75000000000000e+00 1.33071323762382e-03 + 2.50000000000000e-01 1.98901157282260e-03 + 7.50000000000000e-01 1.98901157282260e-03 + 1.25000000000000e+00 1.98901157282260e-03 + 1.75000000000000e+00 1.98897688077326e-03 + 2.25000000000000e+00 1.97193947178884e-03 + 2.75000000000000e+00 1.33071323711552e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.51810946847522e-03 - 4.25000000000000e+00 1.98027577214821e-03 - 4.75000000000000e+00 1.98901157291202e-03 - 5.25000000000000e+00 1.98901157291202e-03 - 5.75000000000000e+00 1.98901157291202e-03 - 6.25000000000000e+00 1.98901157291202e-03 - 6.75000000000000e+00 1.98901157291202e-03 - 7.25000000000000e+00 1.98901157291202e-03 - 7.75000000000000e+00 1.98901157291202e-03 - 8.25000000000000e+00 1.98901157291202e-03 - 8.75000000000000e+00 1.98901157291202e-03 - 9.25000000000000e+00 1.98901157291202e-03 - 9.75000000000000e+00 1.98901157291202e-03 + 3.75000000000000e+00 1.51810946872738e-03 + 4.25000000000000e+00 1.98027577207107e-03 + 4.75000000000000e+00 1.98901157282260e-03 + 5.25000000000000e+00 1.98901157282260e-03 + 5.75000000000000e+00 1.98901157282260e-03 + 6.25000000000000e+00 1.98901157282260e-03 + 6.75000000000000e+00 1.98901157282260e-03 + 7.25000000000000e+00 1.98901157282260e-03 + 7.75000000000000e+00 1.98901157282260e-03 + 8.25000000000000e+00 1.98901157282260e-03 + 8.75000000000000e+00 1.98901157282260e-03 + 9.25000000000000e+00 1.98901157282260e-03 + 9.75000000000000e+00 1.98901157282260e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out index adabe2e3d..2bb4389fd 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -134,20 +138,34 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped index 235b1896e..5f97bd617 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405136134992e+00 + x 3.21405136086868e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 7.43923403227782e-08 3.57122155647627e-05 1.34466139685731e-03 - 3.97104317655277e-03 9.19770327415716e-04 1.67080044623168e-05 + 7.43923406409864e-08 3.57122156643391e-05 1.34466139863962e-03 + 3.97104317611064e-03 9.19770326015385e-04 1.67080044137238e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1.10794466055357e-06 3.50062167930554e-04 6.33510417866273e-03 - -1.50805868972440e-03 -5.03195891853835e-03 -1.76471077879577e-04 + 1.10794466506920e-06 3.50062168801214e-04 6.33510418316085e-03 + -1.50805870086533e-03 -5.03195891344979e-03 -1.76471077412228e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj index 6b959f565..e23343a0c 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688278597333e+00 6.66334787942696e-04 - 21 3.21458283262116e+00 6.66334787942696e-04 - 22 3.21223351074552e+00 6.66334787942696e-04 - 23 3.20995434276490e+00 6.66334787942696e-04 - 24 3.20785376300757e+00 6.66334787942696e-04 - 25 3.20602301895356e+00 6.66334787942696e-04 - 26 3.20453185497061e+00 6.66334787942696e-04 - 27 3.20342630674324e+00 6.66334787942696e-04 - 28 3.20272853390700e+00 6.66334787942696e-04 - 29 3.20243824119566e+00 6.66334787942696e-04 - 30 3.20253526877602e+00 1.14429095260314e-03 - 31 3.20298298275490e+00 1.14429095260314e-03 - 32 3.20373228243844e+00 1.14429095260314e-03 - 33 3.20472609508842e+00 1.14429095260314e-03 - 34 3.20590411372385e+00 1.14429095260314e-03 - 35 3.20720736612802e+00 1.14429095260314e-03 - 36 3.20858216980690e+00 1.14429095260314e-03 - 37 3.20998315211066e+00 1.14429095260314e-03 - 38 3.21137529195283e+00 1.14429095260314e-03 - 39 3.21273513276742e+00 1.14429095260314e-03 - 40 3.21405136134992e+00 1.50805868972440e-03 + 20 3.21688278576757e+00 6.66334790621162e-04 + 21 3.21458283239873e+00 6.66334790621162e-04 + 22 3.21223351050617e+00 6.66334790621162e-04 + 23 3.20995434250849e+00 6.66334790621162e-04 + 24 3.20785376273403e+00 6.66334790621162e-04 + 25 3.20602301866294e+00 6.66334790621162e-04 + 26 3.20453185466307e+00 6.66334790621162e-04 + 27 3.20342630641905e+00 6.66334790621162e-04 + 28 3.20272853356652e+00 6.66334790621162e-04 + 29 3.20243824083933e+00 6.66334790621162e-04 + 30 3.20253526840434e+00 1.14429095893840e-03 + 31 3.20298298236841e+00 1.14429095893840e-03 + 32 3.20373228203772e+00 1.14429095893840e-03 + 33 3.20472609467411e+00 1.14429095893840e-03 + 34 3.20590411329665e+00 1.14429095893840e-03 + 35 3.20720736568876e+00 1.14429095893840e-03 + 36 3.20858216935653e+00 1.14429095893840e-03 + 37 3.20998315165031e+00 1.14429095893840e-03 + 38 3.21137529148386e+00 1.14429095893840e-03 + 39 3.21273513229142e+00 1.14429095893840e-03 + 40 3.21405136086868e+00 1.50805870086533e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf index 051812fec..38a897e10 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.97104317655277e-03 - 7.50000000000000e-01 3.97104317655277e-03 - 1.25000000000000e+00 3.97104317655277e-03 - 1.75000000000000e+00 3.97096878421245e-03 - 2.25000000000000e+00 3.93533096098801e-03 - 2.75000000000000e+00 2.62638177969546e-03 + 2.50000000000000e-01 3.97104317611064e-03 + 7.50000000000000e-01 3.97104317611064e-03 + 1.25000000000000e+00 3.97104317611064e-03 + 1.75000000000000e+00 3.97096878377000e-03 + 2.25000000000000e+00 3.93533096044630e-03 + 2.75000000000000e+00 2.62638177747102e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 3.05127284913705e-03 - 4.25000000000000e+00 3.95433517209045e-03 - 4.75000000000000e+00 3.97104317655277e-03 - 5.25000000000000e+00 3.97104317655277e-03 - 5.75000000000000e+00 3.97104317655277e-03 - 6.25000000000000e+00 3.97104317655277e-03 - 6.75000000000000e+00 3.97104317655277e-03 - 7.25000000000000e+00 3.97104317655277e-03 - 7.75000000000000e+00 3.97104317655277e-03 - 8.25000000000000e+00 3.97104317655277e-03 - 8.75000000000000e+00 3.97104317655277e-03 - 9.25000000000000e+00 3.97104317655277e-03 - 9.75000000000000e+00 3.97104317655277e-03 + 3.75000000000000e+00 3.05127285009526e-03 + 4.25000000000000e+00 3.95433517169692e-03 + 4.75000000000000e+00 3.97104317611064e-03 + 5.25000000000000e+00 3.97104317611064e-03 + 5.75000000000000e+00 3.97104317611064e-03 + 6.25000000000000e+00 3.97104317611064e-03 + 6.75000000000000e+00 3.97104317611064e-03 + 7.25000000000000e+00 3.97104317611064e-03 + 7.75000000000000e+00 3.97104317611064e-03 + 8.25000000000000e+00 3.97104317611064e-03 + 8.75000000000000e+00 3.97104317611064e-03 + 9.25000000000000e+00 3.97104317611064e-03 + 9.75000000000000e+00 3.97104317611064e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt index e2b19c981..157cac038 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out index 5fcb5a777..60aee7ad6 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -136,15 +140,30 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped index 2e2ab665b..7dc8c95f8 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688278597333e+00 + x 3.21688278576757e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.46920492770083e-08 1.70721010112539e-05 6.58298335288197e-04 - 1.98901157291202e-03 4.70902104436801e-04 8.73580076380761e-06 + 3.46920493464415e-08 1.70721010337625e-05 6.58298335707084e-04 + 1.98901157282260e-03 4.70902104095221e-04 8.73580075153432e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 5.18433073974142e-07 1.68175610579987e-04 3.13214890940428e-03 - -6.66334787942696e-04 -2.55603942784152e-03 -9.19086519769792e-05 + 5.18433074964325e-07 1.68175610778412e-04 3.13214891049980e-03 + -6.66334790621162e-04 -2.55603942662786e-03 -9.19086518597186e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -56,7 +56,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -1.46245122218042e+00 0.00000000000000e+00 0.00000000000000e+00 + -1.46245128120959e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj index 3ac32bb03..56616ce4c 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 3.30884583259955e-04 - 11 3.21950367891521e+00 3.30884583259955e-04 - 12 3.22130501376020e+00 3.30884583259955e-04 - 13 3.22263482513293e+00 3.30884583259955e-04 - 14 3.22341774651982e+00 3.30884583259955e-04 - 15 3.22361481079113e+00 3.30884583259955e-04 - 16 3.22322427751010e+00 3.30884583259955e-04 - 17 3.22227956023865e+00 3.30884583259955e-04 - 18 3.22084496840419e+00 3.30884583259955e-04 - 19 3.21901000786075e+00 3.30884583259955e-04 - 20 3.21688278597333e+00 6.66334787942696e-04 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 3.30884583877525e-04 + 11 3.21950367884164e+00 3.30884583877525e-04 + 12 3.22130501367398e+00 3.30884583877525e-04 + 13 3.22263482503343e+00 3.30884583877525e-04 + 14 3.22341774640647e+00 3.30884583877525e-04 + 15 3.22361481066343e+00 3.30884583877525e-04 + 16 3.22322427736760e+00 3.30884583877525e-04 + 17 3.22227956008091e+00 3.30884583877525e-04 + 18 3.22084496823082e+00 3.30884583877525e-04 + 19 3.21901000767136e+00 3.30884583877525e-04 + 20 3.21688278576757e+00 6.66334790621162e-04 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf index 3a05a7c71..7a24c6664 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.98901157291202e-03 - 7.50000000000000e-01 1.98901157291202e-03 - 1.25000000000000e+00 1.98901157291202e-03 - 1.75000000000000e+00 1.98897688086274e-03 - 2.25000000000000e+00 1.97193947190077e-03 - 2.75000000000000e+00 1.33071323762382e-03 + 2.50000000000000e-01 1.98901157282260e-03 + 7.50000000000000e-01 1.98901157282260e-03 + 1.25000000000000e+00 1.98901157282260e-03 + 1.75000000000000e+00 1.98897688077326e-03 + 2.25000000000000e+00 1.97193947178884e-03 + 2.75000000000000e+00 1.33071323711552e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.51810946847522e-03 - 4.25000000000000e+00 1.98027577214821e-03 - 4.75000000000000e+00 1.98901157291202e-03 - 5.25000000000000e+00 1.98901157291202e-03 - 5.75000000000000e+00 1.98901157291202e-03 - 6.25000000000000e+00 1.98901157291202e-03 - 6.75000000000000e+00 1.98901157291202e-03 - 7.25000000000000e+00 1.98901157291202e-03 - 7.75000000000000e+00 1.98901157291202e-03 - 8.25000000000000e+00 1.98901157291202e-03 - 8.75000000000000e+00 1.98901157291202e-03 - 9.25000000000000e+00 1.98901157291202e-03 - 9.75000000000000e+00 1.98901157291202e-03 + 3.75000000000000e+00 1.51810946872738e-03 + 4.25000000000000e+00 1.98027577207107e-03 + 4.75000000000000e+00 1.98901157282260e-03 + 5.25000000000000e+00 1.98901157282260e-03 + 5.75000000000000e+00 1.98901157282260e-03 + 6.25000000000000e+00 1.98901157282260e-03 + 6.75000000000000e+00 1.98901157282260e-03 + 7.25000000000000e+00 1.98901157282260e-03 + 7.75000000000000e+00 1.98901157282260e-03 + 8.25000000000000e+00 1.98901157282260e-03 + 8.75000000000000e+00 1.98901157282260e-03 + 9.25000000000000e+00 1.98901157282260e-03 + 9.75000000000000e+00 1.98901157282260e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out index 8704eef89..60a73ce49 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -136,20 +140,37 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped index d3e71c6bd..c9a85fb5b 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405136134992e+00 + x 3.21405136086868e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 7.43923403227782e-08 3.57122155647627e-05 1.34466139685731e-03 - 3.97104317655277e-03 9.19770327415716e-04 1.67080044623168e-05 + 7.43923406409864e-08 3.57122156643391e-05 1.34466139863962e-03 + 3.97104317611064e-03 9.19770326015385e-04 1.67080044137238e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1.10794466055357e-06 3.50062167930554e-04 6.33510417866273e-03 - -1.50805868972440e-03 -5.03195891853835e-03 -1.76471077879577e-04 + 1.10794466506920e-06 3.50062168801214e-04 6.33510418316085e-03 + -1.50805870086533e-03 -5.03195891344979e-03 -1.76471077412228e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -56,7 +56,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 4.71618561911262e+00 0.00000000000000e+00 0.00000000000000e+00 + 4.71618560685502e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj index 6b959f565..e23343a0c 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688278597333e+00 6.66334787942696e-04 - 21 3.21458283262116e+00 6.66334787942696e-04 - 22 3.21223351074552e+00 6.66334787942696e-04 - 23 3.20995434276490e+00 6.66334787942696e-04 - 24 3.20785376300757e+00 6.66334787942696e-04 - 25 3.20602301895356e+00 6.66334787942696e-04 - 26 3.20453185497061e+00 6.66334787942696e-04 - 27 3.20342630674324e+00 6.66334787942696e-04 - 28 3.20272853390700e+00 6.66334787942696e-04 - 29 3.20243824119566e+00 6.66334787942696e-04 - 30 3.20253526877602e+00 1.14429095260314e-03 - 31 3.20298298275490e+00 1.14429095260314e-03 - 32 3.20373228243844e+00 1.14429095260314e-03 - 33 3.20472609508842e+00 1.14429095260314e-03 - 34 3.20590411372385e+00 1.14429095260314e-03 - 35 3.20720736612802e+00 1.14429095260314e-03 - 36 3.20858216980690e+00 1.14429095260314e-03 - 37 3.20998315211066e+00 1.14429095260314e-03 - 38 3.21137529195283e+00 1.14429095260314e-03 - 39 3.21273513276742e+00 1.14429095260314e-03 - 40 3.21405136134992e+00 1.50805868972440e-03 + 20 3.21688278576757e+00 6.66334790621162e-04 + 21 3.21458283239873e+00 6.66334790621162e-04 + 22 3.21223351050617e+00 6.66334790621162e-04 + 23 3.20995434250849e+00 6.66334790621162e-04 + 24 3.20785376273403e+00 6.66334790621162e-04 + 25 3.20602301866294e+00 6.66334790621162e-04 + 26 3.20453185466307e+00 6.66334790621162e-04 + 27 3.20342630641905e+00 6.66334790621162e-04 + 28 3.20272853356652e+00 6.66334790621162e-04 + 29 3.20243824083933e+00 6.66334790621162e-04 + 30 3.20253526840434e+00 1.14429095893840e-03 + 31 3.20298298236841e+00 1.14429095893840e-03 + 32 3.20373228203772e+00 1.14429095893840e-03 + 33 3.20472609467411e+00 1.14429095893840e-03 + 34 3.20590411329665e+00 1.14429095893840e-03 + 35 3.20720736568876e+00 1.14429095893840e-03 + 36 3.20858216935653e+00 1.14429095893840e-03 + 37 3.20998315165031e+00 1.14429095893840e-03 + 38 3.21137529148386e+00 1.14429095893840e-03 + 39 3.21273513229142e+00 1.14429095893840e-03 + 40 3.21405136086868e+00 1.50805870086533e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf index 051812fec..38a897e10 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.97104317655277e-03 - 7.50000000000000e-01 3.97104317655277e-03 - 1.25000000000000e+00 3.97104317655277e-03 - 1.75000000000000e+00 3.97096878421245e-03 - 2.25000000000000e+00 3.93533096098801e-03 - 2.75000000000000e+00 2.62638177969546e-03 + 2.50000000000000e-01 3.97104317611064e-03 + 7.50000000000000e-01 3.97104317611064e-03 + 1.25000000000000e+00 3.97104317611064e-03 + 1.75000000000000e+00 3.97096878377000e-03 + 2.25000000000000e+00 3.93533096044630e-03 + 2.75000000000000e+00 2.62638177747102e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 3.05127284913705e-03 - 4.25000000000000e+00 3.95433517209045e-03 - 4.75000000000000e+00 3.97104317655277e-03 - 5.25000000000000e+00 3.97104317655277e-03 - 5.75000000000000e+00 3.97104317655277e-03 - 6.25000000000000e+00 3.97104317655277e-03 - 6.75000000000000e+00 3.97104317655277e-03 - 7.25000000000000e+00 3.97104317655277e-03 - 7.75000000000000e+00 3.97104317655277e-03 - 8.25000000000000e+00 3.97104317655277e-03 - 8.75000000000000e+00 3.97104317655277e-03 - 9.25000000000000e+00 3.97104317655277e-03 - 9.75000000000000e+00 3.97104317655277e-03 + 3.75000000000000e+00 3.05127285009526e-03 + 4.25000000000000e+00 3.95433517169692e-03 + 4.75000000000000e+00 3.97104317611064e-03 + 5.25000000000000e+00 3.97104317611064e-03 + 5.75000000000000e+00 3.97104317611064e-03 + 6.25000000000000e+00 3.97104317611064e-03 + 6.75000000000000e+00 3.97104317611064e-03 + 7.25000000000000e+00 3.97104317611064e-03 + 7.75000000000000e+00 3.97104317611064e-03 + 8.25000000000000e+00 3.97104317611064e-03 + 8.75000000000000e+00 3.97104317611064e-03 + 9.25000000000000e+00 3.97104317611064e-03 + 9.75000000000000e+00 3.97104317611064e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt index e2b19c981..157cac038 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj index a66046fd3..fa1b525d4 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj @@ -1,4 +1,4 @@ 5 3.20606308065050e+00 5.00000000000000e-01 1.00000000000000e-01 10 3.21734242206787e+00 5.00000000000000e-01 8.46119581367384e-02 - 15 3.22363050330139e+00 5.00000000000000e-01 7.34385578106080e-02 + 15 3.22363050330140e+00 5.00000000000000e-01 7.34385578106080e-02 20 3.21691895295305e+00 5.00000000000000e-01 6.49380514240066e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out index 8e00aed34..689bb1bf4 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -139,16 +143,26 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped index 2b4ef2420..87801e244 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped @@ -21,10 +21,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.42973919084570e-04 - 4.41360461286586e-03 5.01317117210114e-02 2.09514390772554e-01 - 3.22178897971626e-01 1.82289606890752e-01 3.79496667604971e-02 - 2.90693223696984e-03 8.19298874561855e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.42973919084568e-04 + 4.41360461286583e-03 5.01317117210112e-02 2.09514390772553e-01 + 3.22178897971626e-01 1.82289606890753e-01 3.79496667604973e-02 + 2.90693223696987e-03 8.19298874561864e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -36,10 +36,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.12368805589938e-03 - 2.58626065712129e-02 1.93513466997636e-01 3.89791769357681e-01 - -4.48458537631430e-02 -3.89889393515630e-01 -1.57054622900226e-01 - -1.78431915109615e-02 -6.66729644383001e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.12368805589937e-03 + 2.58626065712127e-02 1.93513466997635e-01 3.89791769357681e-01 + -4.48458537631413e-02 -3.89889393515630e-01 -1.57054622900226e-01 + -1.78431915109616e-02 -6.66729644383008e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj index b0936f14b..89043bf99 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj @@ -4,19 +4,19 @@ 2 3.20384028588952e+00 0.00000000000000e+00 3 3.20396721186862e+00 0.00000000000000e+00 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 1.75070440392768e-02 - 6 3.20788015841690e+00 1.75070440392768e-02 - 7 3.21006078117990e+00 1.75070440392768e-02 - 8 3.21246619986317e+00 1.75070440392768e-02 - 9 3.21494510727501e+00 1.75070440392768e-02 - 10 3.21734242206787e+00 2.85363794417943e-02 - 11 3.21950925117359e+00 2.85363794417943e-02 - 12 3.22131261706854e+00 2.85363794417943e-02 - 13 3.22264480741010e+00 2.85363794417943e-02 - 14 3.22343043310305e+00 2.85363794417943e-02 - 15 3.22363050330139e+00 3.62717655819535e-02 - 16 3.22324337253598e+00 3.62717655819535e-02 - 17 3.22230242928906e+00 3.62717655819535e-02 - 18 3.22087195749114e+00 3.62717655819535e-02 - 19 3.21904143773479e+00 3.62717655819535e-02 - 20 3.21691895295305e+00 4.48458537631430e-02 + 5 3.20606308065050e+00 1.75070440392767e-02 + 6 3.20788015841690e+00 1.75070440392767e-02 + 7 3.21006078117990e+00 1.75070440392767e-02 + 8 3.21246619986317e+00 1.75070440392767e-02 + 9 3.21494510727501e+00 1.75070440392767e-02 + 10 3.21734242206787e+00 2.85363794417937e-02 + 11 3.21950925117359e+00 2.85363794417937e-02 + 12 3.22131261706854e+00 2.85363794417937e-02 + 13 3.22264480741010e+00 2.85363794417937e-02 + 14 3.22343043310305e+00 2.85363794417937e-02 + 15 3.22363050330140e+00 3.62717655819525e-02 + 16 3.22324337253598e+00 3.62717655819525e-02 + 17 3.22230242928906e+00 3.62717655819525e-02 + 18 3.22087195749114e+00 3.62717655819525e-02 + 19 3.21904143773479e+00 3.62717655819525e-02 + 20 3.21691895295305e+00 4.48458537631413e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf index 1433280e7..a4a179906 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.22178897974989e-01 - 7.50000000000000e-01 3.22178897974989e-01 - 1.25000000000000e+00 3.22035924056005e-01 - 1.75000000000000e+00 3.17765293364453e-01 - 2.25000000000000e+00 2.72047186271566e-01 - 2.75000000000000e+00 1.12664507238354e-01 + 2.50000000000000e-01 3.22178897971626e-01 + 7.50000000000000e-01 3.22178897971626e-01 + 1.25000000000000e+00 3.22035924052542e-01 + 1.75000000000000e+00 3.17765293358761e-01 + 2.25000000000000e+00 2.72047186250615e-01 + 2.75000000000000e+00 1.12664507199074e-01 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.39889291048735e-01 - 4.25000000000000e+00 2.84229231200015e-01 - 4.75000000000000e+00 3.19271965736361e-01 - 5.25000000000000e+00 3.22096968087471e-01 - 5.75000000000000e+00 3.22178897974989e-01 - 6.25000000000000e+00 3.22178897974989e-01 - 6.75000000000000e+00 3.22178897974989e-01 - 7.25000000000000e+00 3.22178897974989e-01 - 7.75000000000000e+00 3.22178897974989e-01 - 8.25000000000000e+00 3.22178897974989e-01 - 8.75000000000000e+00 3.22178897974989e-01 - 9.25000000000000e+00 3.22178897974989e-01 - 9.75000000000000e+00 3.22178897974989e-01 + 3.75000000000000e+00 1.39889291080873e-01 + 4.25000000000000e+00 2.84229231211129e-01 + 4.75000000000000e+00 3.19271965734657e-01 + 5.25000000000000e+00 3.22096968084170e-01 + 5.75000000000000e+00 3.22178897971626e-01 + 6.25000000000000e+00 3.22178897971626e-01 + 6.75000000000000e+00 3.22178897971626e-01 + 7.25000000000000e+00 3.22178897971626e-01 + 7.75000000000000e+00 3.22178897971626e-01 + 8.25000000000000e+00 3.22178897971626e-01 + 8.75000000000000e+00 3.22178897971626e-01 + 9.25000000000000e+00 3.22178897971626e-01 + 9.75000000000000e+00 3.22178897971626e-01 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out index 817eae3a8..857505a84 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -139,21 +143,33 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21692 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped index 86220cc57..37445afe6 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped @@ -21,10 +21,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 2.39032008958375e-04 - 7.33347556564719e-03 8.27850280039980e-02 3.43860479556677e-01 - 5.25534912996650e-01 2.95535757364178e-01 6.11516158055115e-02 - 4.65581319200500e-03 1.30428682628952e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 2.39032008958370e-04 + 7.33347556564710e-03 8.27850280039973e-02 3.43860479556675e-01 + 5.25534912996650e-01 2.95535757364180e-01 6.11516158055121e-02 + 4.65581319200507e-03 1.30428682628954e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -36,10 +36,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.87569014992074e-03 - 4.28817998866076e-02 3.18539085938464e-01 6.35512332470772e-01 - -7.95903631638470e-02 -6.35715309684715e-01 -2.53820387793995e-01 - -2.86345787796509e-02 -1.06298017276160e-03 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.87569014992071e-03 + 4.28817998866071e-02 3.18539085938462e-01 6.35512332470773e-01 + -7.95903631638424e-02 -6.35715309684715e-01 -2.53820387793996e-01 + -2.86345787796512e-02 -1.06298017276162e-03 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj index dba722227..f184c4075 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21691895295305e+00 4.48458537631430e-02 - 21 3.21462413660771e+00 4.48458537631430e-02 - 22 3.21228032841214e+00 4.48458537631430e-02 - 23 3.21000702769477e+00 4.48458537631430e-02 - 24 3.20791264597674e+00 4.48458537631430e-02 - 25 3.20608840817769e+00 5.50378747704786e-02 - 26 3.20460419289258e+00 5.50378747704786e-02 - 27 3.20350601131064e+00 5.50378747704786e-02 - 28 3.20281599649047e+00 5.50378747704786e-02 - 29 3.20253382453620e+00 5.50378747704786e-02 - 30 3.20263930510781e+00 6.50046475230917e-02 - 31 3.20309591808115e+00 6.50046475230917e-02 - 32 3.20385452785452e+00 6.50046475230917e-02 - 33 3.20485802441983e+00 6.50046475230917e-02 - 34 3.20604606196811e+00 6.50046475230917e-02 - 35 3.20735962915093e+00 7.32270721427131e-02 - 36 3.20874513121416e+00 7.32270721427131e-02 - 37 3.21015715709204e+00 7.32270721427131e-02 - 38 3.21156064829882e+00 7.32270721427131e-02 - 39 3.21293211249027e+00 7.32270721427131e-02 - 40 3.21426020264931e+00 7.95903631638470e-02 + 20 3.21691895295305e+00 4.48458537631413e-02 + 21 3.21462413660772e+00 4.48458537631413e-02 + 22 3.21228032841215e+00 4.48458537631413e-02 + 23 3.21000702769477e+00 4.48458537631413e-02 + 24 3.20791264597674e+00 4.48458537631413e-02 + 25 3.20608840817769e+00 5.50378747704764e-02 + 26 3.20460419289259e+00 5.50378747704764e-02 + 27 3.20350601131064e+00 5.50378747704764e-02 + 28 3.20281599649048e+00 5.50378747704764e-02 + 29 3.20253382453620e+00 5.50378747704764e-02 + 30 3.20263930510781e+00 6.50046475230887e-02 + 31 3.20309591808115e+00 6.50046475230887e-02 + 32 3.20385452785452e+00 6.50046475230887e-02 + 33 3.20485802441983e+00 6.50046475230887e-02 + 34 3.20604606196811e+00 6.50046475230887e-02 + 35 3.20735962915093e+00 7.32270721427094e-02 + 36 3.20874513121416e+00 7.32270721427094e-02 + 37 3.21015715709204e+00 7.32270721427094e-02 + 38 3.21156064829882e+00 7.32270721427094e-02 + 39 3.21293211249028e+00 7.32270721427094e-02 + 40 3.21426020264931e+00 7.95903631638424e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf index f2f4c584a..29265ec37 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 5.25534913010848e-01 - 7.50000000000000e-01 5.25534913010848e-01 - 1.25000000000000e+00 5.25295881002282e-01 - 1.75000000000000e+00 5.18201437454156e-01 - 2.25000000000000e+00 4.42749885073309e-01 - 2.75000000000000e+00 1.81674433587149e-01 + 2.50000000000000e-01 5.25534912996650e-01 + 7.50000000000000e-01 5.25534912996650e-01 + 1.25000000000000e+00 5.25295880987692e-01 + 1.75000000000000e+00 5.18201437431003e-01 + 2.25000000000000e+00 4.42749884992653e-01 + 2.75000000000000e+00 1.81674433439975e-01 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 2.29999155517106e-01 - 4.25000000000000e+00 4.64383297153516e-01 - 4.75000000000000e+00 5.20879099813004e-01 - 5.25000000000000e+00 5.25404484328003e-01 - 5.75000000000000e+00 5.25534913010848e-01 - 6.25000000000000e+00 5.25534913010848e-01 - 6.75000000000000e+00 5.25534913010848e-01 - 7.25000000000000e+00 5.25534913010848e-01 - 7.75000000000000e+00 5.25534913010848e-01 - 8.25000000000000e+00 5.25534913010848e-01 - 8.75000000000000e+00 5.25534913010848e-01 - 9.25000000000000e+00 5.25534913010848e-01 - 9.75000000000000e+00 5.25534913010848e-01 + 3.75000000000000e+00 2.29999155632470e-01 + 4.25000000000000e+00 4.64383297191138e-01 + 4.75000000000000e+00 5.20879099804645e-01 + 5.25000000000000e+00 5.25404484314022e-01 + 5.75000000000000e+00 5.25534912996650e-01 + 6.25000000000000e+00 5.25534912996650e-01 + 6.75000000000000e+00 5.25534912996650e-01 + 7.25000000000000e+00 5.25534912996650e-01 + 7.75000000000000e+00 5.25534912996650e-01 + 8.25000000000000e+00 5.25534912996650e-01 + 8.75000000000000e+00 5.25534912996650e-01 + 9.25000000000000e+00 5.25534912996650e-01 + 9.75000000000000e+00 5.25534912996650e-01 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt index 617210efd..157cac038 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-07-07". -colvars: Using NAMD interface, version "2020-05-04". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out index 0343b9172..bc1e4dfcd 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -136,15 +140,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped index 6de09bffd..ab45cb882 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688278597333e+00 + x 3.21688278576757e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.46920492770083e-08 1.70721010112539e-05 6.58298335288197e-04 - 1.98901157291202e-03 4.70902104436801e-04 8.73580076380761e-06 + 3.46920493464415e-08 1.70721010337625e-05 6.58298335707084e-04 + 1.98901157282260e-03 4.70902104095221e-04 8.73580075153432e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 5.18433073974142e-07 1.68175610579987e-04 3.13214890940428e-03 - -6.66334787942696e-04 -2.55603942784152e-03 -9.19086519769792e-05 + 5.18433074964325e-07 1.68175610778412e-04 3.13214891049980e-03 + -6.66334790621162e-04 -2.55603942662786e-03 -9.19086518597186e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj index 3ac32bb03..56616ce4c 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 3.30884583259955e-04 - 11 3.21950367891521e+00 3.30884583259955e-04 - 12 3.22130501376020e+00 3.30884583259955e-04 - 13 3.22263482513293e+00 3.30884583259955e-04 - 14 3.22341774651982e+00 3.30884583259955e-04 - 15 3.22361481079113e+00 3.30884583259955e-04 - 16 3.22322427751010e+00 3.30884583259955e-04 - 17 3.22227956023865e+00 3.30884583259955e-04 - 18 3.22084496840419e+00 3.30884583259955e-04 - 19 3.21901000786075e+00 3.30884583259955e-04 - 20 3.21688278597333e+00 6.66334787942696e-04 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 3.30884583877525e-04 + 11 3.21950367884164e+00 3.30884583877525e-04 + 12 3.22130501367398e+00 3.30884583877525e-04 + 13 3.22263482503343e+00 3.30884583877525e-04 + 14 3.22341774640647e+00 3.30884583877525e-04 + 15 3.22361481066343e+00 3.30884583877525e-04 + 16 3.22322427736760e+00 3.30884583877525e-04 + 17 3.22227956008091e+00 3.30884583877525e-04 + 18 3.22084496823082e+00 3.30884583877525e-04 + 19 3.21901000767136e+00 3.30884583877525e-04 + 20 3.21688278576757e+00 6.66334790621162e-04 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf index 3a05a7c71..7a24c6664 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.98901157291202e-03 - 7.50000000000000e-01 1.98901157291202e-03 - 1.25000000000000e+00 1.98901157291202e-03 - 1.75000000000000e+00 1.98897688086274e-03 - 2.25000000000000e+00 1.97193947190077e-03 - 2.75000000000000e+00 1.33071323762382e-03 + 2.50000000000000e-01 1.98901157282260e-03 + 7.50000000000000e-01 1.98901157282260e-03 + 1.25000000000000e+00 1.98901157282260e-03 + 1.75000000000000e+00 1.98897688077326e-03 + 2.25000000000000e+00 1.97193947178884e-03 + 2.75000000000000e+00 1.33071323711552e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.51810946847522e-03 - 4.25000000000000e+00 1.98027577214821e-03 - 4.75000000000000e+00 1.98901157291202e-03 - 5.25000000000000e+00 1.98901157291202e-03 - 5.75000000000000e+00 1.98901157291202e-03 - 6.25000000000000e+00 1.98901157291202e-03 - 6.75000000000000e+00 1.98901157291202e-03 - 7.25000000000000e+00 1.98901157291202e-03 - 7.75000000000000e+00 1.98901157291202e-03 - 8.25000000000000e+00 1.98901157291202e-03 - 8.75000000000000e+00 1.98901157291202e-03 - 9.25000000000000e+00 1.98901157291202e-03 - 9.75000000000000e+00 1.98901157291202e-03 + 3.75000000000000e+00 1.51810946872738e-03 + 4.25000000000000e+00 1.98027577207107e-03 + 4.75000000000000e+00 1.98901157282260e-03 + 5.25000000000000e+00 1.98901157282260e-03 + 5.75000000000000e+00 1.98901157282260e-03 + 6.25000000000000e+00 1.98901157282260e-03 + 6.75000000000000e+00 1.98901157282260e-03 + 7.25000000000000e+00 1.98901157282260e-03 + 7.75000000000000e+00 1.98901157282260e-03 + 8.25000000000000e+00 1.98901157282260e-03 + 8.75000000000000e+00 1.98901157282260e-03 + 9.25000000000000e+00 1.98901157282260e-03 + 9.75000000000000e+00 1.98901157282260e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out index 1c3db0232..625d7c300 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -136,20 +140,34 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped index 235b1896e..5f97bd617 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405136134992e+00 + x 3.21405136086868e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 7.43923403227782e-08 3.57122155647627e-05 1.34466139685731e-03 - 3.97104317655277e-03 9.19770327415716e-04 1.67080044623168e-05 + 7.43923406409864e-08 3.57122156643391e-05 1.34466139863962e-03 + 3.97104317611064e-03 9.19770326015385e-04 1.67080044137238e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1.10794466055357e-06 3.50062167930554e-04 6.33510417866273e-03 - -1.50805868972440e-03 -5.03195891853835e-03 -1.76471077879577e-04 + 1.10794466506920e-06 3.50062168801214e-04 6.33510418316085e-03 + -1.50805870086533e-03 -5.03195891344979e-03 -1.76471077412228e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj index 6b959f565..e23343a0c 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688278597333e+00 6.66334787942696e-04 - 21 3.21458283262116e+00 6.66334787942696e-04 - 22 3.21223351074552e+00 6.66334787942696e-04 - 23 3.20995434276490e+00 6.66334787942696e-04 - 24 3.20785376300757e+00 6.66334787942696e-04 - 25 3.20602301895356e+00 6.66334787942696e-04 - 26 3.20453185497061e+00 6.66334787942696e-04 - 27 3.20342630674324e+00 6.66334787942696e-04 - 28 3.20272853390700e+00 6.66334787942696e-04 - 29 3.20243824119566e+00 6.66334787942696e-04 - 30 3.20253526877602e+00 1.14429095260314e-03 - 31 3.20298298275490e+00 1.14429095260314e-03 - 32 3.20373228243844e+00 1.14429095260314e-03 - 33 3.20472609508842e+00 1.14429095260314e-03 - 34 3.20590411372385e+00 1.14429095260314e-03 - 35 3.20720736612802e+00 1.14429095260314e-03 - 36 3.20858216980690e+00 1.14429095260314e-03 - 37 3.20998315211066e+00 1.14429095260314e-03 - 38 3.21137529195283e+00 1.14429095260314e-03 - 39 3.21273513276742e+00 1.14429095260314e-03 - 40 3.21405136134992e+00 1.50805868972440e-03 + 20 3.21688278576757e+00 6.66334790621162e-04 + 21 3.21458283239873e+00 6.66334790621162e-04 + 22 3.21223351050617e+00 6.66334790621162e-04 + 23 3.20995434250849e+00 6.66334790621162e-04 + 24 3.20785376273403e+00 6.66334790621162e-04 + 25 3.20602301866294e+00 6.66334790621162e-04 + 26 3.20453185466307e+00 6.66334790621162e-04 + 27 3.20342630641905e+00 6.66334790621162e-04 + 28 3.20272853356652e+00 6.66334790621162e-04 + 29 3.20243824083933e+00 6.66334790621162e-04 + 30 3.20253526840434e+00 1.14429095893840e-03 + 31 3.20298298236841e+00 1.14429095893840e-03 + 32 3.20373228203772e+00 1.14429095893840e-03 + 33 3.20472609467411e+00 1.14429095893840e-03 + 34 3.20590411329665e+00 1.14429095893840e-03 + 35 3.20720736568876e+00 1.14429095893840e-03 + 36 3.20858216935653e+00 1.14429095893840e-03 + 37 3.20998315165031e+00 1.14429095893840e-03 + 38 3.21137529148386e+00 1.14429095893840e-03 + 39 3.21273513229142e+00 1.14429095893840e-03 + 40 3.21405136086868e+00 1.50805870086533e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf index 051812fec..38a897e10 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.97104317655277e-03 - 7.50000000000000e-01 3.97104317655277e-03 - 1.25000000000000e+00 3.97104317655277e-03 - 1.75000000000000e+00 3.97096878421245e-03 - 2.25000000000000e+00 3.93533096098801e-03 - 2.75000000000000e+00 2.62638177969546e-03 + 2.50000000000000e-01 3.97104317611064e-03 + 7.50000000000000e-01 3.97104317611064e-03 + 1.25000000000000e+00 3.97104317611064e-03 + 1.75000000000000e+00 3.97096878377000e-03 + 2.25000000000000e+00 3.93533096044630e-03 + 2.75000000000000e+00 2.62638177747102e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 3.05127284913705e-03 - 4.25000000000000e+00 3.95433517209045e-03 - 4.75000000000000e+00 3.97104317655277e-03 - 5.25000000000000e+00 3.97104317655277e-03 - 5.75000000000000e+00 3.97104317655277e-03 - 6.25000000000000e+00 3.97104317655277e-03 - 6.75000000000000e+00 3.97104317655277e-03 - 7.25000000000000e+00 3.97104317655277e-03 - 7.75000000000000e+00 3.97104317655277e-03 - 8.25000000000000e+00 3.97104317655277e-03 - 8.75000000000000e+00 3.97104317655277e-03 - 9.25000000000000e+00 3.97104317655277e-03 - 9.75000000000000e+00 3.97104317655277e-03 + 3.75000000000000e+00 3.05127285009526e-03 + 4.25000000000000e+00 3.95433517169692e-03 + 4.75000000000000e+00 3.97104317611064e-03 + 5.25000000000000e+00 3.97104317611064e-03 + 5.75000000000000e+00 3.97104317611064e-03 + 6.25000000000000e+00 3.97104317611064e-03 + 6.75000000000000e+00 3.97104317611064e-03 + 7.25000000000000e+00 3.97104317611064e-03 + 7.75000000000000e+00 3.97104317611064e-03 + 8.25000000000000e+00 3.97104317611064e-03 + 8.75000000000000e+00 3.97104317611064e-03 + 9.25000000000000e+00 3.97104317611064e-03 + 9.75000000000000e+00 3.97104317611064e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt index e2b19c981..157cac038 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out index 2fccbc3b5..dbedf374d 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -111,15 +115,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped index c1e336541..5268daf85 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21688253464583e+00 + x 3.21688253444007e+00 } diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj index 787f78aa5..9f55268e7 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 0.00000000000000e+00 - 11 3.21950367383415e+00 0.00000000000000e+00 - 12 3.22130499858006e+00 0.00000000000000e+00 - 13 3.22263479496347e+00 0.00000000000000e+00 - 14 3.22341769665784e+00 0.00000000000000e+00 - 15 3.22361473677138e+00 0.00000000000000e+00 - 16 3.22322417514557e+00 0.00000000000000e+00 - 17 3.22227942564879e+00 0.00000000000000e+00 - 18 3.22084479803044e+00 0.00000000000000e+00 - 19 3.21900979846930e+00 0.00000000000000e+00 - 20 3.21688253464583e+00 0.00000000000000e+00 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 0.00000000000000e+00 + 11 3.21950367376059e+00 0.00000000000000e+00 + 12 3.22130499849384e+00 0.00000000000000e+00 + 13 3.22263479486396e+00 0.00000000000000e+00 + 14 3.22341769654449e+00 0.00000000000000e+00 + 15 3.22361473664369e+00 0.00000000000000e+00 + 16 3.22322417500307e+00 0.00000000000000e+00 + 17 3.22227942549106e+00 0.00000000000000e+00 + 18 3.22084479785707e+00 0.00000000000000e+00 + 19 3.21900979827991e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj b/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj index 1a1e986ed..31a359570 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj @@ -1,8 +1,8 @@ # step running average running stddev - 8 3.20722823883620e+00 7.80321483722600e-03 - 10 4.01156286692710e+00 4.58710790751680e-01 - 12 4.01592904509911e+00 4.58975774793035e-01 - 14 4.02060142604598e+00 4.60400083982649e-01 - 16 4.02443749732474e+00 4.62636256566416e-01 - 18 4.02653254519438e+00 4.65172918743354e-01 - 20 4.02641855076493e+00 4.67427978002713e-01 + 8 3.20722823881721e+00 7.80321480520572e-03 + 10 4.01156286689271e+00 4.58710790766007e-01 + 12 4.01592904504379e+00 4.58975774808969e-01 + 14 4.02060142596487e+00 4.60400083999393e-01 + 16 4.02443749721375e+00 4.62636256583393e-01 + 18 4.02653254505012e+00 4.65172918760069e-01 + 20 4.02641855058464e+00 4.67427978018598e-01 diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out index 98b6025c4..33058590a 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -111,19 +115,30 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped index 139366ade..b307ede0d 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21404878547144e+00 + x 3.21404878499019e+00 } diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj index 3b596ebde..177b1bbb8 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253464583e+00 0.00000000000000e+00 - 21 3.21458253157603e+00 0.00000000000000e+00 - 22 3.21223315254029e+00 0.00000000000000e+00 - 23 3.20995392032979e+00 0.00000000000000e+00 - 24 3.20785326966943e+00 0.00000000000000e+00 - 25 3.20602244845117e+00 0.00000000000000e+00 - 26 3.20453120146139e+00 0.00000000000000e+00 - 27 3.20342556480347e+00 0.00000000000000e+00 - 28 3.20272769852622e+00 0.00000000000000e+00 - 29 3.20243730776714e+00 0.00000000000000e+00 - 30 3.20253423308456e+00 0.00000000000000e+00 - 31 3.20298183362156e+00 0.00000000000000e+00 - 32 3.20373100914607e+00 0.00000000000000e+00 - 33 3.20472468746373e+00 0.00000000000000e+00 - 34 3.20590256221113e+00 0.00000000000000e+00 - 35 3.20720566184671e+00 0.00000000000000e+00 - 36 3.20858030459458e+00 0.00000000000000e+00 - 37 3.20998111854285e+00 0.00000000000000e+00 - 38 3.21137308334419e+00 0.00000000000000e+00 - 39 3.21273274315657e+00 0.00000000000000e+00 - 40 3.21404878547144e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 + 21 3.21458253135360e+00 0.00000000000000e+00 + 22 3.21223315230095e+00 0.00000000000000e+00 + 23 3.20995392007338e+00 0.00000000000000e+00 + 24 3.20785326939589e+00 0.00000000000000e+00 + 25 3.20602244816055e+00 0.00000000000000e+00 + 26 3.20453120115385e+00 0.00000000000000e+00 + 27 3.20342556447929e+00 0.00000000000000e+00 + 28 3.20272769818575e+00 0.00000000000000e+00 + 29 3.20243730741081e+00 0.00000000000000e+00 + 30 3.20253423271288e+00 0.00000000000000e+00 + 31 3.20298183323508e+00 0.00000000000000e+00 + 32 3.20373100874536e+00 0.00000000000000e+00 + 33 3.20472468704943e+00 0.00000000000000e+00 + 34 3.20590256178394e+00 0.00000000000000e+00 + 35 3.20720566140745e+00 0.00000000000000e+00 + 36 3.20858030414420e+00 0.00000000000000e+00 + 37 3.20998111808250e+00 0.00000000000000e+00 + 38 3.21137308287521e+00 0.00000000000000e+00 + 39 3.21273274268056e+00 0.00000000000000e+00 + 40 3.21404878499019e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-runave/namd-version.txt b/namd/tests/library/000_distance-runave/namd-version.txt index b7bf5455c..157cac038 100644 --- a/namd/tests/library/000_distance-runave/namd-version.txt +++ b/namd/tests/library/000_distance-runave/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-10-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out index f9858b5a8..5b1c03881 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out @@ -4,10 +4,9 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -91,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -127,6 +127,7 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -143,11 +144,12 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: colvars: colvars: - Colvars module: colvars: - Colvars-NAMD interface: -colvars: - Linear and polynomial combination of colvar components: +colvars: - Optimal rotation via flexible fitting: colvars: - distance colvar component: colvars: - harmonicWalls colvar bias implementation: colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 @@ -155,22 +157,13 @@ colvars: colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Linear and polynomial combination of colvar components: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped index 747b45745..83b0d62b7 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21549617606775e+00 - v 1.63765400741131e-04 - extended_x 3.20653014355194e+00 - extended_v 1.63765400741131e-04 + x 3.21549617587205e+00 + v 1.63765399419808e-04 + extended_x 3.20653014354441e+00 + extended_v 1.63765399419808e-04 } restraint { diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj index e78c74303..ea3cb4584 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 -1.20221869387334e-02 - 1 3.20437148316546e+00 3.20554661526430e+00 -1.17525151787978e-03 -1.19419048416828e-07 -1.20221864610572e-02 - 2 3.20384207658450e+00 3.20554521661731e+00 -5.29406580961123e-04 -1.39864698553752e-06 -1.20221808664692e-02 - 3 3.20397336372901e+00 3.20554201761950e+00 1.31287144503833e-04 -3.19899780998369e-06 -1.20221680704780e-02 - 4 3.20474099373313e+00 3.20553715100349e+00 7.67630004118391e-04 -4.86661600511761e-06 -1.20221486040140e-02 - 5 3.20608361727106e+00 3.20553137919309e+00 1.34262353793657e-03 -5.77181040270690e-06 -1.20221255167724e-02 - 6 3.20790704368963e+00 3.20552603300139e+00 1.82342641856614e-03 -5.34619170452791e-06 -1.20221041320056e-02 - 7 3.21008979711353e+00 3.20552291735481e+00 2.18275342390539e-03 -3.11564657363747e-06 -1.20220916694193e-02 - 8 3.21248979695188e+00 3.20552418961980e+00 2.39999983834460e-03 1.27226498086710e-06 -1.20220967584792e-02 - 9 3.21495218471243e+00 3.20553221724550e+00 2.46238776055163e-03 8.02762570632936e-06 -1.20221288689820e-02 - 10 3.21731838890489e+00 3.20554942258797e+00 2.36620419245748e-03 1.72053424717036e-05 -1.20221976903519e-02 - 11 3.21943620059508e+00 3.20557812401547e+00 2.11781169019343e-03 2.87014274922572e-05 -1.20223124960619e-02 - 12 3.22117010496679e+00 3.20562038339602e+00 1.73390437170573e-03 4.22593805567318e-05 -1.20224815335841e-02 - 13 3.22241068511834e+00 3.20567787031465e+00 1.24058015155670e-03 5.74869186270917e-05 -1.20227114812586e-02 - 14 3.22308184575111e+00 3.20575175243528e+00 6.71160632762735e-04 7.38821206311925e-05 -1.20230070097411e-02 - 15 3.22314498306341e+00 3.20584261924524e+00 6.31373123058943e-05 9.08668099629442e-05 -1.20233704769810e-02 - 16 3.22259983061978e+00 3.20595044337301e+00 -5.45152443630847e-04 1.07824127767084e-04 -1.20238017734920e-02 - 17 3.22148232868433e+00 3.20607458035225e+00 -1.11750193545301e-03 1.24136979242771e-04 -1.20242983214090e-02 - 18 3.21986023812409e+00 3.20621380472955e+00 -1.62209056023332e-03 1.39224377296434e-04 -1.20248552189182e-02 - 19 3.21782725362733e+00 3.20636637815120e+00 -2.03298449676304e-03 1.52573421652395e-04 -1.20254655126048e-02 - 20 3.21549617606775e+00 3.20653014355194e+00 -2.33107755958173e-03 1.63765400741131e-04 -1.20261205742078e-02 + 1 3.20437148316484e+00 3.20554661526430e+00 -1.17525151850328e-03 -1.19419048416827e-07 -1.20221864610572e-02 + 2 3.20384207658198e+00 3.20554521661731e+00 -5.29406582859160e-04 -1.39864698615333e-06 -1.20221808664692e-02 + 3 3.20397336372329e+00 3.20554201761950e+00 1.31287141313052e-04 -3.19899781308815e-06 -1.20221680704780e-02 + 4 3.20474099372294e+00 3.20553715100348e+00 7.67629999647745e-04 -4.86661601385684e-06 -1.20221486040139e-02 + 5 3.20608361725515e+00 3.20553137919306e+00 1.34262353221182e-03 -5.77181042148448e-06 -1.20221255167722e-02 + 6 3.20790704366680e+00 3.20552603300132e+00 1.82342641164146e-03 -5.34619173897510e-06 -1.20221041320053e-02 + 7 3.21008979708265e+00 3.20552291735469e+00 2.18275341585361e-03 -3.11564663055446e-06 -1.20220916694188e-02 + 8 3.21248979691190e+00 3.20552418961958e+00 2.39999982925276e-03 1.27226489358961e-06 -1.20220967584783e-02 + 9 3.21495218466242e+00 3.20553221724516e+00 2.46238775052099e-03 8.02762557980444e-06 -1.20221288689807e-02 + 10 3.21731838884401e+00 3.20554942258746e+00 2.36620418158973e-03 1.72053422961567e-05 -1.20221976903498e-02 + 11 3.21943620052261e+00 3.20557812401472e+00 2.11781167860092e-03 2.87014272571360e-05 -1.20223124960589e-02 + 12 3.22117010488210e+00 3.20562038339497e+00 1.73390435948928e-03 4.22593802508272e-05 -1.20224815335799e-02 + 13 3.22241068502092e+00 3.20567787031321e+00 1.24058013882022e-03 5.74869182386481e-05 -1.20227114812528e-02 + 14 3.22308184564051e+00 3.20575175243336e+00 6.71160619590605e-04 7.38821201480224e-05 -1.20230070097334e-02 + 15 3.22314498293928e+00 3.20584261924273e+00 6.31372987673906e-05 9.08668093725243e-05 -1.20233704769709e-02 + 16 3.22259983048180e+00 3.20595044336978e+00 -5.45152457477549e-04 1.07824127056634e-04 -1.20238017734791e-02 + 17 3.22148232853223e+00 3.20607458034818e+00 -1.11750194957105e-03 1.24136978399328e-04 -1.20242983213927e-02 + 18 3.21986023795765e+00 3.20621380472449e+00 -1.62209057458140e-03 1.39224376306895e-04 -1.20248552188980e-02 + 19 3.21782725344634e+00 3.20636637814499e+00 -2.03298451131184e-03 1.52573420503577e-04 -1.20254655125800e-02 + 20 3.21549617587205e+00 3.20653014354441e+00 -2.33107757428819e-03 1.63765399419808e-04 -1.20261205741777e-02 diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out index e7b81c1e7..71e67a3d0 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out @@ -4,10 +4,9 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -91,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -127,6 +127,7 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -143,11 +144,12 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: colvars: colvars: - Colvars module: colvars: - Colvars-NAMD interface: -colvars: - Linear and polynomial combination of colvar components: +colvars: - Optimal rotation via flexible fitting: colvars: - distance colvar component: colvars: - harmonicWalls colvar bias implementation: colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 @@ -155,6 +157,8 @@ colvars: colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.2155 @@ -164,18 +168,7 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Linear and polynomial combination of colvar components: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped index 38e912279..740730ef2 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21130917331427e+00 - v 1.00951355693882e-04 - extended_x 3.20938126640048e+00 - extended_v 1.00951355693882e-04 + x 3.21130917292044e+00 + v 1.00951348854985e-04 + extended_x 3.20938126631322e+00 + extended_v 1.00951348854985e-04 } restraint { diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj index 532fb06c0..e35e1b0ba 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 20 3.21549617606775e+00 3.20653014355194e+00 0.00000000000000e+00 1.63765400741131e-04 -1.20261205742078e-02 - 21 3.21299146712053e+00 3.20670263861396e+00 -2.50470894721611e-03 1.72495062016875e-04 -1.20268105544558e-02 - 22 3.21044140024819e+00 3.20688122103595e+00 -2.55006687233861e-03 1.78582421991679e-04 -1.20275248841438e-02 - 23 3.20797012460099e+00 3.20706319774191e+00 -2.47127564720051e-03 1.81976705962452e-04 -1.20282527909676e-02 - 24 3.20569019005604e+00 3.20724595006950e+00 -2.27993454495001e-03 1.82752327592568e-04 -1.20289838002780e-02 - 25 3.20369626869598e+00 3.20742704743694e+00 -1.99392136005994e-03 1.81097367441832e-04 -1.20297081897478e-02 - 26 3.20206071223530e+00 3.20760434317960e+00 -1.63555646068803e-03 1.77295742655034e-04 -1.20304173727184e-02 - 27 3.20083128336097e+00 3.20777604807702e+00 -1.22942887432353e-03 1.71704897415300e-04 -1.20311041923081e-02 - 28 3.20003097928630e+00 3.20794077925876e+00 -8.00304074670688e-04 1.64731181749229e-04 -1.20317631170351e-02 - 29 3.19965949840204e+00 3.20809758426668e+00 -3.71480884266973e-04 1.56805007916514e-04 -1.20323903370667e-02 - 30 3.19969592099552e+00 3.20824594169726e+00 3.64225934861295e-05 1.48357430576832e-04 -1.20329837667890e-02 - 31 3.20010221789303e+00 3.20838574106934e+00 4.06296897506930e-04 1.39799372086402e-04 -1.20335429642774e-02 - 32 3.20082742014926e+00 3.20851724539990e+00 7.25202256227853e-04 1.31504330556317e-04 -1.20340689815996e-02 - 33 3.20181227147044e+00 3.20864104064007e+00 9.84851321187641e-04 1.23795240167197e-04 -1.20345641625603e-02 - 34 3.20299412090831e+00 3.20875797661322e+00 1.18184943786748e-03 1.16935973148017e-04 -1.20350319064529e-02 - 35 3.20431162299519e+00 3.20886910434216e+00 1.31750208687542e-03 1.11127728944451e-04 -1.20354764173686e-02 - 36 3.20570880341320e+00 3.20897561446625e+00 1.39718041801373e-03 1.06510124092699e-04 -1.20359024578650e-02 - 37 3.20713815074963e+00 3.20907878082178e+00 1.42934733642930e-03 1.03166355530316e-04 -1.20363151232871e-02 - 38 3.20856270857345e+00 3.20917991229282e+00 1.42455782382234e-03 1.01131471033408e-04 -1.20367196491713e-02 - 39 3.20995731392663e+00 3.20928031504479e+00 1.39460535317548e-03 1.00402751973855e-04 -1.20371212601792e-02 - 40 3.21130917331427e+00 3.20938126640048e+00 1.35185938764515e-03 1.00951355693882e-04 -1.20375250656019e-02 + 20 3.21549617587205e+00 3.20653014354441e+00 0.00000000000000e+00 1.63765399419808e-04 -1.20261205741776e-02 + 21 3.21299146691002e+00 3.20670263860492e+00 -2.50470896202648e-03 1.72495060509838e-04 -1.20268105544197e-02 + 22 3.21044140002284e+00 3.20688122102521e+00 -2.55006688718051e-03 1.78582420285797e-04 -1.20275248841008e-02 + 23 3.20797012436086e+00 3.20706319772925e+00 -2.47127566198468e-03 1.81976704044760e-04 -1.20282527909170e-02 + 24 3.20569018980129e+00 3.20724595005470e+00 -2.27993455957121e-03 1.82752325450367e-04 -1.20289838002188e-02 + 25 3.20369626842688e+00 3.20742704741977e+00 -1.99392137440801e-03 1.81097365062805e-04 -1.20297081896791e-02 + 26 3.20206071195224e+00 3.20760434315979e+00 -1.63555647464264e-03 1.77295740027368e-04 -1.20304173726392e-02 + 27 3.20083128306446e+00 3.20777604805432e+00 -1.22942888777944e-03 1.71704894527817e-04 -1.20311041922173e-02 + 28 3.20003097897692e+00 3.20794077923291e+00 -8.00304087535064e-04 1.64731178591497e-04 -1.20317631169316e-02 + 29 3.19965949808046e+00 3.20809758423739e+00 -3.71480896461218e-04 1.56805004478955e-04 -1.20323903369496e-02 + 30 3.19969592066247e+00 3.20824594166424e+00 3.64225820090880e-05 1.48357426850803e-04 -1.20329837666570e-02 + 31 3.20010221754926e+00 3.20838574103230e+00 4.06296886787061e-04 1.39799368064253e-04 -1.20335429641292e-02 + 32 3.20082741979556e+00 3.20851724535854e+00 7.25202246302015e-04 1.31504326231438e-04 -1.20340689814341e-02 + 33 3.20181227110765e+00 3.20864104059407e+00 9.84851312094914e-04 1.23795235534061e-04 -1.20345641623763e-02 + 34 3.20299412053733e+00 3.20875797656227e+00 1.18184942967092e-03 1.16935968202223e-04 -1.20350319062491e-02 + 35 3.20431162261699e+00 3.20886910428595e+00 1.31750207966386e-03 1.11127723682791e-04 -1.20354764171438e-02 + 36 3.20570880302891e+00 3.20897561440447e+00 1.39718041191950e-03 1.06510118513249e-04 -1.20359024576179e-02 + 37 3.20713815036053e+00 3.20907878075410e+00 1.42934733162248e-03 1.03166349632568e-04 -1.20363151230164e-02 + 38 3.20856270818102e+00 3.20917991221892e+00 1.42455782049122e-03 1.01131464818439e-04 -1.20367196488757e-02 + 39 3.20995731353255e+00 3.20928031496436e+00 1.39460535153013e-03 1.00402745444511e-04 -1.20371212598575e-02 + 40 3.21130917292044e+00 3.20938126631322e+00 1.35185938788940e-03 1.00951348854985e-04 -1.20375250652529e-02 diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt b/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt index de8afabca..157cac038 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2021-08-30. -colvars: Using NAMD interface, version "2021-08-30". +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance/AutoDiff/test.colvars.out b/namd/tests/library/000_distance/AutoDiff/test.colvars.out index 1edf5300b..27f0966fb 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -108,15 +112,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped index 283a80870..5268daf85 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21688253462243e+00 + x 3.21688253444007e+00 } diff --git a/namd/tests/library/000_distance/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance/AutoDiff/test.colvars.traj index d19a63aaf..9f55268e7 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316545e+00 0.00000000000000e+00 - 2 3.20384028594369e+00 0.00000000000000e+00 - 3 3.20396721187615e+00 0.00000000000000e+00 - 4 3.20472817290791e+00 0.00000000000000e+00 - 5 3.20606308065559e+00 0.00000000000000e+00 - 6 3.20787989002674e+00 0.00000000000000e+00 - 7 3.21005997944336e+00 0.00000000000000e+00 - 8 3.21246460656400e+00 0.00000000000000e+00 - 9 3.21494247390735e+00 0.00000000000000e+00 - 10 3.21733851238969e+00 0.00000000000000e+00 - 11 3.21950367386500e+00 0.00000000000000e+00 - 12 3.22130499861355e+00 0.00000000000000e+00 - 13 3.22263479499712e+00 0.00000000000000e+00 - 14 3.22341769668903e+00 0.00000000000000e+00 - 15 3.22361473679752e+00 0.00000000000000e+00 - 16 3.22322417516431e+00 0.00000000000000e+00 - 17 3.22227942565775e+00 0.00000000000000e+00 - 18 3.22084479802894e+00 0.00000000000000e+00 - 19 3.21900979846159e+00 0.00000000000000e+00 - 20 3.21688253462243e+00 0.00000000000000e+00 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 0.00000000000000e+00 + 11 3.21950367376059e+00 0.00000000000000e+00 + 12 3.22130499849384e+00 0.00000000000000e+00 + 13 3.22263479486396e+00 0.00000000000000e+00 + 14 3.22341769654449e+00 0.00000000000000e+00 + 15 3.22361473664369e+00 0.00000000000000e+00 + 16 3.22322417500307e+00 0.00000000000000e+00 + 17 3.22227942549106e+00 0.00000000000000e+00 + 18 3.22084479785707e+00 0.00000000000000e+00 + 19 3.21900979827991e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out index 3a7264d71..f4778ef00 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -108,19 +112,30 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped index 9b4200d28..b307ede0d 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21404878546491e+00 + x 3.21404878499019e+00 } diff --git a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj index 2f8dd9cef..177b1bbb8 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253462243e+00 0.00000000000000e+00 - 21 3.21458253154238e+00 0.00000000000000e+00 - 22 3.21223315249804e+00 0.00000000000000e+00 - 23 3.20995392028117e+00 0.00000000000000e+00 - 24 3.20785326961705e+00 0.00000000000000e+00 - 25 3.20602244839787e+00 0.00000000000000e+00 - 26 3.20453120140997e+00 0.00000000000000e+00 - 27 3.20342556475651e+00 0.00000000000000e+00 - 28 3.20272769848587e+00 0.00000000000000e+00 - 29 3.20243730773497e+00 0.00000000000000e+00 - 30 3.20253423306146e+00 0.00000000000000e+00 - 31 3.20298183360766e+00 0.00000000000000e+00 - 32 3.20373100914076e+00 0.00000000000000e+00 - 33 3.20472468746573e+00 0.00000000000000e+00 - 34 3.20590256221861e+00 0.00000000000000e+00 - 35 3.20720566185745e+00 0.00000000000000e+00 - 36 3.20858030460613e+00 0.00000000000000e+00 - 37 3.20998111855282e+00 0.00000000000000e+00 - 38 3.21137308335033e+00 0.00000000000000e+00 - 39 3.21273274315706e+00 0.00000000000000e+00 - 40 3.21404878546491e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 + 21 3.21458253135360e+00 0.00000000000000e+00 + 22 3.21223315230095e+00 0.00000000000000e+00 + 23 3.20995392007338e+00 0.00000000000000e+00 + 24 3.20785326939589e+00 0.00000000000000e+00 + 25 3.20602244816055e+00 0.00000000000000e+00 + 26 3.20453120115385e+00 0.00000000000000e+00 + 27 3.20342556447929e+00 0.00000000000000e+00 + 28 3.20272769818575e+00 0.00000000000000e+00 + 29 3.20243730741081e+00 0.00000000000000e+00 + 30 3.20253423271288e+00 0.00000000000000e+00 + 31 3.20298183323508e+00 0.00000000000000e+00 + 32 3.20373100874536e+00 0.00000000000000e+00 + 33 3.20472468704943e+00 0.00000000000000e+00 + 34 3.20590256178394e+00 0.00000000000000e+00 + 35 3.20720566140745e+00 0.00000000000000e+00 + 36 3.20858030414420e+00 0.00000000000000e+00 + 37 3.20998111808250e+00 0.00000000000000e+00 + 38 3.21137308287521e+00 0.00000000000000e+00 + 39 3.21273274268056e+00 0.00000000000000e+00 + 40 3.21404878499019e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance/namd-version.txt b/namd/tests/library/000_distance/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distance/namd-version.txt +++ b/namd/tests/library/000_distance/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out index 3ab6145e8..aa012e652 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -118,6 +122,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,15 +133,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped index 4e365695b..7932133bf 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685433519314e+00 + x 3.21685433498741e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22496300318146e-03 + accumulatedWork -1.22496300314925e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj index 7f6576778..036216748 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788663e+00 -1.23974855515465e-02 1.92122060001005e-02 1.05000000000000e-01 -6.19874277577326e-05 - 2 3.20383990649994e+00 -1.23753596259998e-02 1.91436907341031e-02 1.10000000000000e-01 -1.23864225887731e-04 - 3 3.20396636369412e+00 -1.23558654547765e-02 1.90834263920673e-02 1.15000000000000e-01 -1.85643553161614e-04 - 4 3.20472667756370e+00 -1.23389067102548e-02 1.90310773505463e-02 1.20000000000000e-01 -2.47338086712888e-04 - 5 3.20606076807835e+00 -1.23242430723134e-02 1.89858709131831e-02 1.25000000000000e-01 -3.08959302074455e-04 - 6 3.20787659964770e+00 -1.23115063985908e-02 1.89466487253177e-02 1.30000000000000e-01 -3.70516834067408e-04 - 7 3.21005556143417e+00 -1.23002222457367e-02 1.89119334118145e-02 1.35000000000000e-01 -4.32017945296092e-04 - 8 3.21245892240487e+00 -1.22898356896195e-02 1.88800076597306e-02 1.40000000000000e-01 -4.93467123744190e-04 - 9 3.21493539658876e+00 -1.22797415863550e-02 1.88490066784571e-02 1.45000000000000e-01 -5.54865831675965e-04 - 10 3.21732992620853e+00 -1.22693197048341e-02 1.88170257524289e-02 1.50000000000000e-01 -6.16212430200135e-04 - 11 3.21949347384418e+00 -1.22579738953767e-02 1.87822405024671e-02 1.55000000000000e-01 -6.77502299677019e-04 - 12 3.22129308961685e+00 -1.22451723584674e-02 1.87430307610718e-02 1.60000000000000e-01 -7.38728161469356e-04 - 13 3.22262109059558e+00 -1.22304843623823e-02 1.86980934673098e-02 1.65000000000000e-01 -7.99880583281267e-04 - 14 3.22340211792757e+00 -1.22136084717103e-02 1.86465289875292e-02 1.70000000000000e-01 -8.60948625639819e-04 - 15 3.22359721096965e+00 -1.21943888438786e-02 1.85878899094638e-02 1.75000000000000e-01 -9.21920569859212e-04 - 16 3.22320463469100e+00 -1.21728185387640e-02 1.85221888972096e-02 1.80000000000000e-01 -9.82784662553032e-04 - 17 3.22225780715853e+00 -1.21490312286341e-02 1.84498699742909e-02 1.85000000000000e-01 -1.04352981869620e-03 - 18 3.22082104163962e+00 -1.21232841665585e-02 1.83717523728909e-02 1.90000000000000e-01 -1.10414623952900e-03 - 19 3.21898384742989e+00 -1.20959353897195e-02 1.82889566190337e-02 1.95000000000000e-01 -1.16462591647759e-03 - 20 3.21685433519314e+00 -1.20674173407726e-02 1.82028201595473e-02 2.00000000000000e-01 -1.22496300318146e-03 + 1 3.20437138788600e+00 -1.23974855515440e-02 1.92122060000928e-02 1.05000000000000e-01 -6.19874277577201e-05 + 2 3.20383990649741e+00 -1.23753596259897e-02 1.91436907340719e-02 1.10000000000000e-01 -1.23864225887668e-04 + 3 3.20396636368840e+00 -1.23558654547536e-02 1.90834263919967e-02 1.15000000000000e-01 -1.85643553161436e-04 + 4 3.20472667755350e+00 -1.23389067102140e-02 1.90310773504205e-02 1.20000000000000e-01 -2.47338086712507e-04 + 5 3.20606076806240e+00 -1.23242430722496e-02 1.89858709129865e-02 1.25000000000000e-01 -3.08959302073754e-04 + 6 3.20787659962477e+00 -1.23115063984991e-02 1.89466487250355e-02 1.30000000000000e-01 -3.70516834066250e-04 + 7 3.21005556140311e+00 -1.23002222456125e-02 1.89119334114324e-02 1.35000000000000e-01 -4.32017945294312e-04 + 8 3.21245892236459e+00 -1.22898356894584e-02 1.88800076592355e-02 1.40000000000000e-01 -4.93467123741604e-04 + 9 3.21493539653826e+00 -1.22797415861530e-02 1.88490066778370e-02 1.45000000000000e-01 -5.54865831672369e-04 + 10 3.21732992614691e+00 -1.22693197045876e-02 1.88170257516728e-02 1.50000000000000e-01 -6.16212430195307e-04 + 11 3.21949347377062e+00 -1.22579738950825e-02 1.87822405015655e-02 1.55000000000000e-01 -6.77502299670720e-04 + 12 3.22129308953064e+00 -1.22451723581226e-02 1.87430307600161e-02 1.60000000000000e-01 -7.38728161461332e-04 + 13 3.22262109049609e+00 -1.22304843619843e-02 1.86980934660929e-02 1.65000000000000e-01 -7.99880583271254e-04 + 14 3.22340211781424e+00 -1.22136084712570e-02 1.86465289861450e-02 1.70000000000000e-01 -8.60948625627539e-04 + 15 3.22359721084197e+00 -1.21943888433679e-02 1.85878899079069e-02 1.75000000000000e-01 -9.21920569844378e-04 + 16 3.22320463454852e+00 -1.21728185381941e-02 1.85221888954752e-02 1.80000000000000e-01 -9.82784662535349e-04 + 17 3.22225780700082e+00 -1.21490312280033e-02 1.84498699723748e-02 1.85000000000000e-01 -1.04352981867537e-03 + 18 3.22082104146627e+00 -1.21232841658651e-02 1.83717523707893e-02 1.90000000000000e-01 -1.10414623950469e-03 + 19 3.21898384724052e+00 -1.20959353889621e-02 1.82889566167431e-02 1.95000000000000e-01 -1.16462591644950e-03 + 20 3.21685433498741e+00 -1.20674173399496e-02 1.82028201570646e-02 2.00000000000000e-01 -1.22496300314925e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out index baca0fc5b..fb727736f 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -118,6 +122,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,20 +133,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped index e0888c9dd..1f650f086 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397283843462e+00 + x 3.21397283795342e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22496300318146e-03 + accumulatedWork -1.22496300314925e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj index d650368f1..ad5f71a3c 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685433519314e+00 -1.20674173407726e-02 1.82028201595473e-02 2.00000000000000e-01 -1.22496300318146e-03 - 21 3.21455203305750e+00 -1.20582081322300e-02 1.81750479200222e-02 2.00000000000000e-01 -1.22496300318146e-03 - 22 3.21220030749260e+00 -1.20488012299704e-02 1.81467013849170e-02 2.00000000000000e-01 -1.22496300318146e-03 - 23 3.20991868511508e+00 -1.20396747404603e-02 1.81192209820098e-02 2.00000000000000e-01 -1.22496300318146e-03 - 24 3.20781560529541e+00 -1.20312624211816e-02 1.80939094309172e-02 2.00000000000000e-01 -1.22496300318146e-03 - 25 3.20598232154492e+00 -1.20239292861797e-02 1.80718594348811e-02 2.00000000000000e-01 -1.22496300318146e-03 - 26 3.20448858523800e+00 -1.20179543409520e-02 1.80539033176509e-02 2.00000000000000e-01 -1.22496300318146e-03 - 27 3.20338043999211e+00 -1.20135217599685e-02 1.80405881346544e-02 2.00000000000000e-01 -1.22496300318146e-03 - 28 3.20268005411016e+00 -1.20107202164406e-02 1.80321750147019e-02 2.00000000000000e-01 -1.22496300318146e-03 - 29 3.20238714153578e+00 -1.20095485661431e-02 1.80286570953188e-02 2.00000000000000e-01 -1.22496300318146e-03 - 30 3.20248155191901e+00 -1.20099262076760e-02 1.80297909392280e-02 2.00000000000000e-01 -1.22496300318146e-03 - 31 3.20292665341239e+00 -1.20117066136495e-02 1.80351369715490e-02 2.00000000000000e-01 -1.22496300318146e-03 - 32 3.20367335432625e+00 -1.20146934173050e-02 1.80441072389790e-02 2.00000000000000e-01 -1.22496300318146e-03 - 33 3.20466459020028e+00 -1.20186583608011e-02 1.80560185992068e-02 2.00000000000000e-01 -1.22496300318146e-03 - 34 3.20584006126686e+00 -1.20233602450674e-02 1.80701489478335e-02 2.00000000000000e-01 -1.22496300318146e-03 - 35 3.20714080103121e+00 -1.20285632041248e-02 1.80857915944533e-02 2.00000000000000e-01 -1.22496300318146e-03 - 36 3.20851313109546e+00 -1.20340525243818e-02 1.81023025199476e-02 2.00000000000000e-01 -1.22496300318146e-03 - 37 3.20991168105067e+00 -1.20396467242027e-02 1.81191366554506e-02 2.00000000000000e-01 -1.22496300318146e-03 - 38 3.21130143028320e+00 -1.20452057211328e-02 1.81358726080512e-02 2.00000000000000e-01 -1.22496300318146e-03 - 39 3.21265892119573e+00 -1.20506356847829e-02 1.81522275509204e-02 2.00000000000000e-01 -1.22496300318146e-03 - 40 3.21397283843462e+00 -1.20558913537385e-02 1.81680645416433e-02 2.00000000000000e-01 -1.22496300318146e-03 + 20 3.21685433498741e+00 -1.20674173399496e-02 1.82028201570646e-02 2.00000000000000e-01 -1.22496300314925e-03 + 21 3.21455203283509e+00 -1.20582081313404e-02 1.81750479173404e-02 2.00000000000000e-01 -1.22496300314925e-03 + 22 3.21220030725328e+00 -1.20488012290131e-02 1.81467013820335e-02 2.00000000000000e-01 -1.22496300314925e-03 + 23 3.20991868485870e+00 -1.20396747394348e-02 1.81192209789231e-02 2.00000000000000e-01 -1.22496300314925e-03 + 24 3.20781560502190e+00 -1.20312624200876e-02 1.80939094276265e-02 2.00000000000000e-01 -1.22496300314925e-03 + 25 3.20598232125433e+00 -1.20239292850173e-02 1.80718594313871e-02 2.00000000000000e-01 -1.22496300314925e-03 + 26 3.20448858493049e+00 -1.20179543397220e-02 1.80539033139553e-02 2.00000000000000e-01 -1.22496300314925e-03 + 27 3.20338043966796e+00 -1.20135217586718e-02 1.80405881307602e-02 2.00000000000000e-01 -1.22496300314925e-03 + 28 3.20268005376972e+00 -1.20107202150789e-02 1.80321750106130e-02 2.00000000000000e-01 -1.22496300314925e-03 + 29 3.20238714117950e+00 -1.20095485647180e-02 1.80286570910400e-02 2.00000000000000e-01 -1.22496300314925e-03 + 30 3.20248155154737e+00 -1.20099262061895e-02 1.80297909347646e-02 2.00000000000000e-01 -1.22496300314925e-03 + 31 3.20292665302594e+00 -1.20117066121038e-02 1.80351369669071e-02 2.00000000000000e-01 -1.22496300314925e-03 + 32 3.20367335392557e+00 -1.20146934157023e-02 1.80441072341650e-02 2.00000000000000e-01 -1.22496300314925e-03 + 33 3.20466458978601e+00 -1.20186583591440e-02 1.80560185942279e-02 2.00000000000000e-01 -1.22496300314925e-03 + 34 3.20584006083970e+00 -1.20233602433588e-02 1.80701489426977e-02 2.00000000000000e-01 -1.22496300314925e-03 + 35 3.20714080059199e+00 -1.20285632023680e-02 1.80857915891700e-02 2.00000000000000e-01 -1.22496300314925e-03 + 36 3.20851313064513e+00 -1.20340525225805e-02 1.81023025145283e-02 2.00000000000000e-01 -1.22496300314925e-03 + 37 3.20991168059037e+00 -1.20396467223615e-02 1.81191366499087e-02 2.00000000000000e-01 -1.22496300314925e-03 + 38 3.21130142981427e+00 -1.20452057192571e-02 1.81358726024029e-02 2.00000000000000e-01 -1.22496300314925e-03 + 39 3.21265892071976e+00 -1.20506356828790e-02 1.81522275451847e-02 2.00000000000000e-01 -1.22496300314925e-03 + 40 3.21397283795342e+00 -1.20558913518137e-02 1.81680645358420e-02 2.00000000000000e-01 -1.22496300314925e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt b/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out index 9d06eb030..2bce89042 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -118,6 +122,7 @@ colvars: # targetNumStages = 4 colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,15 +133,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped index 1cf9a8664..e298649e7 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685409696506e+00 + x 3.21685409675932e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj index 66081f9e6..5c980cf93 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 - 1 3.20437138788663e+00 -1.24174855515465e-02 1.92742434278583e-02 1.00000000000000e-01 - 2 3.20383990619321e+00 -1.24153596247728e-02 1.92676443265549e-02 1.00000000000000e-01 - 3 3.20396636247149e+00 -1.24158654498859e-02 1.92692143587090e-02 1.00000000000000e-01 - 4 3.20472667452156e+00 -1.24189066980862e-02 1.92786554469713e-02 1.00000000000000e-01 - 5 3.20606076202988e+00 -1.24242430481195e-02 1.92952269148432e-02 1.00000000000000e-01 - 6 3.20787658913670e+00 -1.24315063565468e-02 1.93177937866079e-02 1.00000000000000e-01 - 7 3.21005554475098e+00 -1.24402221790039e-02 1.93448909828726e-02 1.00000000000000e-01 - 8 3.21245889760366e+00 -1.24498355904147e-02 1.93748007785444e-02 1.00000000000000e-01 - 9 3.21493536150581e+00 -1.23597414460232e-02 1.90954010765681e-02 1.25000000000000e-01 - 10 3.21732988001565e+00 -1.23693195200626e-02 1.91250081736752e-02 1.25000000000000e-01 - 11 3.21949341551286e+00 -1.23779736620515e-02 1.91517789973049e-02 1.25000000000000e-01 - 12 3.22129301791606e+00 -1.23851720716642e-02 1.91740609055915e-02 1.25000000000000e-01 - 13 3.22262100408954e+00 -1.23904840163582e-02 1.91905117699534e-02 1.25000000000000e-01 - 14 3.22340201497448e+00 -1.23936080598979e-02 1.92001900927959e-02 1.25000000000000e-01 - 15 3.22359708972178e+00 -1.23943883588871e-02 1.92026078488646e-02 1.25000000000000e-01 - 16 3.22320449309688e+00 -1.23928179723875e-02 1.91977421620913e-02 1.25000000000000e-01 - 17 3.22225764296745e+00 -1.22890305718698e-02 1.88775340495438e-02 1.50000000000000e-01 - 18 3.22082085394715e+00 -1.22832834157886e-02 1.88598814340734e-02 1.50000000000000e-01 - 19 3.21898363512874e+00 -1.22759345405150e-02 1.88373211053761e-02 1.50000000000000e-01 - 20 3.21685409696506e+00 -1.22674163878602e-02 1.88111881041427e-02 1.50000000000000e-01 + 1 3.20437138788600e+00 -1.24174855515440e-02 1.92742434278505e-02 1.00000000000000e-01 + 2 3.20383990619069e+00 -1.24153596247627e-02 1.92676443265236e-02 1.00000000000000e-01 + 3 3.20396636246577e+00 -1.24158654498631e-02 1.92692143586380e-02 1.00000000000000e-01 + 4 3.20472667451135e+00 -1.24189066980454e-02 1.92786554468447e-02 1.00000000000000e-01 + 5 3.20606076201392e+00 -1.24242430480557e-02 1.92952269146450e-02 1.00000000000000e-01 + 6 3.20787658911377e+00 -1.24315063564551e-02 1.93177937863229e-02 1.00000000000000e-01 + 7 3.21005554471991e+00 -1.24402221788797e-02 1.93448909824861e-02 1.00000000000000e-01 + 8 3.21245889756338e+00 -1.24498355902535e-02 1.93748007780429e-02 1.00000000000000e-01 + 9 3.21493536145531e+00 -1.23597414458212e-02 1.90954010759439e-02 1.25000000000000e-01 + 10 3.21732987995403e+00 -1.23693195198161e-02 1.91250081729130e-02 1.25000000000000e-01 + 11 3.21949341543930e+00 -1.23779736617572e-02 1.91517789963944e-02 1.25000000000000e-01 + 12 3.22129301782985e+00 -1.23851720713194e-02 1.91740609045237e-02 1.25000000000000e-01 + 13 3.22262100399005e+00 -1.23904840159602e-02 1.91905117687206e-02 1.25000000000000e-01 + 14 3.22340201486115e+00 -1.23936080594446e-02 1.92001900913912e-02 1.25000000000000e-01 + 15 3.22359708959410e+00 -1.23943883583764e-02 1.92026078472821e-02 1.25000000000000e-01 + 16 3.22320449295439e+00 -1.23928179718176e-02 1.91977421603256e-02 1.25000000000000e-01 + 17 3.22225764280973e+00 -1.22890305712389e-02 1.88775340476056e-02 1.50000000000000e-01 + 18 3.22082085377380e+00 -1.22832834150952e-02 1.88598814319441e-02 1.50000000000000e-01 + 19 3.21898363493937e+00 -1.22759345397575e-02 1.88373211030514e-02 1.50000000000000e-01 + 20 3.21685409675932e+00 -1.22674163870373e-02 1.88111881016189e-02 1.50000000000000e-01 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out index ac78db1f1..abea13011 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -118,6 +122,7 @@ colvars: # targetNumStages = 4 colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,20 +133,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped index 59699cf48..14415afc1 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397207993279e+00 + x 3.21397207945158e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj index cb822a1c2..c6b191d7a 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one - 20 3.21685409696506e+00 -1.22674163878602e-02 1.88111881041427e-02 1.50000000000000e-01 - 21 3.21455176736891e+00 -1.22582070694756e-02 1.87829550697678e-02 1.50000000000000e-01 - 22 3.21220001290207e+00 -1.22488000516083e-02 1.87541378380349e-02 1.50000000000000e-01 - 23 3.20991836027364e+00 -1.22396734410946e-02 1.87262007430795e-02 1.50000000000000e-01 - 24 3.20781524894743e+00 -1.22312609957897e-02 1.87004681933909e-02 1.50000000000000e-01 - 25 3.20598193253024e+00 -1.21239277301209e-02 1.83737029506495e-02 1.75000000000000e-01 - 26 3.20448816403056e+00 -1.21179526561222e-02 1.83555970720025e-02 1.75000000000000e-01 - 27 3.20337998714552e+00 -1.21135199485821e-02 1.83421706930870e-02 1.75000000000000e-01 - 28 3.20267957024093e+00 -1.21107182809637e-02 1.83336871601086e-02 1.75000000000000e-01 - 29 3.20238662730877e+00 -1.21095465092351e-02 1.83301395824160e-02 1.75000000000000e-01 - 30 3.20248100803512e+00 -1.21099240321405e-02 1.83312825080267e-02 1.75000000000000e-01 - 31 3.20292608059827e+00 -1.21117043223931e-02 1.83366726991344e-02 1.75000000000000e-01 - 32 3.20367275332608e+00 -1.21146910133043e-02 1.83457172934795e-02 1.75000000000000e-01 - 33 3.20466396177004e+00 -1.20186558470801e-02 1.80560110463192e-02 2.00000000000000e-01 - 34 3.20583940770664e+00 -1.20233576308266e-02 1.80701410898444e-02 2.00000000000000e-01 - 35 3.20714012462387e+00 -1.20285604984955e-02 1.80857834582457e-02 2.00000000000000e-01 - 36 3.20851243408350e+00 -1.20340497363340e-02 1.81022941320700e-02 2.00000000000000e-01 - 37 3.20991096561413e+00 -1.20396438624565e-02 1.81191280418484e-02 2.00000000000000e-01 - 38 3.21130069852117e+00 -1.20452027940847e-02 1.81358637938281e-02 2.00000000000000e-01 - 39 3.21265817511275e+00 -1.20506327004510e-02 1.81522185601474e-02 2.00000000000000e-01 - 40 3.21397207993279e+00 -1.20558883197312e-02 1.81680553972288e-02 2.00000000000000e-01 + 20 3.21685409675932e+00 -1.22674163870373e-02 1.88111881016189e-02 1.50000000000000e-01 + 21 3.21455176714650e+00 -1.22582070685860e-02 1.87829550670414e-02 1.50000000000000e-01 + 22 3.21220001266275e+00 -1.22488000506510e-02 1.87541378351035e-02 1.50000000000000e-01 + 23 3.20991836001725e+00 -1.22396734400690e-02 1.87262007399414e-02 1.50000000000000e-01 + 24 3.20781524867392e+00 -1.22312609946957e-02 1.87004681900454e-02 1.50000000000000e-01 + 25 3.20598193223964e+00 -1.21239277289585e-02 1.83737029471263e-02 1.75000000000000e-01 + 26 3.20448816372304e+00 -1.21179526548922e-02 1.83555970682760e-02 1.75000000000000e-01 + 27 3.20337998682136e+00 -1.21135199472854e-02 1.83421706891602e-02 1.75000000000000e-01 + 28 3.20267956990048e+00 -1.21107182796019e-02 1.83336871559855e-02 1.75000000000000e-01 + 29 3.20238662695248e+00 -1.21095465078099e-02 1.83301395781014e-02 1.75000000000000e-01 + 30 3.20248100766347e+00 -1.21099240306539e-02 1.83312825035261e-02 1.75000000000000e-01 + 31 3.20292608021181e+00 -1.21117043208472e-02 1.83366726944537e-02 1.75000000000000e-01 + 32 3.20367275292539e+00 -1.21146910117016e-02 1.83457172886253e-02 1.75000000000000e-01 + 33 3.20466396135575e+00 -1.20186558454230e-02 1.80560110413401e-02 2.00000000000000e-01 + 34 3.20583940727948e+00 -1.20233576291179e-02 1.80701410847085e-02 2.00000000000000e-01 + 35 3.20714012418463e+00 -1.20285604967385e-02 1.80857834529623e-02 2.00000000000000e-01 + 36 3.20851243363315e+00 -1.20340497345326e-02 1.81022941266506e-02 2.00000000000000e-01 + 37 3.20991096515382e+00 -1.20396438606153e-02 1.81191280363064e-02 2.00000000000000e-01 + 38 3.21130069805223e+00 -1.20452027922089e-02 1.81358637881797e-02 2.00000000000000e-01 + 39 3.21265817463677e+00 -1.20506326985471e-02 1.81522185544115e-02 2.00000000000000e-01 + 40 3.21397207945158e+00 -1.20558883178063e-02 1.81680553914274e-02 2.00000000000000e-01 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt b/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out index 437e26dcb..c5200e63f 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -118,6 +122,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,15 +133,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped index 4109af1f5..5ef095f44 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685457639221e+00 + x 3.21685457618647e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486621732e-03 + accumulatedWork -1.22142486620766e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj index c0e02c1fa..5eec6dc1f 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788663e+00 -1.23774855515465e-02 1.91502685723428e-02 1.10000000000000e-01 -1.23774855515465e-04 - 2 3.20383990680667e+00 -1.23353596272267e-02 1.90201371416267e-02 1.20000000000000e-01 -2.47128451787732e-04 - 3 3.20396636491675e+00 -1.22958654596670e-02 1.88985384252790e-02 1.30000000000000e-01 -3.70087106384402e-04 - 4 3.20472668060584e+00 -1.22589067224234e-02 1.87850992536346e-02 1.40000000000000e-01 -4.92676173608635e-04 - 5 3.20606077412683e+00 -1.22242430965073e-02 1.86790149103134e-02 1.50000000000000e-01 -6.14918604573709e-04 - 6 3.20787661015870e+00 -1.21915064406348e-02 1.85791036615050e-02 1.60000000000000e-01 -7.36833668980057e-04 - 7 3.21005557811738e+00 -1.21602223124695e-02 1.84838758360852e-02 1.70000000000000e-01 -8.58435892104752e-04 - 8 3.21245894720608e+00 -1.21298357888243e-02 1.83916145329805e-02 1.80000000000000e-01 -9.79734249992995e-04 - 9 3.21493543167171e+00 -1.20997417266868e-02 1.83004687315658e-02 1.90000000000000e-01 -1.10073166725986e-03 - 10 3.21732997393638e+00 -1.20693198957455e-02 1.82085603432298e-02 2.00000000000000e-01 -1.22142486621732e-03 - 11 3.21949353676140e+00 -1.20779741470456e-02 1.82346824370878e-02 2.00000000000000e-01 -1.22142486621732e-03 - 12 3.22129316981759e+00 -1.20851726792704e-02 1.82564248359729e-02 2.00000000000000e-01 -1.22142486621732e-03 - 13 3.22262118971552e+00 -1.20904847588621e-02 1.82724777130345e-02 2.00000000000000e-01 -1.22142486621732e-03 - 14 3.22340223714544e+00 -1.20936089485818e-02 1.82819221751521e-02 2.00000000000000e-01 -1.22142486621732e-03 - 15 3.22359735101788e+00 -1.20943894040715e-02 1.82842818821647e-02 2.00000000000000e-01 -1.22142486621732e-03 - 16 3.22320479587449e+00 -1.20928191834980e-02 1.82795344755970e-02 2.00000000000000e-01 -1.22142486621732e-03 - 17 3.22225798937996e+00 -1.20890319575198e-02 1.82680867087420e-02 2.00000000000000e-01 -1.22142486621732e-03 - 18 3.22082124442969e+00 -1.20832849777187e-02 1.82507219815954e-02 2.00000000000000e-01 -1.22142486621732e-03 - 19 3.21898406998055e+00 -1.20759362799222e-02 1.82285296295926e-02 2.00000000000000e-01 -1.22142486621732e-03 - 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 + 1 3.20437138788600e+00 -1.23774855515440e-02 1.91502685723351e-02 1.10000000000000e-01 -1.23774855515440e-04 + 2 3.20383990680414e+00 -1.23353596272166e-02 1.90201371415956e-02 1.20000000000000e-01 -2.47128451787606e-04 + 3 3.20396636491103e+00 -1.22958654596441e-02 1.88985384252087e-02 1.30000000000000e-01 -3.70087106384047e-04 + 4 3.20472668059564e+00 -1.22589067223826e-02 1.87850992535096e-02 1.40000000000000e-01 -4.92676173607873e-04 + 5 3.20606077411088e+00 -1.22242430964435e-02 1.86790149101184e-02 1.50000000000000e-01 -6.14918604572308e-04 + 6 3.20787661013578e+00 -1.21915064405431e-02 1.85791036612255e-02 1.60000000000000e-01 -7.36833668977739e-04 + 7 3.21005557808631e+00 -1.21602223123453e-02 1.84838758357074e-02 1.70000000000000e-01 -8.58435892101191e-04 + 8 3.21245894716580e+00 -1.21298357886632e-02 1.83916145324919e-02 1.80000000000000e-01 -9.79734249987824e-04 + 9 3.21493543162121e+00 -1.20997417264848e-02 1.83004687309548e-02 1.90000000000000e-01 -1.10073166725267e-03 + 10 3.21732997387476e+00 -1.20693198954990e-02 1.82085603424861e-02 2.00000000000000e-01 -1.22142486620766e-03 + 11 3.21949353668785e+00 -1.20779741467514e-02 1.82346824361994e-02 2.00000000000000e-01 -1.22142486620766e-03 + 12 3.22129316973139e+00 -1.20851726789256e-02 1.82564248349311e-02 2.00000000000000e-01 -1.22142486620766e-03 + 13 3.22262118961603e+00 -1.20904847584641e-02 1.82724777118316e-02 2.00000000000000e-01 -1.22142486620766e-03 + 14 3.22340223703211e+00 -1.20936089481284e-02 1.82819221737815e-02 2.00000000000000e-01 -1.22142486620766e-03 + 15 3.22359735089020e+00 -1.20943894035608e-02 1.82842818806205e-02 2.00000000000000e-01 -1.22142486620766e-03 + 16 3.22320479573201e+00 -1.20928191829280e-02 1.82795344738740e-02 2.00000000000000e-01 -1.22142486620766e-03 + 17 3.22225798922225e+00 -1.20890319568890e-02 1.82680867068354e-02 2.00000000000000e-01 -1.22142486620766e-03 + 18 3.22082124425633e+00 -1.20832849770253e-02 1.82507219795008e-02 2.00000000000000e-01 -1.22142486620766e-03 + 19 3.21898406979118e+00 -1.20759362791647e-02 1.82285296273058e-02 2.00000000000000e-01 -1.22142486620766e-03 + 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out index ec62b7868..c92a324d4 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -118,6 +122,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,20 +133,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped index 100eebdff..a27db3dc3 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397324487089e+00 + x 3.21397324438969e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486621732e-03 + accumulatedWork -1.22142486620766e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj index 82871cb9e..9592912c4 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 - 21 3.21455229152270e+00 -1.20582091660908e-02 1.81750510366495e-02 2.00000000000000e-01 -1.22142486621732e-03 - 22 3.21220058191067e+00 -1.20488023276427e-02 1.81467046913260e-02 2.00000000000000e-01 -1.22142486621732e-03 - 23 3.20991897426449e+00 -1.20396758970580e-02 1.81192244632749e-02 2.00000000000000e-01 -1.22142486621732e-03 - 24 3.20781590805930e+00 -1.20312636322372e-02 1.80939130735492e-02 2.00000000000000e-01 -1.22142486621732e-03 - 25 3.20598263691365e+00 -1.20239305476546e-02 1.80718632268527e-02 2.00000000000000e-01 -1.22142486621732e-03 - 26 3.20448891230251e+00 -1.20179556492100e-02 1.80539072482974e-02 2.00000000000000e-01 -1.22142486621732e-03 - 27 3.20338077792898e+00 -1.20135231117159e-02 1.80405921944666e-02 2.00000000000000e-01 -1.22142486621732e-03 - 28 3.20268040216098e+00 -1.20107216086439e-02 1.80321791950433e-02 2.00000000000000e-01 -1.22142486621732e-03 - 29 3.20238749898247e+00 -1.20095499959299e-02 1.80286613880924e-02 2.00000000000000e-01 -1.22142486621732e-03 - 30 3.20248191805753e+00 -1.20099276722301e-02 1.80297953365248e-02 2.00000000000000e-01 -1.22142486621732e-03 - 31 3.20292702752774e+00 -1.20117081101110e-02 1.80351414653132e-02 2.00000000000000e-01 -1.22142486621732e-03 - 32 3.20367373567078e+00 -1.20146949426831e-02 1.80441118207169e-02 2.00000000000000e-01 -1.22142486621732e-03 - 33 3.20466497797716e+00 -1.20186599119087e-02 1.80560232597650e-02 2.00000000000000e-01 -1.22142486621732e-03 - 34 3.20584045462068e+00 -1.20233618184827e-02 1.80701536772685e-02 2.00000000000000e-01 -1.22142486621732e-03 - 35 3.20714119904756e+00 -1.20285647961903e-02 1.80857963820184e-02 2.00000000000000e-01 -1.22142486621732e-03 - 36 3.20851353280837e+00 -1.20340541312335e-02 1.81023073541822e-02 2.00000000000000e-01 -1.22142486621732e-03 - 37 3.20991208545797e+00 -1.20396483418319e-02 1.81191415243719e-02 2.00000000000000e-01 -1.22142486621732e-03 - 38 3.21130183636701e+00 -1.20452073454680e-02 1.81358774994146e-02 2.00000000000000e-01 -1.22142486621732e-03 - 39 3.21265932794554e+00 -1.20506373117822e-02 1.81522324525146e-02 2.00000000000000e-01 -1.22142486621732e-03 - 40 3.21397324487089e+00 -1.20558929794836e-02 1.81680694415952e-02 2.00000000000000e-01 -1.22142486621732e-03 + 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 + 21 3.21455229130029e+00 -1.20582091652012e-02 1.81750510339676e-02 2.00000000000000e-01 -1.22142486620766e-03 + 22 3.21220058167135e+00 -1.20488023266854e-02 1.81467046884425e-02 2.00000000000000e-01 -1.22142486620766e-03 + 23 3.20991897400811e+00 -1.20396758960324e-02 1.81192244601880e-02 2.00000000000000e-01 -1.22142486620766e-03 + 24 3.20781590778578e+00 -1.20312636311431e-02 1.80939130702584e-02 2.00000000000000e-01 -1.22142486620766e-03 + 25 3.20598263662306e+00 -1.20239305464922e-02 1.80718632233586e-02 2.00000000000000e-01 -1.22142486620766e-03 + 26 3.20448891199500e+00 -1.20179556479800e-02 1.80539072446018e-02 2.00000000000000e-01 -1.22142486620766e-03 + 27 3.20338077760483e+00 -1.20135231104193e-02 1.80405921905723e-02 2.00000000000000e-01 -1.22142486620766e-03 + 28 3.20268040182054e+00 -1.20107216072822e-02 1.80321791909543e-02 2.00000000000000e-01 -1.22142486620766e-03 + 29 3.20238749862618e+00 -1.20095499945047e-02 1.80286613838135e-02 2.00000000000000e-01 -1.22142486620766e-03 + 30 3.20248191768589e+00 -1.20099276707435e-02 1.80297953320614e-02 2.00000000000000e-01 -1.22142486620766e-03 + 31 3.20292702714129e+00 -1.20117081085652e-02 1.80351414606713e-02 2.00000000000000e-01 -1.22142486620766e-03 + 32 3.20367373527010e+00 -1.20146949410804e-02 1.80441118159029e-02 2.00000000000000e-01 -1.22142486620766e-03 + 33 3.20466497756289e+00 -1.20186599102516e-02 1.80560232547861e-02 2.00000000000000e-01 -1.22142486620766e-03 + 34 3.20584045419353e+00 -1.20233618167741e-02 1.80701536721327e-02 2.00000000000000e-01 -1.22142486620766e-03 + 35 3.20714119860834e+00 -1.20285647944334e-02 1.80857963767352e-02 2.00000000000000e-01 -1.22142486620766e-03 + 36 3.20851353235803e+00 -1.20340541294321e-02 1.81023073487628e-02 2.00000000000000e-01 -1.22142486620766e-03 + 37 3.20991208499767e+00 -1.20396483399907e-02 1.81191415188300e-02 2.00000000000000e-01 -1.22142486620766e-03 + 38 3.21130183589808e+00 -1.20452073435923e-02 1.81358774937663e-02 2.00000000000000e-01 -1.22142486620766e-03 + 39 3.21265932746957e+00 -1.20506373098783e-02 1.81522324467788e-02 2.00000000000000e-01 -1.22142486620766e-03 + 40 3.21397324438969e+00 -1.20558929775587e-02 1.81680694357938e-02 2.00000000000000e-01 -1.22142486620766e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt b/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out index 908c0f068..99cf50a61 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,6 +119,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -125,15 +130,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 9eef8b44e..fec1e803e 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685399835649e+00 + x 3.21685399817416e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj index 5a6aa23cd..2cd06ea2b 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.24221869387334e-02 - 1 3.20437138788661e+00 -1.24174855515465e-02 - 2 3.20383990624489e+00 -1.24153596249795e-02 - 3 3.20396636247331e+00 -1.24158654498932e-02 - 4 3.20472667455914e+00 -1.24189066982366e-02 - 5 3.20606076201901e+00 -1.24242430480760e-02 - 6 3.20787658913293e+00 -1.24315063565317e-02 - 7 3.21005554475517e+00 -1.24402221790207e-02 - 8 3.21245889761578e+00 -1.24498355904631e-02 - 9 3.21493536152545e+00 -1.24597414461018e-02 - 10 3.21732987850678e+00 -1.24693195140271e-02 - 11 3.21949341095784e+00 -1.24779736438313e-02 - 12 3.22129300883514e+00 -1.24851720353406e-02 - 13 3.22262098905883e+00 -1.24904839562353e-02 - 14 3.22340199264132e+00 -1.24936079705653e-02 - 15 3.22359705881703e+00 -1.24943882352681e-02 - 16 3.22320445244359e+00 -1.24928178097743e-02 - 17 3.22225759148518e+00 -1.24890303659407e-02 - 18 3.22082078911634e+00 -1.24832831564654e-02 - 19 3.21898355455034e+00 -1.24759342182014e-02 - 20 3.21685399835649e+00 -1.24674159934260e-02 + 1 3.20437138788600e+00 -1.24174855515440e-02 + 2 3.20383990619069e+00 -1.24153596247627e-02 + 3 3.20396636246577e+00 -1.24158654498631e-02 + 4 3.20472667451135e+00 -1.24189066980454e-02 + 5 3.20606076201392e+00 -1.24242430480557e-02 + 6 3.20787658911377e+00 -1.24315063564551e-02 + 7 3.21005554471991e+00 -1.24402221788797e-02 + 8 3.21245889756338e+00 -1.24498355902535e-02 + 9 3.21493536145531e+00 -1.24597414458212e-02 + 10 3.21732987841907e+00 -1.24693195136763e-02 + 11 3.21949341085340e+00 -1.24779736434136e-02 + 12 3.22129300871542e+00 -1.24851720348617e-02 + 13 3.22262098892565e+00 -1.24904839557026e-02 + 14 3.22340199249676e+00 -1.24936079699870e-02 + 15 3.22359705866319e+00 -1.24943882346527e-02 + 16 3.22320445228234e+00 -1.24928178091294e-02 + 17 3.22225759131848e+00 -1.24890303652739e-02 + 18 3.22082078894448e+00 -1.24832831557779e-02 + 19 3.21898355436871e+00 -1.24759342174748e-02 + 20 3.21685399817416e+00 -1.24674159926967e-02 diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out index 8752f5403..a71fdf83a 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,6 +119,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -125,20 +130,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index ba9e5b167..086f80ad0 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397114764396e+00 + x 3.21397114716924e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj index d18eb0fa7..8924671f5 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685399835649e+00 -1.24674159934260e-02 - 21 3.21455164860269e+00 -1.24582065944107e-02 - 22 3.21219987199261e+00 -1.24487994879705e-02 - 23 3.20991819538261e+00 -1.24396727815305e-02 - 24 3.20781505838050e+00 -1.24312602335220e-02 - 25 3.20598171473079e+00 -1.24239268589232e-02 - 26 3.20448791603500e+00 -1.24179516641400e-02 - 27 3.20337970613153e+00 -1.24135188245261e-02 - 28 3.20267925353770e+00 -1.24107170141508e-02 - 29 3.20238627240592e+00 -1.24095450896237e-02 - 30 3.20248061259023e+00 -1.24099224503609e-02 - 31 3.20292564244219e+00 -1.24117025697688e-02 - 32 3.20367227046597e+00 -1.24146890818639e-02 - 33 3.20466343239054e+00 -1.24186537295621e-02 - 34 3.20583882863293e+00 -1.24233553145317e-02 - 35 3.20713949287508e+00 -1.24285579715003e-02 - 36 3.20851174688770e+00 -1.24340469875508e-02 - 37 3.20991022041763e+00 -1.24396408816705e-02 - 38 3.21129989299330e+00 -1.24451995719732e-02 - 39 3.21265730714688e+00 -1.24506292285875e-02 - 40 3.21397114764396e+00 -1.24558845905758e-02 + 20 3.21685399817416e+00 -1.24674159926967e-02 + 21 3.21455164841394e+00 -1.24582065936557e-02 + 22 3.21219987179556e+00 -1.24487994871822e-02 + 23 3.20991819517487e+00 -1.24396727806995e-02 + 24 3.20781505815938e+00 -1.24312602326375e-02 + 25 3.20598171449351e+00 -1.24239268579740e-02 + 26 3.20448791577891e+00 -1.24179516631157e-02 + 27 3.20337970585434e+00 -1.24135188234173e-02 + 28 3.20267925323760e+00 -1.24107170129504e-02 + 29 3.20238627208178e+00 -1.24095450883271e-02 + 30 3.20248061224166e+00 -1.24099224489666e-02 + 31 3.20292564206961e+00 -1.24117025682784e-02 + 32 3.20367227007056e+00 -1.24146890802823e-02 + 33 3.20466343197421e+00 -1.24186537278969e-02 + 34 3.20583882819824e+00 -1.24233553127930e-02 + 35 3.20713949242506e+00 -1.24285579697002e-02 + 36 3.20851174642574e+00 -1.24340469857030e-02 + 37 3.20991021994729e+00 -1.24396408797892e-02 + 38 3.21129989251817e+00 -1.24451995700727e-02 + 39 3.21265730667037e+00 -1.24506292266815e-02 + 40 3.21397114716924e+00 -1.24558845886769e-02 diff --git a/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out index db180cf49..8085f9903 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out @@ -1,118 +1,174 @@ colvars: ---------------------------------------------------------------------- +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. +colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # indexFile = index.ndx -colvars: The following index groups were read from the index file "index.ndx": -colvars: Protein (104 atoms). -colvars: Protein_noH (51 atoms). -colvars: Protein_Backbone (40 atoms). -colvars: Protein_C-alpha (10 atoms). -colvars: RMSD_atoms (10 atoms). -colvars: Protein_C-alpha_1_2 (2 atoms). -colvars: Protein_C-alpha_9_10 (2 atoms). -colvars: Protein_C-alpha_1 (1 atoms). -colvars: group1 (4 atoms). -colvars: Protein_C-alpha_2 (1 atoms). -colvars: group2 (4 atoms). -colvars: Protein_C-alpha_3 (1 atoms). -colvars: group3 (4 atoms). -colvars: Protein_C-alpha_4 (1 atoms). -colvars: group4 (4 atoms). -colvars: Protein_C-alpha_5 (1 atoms). -colvars: group5 (4 atoms). -colvars: Protein_C-alpha_6 (1 atoms). -colvars: group6 (4 atoms). -colvars: Protein_C-alpha_7 (1 atoms). -colvars: group7 (4 atoms). -colvars: Protein_C-alpha_8 (1 atoms). -colvars: group8 (4 atoms). -colvars: Protein_C-alpha_9 (1 atoms). -colvars: group9 (4 atoms). -colvars: Protein_C-alpha_10 (1 atoms). -colvars: group10 (4 atoms). -colvars: heavy_atoms (51 atoms). -colvars: # analysis = off [default] +colvars: # units = "" [default] +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) +colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 -colvars: # colvarsTrajAppend = off [default] +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. -colvars: # name = one +colvars: # name = "one" colvars: Initializing a new "distance" component. +colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] +colvars: # scalable = on [default] colvars: Initializing atom group "group1". -colvars: # indexGroup = group1 +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028. +colvars: Enabling scalable calculation for group "group1". +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". -colvars: # indexGroup = group2 +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028. +colvars: Enabling scalable calculation for group "group2". +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] +colvars: # upperBoundary = 0.5 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] +colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = on +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } +colvars: # stepZeroData = off [default] colvars: # outputEnergy = on -colvars: # forceConstant = 0.001 +colvars: # outputFreq = 10 [default] +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] +colvars: # outputCenters = off [default] +colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 -colvars: # targetEquilSteps = 0 [default] -colvars: # lambdaSchedule = [default] colvars: # targetNumSteps = 8 colvars: # targetNumStages = 4 -colvars: # targetForceExponent = 1 [default] -colvars: # outputCenters = off [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. +colvars: # outputAccumulatedWork = off [default] +colvars: # targetEquilSteps = 0 [default] +colvars: # lambdaSchedule = [default] +colvars: # lambdaExponent = 1 [default] +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (0 atoms). +colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). +colvars: Updating NAMD interface: +colvars: updating atomic data (0 atoms). +colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Writing to colvar trajectory file "test.colvars.traj". -colvars: Restraint harmonic1, stage 0 : lambda = 0 -colvars: Setting force constant to 0.001 -colvars: Lambda= 0 dA/dLambda= -0.0195425 -colvars: Restraint harmonic1, stage 1 : lambda = 0.25 -colvars: Setting force constant to 0.000775 -colvars: Writing the state file "test.tmp.colvars.state". +colvars: Restraint harmonic1, stage 0 : lambda = 0, k = 0.001 +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Restraint harmonic1 Lambda= 0 dA/dLambda= -0.0195425 +colvars: Restraint harmonic1, stage 1 : lambda = 0.25, k = 0.000775 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Lambda= 0.25 dA/dLambda= -0.0175302 -colvars: Restraint harmonic1, stage 2 : lambda = 0.5 -colvars: Setting force constant to 0.00055 -colvars: Writing the state file "test.tmp.colvars.state". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Restraint harmonic1 Lambda= 0.25 dA/dLambda= -0.0175302 +colvars: Restraint harmonic1, stage 2 : lambda = 0.5, k = 0.00055 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped index 57c7b11d1..199ba99ec 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685733313543e+00 + x 3.21685733295311e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj index ec772e9bf..b1edac98e 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 - 1 3.20437138788661e+00 -1.24174855515465e-02 1.92742434278581e-02 - 2 3.20383990624489e+00 -1.24153596249795e-02 1.92676443271965e-02 - 3 3.20396636247331e+00 -1.24158654498932e-02 1.92692143587316e-02 - 4 3.20472667455914e+00 -1.24189066982366e-02 1.92786554474381e-02 - 5 3.20606076201901e+00 -1.24242430480760e-02 1.92952269147082e-02 - 6 3.20787658913293e+00 -1.24315063565317e-02 1.93177937865610e-02 - 7 3.21005554475517e+00 -1.24402221790207e-02 1.93448909829248e-02 - 8 3.21245889761578e+00 -9.64862258260892e-03 1.50154706034888e-02 - 9 3.21493540450586e+00 -9.65629975396818e-03 1.50393749900784e-02 - 10 3.21733000694964e+00 -9.66372302154388e-03 1.50625068769544e-02 - 11 3.21949366630678e+00 -9.67043036555102e-03 1.50834231378986e-02 - 12 3.22129343099816e+00 -9.67600963609430e-03 1.51008326577080e-02 - 13 3.22262161597842e+00 -9.68012700953309e-03 1.51136869226923e-02 - 14 3.22340285995130e+00 -9.68254886584905e-03 1.51212504096056e-02 - 15 3.22359819959959e+00 -9.68315441875872e-03 1.51231418544397e-02 - 16 3.22320589709283e+00 -6.87105297360423e-03 1.07298565831990e-02 - 17 3.22225941091162e+00 -6.86897070400556e-03 1.07233542119288e-02 - 18 3.22082305098640e+00 -6.86581071217007e-03 1.07134901671248e-02 - 19 3.21898632286159e+00 -6.86176991029550e-03 1.07008832504174e-02 - 20 3.21685733313543e+00 -6.85708613289795e-03 1.06862795986321e-02 + 1 3.20437138788600e+00 -1.24174855515440e-02 1.92742434278505e-02 + 2 3.20383990619069e+00 -1.24153596247627e-02 1.92676443265236e-02 + 3 3.20396636246577e+00 -1.24158654498631e-02 1.92692143586380e-02 + 4 3.20472667451135e+00 -1.24189066980454e-02 1.92786554468447e-02 + 5 3.20606076201392e+00 -1.24242430480557e-02 1.92952269146450e-02 + 6 3.20787658911377e+00 -1.24315063564551e-02 1.93177937863229e-02 + 7 3.21005554471991e+00 -1.24402221788797e-02 1.93448909824861e-02 + 8 3.21245889756338e+00 -9.64862258244647e-03 1.50154706029832e-02 + 9 3.21493540443572e+00 -9.65629975375074e-03 1.50393749894011e-02 + 10 3.21733000686193e+00 -9.66372302127197e-03 1.50625068761068e-02 + 11 3.21949366620235e+00 -9.67043036522729e-03 1.50834231368887e-02 + 12 3.22129343087844e+00 -9.67600963572316e-03 1.51008326565496e-02 + 13 3.22262161584524e+00 -9.68012700912024e-03 1.51136869214031e-02 + 14 3.22340285980675e+00 -9.68254886540093e-03 1.51212504082059e-02 + 15 3.22359819944574e+00 -9.68315441828180e-03 1.51231418529500e-02 + 16 3.22320589693159e+00 -6.87105297324950e-03 1.07298565820911e-02 + 17 3.22225941074492e+00 -6.86897070363883e-03 1.07233542107838e-02 + 18 3.22082305081454e+00 -6.86581071179198e-03 1.07134901659449e-02 + 19 3.21898632267996e+00 -6.86176990989590e-03 1.07008832491711e-02 + 20 3.21685733295311e+00 -6.85708613249684e-03 1.06862795973819e-02 diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out index cd19260d0..e5fe4122e 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out @@ -1,123 +1,179 @@ colvars: ---------------------------------------------------------------------- +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. +colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # indexFile = index.ndx -colvars: The following index groups were read from the index file "index.ndx": -colvars: Protein (104 atoms). -colvars: Protein_noH (51 atoms). -colvars: Protein_Backbone (40 atoms). -colvars: Protein_C-alpha (10 atoms). -colvars: RMSD_atoms (10 atoms). -colvars: Protein_C-alpha_1_2 (2 atoms). -colvars: Protein_C-alpha_9_10 (2 atoms). -colvars: Protein_C-alpha_1 (1 atoms). -colvars: group1 (4 atoms). -colvars: Protein_C-alpha_2 (1 atoms). -colvars: group2 (4 atoms). -colvars: Protein_C-alpha_3 (1 atoms). -colvars: group3 (4 atoms). -colvars: Protein_C-alpha_4 (1 atoms). -colvars: group4 (4 atoms). -colvars: Protein_C-alpha_5 (1 atoms). -colvars: group5 (4 atoms). -colvars: Protein_C-alpha_6 (1 atoms). -colvars: group6 (4 atoms). -colvars: Protein_C-alpha_7 (1 atoms). -colvars: group7 (4 atoms). -colvars: Protein_C-alpha_8 (1 atoms). -colvars: group8 (4 atoms). -colvars: Protein_C-alpha_9 (1 atoms). -colvars: group9 (4 atoms). -colvars: Protein_C-alpha_10 (1 atoms). -colvars: group10 (4 atoms). -colvars: heavy_atoms (51 atoms). -colvars: # analysis = off [default] +colvars: # units = "" [default] +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) +colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 -colvars: # colvarsTrajAppend = off [default] +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. -colvars: # name = one +colvars: # name = "one" colvars: Initializing a new "distance" component. +colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] +colvars: # scalable = on [default] colvars: Initializing atom group "group1". -colvars: # indexGroup = group1 +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028. +colvars: Enabling scalable calculation for group "group1". +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". -colvars: # indexGroup = group2 +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028. +colvars: Enabling scalable calculation for group "group2". +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] +colvars: # upperBoundary = 0.5 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] +colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = on +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } +colvars: # stepZeroData = off [default] colvars: # outputEnergy = on -colvars: # forceConstant = 0.001 +colvars: # outputFreq = 10 [default] +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] +colvars: # outputCenters = off [default] +colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 -colvars: # targetEquilSteps = 0 [default] -colvars: # lambdaSchedule = [default] colvars: # targetNumSteps = 8 colvars: # targetNumStages = 4 -colvars: # targetForceExponent = 1 [default] -colvars: # outputCenters = off [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. +colvars: # outputAccumulatedWork = off [default] +colvars: # targetEquilSteps = 0 [default] +colvars: # lambdaSchedule = [default] +colvars: # lambdaExponent = 1 [default] +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Updating NAMD interface: +colvars: updating atomic data (0 atoms). +colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). +colvars: ---------------------------------------------------------------------- +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21686 -colvars: Restarting restraint bias "harmonic1". -colvars: # forceConstant = 0.00055 -colvars: # stage = 2 +colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (0 atoms). +colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Writing to colvar trajectory file "test.restart.colvars.traj". -colvars: Lambda= 0.5 dA/dLambda= -0.010897 -colvars: Restraint harmonic1, stage 3 : lambda = 0.75 -colvars: Setting force constant to 0.000325 -colvars: Writing the state file "test.restart.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Lambda= 0.75 dA/dLambda= -0.0173372 -colvars: Restraint harmonic1, stage 4 : lambda = 1 -colvars: Setting force constant to 0.0001 -colvars: Lambda= 1 dA/dLambda= -0.0174016 -colvars: Writing the state file "test.restart.tmp.colvars.state". +colvars: Restraint harmonic1 Lambda= 0.5 dA/dLambda= -0.010897 +colvars: Restraint harmonic1, stage 3 : lambda = 0.75, k = 0.000325 +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "test.restart.tmp.colvars.state". +colvars: Restraint harmonic1 Lambda= 0.75 dA/dLambda= -0.0173372 +colvars: Restraint harmonic1, stage 4 : lambda = 1, k = 0.0001 +colvars: Restraint harmonic1 Lambda= 1 dA/dLambda= -0.0174016 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "test.restart.tmp.colvars.state". colvars: Saving collective variables state to "test.restart.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped index b91f1692e..74a01de19 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21399913267948e+00 + x 3.21399913220478e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj index 9b8f32622..d899a4145 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 - 20 3.21685733313543e+00 -6.85708613289795e-03 1.06862795986321e-02 - 21 3.21455560573336e+00 -6.85202233261338e-03 1.06705022833256e-02 - 22 3.21220450317535e+00 -6.84684990698578e-03 1.06543985565434e-02 - 23 3.20992354821064e+00 -6.84183180606342e-03 1.06387869232866e-02 - 24 3.20782117651646e+00 -4.04016752947140e-03 6.27805910238270e-03 - 25 3.20598868112038e+00 -4.03778528545649e-03 6.27065769671115e-03 - 26 3.20449580957973e+00 -4.03584455245364e-03 6.26463125060375e-03 - 27 3.20338860141795e+00 -4.03440518184334e-03 6.26016352741707e-03 - 28 3.20268922061319e+00 -4.03349598679715e-03 6.25734225981105e-03 - 29 3.20239737659378e+00 -4.03311658957192e-03 6.25616516349240e-03 - 30 3.20249291434882e+00 -4.03324078865346e-03 6.25655048433000e-03 - 31 3.20293919728737e+00 -4.03382095647358e-03 6.25835058034053e-03 - 32 3.20368712895776e+00 -1.24147485158310e-03 1.92657475889161e-03 - 33 3.20467968307286e+00 -1.24187187322914e-03 1.92780718689708e-03 - 34 3.20585655463118e+00 -1.24234262185247e-03 1.92926898758910e-03 - 35 3.20715877149842e+00 -1.24286350859937e-03 1.93088712625992e-03 - 36 3.20853264932110e+00 -1.24341305972844e-03 1.93259504637905e-03 - 37 3.20993281159222e+00 -1.24397312463689e-03 1.93433641852358e-03 - 38 3.21132423158529e+00 -1.24452969263412e-03 1.93606769480996e-03 - 39 3.21268344568196e+00 -1.24507337827279e-03 1.93775964660451e-03 - 40 3.21399913267948e+00 -1.24559965307179e-03 1.93939811966572e-03 + 20 3.21685733295311e+00 -6.85708613249684e-03 1.06862795973819e-02 + 21 3.21455560554461e+00 -6.85202233219815e-03 1.06705022820323e-02 + 22 3.21220450297830e+00 -6.84684990655226e-03 1.06543985551943e-02 + 23 3.20992354800290e+00 -6.84183180560639e-03 1.06387869218653e-02 + 24 3.20782117629534e+00 -4.04016752918394e-03 6.27805910148934e-03 + 25 3.20598868088311e+00 -4.03778528514804e-03 6.27065769575309e-03 + 26 3.20449580932365e+00 -4.03584455212074e-03 6.26463124957027e-03 + 27 3.20338860114077e+00 -4.03440518148300e-03 6.26016352629879e-03 + 28 3.20268922031311e+00 -4.03349598640704e-03 6.25734225860066e-03 + 29 3.20239737626966e+00 -4.03311658915055e-03 6.25616516218516e-03 + 30 3.20249291400027e+00 -4.03324078820035e-03 6.25655048292422e-03 + 31 3.20293919691480e+00 -4.03382095598924e-03 6.25835057883767e-03 + 32 3.20368712856237e+00 -1.24147485142495e-03 1.92657475840075e-03 + 33 3.20467968265656e+00 -1.24187187306262e-03 1.92780718638008e-03 + 34 3.20585655419651e+00 -1.24234262167861e-03 1.92926898704909e-03 + 35 3.20715877104842e+00 -1.24286350841937e-03 1.93088712570063e-03 + 36 3.20853264885916e+00 -1.24341305954367e-03 1.93259504580467e-03 + 37 3.20993281112190e+00 -1.24397312444876e-03 1.93433641793852e-03 + 38 3.21132423111018e+00 -1.24452969244407e-03 1.93606769421867e-03 + 39 3.21268344520547e+00 -1.24507337808219e-03 1.93775964601125e-03 + 40 3.21399913220478e+00 -1.24559965288191e-03 1.93939811907443e-03 diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt b/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt index 494519348..157cac038 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2015-09-16. -colvars: Using NAMD interface, version 2015-07-24. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out index 11f61358e..d2be0212a 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,13 +119,14 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -131,15 +136,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped index 4507a2d83..6d65b453d 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687020515258e+00 + x 3.21687020497026e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj index f58ff8ba4..a79591894 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 - 1 3.20437138788661e+00 -1.12999118519073e-02 1.75395615193509e-02 - 2 3.20383992338449e+00 -1.01805949487011e-02 1.57994685227925e-02 - 3 3.20396643078647e+00 -9.06358197789650e-03 1.40665271010360e-02 - 4 3.20472684453174e+00 -7.94810072200125e-03 1.23383408373197e-02 - 5 3.20606109997726e+00 -6.83333441994998e-03 1.06123771124712e-02 - 6 3.20787717649369e+00 -5.71849400474838e-03 8.88618850063674e-03 - 7 3.21005647716855e+00 -4.60288358620946e-03 7.15761395547176e-03 - 8 3.21246028402867e+00 -3.48595551811211e-03 5.42494905100725e-03 - 9 3.21493732319445e+00 -2.36735236562779e-03 3.68707712042334e-03 - 10 3.21733254799115e+00 -1.24693301919646e-03 1.94355244295300e-03 - 11 3.21949693112495e+00 -1.24779877244998e-03 1.94625222065960e-03 - 12 3.22129751465341e+00 -1.24851900586136e-03 1.94849963499631e-03 - 13 3.22262660690669e+00 -1.24905064276268e-03 1.95015938523232e-03 - 14 3.22340883992570e+00 -1.24936353597028e-03 1.95113655626521e-03 - 15 3.22360524389145e+00 -1.24944209755658e-03 1.95138194393324e-03 - 16 3.22321407479779e+00 -1.24928562991912e-03 1.95089323140301e-03 - 17 3.22226874215941e+00 -1.24890749686377e-03 1.94971241965315e-03 - 18 3.22083355128627e+00 -1.24833342051451e-03 1.94792041096681e-03 - 19 3.21899800422646e+00 -1.24759920169058e-03 1.94562971007373e-03 - 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 + 1 3.20437138788600e+00 -1.12999118519050e-02 1.75395615193440e-02 + 2 3.20383992333029e+00 -1.01805949485234e-02 1.57994685222408e-02 + 3 3.20396643077894e+00 -9.06358197787450e-03 1.40665271009677e-02 + 4 3.20472684448397e+00 -7.94810072187895e-03 1.23383408369400e-02 + 5 3.20606109997218e+00 -6.83333441993879e-03 1.06123771124364e-02 + 6 3.20787717647453e+00 -5.71849400471313e-03 8.88618850052717e-03 + 7 3.21005647713329e+00 -4.60288358615728e-03 7.15761395530948e-03 + 8 3.21246028397626e+00 -3.48595551805342e-03 5.42494905082458e-03 + 9 3.21493732312431e+00 -2.36735236557448e-03 3.68707712025729e-03 + 10 3.21733254790344e+00 -1.24693301916138e-03 1.94355244284363e-03 + 11 3.21949693102052e+00 -1.24779877240821e-03 1.94625222052929e-03 + 12 3.22129751453369e+00 -1.24851900581348e-03 1.94849963484684e-03 + 13 3.22262660677352e+00 -1.24905064270941e-03 1.95015938506598e-03 + 14 3.22340883978115e+00 -1.24936353591246e-03 1.95113655608461e-03 + 15 3.22360524373761e+00 -1.24944209749504e-03 1.95138194374102e-03 + 16 3.22321407463655e+00 -1.24928562985462e-03 1.95089323120157e-03 + 17 3.22226874199272e+00 -1.24890749679709e-03 1.94971241944496e-03 + 18 3.22083355111441e+00 -1.24833342044576e-03 1.94792041075227e-03 + 19 3.21899800404481e+00 -1.24759920161792e-03 1.94562970984710e-03 + 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out index 126710c7e..4e433433c 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,13 +119,14 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -131,20 +136,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped index 32715071f..226b212c1 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21402990715919e+00 + x 3.21402990668451e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj index 0970380b3..2753d1963 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 - 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 - 21 3.21456967651805e+00 -1.24582787060722e-03 1.94010885397715e-03 - 22 3.21221978014351e+00 -1.24488791205741e-03 1.93718239198331e-03 - 23 3.20994003861018e+00 -1.24397601544407e-03 1.93434540875013e-03 - 24 3.20783888769037e+00 -1.24313555507615e-03 1.93173251036810e-03 - 25 3.20600757749894e+00 -1.24240303099958e-03 1.92945661429617e-03 - 26 3.20451585601250e+00 -1.24180634240500e-03 1.92760374004661e-03 - 27 3.20340976322452e+00 -1.24136390528981e-03 1.92623043169546e-03 - 28 3.20271146343875e+00 -1.24108458537550e-03 1.92536368507084e-03 - 29 3.20242066608521e+00 -1.24096826643409e-03 1.92500279787052e-03 - 30 3.20251721571819e+00 -1.24100688628728e-03 1.92512261476555e-03 - 31 3.20296447484878e+00 -1.24118578993951e-03 1.92567770643472e-03 - 32 3.20371334569543e+00 -1.24148533827817e-03 1.92660730644958e-03 - 33 3.20470675738049e+00 -1.24188270295219e-03 1.92784080986481e-03 - 34 3.20588440358750e+00 -1.24235376143500e-03 1.92930358568961e-03 - 35 3.20718731148154e+00 -1.24287492459262e-03 1.93092259772638e-03 - 36 3.20856179675119e+00 -1.24342471870048e-03 1.93263128884420e-03 - 37 3.20996248385038e+00 -1.24398499354015e-03 1.93437333019136e-03 - 38 3.21135434796541e+00 -1.24454173918616e-03 1.93610517572065e-03 - 39 3.21271392828201e+00 -1.24508557131280e-03 1.93779759986417e-03 - 40 3.21402990715919e+00 -1.24561196286367e-03 1.93943645253637e-03 + 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 + 21 3.21456967632931e+00 -1.24582787053172e-03 1.94010885374201e-03 + 22 3.21221977994646e+00 -1.24488791197858e-03 1.93718239173800e-03 + 23 3.20994003840243e+00 -1.24397601536097e-03 1.93434540849171e-03 + 24 3.20783888746925e+00 -1.24313555498770e-03 1.93173251009322e-03 + 25 3.20600757726167e+00 -1.24240303090467e-03 1.92945661400138e-03 + 26 3.20451585575643e+00 -1.24180634230257e-03 1.92760373972862e-03 + 27 3.20340976294734e+00 -1.24136390517894e-03 1.92623043135138e-03 + 28 3.20271146313867e+00 -1.24108458525547e-03 1.92536368469842e-03 + 29 3.20242066576110e+00 -1.24096826630444e-03 1.92500279746831e-03 + 30 3.20251721536965e+00 -1.24100688614786e-03 1.92512261433301e-03 + 31 3.20296447447623e+00 -1.24118578979049e-03 1.92567770597231e-03 + 32 3.20371334530005e+00 -1.24148533812002e-03 1.92660730595873e-03 + 33 3.20470675696420e+00 -1.24188270278568e-03 1.92784080934784e-03 + 34 3.20588440315285e+00 -1.24235376126114e-03 1.92930358514962e-03 + 35 3.20718731103156e+00 -1.24287492441263e-03 1.93092259716711e-03 + 36 3.20856179628928e+00 -1.24342471851571e-03 1.93263128826985e-03 + 37 3.20996248338009e+00 -1.24398499335204e-03 1.93437332960633e-03 + 38 3.21135434749032e+00 -1.24454173899613e-03 1.93610517512938e-03 + 39 3.21271392780555e+00 -1.24508557112222e-03 1.93779759927093e-03 + 40 3.21402990668451e+00 -1.24561196267380e-03 1.93943645194510e-03 diff --git a/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out index 454648299..e8ce74ce1 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,6 +116,7 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -127,15 +132,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped index ed4ff587f..a0bbaca3d 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491541898e+00 + x 3.21685491521323e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj index dfbf0ebd2..d5d525eb6 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095465e+00 -1.20174855638186e-02 - 2 3.20383991842200e+00 -1.20153596736880e-02 - 3 3.20396638983062e+00 -1.20158655593225e-02 - 4 3.20472672278571e+00 -1.20189068911429e-02 - 5 3.20606083671774e+00 -1.20242433468710e-02 - 6 3.20787669546241e+00 -1.20315067818496e-02 - 7 3.21005568758906e+00 -1.20402227503562e-02 - 8 3.21245908146782e+00 -1.20498363258713e-02 - 9 3.21493559054151e+00 -1.20597423621660e-02 - 10 3.21733015647118e+00 -1.20693206258847e-02 - 11 3.21949374131176e+00 -1.20779749652470e-02 - 12 3.22129339470521e+00 -1.20851735788208e-02 - 13 3.22262143329394e+00 -1.20904857331758e-02 - 14 3.22340249785300e+00 -1.20936099914120e-02 - 15 3.22359762741961e+00 -1.20943905096784e-02 - 16 3.22320508669112e+00 -1.20928203467645e-02 - 17 3.22225829350267e+00 -1.20890331740107e-02 - 18 3.22082156092082e+00 -1.20832862436833e-02 - 19 3.21898439806125e+00 -1.20759375922450e-02 - 20 3.21685491541898e+00 -1.20674196616759e-02 + 1 3.20437139095402e+00 -1.20174855638161e-02 + 2 3.20383991841948e+00 -1.20153596736779e-02 + 3 3.20396638982490e+00 -1.20158655592996e-02 + 4 3.20472672277551e+00 -1.20189068911021e-02 + 5 3.20606083670179e+00 -1.20242433468072e-02 + 6 3.20787669543948e+00 -1.20315067817579e-02 + 7 3.21005568755800e+00 -1.20402227502320e-02 + 8 3.21245908142754e+00 -1.20498363257101e-02 + 9 3.21493559049101e+00 -1.20597423619640e-02 + 10 3.21733015640955e+00 -1.20693206256382e-02 + 11 3.21949374123820e+00 -1.20779749649528e-02 + 12 3.22129339461899e+00 -1.20851735784760e-02 + 13 3.22262143319445e+00 -1.20904857327778e-02 + 14 3.22340249773966e+00 -1.20936099909586e-02 + 15 3.22359762729192e+00 -1.20943905091677e-02 + 16 3.22320508654863e+00 -1.20928203461945e-02 + 17 3.22225829334495e+00 -1.20890331733798e-02 + 18 3.22082156074746e+00 -1.20832862429898e-02 + 19 3.21898439787187e+00 -1.20759375914875e-02 + 20 3.21685491521323e+00 -1.20674196608529e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out index 57651fe22..5da67b4d9 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,6 +116,7 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -127,20 +132,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped index 8719ed7ca..f58df11b7 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397364248195e+00 + x 3.21397364200070e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj index fec7bdbdb..8b5e494a7 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685491541898e+00 -1.20674196616759e-02 - 21 3.21455264095509e+00 -1.20582105638204e-02 - 22 3.21220094127252e+00 -1.20488037650901e-02 - 23 3.20991934310164e+00 -1.20396773724066e-02 - 24 3.20781628589752e+00 -1.20312651435901e-02 - 25 3.20598302322006e+00 -1.20239320928802e-02 - 26 3.20448930645441e+00 -1.20179572258176e-02 - 27 3.20338117919211e+00 -1.20135247167684e-02 - 28 3.20268080967909e+00 -1.20107232387163e-02 - 29 3.20238791177794e+00 -1.20095516471117e-02 - 30 3.20248233504303e+00 -1.20099293401721e-02 - 31 3.20292744752838e+00 -1.20117097901135e-02 - 32 3.20367415745526e+00 -1.20146966298210e-02 - 33 3.20466540029545e+00 -1.20186616011818e-02 - 34 3.20584087624535e+00 -1.20233635049814e-02 - 35 3.20714161881621e+00 -1.20285664752649e-02 - 36 3.20851394966204e+00 -1.20340557986482e-02 - 37 3.20991249847373e+00 -1.20396499938949e-02 - 38 3.21130224478131e+00 -1.20452089791253e-02 - 39 3.21265973116698e+00 -1.20506389246679e-02 - 40 3.21397364248195e+00 -1.20558945699278e-02 + 20 3.21685491521323e+00 -1.20674196608529e-02 + 21 3.21455264073267e+00 -1.20582105629307e-02 + 22 3.21220094103318e+00 -1.20488037641327e-02 + 23 3.20991934284523e+00 -1.20396773713809e-02 + 24 3.20781628562398e+00 -1.20312651424959e-02 + 25 3.20598302292944e+00 -1.20239320917178e-02 + 26 3.20448930614687e+00 -1.20179572245875e-02 + 27 3.20338117886792e+00 -1.20135247154717e-02 + 28 3.20268080933861e+00 -1.20107232373544e-02 + 29 3.20238791142161e+00 -1.20095516456865e-02 + 30 3.20248233467135e+00 -1.20099293386854e-02 + 31 3.20292744714189e+00 -1.20117097885676e-02 + 32 3.20367415705454e+00 -1.20146966282182e-02 + 33 3.20466539988114e+00 -1.20186615995246e-02 + 34 3.20584087581816e+00 -1.20233635032726e-02 + 35 3.20714161837695e+00 -1.20285664735078e-02 + 36 3.20851394921166e+00 -1.20340557968466e-02 + 37 3.20991249801338e+00 -1.20396499920535e-02 + 38 3.21130224431234e+00 -1.20452089772494e-02 + 39 3.21265973069097e+00 -1.20506389227639e-02 + 40 3.21397364200070e+00 -1.20558945680028e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out index a58050110..9064d17fa 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,13 +116,14 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.002 @@ -133,15 +138,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped index 75c48b998..bf89cca29 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687111250546e+00 + x 3.21687111229972e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.37880405409319e-02 + accumulatedWork -3.37880405391244e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj index 260962906..dfafafb40 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 0 3.20554673468334e+00 -1.20221869387334e-02 1.80666223487314e-02 0.00000000000000e+00 - 1 3.20437139095465e+00 -1.09007134627866e-02 1.63748958342951e-02 -1.67759907527840e-03 - 2 3.20383993554932e+00 -9.78221064079988e-03 1.46920974903951e-02 -3.35460468848178e-03 - 3 3.20396645809459e+00 -8.66600108902194e-03 1.30161882986166e-02 -5.03175157651451e-03 - 4 3.20472689263580e+00 -7.55129058414933e-03 1.13447829461505e-02 -6.70974768964128e-03 - 5 3.20606117443283e+00 -6.43724359708628e-03 9.67537402378371e-03 -8.38923439865754e-03 - 6 3.20787728240253e+00 -5.32305735345136e-03 8.00555164318605e-03 -1.00707510401243e-02 - 7 3.21005661933959e+00 -4.20802874844884e-03 6.33320239431985e-03 -1.17547052271157e-02 - 8 3.21246046690473e+00 -3.09161036526929e-03 4.65667700222331e-03 -1.34413501180038e-02 - 9 3.21493755084609e+00 -1.97345282367904e-03 2.97491851146660e-03 -1.51307699357301e-02 - 10 3.21733282412455e+00 -8.53430600414092e-04 1.28754208187088e-03 -1.68228752018509e-02 - 11 3.21949725910164e+00 -8.54042795073986e-04 1.28938993944070e-03 -1.85174089474513e-02 - 12 3.22129789752922e+00 -8.54552092531030e-04 1.29092822024660e-03 -2.02139643225496e-02 - 13 3.22262704746820e+00 -8.54928032905055e-04 1.29206429794880e-03 -2.19120127463720e-02 - 14 3.22340934072964e+00 -8.55149298853072e-04 1.29273318893539e-03 -2.36109402358007e-02 - 15 3.22360580730372e+00 -8.55204867991794e-04 1.29290120264720e-03 -2.53100885311281e-02 - 16 3.22321470302893e+00 -8.55094246997852e-04 1.29256674999968e-03 -2.70087972842502e-02 - 17 3.22226943729432e+00 -8.54826885473466e-04 1.29175858507197e-03 -2.87064439360637e-02 - 18 3.22083431530374e+00 -8.54420971676919e-04 1.29053209547840e-03 -3.04024787186191e-02 - 19 3.21899883900822e+00 -8.53901820582810e-04 1.28896430248325e-03 -3.20964530863574e-02 - 20 3.21687111250546e+00 -8.53300008647365e-04 1.28714807319445e-03 -3.37880405409319e-02 + 1 3.20437139095402e+00 -1.09007134627843e-02 1.63748958342883e-02 -1.67759907527770e-03 + 2 3.20383993554679e+00 -9.78221064079167e-03 1.46920974903704e-02 -3.35460468847827e-03 + 3 3.20396645808888e+00 -8.66600108900544e-03 1.30161882985670e-02 -5.03175157650461e-03 + 4 3.20472689262560e+00 -7.55129058412370e-03 1.13447829460735e-02 -6.70974768961999e-03 + 5 3.20606117441688e+00 -6.43724359705212e-03 9.67537402368102e-03 -8.38923439861843e-03 + 6 3.20787728237960e+00 -5.32305735341078e-03 8.00555164306400e-03 -1.00707510400595e-02 + 7 3.21005661930852e+00 -4.20802874840541e-03 6.33320239418913e-03 -1.17547052270162e-02 + 8 3.21246046686444e+00 -3.09161036522795e-03 4.65667700209877e-03 -1.34413501178592e-02 + 9 3.21493755079559e+00 -1.97345282364599e-03 2.97491851136694e-03 -1.51307699355289e-02 + 10 3.21733282406293e+00 -8.53430600396662e-04 1.28754208181829e-03 -1.68228752015806e-02 + 11 3.21949725902808e+00 -8.54042795053181e-04 1.28938993937788e-03 -1.85174089470984e-02 + 12 3.22129789744302e+00 -8.54552092506647e-04 1.29092822017293e-03 -2.02139643220999e-02 + 13 3.22262704736871e+00 -8.54928032876915e-04 1.29206429786374e-03 -2.19120127458105e-02 + 14 3.22340934061631e+00 -8.55149298821016e-04 1.29273318883847e-03 -2.36109402351118e-02 + 15 3.22360580717604e+00 -8.55204867955681e-04 1.29290120253801e-03 -2.53100885302957e-02 + 16 3.22321470288645e+00 -8.55094246957553e-04 1.29256674987784e-03 -2.70087972832577e-02 + 17 3.22226943713660e+00 -8.54826885428858e-04 1.29175858493715e-03 -2.87064439348940e-02 + 18 3.22083431513039e+00 -8.54420971627888e-04 1.29053209533029e-03 -3.04024787172548e-02 + 19 3.21899883881885e+00 -8.53901820529248e-04 1.28896430232155e-03 -3.20964530847806e-02 + 20 3.21687111229972e+00 -8.53300008589174e-04 1.28714807301889e-03 -3.37880405391244e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out index 942b809b4..9014734ce 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,13 +116,14 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.002 @@ -133,20 +138,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped index 520580d86..fc7a79383 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403236536445e+00 + x 3.21403236488325e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.37880405409319e-02 + accumulatedWork -3.37880405391244e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj index 2e304633f..d0e1dbfa0 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 - 20 3.21687111250546e+00 -8.53300008647364e-04 1.28714807319444e-03 -3.37880405409319e-02 - 21 3.21457065814050e+00 -8.52649341894857e-04 1.28518584387952e-03 -3.37880405409319e-02 - 22 3.21222083763125e+00 -8.51984712288192e-04 1.28318305184888e-03 -3.37880405409319e-02 - 23 3.20994117343080e+00 -8.51339925882205e-04 1.28124154774919e-03 -3.37880405409319e-02 - 24 3.20784010115684e+00 -8.50745652901133e-04 1.27945344534044e-03 -3.37880405409319e-02 - 25 3.20600887073836e+00 -8.50227702722403e-04 1.27789600826552e-03 -3.37880405409319e-02 - 26 3.20451722993525e+00 -8.49805802991615e-04 1.27662808859363e-03 -3.37880405409319e-02 - 27 3.20341121849498e+00 -8.49492975715819e-04 1.27568836664879e-03 -3.37880405409319e-02 - 28 3.20271300045200e+00 -8.49295489830646e-04 1.27509530426987e-03 -3.37880405409319e-02 - 29 3.20242228494997e+00 -8.49213263069492e-04 1.27484841285746e-03 -3.37880405409319e-02 - 30 3.20251891624817e+00 -8.49240594527986e-04 1.27493047475806e-03 -3.37880405409319e-02 - 31 3.20296625656595e+00 -8.49367121476866e-04 1.27531040261579e-03 -3.37880405409319e-02 - 32 3.20371520784545e+00 -8.49578956888271e-04 1.27594661653539e-03 -3.37880405409319e-02 - 33 3.20470869895909e+00 -8.49859958609671e-04 1.27679080526574e-03 -3.37880405409319e-02 - 34 3.20588642337721e+00 -8.50193069378641e-04 1.27779190224733e-03 -3.37880405409319e-02 - 35 3.20718940810155e+00 -8.50561609112386e-04 1.27889993093029e-03 -3.37880405409319e-02 - 36 3.20856396871082e+00 -8.50950393563573e-04 1.28006934661783e-03 -3.37880405409319e-02 - 37 3.20996472960913e+00 -8.51346588575580e-04 1.28126160214278e-03 -3.37880405409319e-02 - 38 3.21135666598954e+00 -8.51740287637006e-04 1.28244689643377e-03 -3.37880405409319e-02 - 39 3.21271631709201e+00 -8.52124855042849e-04 1.28360522749363e-03 -3.37880405409319e-02 - 40 3.21403236536445e+00 -8.52497089705972e-04 1.28472690987640e-03 -3.37880405409319e-02 + 20 3.21687111229972e+00 -8.53300008589174e-04 1.28714807301889e-03 -3.37880405391244e-02 + 21 3.21457065791810e+00 -8.52649341831951e-04 1.28518584368989e-03 -3.37880405391244e-02 + 22 3.21222083739193e+00 -8.51984712220503e-04 1.28318305164498e-03 -3.37880405391244e-02 + 23 3.20994117317441e+00 -8.51339925809688e-04 1.28124154753091e-03 -3.37880405391244e-02 + 24 3.20784010088332e+00 -8.50745652823771e-04 1.27945344510775e-03 -3.37880405391244e-02 + 25 3.20600887044777e+00 -8.50227702640212e-04 1.27789600801845e-03 -3.37880405391244e-02 + 26 3.20451722962774e+00 -8.49805802904639e-04 1.27662808833231e-03 -3.37880405391244e-02 + 27 3.20341121817082e+00 -8.49492975624134e-04 1.27568836637342e-03 -3.37880405391244e-02 + 28 3.20271300011156e+00 -8.49295489734355e-04 1.27509530398073e-03 -3.37880405391244e-02 + 29 3.20242228459368e+00 -8.49213262968719e-04 1.27484841255490e-03 -3.37880405391244e-02 + 30 3.20251891587653e+00 -8.49240594422870e-04 1.27493047444245e-03 -3.37880405391244e-02 + 31 3.20296625617950e+00 -8.49367121367561e-04 1.27531040228755e-03 -3.37880405391244e-02 + 32 3.20371520744477e+00 -8.49578956774942e-04 1.27594661619498e-03 -3.37880405391244e-02 + 33 3.20470869854482e+00 -8.49859958492498e-04 1.27679080491367e-03 -3.37880405391244e-02 + 34 3.20588642295006e+00 -8.50193069257824e-04 1.27779190188417e-03 -3.37880405391244e-02 + 35 3.20718940766233e+00 -8.50561608988155e-04 1.27889993055670e-03 -3.37880405391244e-02 + 36 3.20856396826048e+00 -8.50950393436199e-04 1.28006934623462e-03 -3.37880405391244e-02 + 37 3.20996472914883e+00 -8.51346588445386e-04 1.28126160175090e-03 -3.37880405391244e-02 + 38 3.21135666552061e+00 -8.51740287504375e-04 1.28244689603437e-03 -3.37880405391244e-02 + 39 3.21271631661605e+00 -8.52124854908226e-04 1.28360522708805e-03 -3.37880405391244e-02 + 40 3.21403236488325e+00 -8.52497089569868e-04 1.28472690946618e-03 -3.37880405391244e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out index 333ed7f0a..a29b506dc 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,13 +116,14 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.001 [default] @@ -133,15 +138,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped index af765be67..99d5623d0 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687060200527e+00 + x 3.21687060179954e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063098198e-02 + accumulatedWork -3.27231063080692e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj index 6c0216a7f..f2c850ae5 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 0 3.20554673468334e+00 -1.20221869387334e-02 1.80666223487314e-02 0.00000000000000e+00 - 1 3.20437139095465e+00 -1.09359118630749e-02 1.64277703677119e-02 -1.62472454186161e-03 - 2 3.20383993500950e+00 -9.85259498683116e-03 1.47978091424589e-02 -3.24887432579003e-03 - 3 3.20396645594305e+00 -8.77158205135371e-03 1.31747691239093e-02 -4.87316093010762e-03 - 4 3.20472688728247e+00 -7.69210083144311e-03 1.15563310939625e-02 -6.49826999019610e-03 - 5 3.20606116378874e+00 -6.61333456033522e-03 9.94004409248278e-03 -8.12482265987509e-03 - 6 3.20787726390336e+00 -5.53449416558219e-03 8.32353958393024e-03 -9.75334127412231e-03 - 7 3.21005658997269e+00 -4.45488375315958e-03 6.70472609938014e-03 -1.13842205955932e-02 - 8 3.21246042323855e+00 -3.37395567402717e-03 5.08195396888400e-03 -1.30177057998773e-02 - 9 3.21493748906124e+00 -2.29135249168655e-03 3.45414226391983e-03 -1.46538784512077e-02 - 10 3.21733274004549e+00 -1.20693309601820e-03 1.82085937283009e-03 -1.62926518867548e-02 - 11 3.21949714822798e+00 -1.20779885929119e-03 1.82347260563138e-03 -1.79337772318231e-02 - 12 3.22129775560926e+00 -1.20851910224370e-03 1.82564802560991e-03 -1.95768604548720e-02 - 13 3.22262687052069e+00 -1.20905074820828e-03 1.82725463967874e-03 -2.12213896305829e-02 - 14 3.22340912505588e+00 -1.20936365002235e-03 1.82820054749423e-03 -2.28667701233277e-02 - 15 3.22360554949013e+00 -1.20944221979605e-03 1.82843810378150e-03 -2.45123644167310e-02 - 16 3.22321439994115e+00 -1.20928575997646e-03 1.82796506160231e-03 -2.61575329721731e-02 - 17 3.22226908606420e+00 -1.20890763442568e-03 1.82682208571586e-03 -2.78016728493174e-02 - 18 3.22083391331092e+00 -1.20833356532437e-03 1.82508750636188e-03 -2.94442516050430e-02 - 19 3.21899838385817e+00 -1.20759935354327e-03 1.82287024834765e-03 -3.10848348285559e-02 - 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 + 1 3.20437139095402e+00 -1.09359118630726e-02 1.64277703677051e-02 -1.62472454186094e-03 + 2 3.20383993500698e+00 -9.85259498682288e-03 1.47978091424340e-02 -3.24887432578663e-03 + 3 3.20396645593733e+00 -8.77158205133702e-03 1.31747691238592e-02 -4.87316093009804e-03 + 4 3.20472688727227e+00 -7.69210083141700e-03 1.15563310938840e-02 -6.49826999017548e-03 + 5 3.20606116377278e+00 -6.61333456030012e-03 9.94004409237728e-03 -8.12482265983721e-03 + 6 3.20787726388044e+00 -5.53449416554000e-03 8.32353958380334e-03 -9.75334127405960e-03 + 7 3.21005658994163e+00 -4.45488375311361e-03 6.70472609924175e-03 -1.13842205954968e-02 + 8 3.21246042319826e+00 -3.37395567398206e-03 5.08195396874809e-03 -1.30177057997372e-02 + 9 3.21493748901074e+00 -2.29135249164817e-03 3.45414226380412e-03 -1.46538784510129e-02 + 10 3.21733273998387e+00 -1.20693309599355e-03 1.82085937275571e-03 -1.62926518864930e-02 + 11 3.21949714815442e+00 -1.20779885926177e-03 1.82347260554254e-03 -1.79337772314813e-02 + 12 3.22129775552305e+00 -1.20851910220922e-03 1.82564802550573e-03 -1.95768604544364e-02 + 13 3.22262687042120e+00 -1.20905074816848e-03 1.82725463955845e-03 -2.12213896300391e-02 + 14 3.22340912494254e+00 -1.20936364997702e-03 1.82820054735717e-03 -2.28667701226605e-02 + 15 3.22360554936245e+00 -1.20944221974498e-03 1.82843810362708e-03 -2.45123644159249e-02 + 16 3.22321439979867e+00 -1.20928575991947e-03 1.82796506143001e-03 -2.61575329712119e-02 + 17 3.22226908590648e+00 -1.20890763436259e-03 1.82682208552520e-03 -2.78016728481846e-02 + 18 3.22083391313757e+00 -1.20833356525503e-03 1.82508750615241e-03 -2.94442516037217e-02 + 19 3.21899838366880e+00 -1.20759935346752e-03 1.82287024811897e-03 -3.10848348270288e-02 + 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out index 35f57cbba..959f0c552 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,13 +116,14 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.001 [default] @@ -133,20 +138,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped index 1cdd044fd..a9bad9be9 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403051451645e+00 + x 3.21403051403523e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063098198e-02 + accumulatedWork -3.27231063080692e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj index 476fdf462..7cdbd31e7 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 - 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 - 21 3.21457009027428e+00 -1.20582803610971e-03 1.81752656583525e-03 -3.27231063098198e-02 - 22 3.21222021053704e+00 -1.20488808421481e-03 1.81469411935356e-03 -3.27231063098198e-02 - 23 3.20994048538146e+00 -1.20397619415258e-03 1.81194834510767e-03 -3.27231063098198e-02 - 24 3.20783935054617e+00 -1.20313574021847e-03 1.80941951173880e-03 -3.27231063098198e-02 - 25 3.20600805607460e+00 -1.20240322242984e-03 1.80721688663708e-03 -3.27231063098198e-02 - 26 3.20451634984089e+00 -1.20180653993636e-03 1.80542369929224e-03 -3.27231063098198e-02 - 27 3.20341027171365e+00 -1.20136410868546e-03 1.80409465204701e-03 -3.27231063098198e-02 - 28 3.20271198586007e+00 -1.20108479434403e-03 1.80325585400555e-03 -3.27231063098198e-02 - 29 3.20242120157252e+00 -1.20096848062901e-03 1.80290661433043e-03 -3.27231063098198e-02 - 30 3.20251776327717e+00 -1.20100710531087e-03 1.80302258375899e-03 -3.27231063098198e-02 - 31 3.20296503337725e+00 -1.20118601335090e-03 1.80355979833728e-03 -3.27231063098198e-02 - 32 3.20371391401280e+00 -1.20148556560512e-03 1.80445945544681e-03 -3.27231063098198e-02 - 33 3.20470733426422e+00 -1.20188293370569e-03 1.80565323291624e-03 -3.27231063098198e-02 - 34 3.20588498781384e+00 -1.20235399512554e-03 1.80706891199292e-03 -3.27231063098198e-02 - 35 3.20718790186854e+00 -1.20287516074742e-03 1.80863581542890e-03 -3.27231063098198e-02 - 36 3.20856239219851e+00 -1.20342495687940e-03 1.81028953355024e-03 -3.27231063098198e-02 - 37 3.20996308337448e+00 -1.20398523334979e-03 1.81197555265544e-03 -3.27231063098198e-02 - 38 3.21135495072621e+00 -1.20454198029048e-03 1.81365172785265e-03 -3.27231063098198e-02 - 39 3.21271453359899e+00 -1.20508581343960e-03 1.81528977219172e-03 -3.27231063098198e-02 - 40 3.21403051451645e+00 -1.20561220580658e-03 1.81687598848726e-03 -3.27231063098198e-02 + 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 + 21 3.21457009005187e+00 -1.20582803602075e-03 1.81752656556706e-03 -3.27231063080692e-02 + 22 3.21222021029772e+00 -1.20488808411909e-03 1.81469411906520e-03 -3.27231063080692e-02 + 23 3.20994048512507e+00 -1.20397619405003e-03 1.81194834479899e-03 -3.27231063080692e-02 + 24 3.20783935027265e+00 -1.20313574010906e-03 1.80941951140972e-03 -3.27231063080692e-02 + 25 3.20600805578400e+00 -1.20240322231360e-03 1.80721688628766e-03 -3.27231063080692e-02 + 26 3.20451634953337e+00 -1.20180653981335e-03 1.80542369892267e-03 -3.27231063080692e-02 + 27 3.20341027138948e+00 -1.20136410855579e-03 1.80409465165757e-03 -3.27231063080692e-02 + 28 3.20271198551962e+00 -1.20108479420785e-03 1.80325585359664e-03 -3.27231063080692e-02 + 29 3.20242120121622e+00 -1.20096848048649e-03 1.80290661390253e-03 -3.27231063080692e-02 + 30 3.20251776290552e+00 -1.20100710516221e-03 1.80302258331263e-03 -3.27231063080692e-02 + 31 3.20296503299079e+00 -1.20118601319632e-03 1.80355979787307e-03 -3.27231063080692e-02 + 32 3.20371391361211e+00 -1.20148556544484e-03 1.80445945496540e-03 -3.27231063080692e-02 + 33 3.20470733384994e+00 -1.20188293353998e-03 1.80565323241832e-03 -3.27231063080692e-02 + 34 3.20588498738668e+00 -1.20235399495467e-03 1.80706891147932e-03 -3.27231063080692e-02 + 35 3.20718790142930e+00 -1.20287516057172e-03 1.80863581490056e-03 -3.27231063080692e-02 + 36 3.20856239174816e+00 -1.20342495669926e-03 1.81028953300828e-03 -3.27231063080692e-02 + 37 3.20996308291416e+00 -1.20398523316567e-03 1.81197555210123e-03 -3.27231063080692e-02 + 38 3.21135495025727e+00 -1.20454198010291e-03 1.81365172728779e-03 -3.27231063080692e-02 + 39 3.21271453312301e+00 -1.20508581324920e-03 1.81528977161812e-03 -3.27231063080692e-02 + 40 3.21403051403523e+00 -1.20561220561409e-03 1.81687598790710e-03 -3.27231063080692e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out index 2432c858b..29a8ea10b 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,6 +116,7 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -126,15 +131,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped index ed4ff587f..a0bbaca3d 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491541898e+00 + x 3.21685491521323e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj index dfbf0ebd2..d5d525eb6 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095465e+00 -1.20174855638186e-02 - 2 3.20383991842200e+00 -1.20153596736880e-02 - 3 3.20396638983062e+00 -1.20158655593225e-02 - 4 3.20472672278571e+00 -1.20189068911429e-02 - 5 3.20606083671774e+00 -1.20242433468710e-02 - 6 3.20787669546241e+00 -1.20315067818496e-02 - 7 3.21005568758906e+00 -1.20402227503562e-02 - 8 3.21245908146782e+00 -1.20498363258713e-02 - 9 3.21493559054151e+00 -1.20597423621660e-02 - 10 3.21733015647118e+00 -1.20693206258847e-02 - 11 3.21949374131176e+00 -1.20779749652470e-02 - 12 3.22129339470521e+00 -1.20851735788208e-02 - 13 3.22262143329394e+00 -1.20904857331758e-02 - 14 3.22340249785300e+00 -1.20936099914120e-02 - 15 3.22359762741961e+00 -1.20943905096784e-02 - 16 3.22320508669112e+00 -1.20928203467645e-02 - 17 3.22225829350267e+00 -1.20890331740107e-02 - 18 3.22082156092082e+00 -1.20832862436833e-02 - 19 3.21898439806125e+00 -1.20759375922450e-02 - 20 3.21685491541898e+00 -1.20674196616759e-02 + 1 3.20437139095402e+00 -1.20174855638161e-02 + 2 3.20383991841948e+00 -1.20153596736779e-02 + 3 3.20396638982490e+00 -1.20158655592996e-02 + 4 3.20472672277551e+00 -1.20189068911021e-02 + 5 3.20606083670179e+00 -1.20242433468072e-02 + 6 3.20787669543948e+00 -1.20315067817579e-02 + 7 3.21005568755800e+00 -1.20402227502320e-02 + 8 3.21245908142754e+00 -1.20498363257101e-02 + 9 3.21493559049101e+00 -1.20597423619640e-02 + 10 3.21733015640955e+00 -1.20693206256382e-02 + 11 3.21949374123820e+00 -1.20779749649528e-02 + 12 3.22129339461899e+00 -1.20851735784760e-02 + 13 3.22262143319445e+00 -1.20904857327778e-02 + 14 3.22340249773966e+00 -1.20936099909586e-02 + 15 3.22359762729192e+00 -1.20943905091677e-02 + 16 3.22320508654863e+00 -1.20928203461945e-02 + 17 3.22225829334495e+00 -1.20890331733798e-02 + 18 3.22082156074746e+00 -1.20832862429898e-02 + 19 3.21898439787187e+00 -1.20759375914875e-02 + 20 3.21685491521323e+00 -1.20674196608529e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out index 57b080e73..95f077f0b 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,6 +116,7 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -126,20 +131,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped index 8719ed7ca..f58df11b7 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397364248195e+00 + x 3.21397364200070e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj index fec7bdbdb..8b5e494a7 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685491541898e+00 -1.20674196616759e-02 - 21 3.21455264095509e+00 -1.20582105638204e-02 - 22 3.21220094127252e+00 -1.20488037650901e-02 - 23 3.20991934310164e+00 -1.20396773724066e-02 - 24 3.20781628589752e+00 -1.20312651435901e-02 - 25 3.20598302322006e+00 -1.20239320928802e-02 - 26 3.20448930645441e+00 -1.20179572258176e-02 - 27 3.20338117919211e+00 -1.20135247167684e-02 - 28 3.20268080967909e+00 -1.20107232387163e-02 - 29 3.20238791177794e+00 -1.20095516471117e-02 - 30 3.20248233504303e+00 -1.20099293401721e-02 - 31 3.20292744752838e+00 -1.20117097901135e-02 - 32 3.20367415745526e+00 -1.20146966298210e-02 - 33 3.20466540029545e+00 -1.20186616011818e-02 - 34 3.20584087624535e+00 -1.20233635049814e-02 - 35 3.20714161881621e+00 -1.20285664752649e-02 - 36 3.20851394966204e+00 -1.20340557986482e-02 - 37 3.20991249847373e+00 -1.20396499938949e-02 - 38 3.21130224478131e+00 -1.20452089791253e-02 - 39 3.21265973116698e+00 -1.20506389246679e-02 - 40 3.21397364248195e+00 -1.20558945699278e-02 + 20 3.21685491521323e+00 -1.20674196608529e-02 + 21 3.21455264073267e+00 -1.20582105629307e-02 + 22 3.21220094103318e+00 -1.20488037641327e-02 + 23 3.20991934284523e+00 -1.20396773713809e-02 + 24 3.20781628562398e+00 -1.20312651424959e-02 + 25 3.20598302292944e+00 -1.20239320917178e-02 + 26 3.20448930614687e+00 -1.20179572245875e-02 + 27 3.20338117886792e+00 -1.20135247154717e-02 + 28 3.20268080933861e+00 -1.20107232373544e-02 + 29 3.20238791142161e+00 -1.20095516456865e-02 + 30 3.20248233467135e+00 -1.20099293386854e-02 + 31 3.20292744714189e+00 -1.20117097885676e-02 + 32 3.20367415705454e+00 -1.20146966282182e-02 + 33 3.20466539988114e+00 -1.20186615995246e-02 + 34 3.20584087581816e+00 -1.20233635032726e-02 + 35 3.20714161837695e+00 -1.20285664735078e-02 + 36 3.20851394921166e+00 -1.20340557968466e-02 + 37 3.20991249801338e+00 -1.20396499920535e-02 + 38 3.21130224431234e+00 -1.20452089772494e-02 + 39 3.21265973069097e+00 -1.20506389227639e-02 + 40 3.21397364200070e+00 -1.20558945680028e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out index be491208e..188ad78a8 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out @@ -7,7 +7,6 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -153,10 +152,12 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out index 27cae7081..abd39e0f9 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out @@ -7,7 +7,6 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -153,6 +152,7 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.1979 @@ -162,6 +162,7 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt index d885e1c46..157cac038 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2022-05-24. -colvars: Using NAMD interface, version "2022-05-09". +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out index 0dd351c58..c92a480be 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,13 +116,14 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. colvars: # upperWalls = { 0.2 } @@ -132,15 +137,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped index af765be67..99d5623d0 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687060200527e+00 + x 3.21687060179954e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063098198e-02 + accumulatedWork -3.27231063080692e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj index 6c0216a7f..f2c850ae5 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 0 3.20554673468334e+00 -1.20221869387334e-02 1.80666223487314e-02 0.00000000000000e+00 - 1 3.20437139095465e+00 -1.09359118630749e-02 1.64277703677119e-02 -1.62472454186161e-03 - 2 3.20383993500950e+00 -9.85259498683116e-03 1.47978091424589e-02 -3.24887432579003e-03 - 3 3.20396645594305e+00 -8.77158205135371e-03 1.31747691239093e-02 -4.87316093010762e-03 - 4 3.20472688728247e+00 -7.69210083144311e-03 1.15563310939625e-02 -6.49826999019610e-03 - 5 3.20606116378874e+00 -6.61333456033522e-03 9.94004409248278e-03 -8.12482265987509e-03 - 6 3.20787726390336e+00 -5.53449416558219e-03 8.32353958393024e-03 -9.75334127412231e-03 - 7 3.21005658997269e+00 -4.45488375315958e-03 6.70472609938014e-03 -1.13842205955932e-02 - 8 3.21246042323855e+00 -3.37395567402717e-03 5.08195396888400e-03 -1.30177057998773e-02 - 9 3.21493748906124e+00 -2.29135249168655e-03 3.45414226391983e-03 -1.46538784512077e-02 - 10 3.21733274004549e+00 -1.20693309601820e-03 1.82085937283009e-03 -1.62926518867548e-02 - 11 3.21949714822798e+00 -1.20779885929119e-03 1.82347260563138e-03 -1.79337772318231e-02 - 12 3.22129775560926e+00 -1.20851910224370e-03 1.82564802560991e-03 -1.95768604548720e-02 - 13 3.22262687052069e+00 -1.20905074820828e-03 1.82725463967874e-03 -2.12213896305829e-02 - 14 3.22340912505588e+00 -1.20936365002235e-03 1.82820054749423e-03 -2.28667701233277e-02 - 15 3.22360554949013e+00 -1.20944221979605e-03 1.82843810378150e-03 -2.45123644167310e-02 - 16 3.22321439994115e+00 -1.20928575997646e-03 1.82796506160231e-03 -2.61575329721731e-02 - 17 3.22226908606420e+00 -1.20890763442568e-03 1.82682208571586e-03 -2.78016728493174e-02 - 18 3.22083391331092e+00 -1.20833356532437e-03 1.82508750636188e-03 -2.94442516050430e-02 - 19 3.21899838385817e+00 -1.20759935354327e-03 1.82287024834765e-03 -3.10848348285559e-02 - 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 + 1 3.20437139095402e+00 -1.09359118630726e-02 1.64277703677051e-02 -1.62472454186094e-03 + 2 3.20383993500698e+00 -9.85259498682288e-03 1.47978091424340e-02 -3.24887432578663e-03 + 3 3.20396645593733e+00 -8.77158205133702e-03 1.31747691238592e-02 -4.87316093009804e-03 + 4 3.20472688727227e+00 -7.69210083141700e-03 1.15563310938840e-02 -6.49826999017548e-03 + 5 3.20606116377278e+00 -6.61333456030012e-03 9.94004409237728e-03 -8.12482265983721e-03 + 6 3.20787726388044e+00 -5.53449416554000e-03 8.32353958380334e-03 -9.75334127405960e-03 + 7 3.21005658994163e+00 -4.45488375311361e-03 6.70472609924175e-03 -1.13842205954968e-02 + 8 3.21246042319826e+00 -3.37395567398206e-03 5.08195396874809e-03 -1.30177057997372e-02 + 9 3.21493748901074e+00 -2.29135249164817e-03 3.45414226380412e-03 -1.46538784510129e-02 + 10 3.21733273998387e+00 -1.20693309599355e-03 1.82085937275571e-03 -1.62926518864930e-02 + 11 3.21949714815442e+00 -1.20779885926177e-03 1.82347260554254e-03 -1.79337772314813e-02 + 12 3.22129775552305e+00 -1.20851910220922e-03 1.82564802550573e-03 -1.95768604544364e-02 + 13 3.22262687042120e+00 -1.20905074816848e-03 1.82725463955845e-03 -2.12213896300391e-02 + 14 3.22340912494254e+00 -1.20936364997702e-03 1.82820054735717e-03 -2.28667701226605e-02 + 15 3.22360554936245e+00 -1.20944221974498e-03 1.82843810362708e-03 -2.45123644159249e-02 + 16 3.22321439979867e+00 -1.20928575991947e-03 1.82796506143001e-03 -2.61575329712119e-02 + 17 3.22226908590648e+00 -1.20890763436259e-03 1.82682208552520e-03 -2.78016728481846e-02 + 18 3.22083391313757e+00 -1.20833356525503e-03 1.82508750615241e-03 -2.94442516037217e-02 + 19 3.21899838366880e+00 -1.20759935346752e-03 1.82287024811897e-03 -3.10848348270288e-02 + 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out index 0bd2a2834..0187122c8 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,13 +116,14 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. colvars: # upperWalls = { 0.2 } @@ -132,20 +137,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped index 1cdd044fd..a9bad9be9 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403051451645e+00 + x 3.21403051403523e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063098198e-02 + accumulatedWork -3.27231063080692e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj index 476fdf462..7cdbd31e7 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 - 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 - 21 3.21457009027428e+00 -1.20582803610971e-03 1.81752656583525e-03 -3.27231063098198e-02 - 22 3.21222021053704e+00 -1.20488808421481e-03 1.81469411935356e-03 -3.27231063098198e-02 - 23 3.20994048538146e+00 -1.20397619415258e-03 1.81194834510767e-03 -3.27231063098198e-02 - 24 3.20783935054617e+00 -1.20313574021847e-03 1.80941951173880e-03 -3.27231063098198e-02 - 25 3.20600805607460e+00 -1.20240322242984e-03 1.80721688663708e-03 -3.27231063098198e-02 - 26 3.20451634984089e+00 -1.20180653993636e-03 1.80542369929224e-03 -3.27231063098198e-02 - 27 3.20341027171365e+00 -1.20136410868546e-03 1.80409465204701e-03 -3.27231063098198e-02 - 28 3.20271198586007e+00 -1.20108479434403e-03 1.80325585400555e-03 -3.27231063098198e-02 - 29 3.20242120157252e+00 -1.20096848062901e-03 1.80290661433043e-03 -3.27231063098198e-02 - 30 3.20251776327717e+00 -1.20100710531087e-03 1.80302258375899e-03 -3.27231063098198e-02 - 31 3.20296503337725e+00 -1.20118601335090e-03 1.80355979833728e-03 -3.27231063098198e-02 - 32 3.20371391401280e+00 -1.20148556560512e-03 1.80445945544681e-03 -3.27231063098198e-02 - 33 3.20470733426422e+00 -1.20188293370569e-03 1.80565323291624e-03 -3.27231063098198e-02 - 34 3.20588498781384e+00 -1.20235399512554e-03 1.80706891199292e-03 -3.27231063098198e-02 - 35 3.20718790186854e+00 -1.20287516074742e-03 1.80863581542890e-03 -3.27231063098198e-02 - 36 3.20856239219851e+00 -1.20342495687940e-03 1.81028953355024e-03 -3.27231063098198e-02 - 37 3.20996308337448e+00 -1.20398523334979e-03 1.81197555265544e-03 -3.27231063098198e-02 - 38 3.21135495072621e+00 -1.20454198029048e-03 1.81365172785265e-03 -3.27231063098198e-02 - 39 3.21271453359899e+00 -1.20508581343960e-03 1.81528977219172e-03 -3.27231063098198e-02 - 40 3.21403051451645e+00 -1.20561220580658e-03 1.81687598848726e-03 -3.27231063098198e-02 + 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 + 21 3.21457009005187e+00 -1.20582803602075e-03 1.81752656556706e-03 -3.27231063080692e-02 + 22 3.21222021029772e+00 -1.20488808411909e-03 1.81469411906520e-03 -3.27231063080692e-02 + 23 3.20994048512507e+00 -1.20397619405003e-03 1.81194834479899e-03 -3.27231063080692e-02 + 24 3.20783935027265e+00 -1.20313574010906e-03 1.80941951140972e-03 -3.27231063080692e-02 + 25 3.20600805578400e+00 -1.20240322231360e-03 1.80721688628766e-03 -3.27231063080692e-02 + 26 3.20451634953337e+00 -1.20180653981335e-03 1.80542369892267e-03 -3.27231063080692e-02 + 27 3.20341027138948e+00 -1.20136410855579e-03 1.80409465165757e-03 -3.27231063080692e-02 + 28 3.20271198551962e+00 -1.20108479420785e-03 1.80325585359664e-03 -3.27231063080692e-02 + 29 3.20242120121622e+00 -1.20096848048649e-03 1.80290661390253e-03 -3.27231063080692e-02 + 30 3.20251776290552e+00 -1.20100710516221e-03 1.80302258331263e-03 -3.27231063080692e-02 + 31 3.20296503299079e+00 -1.20118601319632e-03 1.80355979787307e-03 -3.27231063080692e-02 + 32 3.20371391361211e+00 -1.20148556544484e-03 1.80445945496540e-03 -3.27231063080692e-02 + 33 3.20470733384994e+00 -1.20188293353998e-03 1.80565323241832e-03 -3.27231063080692e-02 + 34 3.20588498738668e+00 -1.20235399495467e-03 1.80706891147932e-03 -3.27231063080692e-02 + 35 3.20718790142930e+00 -1.20287516057172e-03 1.80863581490056e-03 -3.27231063080692e-02 + 36 3.20856239174816e+00 -1.20342495669926e-03 1.81028953300828e-03 -3.27231063080692e-02 + 37 3.20996308291416e+00 -1.20398523316567e-03 1.81197555210123e-03 -3.27231063080692e-02 + 38 3.21135495025727e+00 -1.20454198010291e-03 1.81365172728779e-03 -3.27231063080692e-02 + 39 3.21271453312301e+00 -1.20508581324920e-03 1.81528977161812e-03 -3.27231063080692e-02 + 40 3.21403051403523e+00 -1.20561220561409e-03 1.81687598790710e-03 -3.27231063080692e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out index a86d5ad83..c19bd65ec 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out @@ -4,10 +4,9 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -142,10 +142,12 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat index 1b0ff42d4..6ff3132f9 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 0.6 0.2 24 0 +# 6.00000000000000e-01 2.00000000000000e-01 24 0 - 0.7 0 - 0.9 0 - 1.1 0 - 1.3 0 - 1.5 0 - 1.7 0 - 1.9 0 - 2.1 0 - 2.3 0 - 2.5 0 - 2.7 0 - 2.9 0 - 3.1 0 - 3.3 20 - 3.5 0 - 3.7 0 - 3.9 0 - 4.1 0 - 4.3 0 - 4.5 0 - 4.7 0 - 4.9 0 - 5.1 0 - 5.3 0 + 7.00000000000000e-01 0.00000000000000e+00 + 9.00000000000000e-01 0.00000000000000e+00 + 1.10000000000000e+00 0.00000000000000e+00 + 1.30000000000000e+00 0.00000000000000e+00 + 1.50000000000000e+00 0.00000000000000e+00 + 1.70000000000000e+00 0.00000000000000e+00 + 1.90000000000000e+00 0.00000000000000e+00 + 2.10000000000000e+00 0.00000000000000e+00 + 2.30000000000000e+00 0.00000000000000e+00 + 2.50000000000000e+00 0.00000000000000e+00 + 2.70000000000000e+00 0.00000000000000e+00 + 2.90000000000000e+00 0.00000000000000e+00 + 3.10000000000000e+00 0.00000000000000e+00 + 3.30000000000000e+00 2.00000000000000e+01 + 3.50000000000000e+00 0.00000000000000e+00 + 3.70000000000000e+00 0.00000000000000e+00 + 3.90000000000000e+00 0.00000000000000e+00 + 4.10000000000000e+00 0.00000000000000e+00 + 4.30000000000000e+00 0.00000000000000e+00 + 4.50000000000000e+00 0.00000000000000e+00 + 4.70000000000000e+00 0.00000000000000e+00 + 4.90000000000000e+00 0.00000000000000e+00 + 5.10000000000000e+00 0.00000000000000e+00 + 5.30000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out index cc179e493..a44f3ed1b 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out @@ -4,10 +4,9 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -142,6 +142,7 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 @@ -151,6 +152,7 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out index 2f8db54b9..6e8a55a99 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,6 +119,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -125,15 +130,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped index 54969f08b..e2cb5b6df 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687794941120e+00 + x 3.21687794922887e+00 } restraint { diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj index 60f1c7042..31625d56a 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -2.00000000000000e-03 - 1 3.20437146782535e+00 -2.00000000000000e-03 - 2 3.20384022479972e+00 -2.00000000000000e-03 - 3 3.20396707508047e+00 -2.00000000000000e-03 - 4 3.20472793158710e+00 -2.00000000000000e-03 - 5 3.20606270721620e+00 -2.00000000000000e-03 - 6 3.20787935839808e+00 -2.00000000000000e-03 - 7 3.21005926525274e+00 -2.00000000000000e-03 - 8 3.21246368724284e+00 -2.00000000000000e-03 - 9 3.21494132872828e+00 -2.00000000000000e-03 - 10 3.21733712243639e+00 -2.00000000000000e-03 - 11 3.21950202193975e+00 -2.00000000000000e-03 - 12 3.22130306909382e+00 -2.00000000000000e-03 - 13 3.22263257365056e+00 -2.00000000000000e-03 - 14 3.22341517047102e+00 -2.00000000000000e-03 - 15 3.22361189364914e+00 -2.00000000000000e-03 - 16 3.22322100382672e+00 -2.00000000000000e-03 - 17 3.22227591551750e+00 -2.00000000000000e-03 - 18 3.22084093900392e+00 -2.00000000000000e-03 - 19 3.21900558093302e+00 -2.00000000000000e-03 - 20 3.21687794941120e+00 -2.00000000000000e-03 + 1 3.20437146782473e+00 -2.00000000000000e-03 + 2 3.20384022474555e+00 -2.00000000000000e-03 + 3 3.20396707507294e+00 -2.00000000000000e-03 + 4 3.20472793153934e+00 -2.00000000000000e-03 + 5 3.20606270721111e+00 -2.00000000000000e-03 + 6 3.20787935837892e+00 -2.00000000000000e-03 + 7 3.21005926521749e+00 -2.00000000000000e-03 + 8 3.21246368719045e+00 -2.00000000000000e-03 + 9 3.21494132865815e+00 -2.00000000000000e-03 + 10 3.21733712234869e+00 -2.00000000000000e-03 + 11 3.21950202183533e+00 -2.00000000000000e-03 + 12 3.22130306897412e+00 -2.00000000000000e-03 + 13 3.22263257351741e+00 -2.00000000000000e-03 + 14 3.22341517032649e+00 -2.00000000000000e-03 + 15 3.22361189349532e+00 -2.00000000000000e-03 + 16 3.22322100366549e+00 -2.00000000000000e-03 + 17 3.22227591535082e+00 -2.00000000000000e-03 + 18 3.22084093883207e+00 -2.00000000000000e-03 + 19 3.21900558075137e+00 -2.00000000000000e-03 + 20 3.21687794922887e+00 -2.00000000000000e-03 diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out index ae73096ad..f25f2a600 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,6 +119,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -125,20 +130,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting linear bias "linear1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped index 7819eca62..8bd282397 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403631097325e+00 + x 3.21403631049857e+00 } restraint { diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj index 22b58b046..feadd768c 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21687794941120e+00 -2.00000000000000e-03 - 21 3.21457756992910e+00 -2.00000000000000e-03 - 22 3.21222780628590e+00 -2.00000000000000e-03 - 23 3.20994818190026e+00 -2.00000000000000e-03 - 24 3.20784713225907e+00 -2.00000000000000e-03 - 25 3.20601590617646e+00 -2.00000000000000e-03 - 26 3.20452424952068e+00 -2.00000000000000e-03 - 27 3.20341819963022e+00 -2.00000000000000e-03 - 28 3.20271991791227e+00 -2.00000000000000e-03 - 29 3.20242911095567e+00 -2.00000000000000e-03 - 30 3.20252562081973e+00 -2.00000000000000e-03 - 31 3.20297280813812e+00 -2.00000000000000e-03 - 32 3.20372157409621e+00 -2.00000000000000e-03 - 33 3.20471484778801e+00 -2.00000000000000e-03 - 34 3.20589232395536e+00 -2.00000000000000e-03 - 35 3.20719503191152e+00 -2.00000000000000e-03 - 36 3.20856929046496e+00 -2.00000000000000e-03 - 37 3.20996972798345e+00 -2.00000000000000e-03 - 38 3.21136132411101e+00 -2.00000000000000e-03 - 39 3.21272062275390e+00 -2.00000000000000e-03 - 40 3.21403631097325e+00 -2.00000000000000e-03 + 20 3.21687794922887e+00 -2.00000000000000e-03 + 21 3.21457756974034e+00 -2.00000000000000e-03 + 22 3.21222780608884e+00 -2.00000000000000e-03 + 23 3.20994818169250e+00 -2.00000000000000e-03 + 24 3.20784713203794e+00 -2.00000000000000e-03 + 25 3.20601590593918e+00 -2.00000000000000e-03 + 26 3.20452424926460e+00 -2.00000000000000e-03 + 27 3.20341819935304e+00 -2.00000000000000e-03 + 28 3.20271991761219e+00 -2.00000000000000e-03 + 29 3.20242911063155e+00 -2.00000000000000e-03 + 30 3.20252562047120e+00 -2.00000000000000e-03 + 31 3.20297280776558e+00 -2.00000000000000e-03 + 32 3.20372157370085e+00 -2.00000000000000e-03 + 33 3.20471484737174e+00 -2.00000000000000e-03 + 34 3.20589232352072e+00 -2.00000000000000e-03 + 35 3.20719503146155e+00 -2.00000000000000e-03 + 36 3.20856929000306e+00 -2.00000000000000e-03 + 37 3.20996972751317e+00 -2.00000000000000e-03 + 38 3.21136132363592e+00 -2.00000000000000e-03 + 39 3.21272062227744e+00 -2.00000000000000e-03 + 40 3.21403631049857e+00 -2.00000000000000e-03 diff --git a/namd/tests/library/000_distance_linear-fixed/namd-version.txt b/namd/tests/library/000_distance_linear-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distance_linear-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_linear-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out index 5461163f6..3d1d47403 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,13 +119,14 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -0.1 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -131,15 +136,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped index d40e34747..7978e66e5 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21716984778310e+00 + x 3.21716984757735e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name linear1 firstStep 0 forceConstant -1.00000000000000e-01 - accumulatedWork -1.25846317032503e+00 + accumulatedWork -1.25846317029250e+00 } } diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj index d7a3f40f3..ab81a1e48 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_linear1 W_linear1 0 3.20554673468334e+00 -2.00000000000000e-03 6.21109346936669e-03 0.00000000000000e+00 - 1 3.20437146782536e+00 1.82000000000000e-02 -5.64995607144215e-02 -6.27083036500722e-02 - 2 3.20384053454426e+00 3.84000000000000e-02 -1.19187476526499e-01 -1.25405882447866e-01 - 3 3.20396830993637e+00 5.86000000000000e-02 -1.81892542962271e-01 -1.88106042308581e-01 - 4 3.20473100411451e+00 7.88000000000000e-02 -2.44652803124223e-01 -2.50821608591694e-01 - 5 3.20606881619079e+00 9.90000000000000e-02 -3.07500812802888e-01 -3.13564198678748e-01 - 6 3.20788997451609e+00 1.19200000000000e-01 -3.70460484962318e-01 -3.76343576163973e-01 - 7 3.21007611528435e+00 1.39400000000000e-01 -4.33544610470638e-01 -4.39167113692717e-01 - 8 3.21248873646155e+00 1.59600000000000e-01 -4.96753202339263e-01 -5.02039386169240e-01 - 9 3.21497676250368e+00 1.79800000000000e-01 -5.60072821898162e-01 -5.64961916771815e-01 - 10 3.21738532756148e+00 2.00000000000000e-01 -6.23477065512297e-01 -6.27933100388556e-01 - 11 3.21956556835082e+00 2.00000000000000e-01 -6.23913113670165e-01 -6.90948324869243e-01 - 12 3.22138438220801e+00 2.00000000000000e-01 -6.24276876441603e-01 -7.54000289389845e-01 - 13 3.22273392239524e+00 2.00000000000000e-01 -6.24546784479049e-01 -8.17079514622229e-01 - 14 3.22353866101367e+00 2.00000000000000e-01 -6.24707732202734e-01 -8.80174995574705e-01 - 15 3.22375946860855e+00 2.00000000000000e-01 -6.24751893721710e-01 -9.43274936840598e-01 - 16 3.22339444640630e+00 2.00000000000000e-01 -6.24678889281260e-01 -1.00636750465800e+00 - 17 3.22247685766515e+00 2.00000000000000e-01 -6.24495371533031e-01 -1.06944153718284e+00 - 18 3.22107087258327e+00 2.00000000000000e-01 -6.24214174516655e-01 -1.13248716880902e+00 - 19 3.21926587083132e+00 2.00000000000000e-01 -6.23853174166263e-01 -1.19549633939982e+00 - 20 3.21716984778310e+00 2.00000000000000e-01 -6.23433969556620e-01 -1.25846317032503e+00 + 1 3.20437146782473e+00 1.82000000000000e-02 -5.64995607144102e-02 -6.27083036500596e-02 + 2 3.20384053454173e+00 3.84000000000000e-02 -1.19187476526403e-01 -1.25405882447803e-01 + 3 3.20396830993065e+00 5.86000000000000e-02 -1.81892542961936e-01 -1.88106042308402e-01 + 4 3.20473100410431e+00 7.88000000000000e-02 -2.44652803123419e-01 -2.50821608591309e-01 + 5 3.20606881617484e+00 9.90000000000000e-02 -3.07500812801309e-01 -3.13564198678041e-01 + 6 3.20788997449316e+00 1.19200000000000e-01 -3.70460484959585e-01 -3.76343576162802e-01 + 7 3.21007611525328e+00 1.39400000000000e-01 -4.33544610466307e-01 -4.39167113690919e-01 + 8 3.21248873642126e+00 1.59600000000000e-01 -4.96753202332834e-01 -5.02039386166628e-01 + 9 3.21497676245318e+00 1.79800000000000e-01 -5.60072821889081e-01 -5.64961916768182e-01 + 10 3.21738532749986e+00 2.00000000000000e-01 -6.23477065499971e-01 -6.27933100383679e-01 + 11 3.21956556827726e+00 2.00000000000000e-01 -6.23913113655452e-01 -6.90948324862880e-01 + 12 3.22138438212180e+00 2.00000000000000e-01 -6.24276876424360e-01 -7.54000289381740e-01 + 13 3.22273392229575e+00 2.00000000000000e-01 -6.24546784459149e-01 -8.17079514612114e-01 + 14 3.22353866090033e+00 2.00000000000000e-01 -6.24707732180065e-01 -8.80174995562301e-01 + 15 3.22375946848086e+00 2.00000000000000e-01 -6.24751893696173e-01 -9.43274936825614e-01 + 16 3.22339444626381e+00 2.00000000000000e-01 -6.24678889252761e-01 -1.00636750464014e+00 + 17 3.22247685750743e+00 2.00000000000000e-01 -6.24495371501486e-01 -1.06944153716179e+00 + 18 3.22107087240991e+00 2.00000000000000e-01 -6.24214174481982e-01 -1.13248716878447e+00 + 19 3.21926587064193e+00 2.00000000000000e-01 -6.23853174128386e-01 -1.19549633937144e+00 + 20 3.21716984757735e+00 2.00000000000000e-01 -6.23433969515469e-01 -1.25846317029250e+00 diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out index bffe886e1..1abc5a030 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,13 +119,14 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -0.1 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # targetForceExponent = 1 [default] +colvars: # lambdaExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -131,20 +136,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21717 colvars: Restarting linear bias "linear1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped index c2d3e24ea..329d673d2 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21509555130398e+00 + x 3.21509555082278e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name linear1 firstStep 0 forceConstant -1.00000000000000e-01 - accumulatedWork -1.25846317032503e+00 + accumulatedWork -1.25846317029250e+00 } } diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj index 105936f55..cd6a6f61c 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_linear1 W_linear1 - 20 3.21716984778310e+00 2.00000000000000e-01 -6.23433969556620e-01 -1.25846317032503e+00 - 21 3.21490223047378e+00 2.00000000000000e-01 -6.22980446094756e-01 -1.25846317032503e+00 - 22 3.21258629748191e+00 2.00000000000000e-01 -6.22517259496383e-01 -1.25846317032503e+00 - 23 3.21034149782971e+00 2.00000000000000e-01 -6.22068299565942e-01 -1.25846317032503e+00 - 24 3.20827620026494e+00 2.00000000000000e-01 -6.21655240052988e-01 -1.25846317032503e+00 - 25 3.20648159014237e+00 2.00000000000000e-01 -6.21296318028474e-01 -1.25846317032503e+00 - 26 3.20502734946283e+00 2.00000000000000e-01 -6.21005469892566e-01 -1.25846317032503e+00 - 27 3.20395944720586e+00 2.00000000000000e-01 -6.20791889441172e-01 -1.25846317032503e+00 - 28 3.20329996925422e+00 2.00000000000000e-01 -6.20659993850845e-01 -1.25846317032503e+00 - 29 3.20304853694008e+00 2.00000000000000e-01 -6.20609707388016e-01 -1.25846317032503e+00 - 30 3.20318489612342e+00 2.00000000000000e-01 -6.20636979224683e-01 -1.25846317032503e+00 - 31 3.20367230114181e+00 2.00000000000000e-01 -6.20734460228362e-01 -1.25846317032503e+00 - 32 3.20446153849181e+00 2.00000000000000e-01 -6.20892307698363e-01 -1.25846317032503e+00 - 33 3.20549541664518e+00 2.00000000000000e-01 -6.21099083329035e-01 -1.25846317032503e+00 - 34 3.20671350741850e+00 2.00000000000000e-01 -6.21342701483699e-01 -1.25846317032503e+00 - 35 3.20805672105962e+00 2.00000000000000e-01 -6.21611344211924e-01 -1.25846317032503e+00 - 36 3.20947126515048e+00 2.00000000000000e-01 -6.21894253030096e-01 -1.25846317032503e+00 - 37 3.21091167114224e+00 2.00000000000000e-01 -6.22182334228447e-01 -1.25846317032503e+00 - 38 3.21234283908886e+00 2.00000000000000e-01 -6.22468567817772e-01 -1.25846317032503e+00 - 39 3.21374125148697e+00 2.00000000000000e-01 -6.22748250297394e-01 -1.25846317032503e+00 - 40 3.21509555130398e+00 2.00000000000000e-01 -6.23019110260796e-01 -1.25846317032503e+00 + 20 3.21716984757735e+00 2.00000000000000e-01 -6.23433969515469e-01 -1.25846317029250e+00 + 21 3.21490223025136e+00 2.00000000000000e-01 -6.22980446050271e-01 -1.25846317029250e+00 + 22 3.21258629724258e+00 2.00000000000000e-01 -6.22517259448516e-01 -1.25846317029250e+00 + 23 3.21034149757330e+00 2.00000000000000e-01 -6.22068299514661e-01 -1.25846317029250e+00 + 24 3.20827619999141e+00 2.00000000000000e-01 -6.21655239998281e-01 -1.25846317029250e+00 + 25 3.20648158985175e+00 2.00000000000000e-01 -6.21296317970351e-01 -1.25846317029250e+00 + 26 3.20502734915530e+00 2.00000000000000e-01 -6.21005469831060e-01 -1.25846317029250e+00 + 27 3.20395944688168e+00 2.00000000000000e-01 -6.20791889376335e-01 -1.25846317029250e+00 + 28 3.20329996891376e+00 2.00000000000000e-01 -6.20659993782751e-01 -1.25846317029250e+00 + 29 3.20304853658376e+00 2.00000000000000e-01 -6.20609707316753e-01 -1.25846317029250e+00 + 30 3.20318489575175e+00 2.00000000000000e-01 -6.20636979150349e-01 -1.25846317029250e+00 + 31 3.20367230075533e+00 2.00000000000000e-01 -6.20734460151066e-01 -1.25846317029250e+00 + 32 3.20446153809111e+00 2.00000000000000e-01 -6.20892307618221e-01 -1.25846317029250e+00 + 33 3.20549541623088e+00 2.00000000000000e-01 -6.21099083246176e-01 -1.25846317029250e+00 + 34 3.20671350699132e+00 2.00000000000000e-01 -6.21342701398263e-01 -1.25846317029250e+00 + 35 3.20805672062037e+00 2.00000000000000e-01 -6.21611344124074e-01 -1.25846317029250e+00 + 36 3.20947126470013e+00 2.00000000000000e-01 -6.21894252940025e-01 -1.25846317029250e+00 + 37 3.21091167068192e+00 2.00000000000000e-01 -6.22182334136383e-01 -1.25846317029250e+00 + 38 3.21234283861993e+00 2.00000000000000e-01 -6.22468567723985e-01 -1.25846317029250e+00 + 39 3.21374125101100e+00 2.00000000000000e-01 -6.22748250202200e-01 -1.25846317029250e+00 + 40 3.21509555082278e+00 2.00000000000000e-01 -6.23019110164555e-01 -1.25846317029250e+00 diff --git a/namd/tests/library/000_distance_linear-k-moving/namd-version.txt b/namd/tests/library/000_distance_linear-k-moving/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distance_linear-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_linear-k-moving/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out index abb32eebd..b7fa6abce 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -87,25 +91,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -148,6 +152,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -158,15 +163,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped index f4d2ca8a0..26945fa08 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) + x ( -3.17274648853048e-01 , -1.89053561545958e-03 , 9.48331810639220e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj index 653638305..84fccc97a 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -3.39806527406457e-01 , 7.75672148823417e-03 , 9.40463373664131e-01 ) ( 2.67961305481292e-03 , -1.55134429764683e-05 , -1.88092674732826e-03 ) - 1 ( -3.39402299531197e-01 , 6.96783241200742e-03 , 9.40615505073361e-01 ) ( 2.67880459906239e-03 , -1.39356648240148e-05 , -1.88123101014672e-03 ) - 2 ( -3.38852268623157e-01 , 6.28615128581265e-03 , 9.40818592689872e-01 ) ( 2.67770453724631e-03 , -1.25723025716253e-05 , -1.88163718537974e-03 ) - 3 ( -3.38144430394757e-01 , 5.71702991439356e-03 , 9.41076861771643e-01 ) ( 2.67628886078951e-03 , -1.14340598287871e-05 , -1.88215372354329e-03 ) - 4 ( -3.37272058710501e-01 , 5.26001267291420e-03 , 9.41392527418750e-01 ) ( 2.67454411742100e-03 , -1.05200253458284e-05 , -1.88278505483750e-03 ) - 5 ( -3.36235002718839e-01 , 4.90828500862304e-03 , 9.41765327289626e-01 ) ( 2.67247000543768e-03 , -9.81657001724609e-06 , -1.88353065457925e-03 ) - 6 ( -3.35040319485078e-01 , 4.64847236523130e-03 , 9.42192324328747e-01 ) ( 2.67008063897016e-03 , -9.29694473046260e-06 , -1.88438464865749e-03 ) - 7 ( -3.33702304368059e-01 , 4.46100232057914e-03 , 9.42667954010182e-01 ) ( 2.66740460873612e-03 , -8.92200464115828e-06 , -1.88533590802036e-03 ) - 8 ( -3.32242055295591e-01 , 4.32116578267109e-03 , 9.43184257830484e-01 ) ( 2.66448411059118e-03 , -8.64233156534219e-06 , -1.88636851566097e-03 ) - 9 ( -3.30686722614415e-01 , 4.20085972373069e-03 , 9.43731235185166e-01 ) ( 2.66137344522883e-03 , -8.40171944746138e-06 , -1.88746247037033e-03 ) - 10 ( -3.29068550340716e-01 , 4.07080426330041e-03 , 9.44297261316218e-01 ) ( 2.65813710068143e-03 , -8.14160852660083e-06 , -1.88859452263244e-03 ) - 11 ( -3.27423742891617e-01 , 3.90288350488177e-03 , 9.44869546599525e-01 ) ( 2.65484748578323e-03 , -7.80576700976354e-06 , -1.88973909319905e-03 ) - 12 ( -3.25791132271727e-01 , 3.67221266789039e-03 , 9.45434637078221e-01 ) ( 2.65158226454345e-03 , -7.34442533578077e-06 , -1.89086927415644e-03 ) - 13 ( -3.24210587689955e-01 , 3.35858640100320e-03 , 9.45978971609370e-01 ) ( 2.64842117537991e-03 , -6.71717280200640e-06 , -1.89195794321874e-03 ) - 14 ( -3.22721152712020e-01 , 2.94710470864841e-03 , 9.46489499237081e-01 ) ( 2.64544230542404e-03 , -5.89420941729682e-06 , -1.89297899847416e-03 ) - 15 ( -3.21358984421525e-01 , 2.42796438390647e-03 , 9.46954332647840e-01 ) ( 2.64271796884305e-03 , -4.85592876781293e-06 , -1.89390866529568e-03 ) - 16 ( -3.20155244264332e-01 , 1.79559468838712e-03 , 9.47363391423672e-01 ) ( 2.64031048852866e-03 , -3.59118937677423e-06 , -1.89472678284734e-03 ) - 17 ( -3.19134137515970e-01 , 1.04747307744542e-03 , 9.47708976992457e-01 ) ( 2.63826827503194e-03 , -2.09494615489084e-06 , -1.89541795398491e-03 ) - 18 ( -3.18311310856538e-01 , 1.83029974893031e-04 , 9.47986221355997e-01 ) ( 2.63662262171308e-03 , -3.66059949786063e-07 , -1.89597244271199e-03 ) - 19 ( -3.17692796906620e-01 , -7.96993701676326e-04 , 9.48193361922919e-01 ) ( 2.63538559381324e-03 , 1.59398740335265e-06 , -1.89638672384584e-03 ) - 20 ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) ( 2.63454929804108e-03 , 3.78107124610862e-06 , -1.89666362116634e-03 ) + 0 ( -3.39806527406457e-01 , 7.75672148823424e-03 , 9.40463373664131e-01 ) ( 2.67961305481292e-03 , -1.55134429764685e-05 , -1.88092674732826e-03 ) + 1 ( -3.39402299530748e-01 , 6.96783241211861e-03 , 9.40615505073522e-01 ) ( 2.67880459906150e-03 , -1.39356648242372e-05 , -1.88123101014704e-03 ) + 2 ( -3.38852268621315e-01 , 6.28615128621521e-03 , 9.40818592690533e-01 ) ( 2.67770453724263e-03 , -1.25723025724304e-05 , -1.88163718538107e-03 ) + 3 ( -3.38144430390545e-01 , 5.71702991523034e-03 , 9.41076861773151e-01 ) ( 2.67628886078109e-03 , -1.14340598304607e-05 , -1.88215372354630e-03 ) + 4 ( -3.37272058702922e-01 , 5.26001267429506e-03 , 9.41392527421457e-01 ) ( 2.67454411740584e-03 , -1.05200253485901e-05 , -1.88278505484291e-03 ) + 5 ( -3.36235002706895e-01 , 4.90828501062859e-03 , 9.41765327293880e-01 ) ( 2.67247000541379e-03 , -9.81657002125718e-06 , -1.88353065458776e-03 ) + 6 ( -3.35040319467782e-01 , 4.64847236791525e-03 , 9.42192324334884e-01 ) ( 2.67008063893556e-03 , -9.29694473583050e-06 , -1.88438464866977e-03 ) + 7 ( -3.33702304344449e-01 , 4.46100232397236e-03 , 9.42667954018524e-01 ) ( 2.66740460868890e-03 , -8.92200464794472e-06 , -1.88533590803705e-03 ) + 8 ( -3.32242055264741e-01 , 4.32116578678476e-03 , 9.43184257841332e-01 ) ( 2.66448411052948e-03 , -8.64233157356951e-06 , -1.88636851568266e-03 ) + 9 ( -3.30686722575443e-01 , 4.20085972855961e-03 , 9.43731235198800e-01 ) ( 2.66137344515089e-03 , -8.40171945711923e-06 , -1.88746247039760e-03 ) + 10 ( -3.29068550292791e-01 , 4.07080426882692e-03 , 9.44297261332895e-01 ) ( 2.65813710058558e-03 , -8.14160853765385e-06 , -1.88859452266579e-03 ) + 11 ( -3.27423742833967e-01 , 3.90288351107626e-03 , 9.44869546619476e-01 ) ( 2.65484748566793e-03 , -7.80576702215252e-06 , -1.88973909323895e-03 ) + 12 ( -3.25791132203644e-01 , 3.67221267471163e-03 , 9.45434637101656e-01 ) ( 2.65158226440729e-03 , -7.34442534942325e-06 , -1.89086927420331e-03 ) + 13 ( -3.24210587610799e-01 , 3.35858640839648e-03 , 9.45978971636472e-01 ) ( 2.64842117522160e-03 , -6.71717281679296e-06 , -1.89195794327294e-03 ) + 14 ( -3.22721152621232e-01 , 2.94710471653878e-03 , 9.46489499268013e-01 ) ( 2.64544230524246e-03 , -5.89420943307757e-06 , -1.89297899853603e-03 ) + 15 ( -3.21358984318630e-01 , 2.42796439219500e-03 , 9.46954332682738e-01 ) ( 2.64271796863726e-03 , -4.85592878438999e-06 , -1.89390866536548e-03 ) + 16 ( -3.20155244148942e-01 , 1.79559469694439e-03 , 9.47363391462651e-01 ) ( 2.64031048829788e-03 , -3.59118939388878e-06 , -1.89472678292530e-03 ) + 17 ( -3.19134137387790e-01 , 1.04747308610593e-03 , 9.47708977035611e-01 ) ( 2.63826827477558e-03 , -2.09494617221186e-06 , -1.89541795407122e-03 ) + 18 ( -3.18311310715357e-01 , 1.83029983452565e-04 , 9.47986221403400e-01 ) ( 2.63662262143071e-03 , -3.66059966905130e-07 , -1.89597244280680e-03 ) + 19 ( -3.17692796752311e-01 , -7.96993693460030e-04 , 9.48193361974628e-01 ) ( 2.63538559350462e-03 , 1.59398738692006e-06 , -1.89638672394926e-03 ) + 20 ( -3.17274648853048e-01 , -1.89053561545958e-03 , 9.48331810639220e-01 ) ( 2.63454929770610e-03 , 3.78107123091915e-06 , -1.89666362127844e-03 ) diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out index 9097222e0..6785f7248 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -87,25 +91,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -148,6 +152,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -158,20 +163,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -0.317275 , -0.00189054 , 0.948332 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped index f3e20f202..0236b3b01 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.11598263889815e-01 , -2.44590603702029e-02 , 9.49899087433323e-01 ) + x ( -3.11598263481038e-01 , -2.44590603951106e-02 , 9.49899087566774e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj index 7d738d1c8..2bb02cd37 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) ( 2.63454929804108e-03 , 3.78107124610862e-06 , -1.89666362116634e-03 ) - 21 ( -3.17043326283096e-01 , -3.09358622124357e-03 , 9.48406009567444e-01 ) ( 2.63408665256619e-03 , 6.18717244248714e-06 , -1.89681201913489e-03 ) - 22 ( -3.16976780479176e-01 , -4.39920685529361e-03 , 9.48423095256595e-01 ) ( 2.63395356095835e-03 , 8.79841371058722e-06 , -1.89684619051319e-03 ) - 23 ( -3.17046097666149e-01 , -5.79657340749948e-03 , 9.48392414399967e-01 ) ( 2.63409219533230e-03 , 1.15931468149990e-05 , -1.89678482879993e-03 ) - 24 ( -3.17217482859608e-01 , -7.27041162129638e-03 , 9.48324949415057e-01 ) ( 2.63443496571922e-03 , 1.45408232425928e-05 , -1.89664989883011e-03 ) - 25 ( -3.17454369154660e-01 , -8.80106277336966e-03 , 9.48232706037224e-01 ) ( 2.63490873830932e-03 , 1.76021255467393e-05 , -1.89646541207445e-03 ) - 26 ( -3.17719471466479e-01 , -1.03652349405030e-02 , 9.48128102819281e-01 ) ( 2.63543894293296e-03 , 2.07304698810060e-05 , -1.89625620563856e-03 ) - 27 ( -3.17976646119255e-01 , -1.19373246135143e-02 , 9.48023392540407e-01 ) ( 2.63595329223851e-03 , 2.38746492270286e-05 , -1.89604678508081e-03 ) - 28 ( -3.18192455781236e-01 , -1.34910475011762e-02 , 9.47930141266342e-01 ) ( 2.63638491156247e-03 , 2.69820950023524e-05 , -1.89586028253268e-03 ) - 29 ( -3.18337378885354e-01 , -1.50010625401725e-02 , 9.47858787650918e-01 ) ( 2.63667475777071e-03 , 3.00021250803450e-05 , -1.89571757530184e-03 ) - 30 ( -3.18386627833720e-01 , -1.64443011529380e-02 , 9.47818305465907e-01 ) ( 2.63677325566744e-03 , 3.28886023058761e-05 , -1.89563661093181e-03 ) - 31 ( -3.18320580791560e-01 , -1.78008340545886e-02 , 9.47815983274963e-01 ) ( 2.63664116158312e-03 , 3.56016681091771e-05 , -1.89563196654993e-03 ) - 32 ( -3.18124861601468e-01 , -1.90542515702588e-02 , 9.47857324668720e-01 ) ( 2.63624972320294e-03 , 3.81085031405176e-05 , -1.89571464933744e-03 ) - 33 ( -3.17790139900921e-01 , -2.01916660122652e-02 , 9.47946055219073e-01 ) ( 2.63558027980184e-03 , 4.03833320245304e-05 , -1.89589211043815e-03 ) - 34 ( -3.17311724965833e-01 , -2.12034927401992e-02 , 9.48084216246017e-01 ) ( 2.63462344993167e-03 , 4.24069854803984e-05 , -1.89616843249203e-03 ) - 35 ( -3.16689033052138e-01 , -2.20831582105308e-02 , 9.48272318729146e-01 ) ( 2.63337806610428e-03 , 4.41663164210616e-05 , -1.89654463745829e-03 ) - 36 ( -3.15924962100982e-01 , -2.28268525064398e-02 , 9.48509542981062e-01 ) ( 2.63184992420196e-03 , 4.56537050128795e-05 , -1.89701908596212e-03 ) - 37 ( -3.15025224091246e-01 , -2.34334009818228e-02 , 9.48793962831070e-01 ) ( 2.63005044818249e-03 , 4.68668019636457e-05 , -1.89758792566214e-03 ) - 38 ( -3.13997688281053e-01 , -2.39042792438929e-02 , 9.49122772452534e-01 ) ( 2.62799537656211e-03 , 4.78085584877859e-05 , -1.89824554490507e-03 ) - 39 ( -3.12851813200530e-01 , -2.42437511657998e-02 , 9.49492487335498e-01 ) ( 2.62570362640106e-03 , 4.84875023315996e-05 , -1.89898497467100e-03 ) - 40 ( -3.11598263889815e-01 , -2.44590603702029e-02 , 9.49899087433323e-01 ) ( 2.62319652777963e-03 , 4.89181207404057e-05 , -1.89979817486665e-03 ) + 20 ( -3.17274648853048e-01 , -1.89053561545958e-03 , 9.48331810639220e-01 ) ( 2.63454929770610e-03 , 3.78107123091915e-06 , -1.89666362127844e-03 ) + 21 ( -3.17043326102425e-01 , -3.09358621457674e-03 , 9.48406009627862e-01 ) ( 2.63408665220485e-03 , 6.18717242915348e-06 , -1.89681201925572e-03 ) + 22 ( -3.16976780285387e-01 , -4.39920684988128e-03 , 9.48423095321387e-01 ) ( 2.63395356057077e-03 , 8.79841369976256e-06 , -1.89684619064277e-03 ) + 23 ( -3.17046097459336e-01 , -5.79657340367589e-03 , 9.48392414469127e-01 ) ( 2.63409219491867e-03 , 1.15931468073518e-05 , -1.89678482893825e-03 ) + 24 ( -3.17217482639898e-01 , -7.27041161938927e-03 , 9.48324949488565e-01 ) ( 2.63443496527980e-03 , 1.45408232387785e-05 , -1.89664989897713e-03 ) + 25 ( -3.17454368922200e-01 , -8.80106277368526e-03 , 9.48232706115045e-01 ) ( 2.63490873784440e-03 , 1.76021255473705e-05 , -1.89646541223009e-03 ) + 26 ( -3.17719471221428e-01 , -1.03652349433106e-02 , 9.48128102901367e-01 ) ( 2.63543894244286e-03 , 2.07304698866213e-05 , -1.89625620580273e-03 ) + 27 ( -3.17976645861785e-01 , -1.19373246190291e-02 , 9.48023392626695e-01 ) ( 2.63595329172357e-03 , 2.38746492380582e-05 , -1.89604678525339e-03 ) + 28 ( -3.18192455511519e-01 , -1.34910475095471e-02 , 9.47930141356759e-01 ) ( 2.63638491102304e-03 , 2.69820950190943e-05 , -1.89586028271352e-03 ) + 29 ( -3.18337378603559e-01 , -1.50010625514700e-02 , 9.47858787745380e-01 ) ( 2.63667475720712e-03 , 3.00021251029400e-05 , -1.89571757549076e-03 ) + 30 ( -3.18386627540012e-01 , -1.64443011671489e-02 , 9.47818305564322e-01 ) ( 2.63677325508002e-03 , 3.28886023342977e-05 , -1.89563661112864e-03 ) + 31 ( -3.18320580486092e-01 , -1.78008340716119e-02 , 9.47815983377233e-01 ) ( 2.63664116097219e-03 , 3.56016681432239e-05 , -1.89563196675447e-03 ) + 32 ( -3.18124861284371e-01 , -1.90542515899086e-02 , 9.47857324774751e-01 ) ( 2.63624972256874e-03 , 3.81085031798172e-05 , -1.89571464954950e-03 ) + 33 ( -3.17790139572305e-01 , -2.01916660342723e-02 , 9.47946055328770e-01 ) ( 2.63558027914461e-03 , 4.03833320685447e-05 , -1.89589211065754e-03 ) + 34 ( -3.17311724625781e-01 , -2.12034927642144e-02 , 9.48084216359291e-01 ) ( 2.63462344925156e-03 , 4.24069855284288e-05 , -1.89616843271858e-03 ) + 35 ( -3.16689032700701e-01 , -2.20831582361305e-02 , 9.48272318845917e-01 ) ( 2.63337806540140e-03 , 4.41663164722610e-05 , -1.89654463769183e-03 ) + 36 ( -3.15924961738176e-01 , -2.28268525331288e-02 , 9.48509543101261e-01 ) ( 2.63184992347635e-03 , 4.56537050662576e-05 , -1.89701908620252e-03 ) + 37 ( -3.15025223717057e-01 , -2.34334010090392e-02 , 9.48793962954638e-01 ) ( 2.63005044743411e-03 , 4.68668020180783e-05 , -1.89758792590928e-03 ) + 38 ( -3.13997687895431e-01 , -2.39042792710176e-02 , 9.49122772579426e-01 ) ( 2.62799537579086e-03 , 4.78085585420352e-05 , -1.89824554515885e-03 ) + 39 ( -3.12851812803389e-01 , -2.42437511921662e-02 , 9.49492487465681e-01 ) ( 2.62570362560678e-03 , 4.84875023843323e-05 , -1.89898497493136e-03 ) + 40 ( -3.11598263481038e-01 , -2.44590603951106e-02 , 9.49899087566774e-01 ) ( 2.62319652696208e-03 , 4.89181207902213e-05 , -1.89979817513355e-03 ) diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt index 129300d44..157cac038 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out index 1d23f8568..6d5786be0 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -113,6 +117,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -123,15 +128,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped index e64cb9b15..ae8e82001 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) + x ( -3.10901432109335e-01 , 2.11904534160048e-01 , 9.26518627937279e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj index 8935a8e9e..b16b4e9e6 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -3.31000066838100e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 2.66200013367620e-03 , -4.30091230223397e-04 , -1.83760097863971e-03 ) - 1 ( -3.30748902386919e-01 , 2.14640582516973e-01 , 9.18985627693177e-01 ) ( 2.66149780477384e-03 , -4.29281165033946e-04 , -1.83797125538635e-03 ) - 2 ( -3.30335278614263e-01 , 2.14351255518651e-01 , 9.19201905437763e-01 ) ( 2.66067055722853e-03 , -4.28702511037302e-04 , -1.83840381087553e-03 ) - 3 ( -3.29748301598012e-01 , 2.14175295385314e-01 , 9.19453642354981e-01 ) ( 2.65949660319602e-03 , -4.28350590770628e-04 , -1.83890728470996e-03 ) - 4 ( -3.28983003286818e-01 , 2.14104941848711e-01 , 9.19744126061344e-01 ) ( 2.65796600657364e-03 , -4.28209883697422e-04 , -1.83948825212269e-03 ) - 5 ( -3.28041624986510e-01 , 2.14126988066820e-01 , 9.20075173699216e-01 ) ( 2.65608324997302e-03 , -4.28253976133641e-04 , -1.84015034739843e-03 ) - 6 ( -3.26934234947895e-01 , 2.14223081728789e-01 , 9.20446889979892e-01 ) ( 2.65386846989579e-03 , -4.28446163457579e-04 , -1.84089377995978e-03 ) - 7 ( -3.25678693151725e-01 , 2.14370527632503e-01 , 9.20857570805359e-01 ) ( 2.65135738630345e-03 , -4.28741055265006e-04 , -1.84171514161072e-03 ) - 8 ( -3.24300051451023e-01 , 2.14543670052469e-01 , 9.21303690576175e-01 ) ( 2.64860010290205e-03 , -4.29087340104938e-04 , -1.84260738115235e-03 ) - 9 ( -3.22829511499202e-01 , 2.14715764651319e-01 , 9.21779934103247e-01 ) ( 2.64565902299840e-03 , -4.29431529302638e-04 , -1.84355986820649e-03 ) - 10 ( -3.21303059779930e-01 , 2.14861065895251e-01 , 9.22279277734468e-01 ) ( 2.64260611955986e-03 , -4.29722131790503e-04 , -1.84455855546894e-03 ) - 11 ( -3.19759879034225e-01 , 2.14956751273127e-01 , 9.22793159295257e-01 ) ( 2.63951975806845e-03 , -4.29913502546255e-04 , -1.84558631859051e-03 ) - 12 ( -3.18240618894718e-01 , 2.14984320891132e-01 , 9.23311783882609e-01 ) ( 2.63648123778944e-03 , -4.29968641782263e-04 , -1.84662356776522e-03 ) - 13 ( -3.16785580628539e-01 , 2.14930240610141e-01 , 9.23824597841553e-01 ) ( 2.63357116125708e-03 , -4.29860481220281e-04 , -1.84764919568311e-03 ) - 14 ( -3.15432869486022e-01 , 2.14785792588681e-01 , 9.24320922704807e-01 ) ( 2.63086573897204e-03 , -4.29571585177362e-04 , -1.84864184540961e-03 ) - 15 ( -3.14216581896700e-01 , 2.14546290781891e-01 , 9.24790694575203e-01 ) ( 2.62843316379340e-03 , -4.29092581563783e-04 , -1.84958138915041e-03 ) - 16 ( -3.13165103302749e-01 , 2.14209940590278e-01 , 9.25225226323671e-01 ) ( 2.62633020660550e-03 , -4.28419881180556e-04 , -1.85045045264734e-03 ) - 17 ( -3.12299612195620e-01 , 2.13776666349982e-01 , 9.25617895865650e-01 ) ( 2.62459922439124e-03 , -4.27553332699964e-04 , -1.85123579173130e-03 ) - 18 ( -3.11632909053414e-01 , 2.13247200164350e-01 , 9.25964665425724e-01 ) ( 2.62326581810683e-03 , -4.26494400328700e-04 , -1.85192933085145e-03 ) - 19 ( -3.11168697605864e-01 , 2.12622637201006e-01 , 9.26264355235566e-01 ) ( 2.62233739521173e-03 , -4.25245274402012e-04 , -1.85252871047113e-03 ) - 20 ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) ( 2.62180286454399e-03 , -4.23809068324612e-04 , -1.85303725576436e-03 ) + 0 ( -3.31000066838099e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 2.66200013367620e-03 , -4.30091230223396e-04 , -1.83760097863971e-03 ) + 1 ( -3.30748902386493e-01 , 2.14640582517095e-01 , 9.18985627693302e-01 ) ( 2.66149780477299e-03 , -4.29281165034190e-04 , -1.83797125538660e-03 ) + 2 ( -3.30335278565548e-01 , 2.14351255511183e-01 , 9.19201905457012e-01 ) ( 2.66067055713110e-03 , -4.28702511022365e-04 , -1.83840381091402e-03 ) + 3 ( -3.29748301584291e-01 , 2.14175295386331e-01 , 9.19453642359664e-01 ) ( 2.65949660316858e-03 , -4.28350590772662e-04 , -1.83890728471933e-03 ) + 4 ( -3.28983003247068e-01 , 2.14104941845713e-01 , 9.19744126076260e-01 ) ( 2.65796600649414e-03 , -4.28209883691426e-04 , -1.83948825215252e-03 ) + 5 ( -3.28041624976885e-01 , 2.14126988072693e-01 , 9.20075173701281e-01 ) ( 2.65608324995377e-03 , -4.28253976145385e-04 , -1.84015034740256e-03 ) + 6 ( -3.26934234935534e-01 , 2.14223081735800e-01 , 9.20446889982651e-01 ) ( 2.65386846987107e-03 , -4.28446163471600e-04 , -1.84089377996530e-03 ) + 7 ( -3.25678693135581e-01 , 2.14370527640576e-01 , 9.20857570809189e-01 ) ( 2.65135738627116e-03 , -4.28741055281152e-04 , -1.84171514161838e-03 ) + 8 ( -3.24300051430000e-01 , 2.14543670061471e-01 , 9.21303690581479e-01 ) ( 2.64860010286000e-03 , -4.29087340122942e-04 , -1.84260738116296e-03 ) + 9 ( -3.22829511472042e-01 , 2.14715764661014e-01 , 9.21779934110501e-01 ) ( 2.64565902294409e-03 , -4.29431529322028e-04 , -1.84355986822100e-03 ) + 10 ( -3.21303059745326e-01 , 2.14861065905351e-01 , 9.22279277744170e-01 ) ( 2.64260611949065e-03 , -4.29722131810702e-04 , -1.84455855548834e-03 ) + 11 ( -3.19759878990855e-01 , 2.14956751283305e-01 , 9.22793159307914e-01 ) ( 2.63951975798171e-03 , -4.29913502566610e-04 , -1.84558631861583e-03 ) + 12 ( -3.18240618841290e-01 , 2.14984320901043e-01 , 9.23311783898716e-01 ) ( 2.63648123768258e-03 , -4.29968641802086e-04 , -1.84662356779743e-03 ) + 13 ( -3.16785580563842e-01 , 2.14930240619444e-01 , 9.23824597861573e-01 ) ( 2.63357116112768e-03 , -4.29860481238888e-04 , -1.84764919572315e-03 ) + 14 ( -3.15432869408985e-01 , 2.14785792597053e-01 , 9.24320922729152e-01 ) ( 2.63086573881797e-03 , -4.29571585194106e-04 , -1.84864184545830e-03 ) + 15 ( -3.14216581806419e-01 , 2.14546290789039e-01 , 9.24790694604220e-01 ) ( 2.62843316361284e-03 , -4.29092581578078e-04 , -1.84958138920844e-03 ) + 16 ( -3.13165103198593e-01 , 2.14209940595846e-01 , 9.25225226357636e-01 ) ( 2.62633020639719e-03 , -4.28419881191692e-04 , -1.85045045271527e-03 ) + 17 ( -3.12299612081994e-01 , 2.13776666346595e-01 , 9.25617895904770e-01 ) ( 2.62459922416399e-03 , -4.27553332693190e-04 , -1.85123579180954e-03 ) + 18 ( -3.11632908920174e-01 , 2.13247200166255e-01 , 9.25964665470127e-01 ) ( 2.62326581784035e-03 , -4.26494400332510e-04 , -1.85192933094025e-03 ) + 19 ( -3.11168697452754e-01 , 2.12622637200253e-01 , 9.26264355287175e-01 ) ( 2.62233739490551e-03 , -4.25245274400506e-04 , -1.85252871057435e-03 ) + 20 ( -3.10901432109335e-01 , 2.11904534160048e-01 , 9.26518627937279e-01 ) ( 2.62180286421867e-03 , -4.23809068320096e-04 , -1.85303725587456e-03 ) diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out index 42c1974d9..7b60a6e6d 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -113,6 +117,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -123,20 +128,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -0.310901 , 0.211905 , 0.926519 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped index 6b8d538b6..99b9e8168 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.08478219385086e-01 , 1.95662054939033e-01 , 9.30890728507939e-01 ) + x ( -3.08478218972664e-01 , 1.95662054911782e-01 , 9.30890728650335e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj index 0b3f5ab28..3c70716e5 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) ( 2.62180286454399e-03 , -4.23809068324612e-04 , -1.85303725576436e-03 ) - 21 ( -3.10816792220306e-01 , 2.11095479027854e-01 , 9.26731687387390e-01 ) ( 2.62163358444061e-03 , -4.22190958055708e-04 , -1.85346337477478e-03 ) - 22 ( -3.10892759748286e-01 , 2.10199933231990e-01 , 9.26909747497221e-01 ) ( 2.62178551949657e-03 , -4.20399866463979e-04 , -1.85381949499444e-03 ) - 23 ( -3.11101193207355e-01 , 2.09225066830326e-01 , 9.27060364266969e-01 ) ( 2.62220238641471e-03 , -4.18450133660652e-04 , -1.85412072853394e-03 ) - 24 ( -3.11409711041452e-01 , 2.08181314903498e-01 , 9.27191744998913e-01 ) ( 2.62281942208290e-03 , -4.16362629806997e-04 , -1.85438348999783e-03 ) - 25 ( -3.11783673453337e-01 , 2.07082466730478e-01 , 9.27312133502395e-01 ) ( 2.62356734690667e-03 , -4.14164933460955e-04 , -1.85462426700479e-03 ) - 26 ( -3.12188067442232e-01 , 2.05945244407307e-01 , 9.27429332538441e-01 ) ( 2.62437613488447e-03 , -4.11890488814613e-04 , -1.85485866507688e-03 ) - 27 ( -3.12589140366756e-01 , 2.04788460697038e-01 , 9.27550384448258e-01 ) ( 2.62517828073351e-03 , -4.09576921394075e-04 , -1.85510076889652e-03 ) - 28 ( -3.12955685129617e-01 , 2.03631959627123e-01 , 9.27681391515142e-01 ) ( 2.62591137025923e-03 , -4.07263919254245e-04 , -1.85536278303028e-03 ) - 29 ( -3.13259948690306e-01 , 2.02495576423685e-01 , 9.27827433349212e-01 ) ( 2.62651989738061e-03 , -4.04991152847370e-04 , -1.85565486669842e-03 ) - 30 ( -3.13478176932022e-01 , 2.01398322580004e-01 , 9.27992536742261e-01 ) ( 2.62695635386404e-03 , -4.02796645160007e-04 , -1.85598507348452e-03 ) - 31 ( -3.13590843998619e-01 , 2.00357900935419e-01 , 9.28179666924991e-01 ) ( 2.62718168799724e-03 , -4.00715801870839e-04 , -1.85635933384998e-03 ) - 32 ( -3.13582621254546e-01 , 1.99390533269725e-01 , 9.28390733952867e-01 ) ( 2.62716524250909e-03 , -3.98781066539451e-04 , -1.85678146790573e-03 ) - 33 ( -3.13442157429236e-01 , 1.98510960989129e-01 , 9.28626626967630e-01 ) ( 2.62688431485847e-03 , -3.97021921978259e-04 , -1.85725325393526e-03 ) - 34 ( -3.13161736572708e-01 , 1.97732440207133e-01 , 9.28887296089519e-01 ) ( 2.62632347314542e-03 , -3.95464880414266e-04 , -1.85777459217904e-03 ) - 35 ( -3.12736895616453e-01 , 1.97066585116309e-01 , 9.29171886763036e-01 ) ( 2.62547379123291e-03 , -3.94133170232619e-04 , -1.85834377352607e-03 ) - 36 ( -3.12166051308255e-01 , 1.96522999367774e-01 , 9.29478922370005e-01 ) ( 2.62433210261651e-03 , -3.93045998735549e-04 , -1.85895784474001e-03 ) - 37 ( -3.11450199612716e-01 , 1.96108732516444e-01 , 9.29806505780634e-01 ) ( 2.62290039922543e-03 , -3.92217465032889e-04 , -1.85961301156127e-03 ) - 38 ( -3.10592727664091e-01 , 1.95827676730295e-01 , 9.30152502844880e-01 ) ( 2.62118545532818e-03 , -3.91655353460590e-04 , -1.86030500568976e-03 ) - 39 ( -3.09599357305329e-01 , 1.95680044131724e-01 , 9.30514673868571e-01 ) ( 2.61919871461066e-03 , -3.91360088263449e-04 , -1.86102934773714e-03 ) - 40 ( -3.08478219385086e-01 , 1.95662054939033e-01 , 9.30890728507939e-01 ) ( 2.61695643877017e-03 , -3.91324109878067e-04 , -1.86178145701588e-03 ) + 20 ( -3.10901432109335e-01 , 2.11904534160048e-01 , 9.26518627937279e-01 ) ( 2.62180286421867e-03 , -4.23809068320096e-04 , -1.85303725587456e-03 ) + 21 ( -3.10816792043180e-01 , 2.11095479023442e-01 , 9.26731687447802e-01 ) ( 2.62163358408636e-03 , -4.22190958046885e-04 , -1.85346337489560e-03 ) + 22 ( -3.10892759556907e-01 , 2.10199933225375e-01 , 9.26909747562911e-01 ) ( 2.62178551911381e-03 , -4.20399866450750e-04 , -1.85381949512582e-03 ) + 23 ( -3.11101193001973e-01 , 2.09225066821485e-01 , 9.27060364337886e-01 ) ( 2.62220238600395e-03 , -4.18450133642970e-04 , -1.85412072867577e-03 ) + 24 ( -3.11409710822334e-01 , 2.08181314892433e-01 , 9.27191745074992e-01 ) ( 2.62281942164467e-03 , -4.16362629784866e-04 , -1.85438349014998e-03 ) + 25 ( -3.11783673220749e-01 , 2.07082466717213e-01 , 9.27312133583558e-01 ) ( 2.62356734644150e-03 , -4.14164933434426e-04 , -1.85462426716712e-03 ) + 26 ( -3.12188067196429e-01 , 2.05945244391887e-01 , 9.27429332624607e-01 ) ( 2.62437613439286e-03 , -4.11890488783774e-04 , -1.85485866524921e-03 ) + 27 ( -3.12589140107981e-01 , 2.04788460679522e-01 , 9.27550384539333e-01 ) ( 2.62517828021596e-03 , -4.09576921359045e-04 , -1.85510076907867e-03 ) + 28 ( -3.12955684858097e-01 , 2.03631959607588e-01 , 9.27681391611028e-01 ) ( 2.62591136971619e-03 , -4.07263919215175e-04 , -1.85536278322206e-03 ) + 29 ( -3.13259948406249e-01 , 2.02495576402221e-01 , 9.27827433449802e-01 ) ( 2.62651989681250e-03 , -4.04991152804443e-04 , -1.85565486689960e-03 ) + 30 ( -3.13478176635625e-01 , 2.01398322556721e-01 , 9.27992536847437e-01 ) ( 2.62695635327125e-03 , -4.02796645113443e-04 , -1.85598507369487e-03 ) + 31 ( -3.13590843690062e-01 , 2.00357900910451e-01 , 9.28179667034628e-01 ) ( 2.62718168738012e-03 , -4.00715801820901e-04 , -1.85635933406926e-03 ) + 32 ( -3.13582620933990e-01 , 1.99390533243234e-01 , 9.28390734066831e-01 ) ( 2.62716524186798e-03 , -3.98781066486467e-04 , -1.85678146813366e-03 ) + 33 ( -3.13442157096821e-01 , 1.98510960961320e-01 , 9.28626627085776e-01 ) ( 2.62688431419364e-03 , -3.97021921922641e-04 , -1.85725325417155e-03 ) + 34 ( -3.13161736228558e-01 , 1.97732440178262e-01 , 9.28887296211691e-01 ) ( 2.62632347245712e-03 , -3.95464880356523e-04 , -1.85777459242338e-03 ) + 35 ( -3.12736895260678e-01 , 1.97066585086681e-01 , 9.29171886889065e-01 ) ( 2.62547379052136e-03 , -3.94133170173362e-04 , -1.85834377377813e-03 ) + 36 ( -3.12166050940956e-01 , 1.96522999337743e-01 , 9.29478922499712e-01 ) ( 2.62433210188191e-03 , -3.93045998675485e-04 , -1.85895784499942e-03 ) + 37 ( -3.11450199233999e-01 , 1.96108732486406e-01 , 9.29806505913826e-01 ) ( 2.62290039846800e-03 , -3.92217464972813e-04 , -1.85961301182765e-03 ) + 38 ( -3.10592727274054e-01 , 1.95827676700691e-01 , 9.30152502981352e-01 ) ( 2.62118545454811e-03 , -3.91655353401382e-04 , -1.86030500596270e-03 ) + 39 ( -3.09599356904062e-01 , 1.95680044103037e-01 , 9.30514674008113e-01 ) ( 2.61919871380812e-03 , -3.91360088206074e-04 , -1.86102934801623e-03 ) + 40 ( -3.08478218972664e-01 , 1.95662054911782e-01 , 9.30890728650335e-01 ) ( 2.61695643794533e-03 , -3.91324109823565e-04 , -1.86178145730067e-03 ) diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out index 5b55b80fb..74c288689 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out @@ -1,13 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -120,6 +120,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -131,10 +132,27 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped index 41cb47258..a3cdd7bbc 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) + x ( -3.10902612073187e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj index 4806fa83f..41394b2d9 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 ( -3.31000066838099e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 2.66200013367620e-03 , -4.30091230223396e-04 , -1.83760097863971e-03 ) 5.32400026735240e-03 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 1 ( -3.30748902386493e-01 , 2.14640582517095e-01 , 9.18985627693302e-01 ) ( 2.65426681755214e-03 , -2.59364533396170e-04 , -1.83797125538660e-03 ) 5.24527031778478e-03 ( 9.96384506389575e-01 , 8.49583158190100e-02 , 0.00000000000000e+00 ) -4.11137793191958e-05 - 2 ( -3.30335278534755e-01 , 2.14351256281980e-01 , 9.19201905288334e-01 ) ( 2.61609431372619e-03 , -8.80022404594755e-06 , -1.83840381057667e-03 ) 5.11187773649830e-03 ( 9.77711878328341e-01 , 2.09951144259006e-01 , 0.00000000000000e+00 ) -1.11474667340389e-04 - 3 ( -3.29748301559333e-01 , 2.14175298816286e-01 , 9.19453641569650e-01 ) ( 2.49361536951405e-03 , 3.69150719454903e-04 , -1.83890728313930e-03 ) 4.86798493036677e-03 ( 9.17059383197694e-01 , 3.98750658543737e-01 , 0.00000000000000e+00 ) -2.40880322518690e-04 - 4 ( -3.28983003639496e-01 , 2.14104951472765e-01 , 9.19744123694835e-01 ) ( 2.15062069976169e-03 , 9.02948227784763e-04 , -1.83948824738967e-03 ) 4.41210095429392e-03 ( 7.46327346241351e-01 , 6.65579065365146e-01 , 0.00000000000000e+00 ) -4.77813021182742e-04 + 2 ( -3.30335278534755e-01 , 2.14351256281980e-01 , 9.19201905288334e-01 ) ( 2.61609431372619e-03 , -8.80022404594749e-06 , -1.83840381057667e-03 ) 5.11187773649830e-03 ( 9.77711878328341e-01 , 2.09951144259006e-01 , 0.00000000000000e+00 ) -1.11474667340389e-04 + 3 ( -3.29748301559332e-01 , 2.14175298816286e-01 , 9.19453641569650e-01 ) ( 2.49361536951405e-03 , 3.69150719454903e-04 , -1.83890728313930e-03 ) 4.86798493036677e-03 ( 9.17059383197694e-01 , 3.98750658543737e-01 , 0.00000000000000e+00 ) -2.40880322518690e-04 + 4 ( -3.28983003639495e-01 , 2.14104951472765e-01 , 9.19744123694835e-01 ) ( 2.15062069976169e-03 , 9.02948227784763e-04 , -1.83948824738967e-03 ) 4.41210095429392e-03 ( 7.46327346241351e-01 , 6.65579065365146e-01 , 0.00000000000000e+00 ) -4.77813021182742e-04 5 ( -3.28041627441930e-01 , 2.14127009680035e-01 , 9.20075167793771e-01 ) ( 1.42145011961404e-03 , 1.41950504566250e-03 , -1.84015033558754e-03 ) 3.71083413738751e-03 ( 3.82683432365090e-01 , 9.23879532511287e-01 , 0.00000000000000e+00 ) -8.12629094252072e-04 - 6 ( -3.26934243989619e-01 , 2.14223123081484e-01 , 9.20446877144005e-01 ) ( 5.39673174025796e-04 , 1.56829094993247e-03 , -1.84089375428801e-03 ) 3.06983672648989e-03 ( -5.70976569767208e-02 , 9.98368598047719e-01 , 0.00000000000000e+00 ) -1.08583725325208e-03 - 7 ( -3.25678716875359e-01 , 2.14370596669932e-01 , 9.20857546343514e-01 ) ( -8.16417941512103e-05 , 1.43209521319758e-03 , -1.84171509268703e-03 ) 2.72473828242341e-03 ( -3.66499613950964e-01 , 9.30418203268721e-01 , 0.00000000000000e+00 ) -1.22624326781898e-03 - 8 ( -3.24300100426941e-01 , 2.14543773657555e-01 , 9.21303649210103e-01 ) ( -4.37177441924495e-04 , 1.25052160675694e-03 , -1.84260729842021e-03 ) 2.57506503044251e-03 ( -5.42888821389189e-01 , 8.39804577036026e-01 , 0.00000000000000e+00 ) -1.28775963537044e-03 - 9 ( -3.22829597532927e-01 , 2.14715908506054e-01 , 9.21779870463197e-01 ) ( -6.43292084741085e-04 , 1.09981786773007e-03 , -1.84355974092639e-03 ) 2.51106828341672e-03 ( -6.44475639903469e-01 , 7.64624842371090e-01 , 0.00000000000000e+00 ) -1.31512027126455e-03 - 10 ( -3.21303195136169e-01 , 2.14861254665660e-01 , 9.22279186601751e-01 ) ( -7.71607172100758e-04 , 9.84491053041776e-04 , -1.84455837320350e-03 ) 2.48349792685589e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 11 ( -3.19760075975256e-01 , 2.14956988805007e-01 , 9.22793035721544e-01 ) ( -7.74693410422582e-04 , 9.84299584763081e-04 , -1.84558607144309e-03 ) 2.48759174991084e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 12 ( -3.18240889009191e-01 , 2.14984610793561e-01 , 9.23311623280342e-01 ) ( -7.77731784354714e-04 , 9.84244340785974e-04 , -1.84662324656068e-03 ) 2.49181053275155e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 13 ( -3.16785934761420e-01 , 2.14930586280875e-01 , 9.23824395985673e-01 ) ( -7.80641692850256e-04 , 9.84352389811345e-04 , -1.84764879197135e-03 ) 2.49607856920830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 6 ( -3.26934243989618e-01 , 2.14223123081484e-01 , 9.20446877144005e-01 ) ( 5.39673174025795e-04 , 1.56829094993247e-03 , -1.84089375428801e-03 ) 3.06983672648989e-03 ( -5.70976569767208e-02 , 9.98368598047719e-01 , 0.00000000000000e+00 ) -1.08583725325208e-03 + 7 ( -3.25678716875358e-01 , 2.14370596669932e-01 , 9.20857546343514e-01 ) ( -8.16417941512113e-05 , 1.43209521319758e-03 , -1.84171509268703e-03 ) 2.72473828242342e-03 ( -3.66499613950964e-01 , 9.30418203268721e-01 , 0.00000000000000e+00 ) -1.22624326781898e-03 + 8 ( -3.24300100426940e-01 , 2.14543773657555e-01 , 9.21303649210103e-01 ) ( -4.37177441924497e-04 , 1.25052160675694e-03 , -1.84260729842021e-03 ) 2.57506503044251e-03 ( -5.42888821389189e-01 , 8.39804577036026e-01 , 0.00000000000000e+00 ) -1.28775963537044e-03 + 9 ( -3.22829597532926e-01 , 2.14715908506054e-01 , 9.21779870463197e-01 ) ( -6.43292084741086e-04 , 1.09981786773007e-03 , -1.84355974092639e-03 ) 2.51106828341672e-03 ( -6.44475639903469e-01 , 7.64624842371090e-01 , 0.00000000000000e+00 ) -1.31512027126455e-03 + 10 ( -3.21303195136168e-01 , 2.14861254665660e-01 , 9.22279186601751e-01 ) ( -7.71607172100759e-04 , 9.84491053041776e-04 , -1.84455837320350e-03 ) 2.48349792685589e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 11 ( -3.19760075975256e-01 , 2.14956988805007e-01 , 9.22793035721544e-01 ) ( -7.74693410422583e-04 , 9.84299584763081e-04 , -1.84558607144309e-03 ) 2.48759174991084e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 12 ( -3.18240889009190e-01 , 2.14984610793561e-01 , 9.23311623280343e-01 ) ( -7.77731784354715e-04 , 9.84244340785974e-04 , -1.84662324656069e-03 ) 2.49181053275156e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 13 ( -3.16785934761419e-01 , 2.14930586280875e-01 , 9.23824395985673e-01 ) ( -7.80641692850257e-04 , 9.84352389811345e-04 , -1.84764879197135e-03 ) 2.49607856920830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 14 ( -3.15433317695425e-01 , 2.14786197242876e-01 , 9.24320675718985e-01 ) ( -7.83346926982245e-04 , 9.84641167887343e-04 , -1.84864135143797e-03 ) 2.50031274187874e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 15 ( -3.14217133435043e-01 , 2.14546757480910e-01 , 9.24790398906851e-01 ) ( -7.85779295503009e-04 , 9.85120047411276e-04 , -1.84958079781370e-03 ) 2.50442986834698e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 16 ( -3.13165766618895e-01 , 2.14210472267861e-01 , 9.25224878712619e-01 ) ( -7.87882029135306e-04 , 9.85792617837373e-04 , -1.85044975742524e-03 ) 2.50835474098607e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 17 ( -3.12300394959219e-01 , 2.13777265827330e-01 , 9.25617493311199e-01 ) ( -7.89612772454658e-04 , 9.86659030718436e-04 , -1.85123498662240e-03 ) 2.51202767450830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 18 ( -3.11633818168871e-01 , 2.13247870196033e-01 , 9.25964205156089e-01 ) ( -7.90945926035354e-04 , 9.87717821981030e-04 , -1.85192841031218e-03 ) 2.51541039534613e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 19 ( -3.11169739281378e-01 , 2.12623380444018e-01 , 9.26263834684329e-01 ) ( -7.91874083810339e-04 , 9.88966801485059e-04 , -1.85252766936866e-03 ) 2.51848933241326e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 20 ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226723e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 16 ( -3.13165766618894e-01 , 2.14210472267861e-01 , 9.25224878712619e-01 ) ( -7.87882029135307e-04 , 9.85792617837373e-04 , -1.85044975742524e-03 ) 2.50835474098607e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 17 ( -3.12300394959219e-01 , 2.13777265827329e-01 , 9.25617493311199e-01 ) ( -7.89612772454658e-04 , 9.86659030718436e-04 , -1.85123498662240e-03 ) 2.51202767450830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 18 ( -3.11633818168871e-01 , 2.13247870196032e-01 , 9.25964205156089e-01 ) ( -7.90945926035354e-04 , 9.87717821981030e-04 , -1.85192841031218e-03 ) 2.51541039534613e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 19 ( -3.11169739281378e-01 , 2.12623380444018e-01 , 9.26263834684329e-01 ) ( -7.91874083810338e-04 , 9.88966801485060e-04 , -1.85252766936866e-03 ) 2.51848933241326e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 20 ( -3.10902612073187e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226722e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out index a610a83f9..28afcc8be 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out @@ -1,13 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -120,6 +120,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -131,6 +132,22 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -0.310903 , 0.211905 , 0.926518 ) @@ -140,6 +157,7 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped index e86a2eb4b..dc793f2a2 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.08482822701290e-01 , 1.95664885198602e-01 , 9.30888608158067e-01 ) + x ( -3.08482822701286e-01 , 1.95664885198602e-01 , 9.30888608158068e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj index d4530bcd2..43f39b9f0 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226723e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 21 ( -3.10818115103370e-01 , 2.11096376432417e-01 , 9.26731039288472e-01 ) ( -7.92577332166356e-04 , 9.92020809508261e-04 , -1.85346207857694e-03 ) 2.52380289534207e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 22 ( -3.10894230143356e-01 , 2.10200911472952e-01 , 9.26909032472718e-01 ) ( -7.92425102086384e-04 , 9.93811739427191e-04 , -1.85381806494544e-03 ) 2.52612036687898e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 23 ( -3.11102815077490e-01 , 2.09226128345936e-01 , 9.27059580430638e-01 ) ( -7.92007932218114e-04 , 9.95761305681222e-04 , -1.85411916086128e-03 ) 2.52828750263065e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 24 ( -3.11411487946955e-01 , 2.08182462090057e-01 , 9.27190890622198e-01 ) ( -7.91390586479184e-04 , 9.97848638192982e-04 , -1.85438178124440e-03 ) 2.53036637786130e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 20 ( -3.10902612073187e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226722e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 21 ( -3.10818115103370e-01 , 2.11096376432417e-01 , 9.26731039288472e-01 ) ( -7.92577332166354e-04 , 9.92020809508262e-04 , -1.85346207857694e-03 ) 2.52380289534206e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 22 ( -3.10894230143356e-01 , 2.10200911472952e-01 , 9.26909032472718e-01 ) ( -7.92425102086383e-04 , 9.93811739427192e-04 , -1.85381806494544e-03 ) 2.52612036687898e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 23 ( -3.11102815077491e-01 , 2.09226128345936e-01 , 9.27059580430638e-01 ) ( -7.92007932218113e-04 , 9.95761305681223e-04 , -1.85411916086128e-03 ) 2.52828750263065e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 24 ( -3.11411487946956e-01 , 2.08182462090056e-01 , 9.27190890622198e-01 ) ( -7.91390586479183e-04 , 9.97848638192983e-04 , -1.85438178124440e-03 ) 2.53036637786130e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 25 ( -3.11785608613730e-01 , 2.07083701948798e-01 , 9.27311207011189e-01 ) ( -7.90642345145636e-04 , 1.00004615847550e-03 , -1.85462241402238e-03 ) 2.53241596780659e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 26 ( -3.12190163793984e-01 , 2.05946569990115e-01 , 9.27428332508551e-01 ) ( -7.89833234785128e-04 , 1.00232042239286e-03 , -1.85485666501710e-03 ) 2.53448800783766e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 26 ( -3.12190163793984e-01 , 2.05946569990115e-01 , 9.27428332508552e-01 ) ( -7.89833234785128e-04 , 1.00232042239287e-03 , -1.85485666501710e-03 ) 2.53448800783766e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 27 ( -3.12591400614140e-01 , 2.04789878956263e-01 , 9.27549309599856e-01 ) ( -7.89030761144815e-04 , 1.00463380446057e-03 , -1.85509861919971e-03 ) 2.53662475502718e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 28 ( -3.12958111790194e-01 , 2.03633472860108e-01 , 9.27680240705626e-01 ) ( -7.88297338792708e-04 , 1.00694661665288e-03 , -1.85536048141125e-03 ) 2.53885834955947e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 29 ( -3.13262544129311e-01 , 2.02497186917752e-01 , 9.27826205566553e-01 ) ( -7.87688474114472e-04 , 1.00921918853759e-03 , -1.85565241113311e-03 ) 2.54121118685469e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 30 ( -3.13480943392436e-01 , 2.01400032613720e-01 , 9.27991231097030e-01 ) ( -7.87251675588223e-04 , 1.01141349714565e-03 , -1.85598246219406e-03 ) 2.54369668144840e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 31 ( -3.13593783631662e-01 , 2.00359712776967e-01 , 9.28178282639445e-01 ) ( -7.87025995109772e-04 , 1.01349413681916e-03 , -1.85635656527889e-03 ) 2.54631998989969e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 32 ( -3.13585736154328e-01 , 1.99392449174349e-01 , 9.28389270345582e-01 ) ( -7.87042090064439e-04 , 1.01542866402440e-03 , -1.85677854069116e-03 ) 2.54907858621329e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 33 ( -3.13445449674932e-01 , 1.98512983197192e-01 , 9.28625083432615e-01 ) ( -7.87322663023230e-04 , 1.01718759597871e-03 , -1.85725016686523e-03 ) 2.55196288172193e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 34 ( -3.13165208280154e-01 , 1.97734570946912e-01 , 9.28885672069113e-01 ) ( -7.87883145812788e-04 , 1.01874442047927e-03 , -1.85777134413823e-03 ) 2.55495720640733e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 35 ( -3.12740549003459e-01 , 1.97068826614834e-01 , 9.29170181713591e-01 ) ( -7.88732464366178e-04 , 1.02007590914343e-03 , -1.85834036342718e-03 ) 2.55804133355130e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 36 ( -3.12169888759603e-01 , 1.96525353868791e-01 , 9.29477135726621e-01 ) ( -7.89873784853888e-04 , 1.02116285463551e-03 , -1.85895427145324e-03 ) 2.56119257752050e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 37 ( -3.11454223752153e-01 , 1.96111202307429e-01 , 9.29804636919218e-01 ) ( -7.91305114868789e-04 , 1.02199115775824e-03 , -1.85960927383844e-03 ) 2.56438818134972e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 38 ( -3.10596941423876e-01 , 1.95830264173120e-01 , 9.30150551046453e-01 ) ( -7.93019679525344e-04 , 1.02255303402686e-03 , -1.86030110209291e-03 ) 2.56760755498004e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 39 ( -3.09603763986273e-01 , 1.95682751690521e-01 , 9.30512638289431e-01 ) ( -7.95006034400549e-04 , 1.02284805899205e-03 , -1.86102527657886e-03 ) 2.57083391329127e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 40 ( -3.08482822701290e-01 , 1.95664885198602e-01 , 9.30888608158067e-01 ) ( -7.97247916970515e-04 , 1.02288379197589e-03 , -1.86177721631613e-03 ) 2.57405494809733e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 28 ( -3.12958111790193e-01 , 2.03633472860108e-01 , 9.27680240705626e-01 ) ( -7.88297338792708e-04 , 1.00694661665288e-03 , -1.85536048141125e-03 ) 2.53885834955947e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 29 ( -3.13262544129310e-01 , 2.02497186917752e-01 , 9.27826205566554e-01 ) ( -7.87688474114474e-04 , 1.00921918853759e-03 , -1.85565241113311e-03 ) 2.54121118685469e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 30 ( -3.13480943392435e-01 , 2.01400032613720e-01 , 9.27991231097030e-01 ) ( -7.87251675588225e-04 , 1.01141349714566e-03 , -1.85598246219406e-03 ) 2.54369668144840e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 31 ( -3.13593783631660e-01 , 2.00359712776967e-01 , 9.28178282639446e-01 ) ( -7.87025995109775e-04 , 1.01349413681916e-03 , -1.85635656527889e-03 ) 2.54631998989970e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 32 ( -3.13585736154326e-01 , 1.99392449174349e-01 , 9.28389270345583e-01 ) ( -7.87042090064442e-04 , 1.01542866402440e-03 , -1.85677854069117e-03 ) 2.54907858621330e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 33 ( -3.13445449674931e-01 , 1.98512983197192e-01 , 9.28625083432615e-01 ) ( -7.87322663023234e-04 , 1.01718759597871e-03 , -1.85725016686523e-03 ) 2.55196288172194e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 34 ( -3.13165208280151e-01 , 1.97734570946912e-01 , 9.28885672069114e-01 ) ( -7.87883145812792e-04 , 1.01874442047927e-03 , -1.85777134413823e-03 ) 2.55495720640733e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 35 ( -3.12740549003456e-01 , 1.97068826614834e-01 , 9.29170181713592e-01 ) ( -7.88732464366183e-04 , 1.02007590914343e-03 , -1.85834036342718e-03 ) 2.55804133355131e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 36 ( -3.12169888759600e-01 , 1.96525353868791e-01 , 9.29477135726622e-01 ) ( -7.89873784853896e-04 , 1.02116285463551e-03 , -1.85895427145324e-03 ) 2.56119257752052e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 37 ( -3.11454223752150e-01 , 1.96111202307429e-01 , 9.29804636919219e-01 ) ( -7.91305114868796e-04 , 1.02199115775824e-03 , -1.85960927383844e-03 ) 2.56438818134973e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 38 ( -3.10596941423872e-01 , 1.95830264173119e-01 , 9.30150551046454e-01 ) ( -7.93019679525352e-04 , 1.02255303402686e-03 , -1.86030110209291e-03 ) 2.56760755498005e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 39 ( -3.09603763986270e-01 , 1.95682751690521e-01 , 9.30512638289433e-01 ) ( -7.95006034400556e-04 , 1.02284805899205e-03 , -1.86102527657887e-03 ) 2.57083391329128e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 40 ( -3.08482822701286e-01 , 1.95664885198602e-01 , 9.30888608158068e-01 ) ( -7.97247916970524e-04 , 1.02288379197589e-03 , -1.86177721631614e-03 ) 2.57405494809734e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt b/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt index 617210efd..157cac038 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-07-07". -colvars: Using NAMD interface, version "2020-05-04". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out index 2724e6331..99a22e5fd 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -84,7 +88,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,6 +116,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -122,15 +127,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distanceInv colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 9745bfb6a..469850fcd 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.42783836132997e+00 + x 2.42783836136749e+00 } restraint { diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj index 0f1bd304e..9b364a5cf 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 2.39061650308305e+00 -9.16246601233221e-03 - 1 2.38234770114368e+00 -9.12939080457472e-03 - 2 2.37511792680581e+00 -9.10047170722326e-03 - 3 2.36945079735818e+00 -9.07780318943272e-03 - 4 2.36577204848084e+00 -9.06308819392336e-03 - 5 2.36436521239393e+00 -9.05746084957573e-03 - 6 2.36534500812203e+00 -9.06138003248811e-03 - 7 2.36864872152266e+00 -9.07459488609063e-03 - 8 2.37404299853629e+00 -9.09617199414514e-03 - 9 2.38114314206215e+00 -9.12457256824860e-03 - 10 2.38944311907187e+00 -9.15777247628748e-03 - 11 2.39835525133988e+00 -9.19342100535952e-03 - 12 2.40725780811812e+00 -9.22903123247246e-03 - 13 2.41554677333277e+00 -9.26218709333110e-03 - 14 2.42268616658529e+00 -9.29074466634115e-03 - 15 2.42825074174577e+00 -9.31300296698308e-03 - 16 2.43195609324583e+00 -9.32782437298332e-03 - 17 2.43367350230322e+00 -9.33469400921286e-03 - 18 2.43342929441762e+00 -9.33371717767048e-03 - 19 2.43139031960514e+00 -9.32556127842056e-03 - 20 2.42783836132997e+00 -9.31135344531990e-03 + 1 2.38234770114191e+00 -9.12939080456763e-03 + 2 2.37511792679912e+00 -9.10047170719648e-03 + 3 2.36945079734406e+00 -9.07780318937623e-03 + 4 2.36577204845768e+00 -9.06308819383071e-03 + 5 2.36436521236120e+00 -9.05746084944482e-03 + 6 2.36534500808037e+00 -9.06138003232147e-03 + 7 2.36864872147381e+00 -9.07459488589523e-03 + 8 2.37404299848291e+00 -9.09617199393162e-03 + 9 2.38114314200753e+00 -9.12457256803010e-03 + 10 2.38944311901955e+00 -9.15777247607821e-03 + 11 2.39835525129330e+00 -9.19342100517319e-03 + 12 2.40725780808025e+00 -9.22903123232098e-03 + 13 2.41554677330587e+00 -9.26218709322349e-03 + 14 2.42268616657072e+00 -9.29074466628286e-03 + 15 2.42825074174393e+00 -9.31300296697570e-03 + 16 2.43195609325616e+00 -9.32782437302463e-03 + 17 2.43367350232427e+00 -9.33469400929707e-03 + 18 2.43342929444717e+00 -9.33371717778869e-03 + 19 2.43139031964034e+00 -9.32556127856135e-03 + 20 2.42783836136749e+00 -9.31135344546996e-03 diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out index fd5a4f5e9..fe78368a1 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -84,7 +88,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,6 +116,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -122,20 +127,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distanceInv colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 2.42784 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 8b74c0b18..d50294abc 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.39535776180124e+00 + x 2.39535776160792e+00 } restraint { diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj index a892a5839..8afdaf44b 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.42783836132997e+00 -9.31135344531990e-03 - 21 2.42313713928297e+00 -9.29254855713189e-03 - 22 2.41769617209907e+00 -9.27078468839628e-03 - 23 2.41193587329818e+00 -9.24774349319270e-03 - 24 2.40625738445557e+00 -9.22502953782229e-03 - 25 2.40101869519443e+00 -9.20407478077773e-03 - 26 2.39651622531912e+00 -9.18606490127647e-03 - 27 2.39296966658990e+00 -9.17187866635958e-03 - 28 2.39050847174201e+00 -9.16203388696806e-03 - 29 2.38916060739287e+00 -9.15664242957147e-03 - 30 2.38884732562697e+00 -9.15538930250787e-03 - 31 2.38938907304455e+00 -9.15755629217820e-03 - 32 2.39052656459227e+00 -9.16210625836907e-03 - 33 2.39195711463777e+00 -9.16782845855110e-03 - 34 2.39338167023812e+00 -9.17352668095248e-03 - 35 2.39455393678809e+00 -9.17821574715235e-03 - 36 2.39532170780857e+00 -9.18128683123430e-03 - 37 2.39565155158960e+00 -9.18260620635839e-03 - 38 2.39563139490110e+00 -9.18252557960440e-03 - 39 2.39545006628275e+00 -9.18180026513099e-03 - 40 2.39535776180124e+00 -9.18143104720494e-03 + 20 2.42783836136749e+00 -9.31135344546996e-03 + 21 2.42313713931922e+00 -9.29254855727687e-03 + 22 2.41769617213041e+00 -9.27078468852164e-03 + 23 2.41193587332118e+00 -9.24774349328473e-03 + 24 2.40625738446726e+00 -9.22502953786906e-03 + 25 2.40101869519248e+00 -9.20407478076994e-03 + 26 2.39651622530201e+00 -9.18606490120804e-03 + 27 2.39296966655697e+00 -9.17187866622788e-03 + 28 2.39050847169341e+00 -9.16203388677364e-03 + 29 2.38916060732936e+00 -9.15664242931743e-03 + 30 2.38884732554973e+00 -9.15538930219891e-03 + 31 2.38938907295485e+00 -9.15755629181939e-03 + 32 2.39052656449122e+00 -9.16210625796488e-03 + 33 2.39195711452612e+00 -9.16782845810448e-03 + 34 2.39338167011611e+00 -9.17352668046446e-03 + 35 2.39455393665551e+00 -9.17821574662203e-03 + 36 2.39532170766483e+00 -9.18128683065931e-03 + 37 2.39565155143393e+00 -9.18260620573574e-03 + 38 2.39563139473288e+00 -9.18252557893151e-03 + 39 2.39545006610174e+00 -9.18180026440696e-03 + 40 2.39535776160792e+00 -9.18143104643170e-03 diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out index 9b43c99fa..18bfc4768 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -120,15 +124,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - distancePairs colvar component: +colvars: - histogramRestraint colvar bias implementation: +colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped index 2fdfb6c4c..76f57335f 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.04650863884945e+00 , 4.49435411437724e+00 , 5.18841527762764e+00 , 6.16645837340779e+00 , 2.49717925480425e+00 , 3.86424836018692e+00 , 4.55750848697779e+00 , 5.34080670765490e+00 , 1.36568581546352e+00 , 2.47047097097987e+00 , 3.12336009885461e+00 , 3.85074280281206e+00 , 2.22178524357949e+00 , 2.73185149414085e+00 , 2.91864419906098e+00 , 3.29101397431997e+00 ) + x ( 3.04650863844542e+00 , 4.49435411373106e+00 , 5.18841527687423e+00 , 6.16645837246753e+00 , 2.49717925475228e+00 , 3.86424835988508e+00 , 4.55750848670402e+00 , 5.34080670712767e+00 , 1.36568581550375e+00 , 2.47047097074510e+00 , 3.12336009876006e+00 , 3.85074280234761e+00 , 2.22178524374518e+00 , 2.73185149420872e+00 , 2.91864419945045e+00 , 3.29101397434784e+00 ) } histogramrestraint { diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj index 703c0aa24..e0a6a3b8e 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hr 0 ( 2.95543971137580e+00 , 4.40149446295507e+00 , 5.19438956774262e+00 , 6.22241603343745e+00 , 2.46985074910253e+00 , 3.82984200895935e+00 , 4.58947829164686e+00 , 5.41000980054028e+00 , 1.34023744154865e+00 , 2.42537620134385e+00 , 3.12639105039661e+00 , 3.90388793384236e+00 , 2.19602098164167e+00 , 2.66815420835178e+00 , 2.96116058328487e+00 , 3.36815290626777e+00 ) ( -5.92960352862036e-03 , 1.10620242770031e-02 , 1.68173891728727e-02 , 1.87723003472394e-02 , -1.12008206156859e-02 , 4.95828158263673e-03 , 1.27336187454413e-02 , 1.77621382788059e-02 , -1.61490029424512e-02 , -1.16075543291348e-02 , -3.82398122724722e-03 , 5.82475954854570e-03 , -1.34483793610802e-02 , -9.21377746348792e-03 , -5.86053342506391e-03 , -7.62252484367914e-04 ) 3.78092070171140e-01 - 1 ( 2.95875719071982e+00 , 4.40108157301290e+00 , 5.19334777145356e+00 , 6.22377033113224e+00 , 2.46917672947515e+00 , 3.82473616688567e+00 , 4.58659307892474e+00 , 5.40932559984203e+00 , 1.33333768535653e+00 , 2.41676016397346e+00 , 3.12170836496849e+00 , 3.90418294782770e+00 , 2.19936580917918e+00 , 2.66448894985085e+00 , 2.96000465033168e+00 , 3.36551108557328e+00 ) ( -5.86283106863594e-03 , 1.10731958752850e-02 , 1.68140327966034e-02 , 1.87597892711556e-02 , -1.11822547405509e-02 , 4.92033089417690e-03 , 1.27214365048402e-02 , 1.77580366645092e-02 , -1.61363624056526e-02 , -1.16601244086755e-02 , -3.85595598393038e-03 , 5.84982545354479e-03 , -1.34023678457367e-02 , -9.22688145620218e-03 , -5.84776463394309e-03 , -7.69953161967240e-04 ) 3.77945851131251e-01 - 2 ( 2.96294215661432e+00 , 4.40226828651527e+00 , 5.19286012272764e+00 , 6.22443374459694e+00 , 2.46935518848109e+00 , 3.82150874456456e+00 , 4.58422849105476e+00 , 5.40818433919542e+00 , 1.32707626479006e+00 , 2.41052101094915e+00 , 3.11822280908199e+00 , 3.90473321717080e+00 , 2.20349735093029e+00 , 2.66304418492767e+00 , 2.95871521200833e+00 , 3.36219610857531e+00 ) ( -5.79800647495339e-03 , 1.10923908557496e-02 , 1.68129107062616e-02 , 1.87535308678082e-02 , -1.11672628468922e-02 , 4.89409954501751e-03 , 1.27081525943855e-02 , 1.77533370847981e-02 , -1.61279245724480e-02 , -1.17024782042702e-02 , -3.88536413834723e-03 , 5.86771262498385e-03 , -1.33609408182631e-02 , -9.22837266286093e-03 , -5.84907998238668e-03 , -7.98316100642240e-04 ) 3.77862223359046e-01 - 3 ( 2.96775402994024e+00 , 4.40516830460360e+00 , 5.19308580986400e+00 , 6.22426614574961e+00 , 2.47031640872298e+00 , 3.82049095747722e+00 , 4.58271436794834e+00 , 5.40668366049041e+00 , 1.32191637303560e+00 , 2.40699048525786e+00 , 3.11597732151607e+00 , 3.90507762177822e+00 , 2.20806859148045e+00 , 2.66384305028015e+00 , 2.95730260669763e+00 , 3.35823946236896e+00 ) ( -5.73812439842742e-03 , 1.11203452480230e-02 , 1.68145007711762e-02 , 1.87535589646727e-02 , -1.11565343479722e-02 , 4.88326606487158e-03 , 1.26961984972676e-02 , 1.77480942242067e-02 , -1.61238345656856e-02 , -1.17319756038901e-02 , -3.91183713334946e-03 , 5.87286048596288e-03 , -1.33265703304735e-02 , -9.21811206406306e-03 , -5.86446396118304e-03 , -8.47126580585897e-04 ) 3.77840179114077e-01 - 4 ( 2.97293625447158e+00 , 4.40980004759664e+00 , 5.19408774076560e+00 , 6.22316886256237e+00 , 2.47196059702916e+00 , 3.82188498631318e+00 , 4.58227967127418e+00 , 5.40493151511998e+00 , 1.31824010724331e+00 , 2.40633376725236e+00 , 3.11491133209108e+00 , 3.90477299815830e+00 , 2.21271348718521e+00 , 2.66679770355164e+00 , 2.95576116722859e+00 , 3.35371179660392e+00 ) ( -5.68562536183138e-03 , 1.11574404636885e-02 , 1.68189720083336e-02 , 1.87595928076098e-02 , -1.11503656065385e-02 , 4.89069779973133e-03 , 1.26876273221314e-02 , 1.77424383833815e-02 , -1.61240913055418e-02 , -1.17467229285959e-02 , -3.93551745867430e-03 , 5.86059410573176e-03 , -1.33013307602379e-02 , -9.19636281544416e-03 , -5.89333166795764e-03 , -9.14911497569518e-04 ) 3.77876668462653e-01 - 5 ( 2.97824318824101e+00 , 4.41608136347726e+00 , 5.19583111699352e+00 , 6.22109580815711e+00 , 2.47416649817960e+00 , 3.82573442794437e+00 , 4.58302854467365e+00 , 5.40302751456301e+00 , 1.31631479783864e+00 , 2.40854057672349e+00 , 3.11487986890582e+00 , 3.90345112768636e+00 , 2.21707823698990e+00 , 2.67171151316098e+00 , 2.95407669271725e+00 , 3.34871521637494e+00 ) ( -5.64215660521570e-03 , 1.12036160408532e-02 , 1.68261920491313e-02 , 1.87710646710979e-02 , -1.11486629031842e-02 , 4.91802392882698e-03 , 1.26838914735522e-02 , 1.77365452169101e-02 , -1.61285450766266e-02 , -1.17456807870724e-02 , -3.95690439737455e-03 , 5.82769712027467e-03 , -1.32867339927564e-02 , -9.16386239633315e-03 , -5.93452420055991e-03 , -9.99112312804834e-04 ) 3.77966928506520e-01 - 6 ( 2.98346272354641e+00 , 4.42383057902279e+00 , 5.19819070221187e+00 , 6.21805993383684e+00 , 2.47679966399307e+00 , 3.83190740551612e+00 , 4.58492741114084e+00 , 5.40104621793262e+00 , 1.31627480646442e+00 , 2.41343034366284e+00 , 3.11567914999535e+00 , 3.90086651034176e+00 , 2.22085290398016e+00 , 2.67829022316575e+00 , 2.95223463727300e+00 , 3.34337409766356e+00 ) ( -5.60843111606338e-03 , 1.12583138090471e-02 , 1.68357668480079e-02 , 1.87871810204228e-02 , -1.11509975018142e-02 , 4.96532034592246e-03 , 1.26856803068378e-02 , 1.77306125297571e-02 , -1.61369024574342e-02 , -1.17287330743696e-02 , -3.97667165972031e-03 , 5.77284958152370e-03 , -1.32835970603912e-02 , -9.12186140048792e-03 , -5.98634736812786e-03 , -1.09632452049312e-03 ) 3.78105088301569e-01 - 7 ( 2.98843276398744e+00 , 4.43277362483451e+00 , 5.20096598215456e+00 , 6.21413473649645e+00 , 2.47971835574389e+00 , 3.84009332258054e+00 , 4.58780406792093e+00 , 5.39902438402581e+00 , 1.31811662219982e+00 , 2.42066789068249e+00 , 3.11707520826167e+00 , 3.89692854958901e+00 , 2.22379944065945e+00 , 2.68616059173228e+00 , 2.95022670924909e+00 , 3.33782534397885e+00 ) ( -5.58418350392305e-03 , 1.13204634820250e-02 , 1.68471093234050e-02 , 1.88070063165611e-02 , -1.11567058554382e-02 , 5.03094217833919e-03 , 1.26928382670779e-02 , 1.77248424341677e-02 , -1.61487389919253e-02 , -1.16967256674628e-02 , -3.99547330134301e-03 , 5.69688275344288e-03 , -1.32919546974225e-02 , -9.07211334097645e-03 , -6.04665602071449e-03 , -1.20257089380199e-03 ) 3.78284907038721e-01 - 8 ( 2.99305095207488e+00 , 4.44255706235088e+00 , 5.20390279809292e+00 , 6.20945090058357e+00 , 2.48277685515950e+00 , 3.84981382800082e+00 , 4.59135934528309e+00 , 5.39695380947607e+00 , 1.32170353603877e+00 , 2.42978572120870e+00 , 3.11883162757640e+00 , 3.89171382389852e+00 , 2.22577247713240e+00 , 2.69489401022899e+00 , 2.94805450424125e+00 , 3.33220883830515e+00 ) ( -5.56820917188656e-03 , 1.13885155086110e-02 , 1.68595280943234e-02 , 1.88295545631365e-02 , -1.11650126057927e-02 , 5.11152770881174e-03 , 1.27043773423435e-02 , 1.77194261760565e-02 , -1.61635185301110e-02 , -1.16514770992267e-02 , -4.01376337810813e-03 , 5.60281550764459e-03 , -1.33110285193646e-02 , -9.01681060097791e-03 , -6.11297722489409e-03 , -1.31358022313040e-03 ) 3.78500459323722e-01 - 9 ( 2.99727803942290e+00 , 4.45276689013810e+00 , 5.20671940505602e+00 , 6.20418843028865e+00 , 2.48582792212175e+00 , 3.86044838531630e+00 , 4.59519142343736e+00 , 5.39478097767364e+00 , 1.32677703129530e+00 , 2.44021023618222e+00 , 3.12073277452649e+00 , 3.88545705730016e+00 , 2.22673027068734e+00 , 2.70403228023088e+00 , 2.94572999605854e+00 , 3.32665870427579e+00 ) ( -5.55846922797675e-03 , 1.14605208116932e-02 , 1.68723226148458e-02 , 1.88538732077974e-02 , -1.11751436040917e-02 , 5.20218321479418e-03 , 1.27185877225548e-02 , 1.77145300273766e-02 , -1.61806180971707e-02 , -1.15957536326590e-02 , -4.03166013252892e-03 , 5.49565596389940e-03 , -1.33392618858248e-02 , -8.95847435071736e-03 , -6.18265892101870e-03 , -1.42505162821923e-03 ) 3.78746600035240e-01 - 10 ( 3.00113590362578e+00 , 4.46295283642265e+00 , 5.20913451147704e+00 , 6.19856492398371e+00 , 2.48872700419815e+00 , 3.87127405646959e+00 , 4.59883180778555e+00 , 5.39241395065204e+00 , 1.33297408012915e+00 , 2.45129095466347e+00 , 3.12259990731229e+00 , 3.87852252742574e+00 , 2.22673463298190e+00 , 2.71311302772409e+00 , 2.94327377801210e+00 , 3.32129591628587e+00 ) ( -5.55224417034228e-03 , 1.15342512231714e-02 , 1.68848695700858e-02 , 1.88791062739624e-02 , -1.11863975631308e-02 , 5.29683799008538e-03 , 1.27332368505308e-02 , 1.77102817911029e-02 , -1.61993578790013e-02 , -1.15331925411162e-02 , -4.04888243585471e-03 , 5.38197720759974e-03 , -1.33744234726094e-02 , -8.89981537283595e-03 , -6.25302646254240e-03 , -1.53289195744994e-03 ) 3.79019107024581e-01 - 11 ( 3.00470125503232e+00 , 4.47265711228424e+00 , 5.21089460531976e+00 , 6.19282083273147e+00 , 2.49134008905727e+00 , 3.88151734630328e+00 , 4.60179016418754e+00 , 5.38973566951884e+00 , 1.33985118526983e+00 , 2.46233295679202e+00 , 3.12429892039402e+00 , 3.87136030320866e+00 , 2.22594006156255e+00 , 2.72169287069741e+00 , 2.94071248075728e+00 , 3.31622273015255e+00 ) ( -5.54632287865549e-03 , 1.16073489553701e-02 , 1.68966879651642e-02 , 1.89045283462007e-02 , -1.11981583558499e-02 , 5.38873432377074e-03 , 1.27458325711537e-02 , 1.77067581962933e-02 , -1.62190359535014e-02 , -1.14681548196382e-02 , -4.06477383520721e-03 , 5.26930541316280e-03 , -1.34137735934670e-02 , -8.84358548360923e-03 , -6.32152819384059e-03 , -1.63341748079868e-03 ) 3.79314492509373e-01 - 12 ( 3.00809583960727e+00 , 4.48144568626711e+00 , 5.21179795363804e+00 , 6.18720282692826e+00 , 2.49355503433962e+00 , 3.89041360016790e+00 , 4.60360319945111e+00 , 5.38662146987011e+00 , 1.34691612073454e+00 , 2.47263280504502e+00 , 3.12573989584620e+00 , 3.86445347605522e+00 , 2.22457351036754e+00 , 2.72936720504478e+00 , 2.93807666839465e+00 , 3.31151936870328e+00 ) ( -5.53721626627702e-03 , 1.16774905538055e-02 , 1.69074760237742e-02 , 1.89295470404025e-02 , -1.12098518644332e-02 , 5.47099418171554e-03 , 1.27539142258515e-02 , 1.77039734246792e-02 , -1.62389653913332e-02 , -1.14054942027861e-02 , -4.07841190467654e-03 , 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6.17725979186124e+00 , 2.49652507991581e+00 , 3.90150978145652e+00 , 4.60234863267193e+00 , 5.37865915172911e+00 , 1.35963468852382e+00 , 2.48838344234272e+00 , 3.12766033461501e+00 , 3.85317752085478e+00 , 2.22122742528990e+00 , 2.74066674500144e+00 , 2.93271867756587e+00 , 3.30343100749719e+00 ) ( -5.49549732658235e-03 , 1.18007441995238e-02 , 1.69256728810072e-02 , 1.89765088165145e-02 , -1.12304979159479e-02 , 5.58188833372983e-03 , 1.27484793022279e-02 , 1.77003118136450e-02 , -1.62771022163553e-02 , -1.13072324023837e-02 , -4.09500221458595e-03 , 5.01132421291456e-03 , -1.35265575665557e-02 , -8.71473341395976e-03 , -6.49440390970358e-03 , -1.86333145710300e-03 ) 3.80303913133154e-01 - 15 ( 3.01885935156514e+00 , 4.49895836137591e+00 , 5.20845880475518e+00 , 6.17330862037168e+00 , 2.49726571449010e+00 , 3.90273958741594e+00 , 4.59886715933612e+00 , 5.37368145671421e+00 , 1.36442685860736e+00 , 2.49273626189266e+00 , 3.12809348128601e+00 , 3.84947011817928e+00 , 2.21980329418561e+00 , 2.74380165821453e+00 , 2.93007263646310e+00 , 3.30010253663009e+00 ) ( -5.45664327201426e-03 , 1.18507598198550e-02 , 1.69333270283853e-02 , 1.89976486913772e-02 , -1.12378675646792e-02 , 5.60103026331286e-03 , 1.27324557178694e-02 , 1.76990895578171e-02 , -1.62942676677129e-02 , -1.12806824573500e-02 , -4.09652022619895e-03 , 4.97117341431712e-03 , -1.35529004613194e-02 , -8.69192881902856e-03 , -6.53579294296637e-03 , -1.91029892090598e-03 ) 3.80653281302327e-01 - 16 ( 3.02318574258621e+00 , 4.50121671756992e+00 , 5.20543347977050e+00 , 6.17020596722025e+00 , 2.49758367079577e+00 , 3.90075791036053e+00 , 4.59345084633747e+00 , 5.36803107369289e+00 , 1.36776218076375e+00 , 2.49422221714921e+00 , 3.12814676412765e+00 , 3.84727076152845e+00 , 2.21885835301271e+00 , 2.74506502292299e+00 , 2.92750329352306e+00 , 3.29726720556305e+00 ) ( -5.40260774968335e-03 , 1.18918394007310e-02 , 1.69403563719583e-02 , 1.90167057097929e-02 , -1.12419666462581e-02 , 5.59228671213132e-03 , 1.27071500721839e-02 , 1.76979317986111e-02 , -1.63096075124309e-02 , -1.12738072071936e-02 , -4.09333242395765e-03 , 4.95876082366399e-03 , -1.35699155636684e-02 , -8.68152857793866e-03 , -6.56737454540186e-03 , -1.94123960822893e-03 ) 3.81001871200905e-01 - 17 ( 3.02809415739285e+00 , 4.50166506152248e+00 , 5.20168811935516e+00 , 6.16800533426867e+00 , 2.49758857966083e+00 , 3.89558236026613e+00 , 4.58626174942138e+00 , 5.36177010663164e+00 , 1.36949463576574e+00 , 2.49265415207740e+00 , 3.12778059657973e+00 , 3.84655116139501e+00 , 2.21854897882363e+00 , 2.74441563391359e+00 , 2.92505081172337e+00 , 3.29493032182962e+00 ) ( -5.33207795196924e-03 , 1.19238375489492e-02 , 1.69470627880117e-02 , 1.90332731835913e-02 , -1.12416911790806e-02 , 5.55523293589804e-03 , 1.26732473351448e-02 , 1.76965367621060e-02 , -1.63227936073129e-02 , -1.12884863405751e-02 , -4.08612201281463e-03 , 4.97341853341229e-03 , -1.35763317146644e-02 , -8.68411432143570e-03 , -6.58877217369707e-03 , -1.95630819012991e-03 ) 3.81341269928444e-01 - 18 ( 3.03363892711023e+00 , 4.50047208617566e+00 , 5.19744285848972e+00 , 6.16669911803858e+00 , 2.49741999767105e+00 , 3.88744865236222e+00 , 4.57759477250720e+00 , 5.35501860480364e+00 , 1.36962096539415e+00 , 2.48802587309199e+00 , 3.12692927012681e+00 , 3.84712592465320e+00 , 2.21895140200526e+00 , 2.74189783522437e+00 , 2.92274822912038e+00 , 3.29309909620042e+00 ) ( -5.24483234153983e-03 , 1.19472351653105e-02 , 1.69537131712506e-02 , 1.90469452579835e-02 , -1.12359373167835e-02 , 5.49144095261838e-03 , 1.26321668651098e-02 , 1.76946183373094e-02 , -1.63335559224151e-02 , -1.13250482243768e-02 , -4.07634438292505e-03 , 5.01204954472087e-03 , -1.35716288071488e-02 , -8.69964479575904e-03 , -6.60008084859376e-03 , -1.95609218183908e-03 ) 3.81662024495540e-01 - 19 ( 3.03980638930293e+00 , 4.49791396578241e+00 , 5.19293926757803e+00 , 6.16622192484240e+00 , 2.49723246067585e+00 , 3.87679761700838e+00 , 4.56785187541893e+00 , 5.34795393898199e+00 , 1.36827142971955e+00 , 2.48051460702728e+00 , 3.12549701705262e+00 , 3.84866874600845e+00 , 2.22005841855173e+00 , 2.73764013697229e+00 , 2.92061396044736e+00 , 3.29178674652055e+00 ) ( -5.14186564988213e-03 , 1.19631117675662e-02 , 1.69604787021299e-02 , 1.90573528714360e-02 , -1.12237144451809e-02 , 5.40445708266560e-03 , 1.25859420474585e-02 , 1.76919640583354e-02 , -1.63416796379246e-02 , -1.13821966907384e-02 , -4.06622804413393e-03 , 5.06938813592078e-03 , -1.35560499548848e-02 , -8.72742264831989e-03 , -6.60191447726332e-03 , -1.94150498787041e-03 ) 3.81954197395723e-01 - 20 ( 3.04650863884945e+00 , 4.49435411437724e+00 , 5.18841527762764e+00 , 6.16645837340779e+00 , 2.49717925480425e+00 , 3.86424836018692e+00 , 4.55750848697779e+00 , 5.34080670765490e+00 , 1.36568581546352e+00 , 2.47047097097987e+00 , 3.12336009885461e+00 , 3.85074280281206e+00 , 2.22178524357949e+00 , 2.73185149414085e+00 , 2.91864419906098e+00 , 3.29101397431997e+00 ) ( -5.02542974750439e-03 , 1.19730728164444e-02 , 1.69673824742426e-02 , 1.90642123537368e-02 , -1.12042672914772e-02 , 5.29965572263668e-03 , 1.25370495916030e-02 , 1.76884949726336e-02 , -1.63470133927038e-02 , -1.14570941759426e-02 , -4.05868153495143e-03 , 5.13846947912402e-03 , -1.35305636185385e-02 , -8.76608365877139e-03 , -6.59544443572543e-03 , -1.91369494935530e-03 ) 3.82208090906906e-01 + 1 ( 2.95875719071828e+00 , 4.40108157301207e+00 , 5.19334777145334e+00 , 6.22377033112801e+00 , 2.46917672947451e+00 , 3.82473616688607e+00 , 4.58659307892583e+00 , 5.40932559983924e+00 , 1.33333768535497e+00 , 2.41676016397270e+00 , 3.12170836496912e+00 , 3.90418294782421e+00 , 2.19936580917941e+00 , 2.66448894985246e+00 , 2.96000465033399e+00 , 3.36551108557249e+00 ) ( -5.86283106865521e-03 , 1.10731958752829e-02 , 1.68140327966110e-02 , 1.87597892711689e-02 , -1.11822547405590e-02 , 4.92033089418465e-03 , 1.27214365048558e-02 , 1.77580366645080e-02 , -1.61363624056552e-02 , -1.16601244086846e-02 , -3.85595598392256e-03 , 5.84982545350766e-03 , -1.34023678457379e-02 , -9.22688145618673e-03 , -5.84776463391588e-03 , -7.69953161976424e-04 ) 3.77945851131380e-01 + 2 ( 2.96294215660827e+00 , 4.40226828651185e+00 , 5.19286012272654e+00 , 6.22443374457976e+00 , 2.46935518847865e+00 , 3.82150874456602e+00 , 4.58422849105882e+00 , 5.40818433918403e+00 , 1.32707626478422e+00 , 2.41052101094634e+00 , 3.11822280908445e+00 , 3.90473321715676e+00 , 2.20349735093127e+00 , 2.66304418493398e+00 , 2.95871521201740e+00 , 3.36219610857201e+00 ) ( -5.79800647502922e-03 , 1.10923908557419e-02 , 1.68129107062924e-02 , 1.87535308678630e-02 , -1.11672628469244e-02 , 4.89409954504780e-03 , 1.27081525944472e-02 , 1.77533370847938e-02 , -1.61279245724598e-02 , -1.17024782043052e-02 , -3.88536413831673e-03 , 5.86771262483623e-03 , -1.33609408182681e-02 , -9.22837266280075e-03 , -5.84907998228004e-03 , -7.98316100680052e-04 ) 3.77862223359593e-01 + 3 ( 2.96775402992694e+00 , 4.40516830459548e+00 , 5.19308580986083e+00 , 6.22426614571086e+00 , 2.47031640871780e+00 , 3.82049095747998e+00 , 4.58271436795677e+00 , 5.40668366046462e+00 , 1.32191637302337e+00 , 2.40699048525175e+00 , 3.11597732152133e+00 , 3.90507762174690e+00 , 2.20806859148285e+00 , 2.66384305029386e+00 , 2.95730260671757e+00 , 3.35823946236147e+00 ) ( -5.73812439859379e-03 , 1.11203452480056e-02 , 1.68145007712454e-02 , 1.87535589647976e-02 , -1.11565343480424e-02 , 4.88326606493625e-03 , 1.26961984974043e-02 , 1.77480942241991e-02 , -1.61238345657143e-02 , -1.17319756039677e-02 , -3.91183713328302e-03 , 5.87286048563701e-03 , -1.33265703304845e-02 , -9.21811206393306e-03 , -5.86446396094804e-03 , -8.47126580670137e-04 ) 3.77840179115355e-01 + 4 ( 2.97293625444857e+00 , 4.40980004758125e+00 , 5.19408774075846e+00 , 6.22316886249381e+00 , 2.47196059702068e+00 , 3.82188498631687e+00 , 4.58227967128769e+00 , 5.40493151507430e+00 , 1.31824010722335e+00 , 2.40633376724167e+00 , 3.11491133209983e+00 , 3.90477299810360e+00 , 2.21271348718989e+00 , 2.66679770357475e+00 , 2.95576116726311e+00 , 3.35371179659075e+00 ) ( -5.68562536211738e-03 , 1.11574404636562e-02 , 1.68189720084544e-02 , 1.87595928078326e-02 , -1.11503656066572e-02 , 4.89069779983769e-03 , 1.26876273223686e-02 , 1.77424383833725e-02 , -1.61240913055969e-02 , -1.17467229287332e-02 , -3.93551745856113e-03 , 5.86059410516952e-03 , -1.33013307602559e-02 , -9.19636281522561e-03 , -5.89333166754952e-03 , -9.14911497713965e-04 ) 3.77876668465000e-01 + 5 ( 2.97824318820620e+00 , 4.41608136345158e+00 , 5.19583111697961e+00 , 6.22109580805119e+00 , 2.47416649816765e+00 , 3.82573442794791e+00 , 4.58302854469209e+00 , 5.40302751449250e+00 , 1.31631479781056e+00 , 2.40854057670679e+00 , 3.11487986891832e+00 , 3.90345112760315e+00 , 2.21707823699791e+00 , 2.67171151319462e+00 , 2.95407669276953e+00 , 3.34871521635490e+00 ) ( -5.64215660564444e-03 , 1.12036160407990e-02 , 1.68261920493138e-02 , 1.87710646714446e-02 , -1.11486629033573e-02 , 4.91802392897703e-03 , 1.26838914739109e-02 , 1.77365452169039e-02 , -1.61285450767192e-02 , -1.17456807872873e-02 , -3.95690439720719e-03 , 5.82769711943081e-03 , -1.32867339927808e-02 , -9.16386239601504e-03 , -5.93452419993883e-03 , -9.99112313017295e-04 ) 3.77966928510290e-01 + 6 ( 2.98346272349810e+00 , 4.42383057898326e+00 , 5.19819070218742e+00 , 6.21805993368695e+00 , 2.47679966397792e+00 , 3.83190740551774e+00 , 4.58492741116317e+00 , 5.40104621783311e+00 , 1.31627480642875e+00 , 2.41343034363858e+00 , 3.11567915001139e+00 , 3.90086651022608e+00 , 2.22085290399274e+00 , 2.67829022321015e+00 , 2.95223463734567e+00 , 3.34337409763593e+00 ) ( -5.60843111665177e-03 , 1.12583138089623e-02 , 1.68357668482585e-02 , 1.87871810209162e-02 , -1.11509975020431e-02 , 4.96532034611288e-03 , 1.26856803073333e-02 , 1.77306125297607e-02 , -1.61369024575768e-02 , -1.17287330746808e-02 , -3.97667165949540e-03 , 5.77284958036822e-03 , -1.32835970604198e-02 , -9.12186140006743e-03 , -5.98634736725953e-03 , -1.09632452077415e-03 ) 3.78105088307123e-01 + 7 ( 2.98843276392426e+00 , 4.43277362477714e+00 , 5.20096598211478e+00 , 6.21413473629710e+00 , 2.47971835572621e+00 , 3.84009332257782e+00 , 4.58780406794513e+00 , 5.39902438389403e+00 , 1.31811662215800e+00 , 2.42066789064899e+00 , 3.11707520828051e+00 , 3.89692854943828e+00 , 2.22379944067799e+00 , 2.68616059178675e+00 , 2.95022670934415e+00 , 3.33782534394336e+00 ) ( -5.58418350468220e-03 , 1.13204634818992e-02 , 1.68471093237251e-02 , 1.88070063172207e-02 , -1.11567058557194e-02 , 5.03094217856181e-03 , 1.26928382677193e-02 , 1.77248424341910e-02 , -1.61487389921320e-02 , -1.16967256678892e-02 , -3.99547330106177e-03 , 5.69688275196239e-03 , -1.32919546974516e-02 , -9.07211334045853e-03 , -6.04665601957078e-03 , -1.20257089414411e-03 ) 3.78284907046422e-01 + 8 ( 2.99305095199572e+00 , 4.44255706227127e+00 , 5.20390279803208e+00 , 6.20945090033049e+00 , 2.48277685514022e+00 , 3.84981382799079e+00 , 4.59135934530626e+00 , 5.39695380930977e+00 , 1.32170353599299e+00 , 2.42978572116422e+00 , 3.11883162759681e+00 , 3.89171382371156e+00 , 2.22577247715835e+00 , 2.69489401029209e+00 , 2.94805450436009e+00 , 3.33220883826211e+00 ) ( -5.56820917282278e-03 , 1.13885155084319e-02 , 1.68595280947096e-02 , 1.88295545639784e-02 , -1.11650126061194e-02 , 5.11152770905446e-03 , 1.27043773431331e-02 , 1.77194261761126e-02 , -1.61635185303969e-02 , -1.16514770997870e-02 , -4.01376337777638e-03 , 5.60281550584254e-03 , -1.33110285193897e-02 , -9.01681060037427e-03 , -6.11297722345335e-03 , -1.31358022351808e-03 ) 3.78500459333923e-01 + 9 ( 2.99727803932683e+00 , 4.45276689003159e+00 , 5.20671940496760e+00 , 6.20418842997876e+00 , 2.48582792210202e+00 , 3.86044838529561e+00 , 4.59519142345580e+00 , 5.39478097747158e+00 , 1.32677703124828e+00 , 2.44021023612503e+00 , 3.12073277454684e+00 , 3.88545705707712e+00 , 2.22673027072218e+00 , 2.70403228030061e+00 , 2.94572999620193e+00 , 3.32665870422601e+00 ) ( -5.55846922909315e-03 , 1.14605208114470e-02 , 1.68723226152897e-02 , 1.88538732088346e-02 , -1.11751436044541e-02 , 5.20218321504213e-03 , 1.27185877234887e-02 , 1.77145300274814e-02 , -1.61806180975511e-02 , -1.15957536333710e-02 , -4.03166013215670e-03 , 5.49565596179502e-03 , -1.33392618858410e-02 , -8.95847435004462e-03 , -6.18265891926579e-03 , -1.42505162862931e-03 ) 3.78746600048281e-01 + 10 ( 3.00113590351193e+00 , 4.46295283628442e+00 , 5.20913451135400e+00 , 6.19856492361509e+00 , 2.48872700417910e+00 , 3.87127405643474e+00 , 4.59883180779499e+00 , 5.39241395041393e+00 , 1.33297408008389e+00 , 2.45129095459194e+00 , 3.12259990733059e+00 , 3.87852252716797e+00 , 2.22673463302703e+00 , 2.71311302779813e+00 , 2.94327377818026e+00 , 3.32129591623069e+00 ) ( -5.55224417164072e-03 , 1.15342512228427e-02 , 1.68848695705750e-02 , 1.88791062752049e-02 , -1.11863975635185e-02 , 5.29683799032226e-03 , 1.27332368515994e-02 , 1.77102817912748e-02 , -1.61993578794913e-02 , -1.15331925419960e-02 , -4.04888243545545e-03 , 5.38197720522603e-03 , -1.33744234726122e-02 , -8.89981537211362e-03 , -6.25302646046828e-03 , -1.53289195785256e-03 ) 3.79019107040781e-01 + 11 ( 3.00470125489972e+00 , 4.47265711210950e+00 , 5.21089460515481e+00 , 6.19282083230316e+00 , 2.49134008903989e+00 , 3.88151734625078e+00 , 4.60179016418336e+00 , 5.38973566924521e+00 , 1.33985118522930e+00 , 2.46233295670471e+00 , 3.12429892040812e+00 , 3.87136030291841e+00 , 2.22594006161918e+00 , 2.72169287077339e+00 , 2.94071248094998e+00 , 3.31622273009373e+00 ) ( -5.54632288013861e-03 , 1.16073489549424e-02 , 1.68966879656824e-02 , 1.89045283476569e-02 , -1.11981583562531e-02 , 5.38873432397986e-03 , 1.27458325723427e-02 , 1.77067581965523e-02 , -1.62190359541145e-02 , -1.14681548206993e-02 , -4.06477383479660e-03 , 5.26930541056336e-03 , -1.34137735934525e-02 , -8.84358548285717e-03 , -6.32152819144142e-03 , -1.63341748115851e-03 ) 3.79314492529018e-01 + 12 ( 3.00809583945475e+00 , 4.48144568605128e+00 , 5.21179795342402e+00 , 6.18720282644011e+00 , 2.49355503432457e+00 , 3.89041360009451e+00 , 4.60360319942864e+00 , 5.38662146956213e+00 , 1.34691612070145e+00 , 2.47263280494077e+00 , 3.12573989585393e+00 , 3.86445347573540e+00 , 2.22457351043668e+00 , 2.72936720512052e+00 , 2.93807666861132e+00 , 3.31151936864297e+00 ) ( -5.53721626795029e-03 , 1.16774905532618e-02 , 1.69074760243028e-02 , 1.89295470420789e-02 , -1.12098518648447e-02 , 5.47099418188079e-03 , 1.27539142271434e-02 , 1.77039734250454e-02 , -1.62389653920810e-02 , -1.14054942040387e-02 , -4.07841190427115e-03 , 5.16538673702184e-03 , -1.34542775132188e-02 , -8.79243550204225e-03 , -6.38585394534860e-03 , -1.72351102574743e-03 ) 3.79629555593815e-01 + 13 ( 3.01147358102753e+00 , 4.48893928194997e+00 , 5.21171292451106e+00 , 6.18194650016787e+00 , 2.49529420874019e+00 , 3.89726774753210e+00 , 4.60388154116292e+00 , 5.38295779117939e+00 , 1.35366684255277e+00 , 2.48151732623380e+00 , 3.12686979147052e+00 , 3.85826315071113e+00 , 2.22290718088401e+00 , 2.73578615464733e+00 , 2.93539988719616e+00 , 3.30724327376658e+00 ) ( -5.52138817482320e-03 , 1.17425495705784e-02 , 1.69171191446419e-02 , 1.89536788062538e-02 , -1.12208703478021e-02 , 5.53719445578204e-03 , 1.27553319589290e-02 , 1.77018696730068e-02 , -1.62585085963099e-02 , -1.13502429741435e-02 , -4.08878426817147e-03 , 5.07741732348955e-03 , -1.34928430954218e-02 , -8.74878890446318e-03 , -6.44401748260910e-03 , -1.80072599449384e-03 ) 3.79960806988138e-01 + 14 ( 3.01500498355936e+00 , 4.49484105603145e+00 , 5.21058888397878e+00 , 6.17725979125500e+00 , 2.49652507990531e+00 , 3.90150978133327e+00 , 4.60234863260006e+00 , 5.37865915135750e+00 , 1.35963468851140e+00 , 2.48838344220267e+00 , 3.12766033460393e+00 , 3.85317752048532e+00 , 2.22122742538576e+00 , 2.74066674507216e+00 , 2.93271867782830e+00 , 3.30343100744147e+00 ) ( -5.49549732867158e-03 , 1.18007441986952e-02 , 1.69256728814974e-02 , 1.89765088186476e-02 , -1.12304979163713e-02 , 5.58188833376368e-03 , 1.27484793036664e-02 , 1.77003118142817e-02 , -1.62771022173966e-02 , -1.13072324040326e-02 , -4.09500221423765e-03 , 5.01132420994778e-03 , -1.35265575664752e-02 , -8.71473341320642e-03 , -6.49440390633471e-03 , -1.86333145708674e-03 ) 3.80303913164440e-01 + 15 ( 3.01885935134200e+00 , 4.49895836101355e+00 , 5.20845880435748e+00 , 6.17330861970770e+00 , 2.49726571448041e+00 , 3.90273958726481e+00 , 4.59886715923434e+00 , 5.37368145631357e+00 , 1.36442685860666e+00 , 2.49273626173455e+00 , 3.12809348126300e+00 , 3.84947011778950e+00 , 2.21980329429498e+00 , 2.74380165828177e+00 , 2.93007263674742e+00 , 3.30010253658084e+00 ) ( -5.45664327434154e-03 , 1.18507598188582e-02 , 1.69333270288283e-02 , 1.89976486937448e-02 , -1.12378675651178e-02 , 5.60103026326155e-03 , 1.27324557193522e-02 , 1.76990895586115e-02 , -1.62942676689069e-02 , -1.12806824591946e-02 , -4.09652022589830e-03 , 4.97117341132816e-03 , -1.35529004612138e-02 , -8.69192881828445e-03 , -6.53579293927686e-03 , -1.91029892067540e-03 ) 3.80653281337756e-01 + 16 ( 3.02318574233431e+00 , 4.50121671715298e+00 , 5.20543347930304e+00 , 6.17020596649946e+00 , 2.49758367078486e+00 , 3.90075791018026e+00 , 4.59345084620333e+00 , 5.36803107326493e+00 , 1.36776218077457e+00 , 2.49422221697351e+00 , 3.12814676409148e+00 , 3.84727076112079e+00 , 2.21885835313521e+00 , 2.74506502298711e+00 , 2.92750329382881e+00 , 3.29726720552320e+00 ) ( -5.40260775227740e-03 , 1.18918393995497e-02 , 1.69403563723388e-02 , 1.90167057123976e-02 , -1.12419666467266e-02 , 5.59228671198299e-03 , 1.27071500736935e-02 , 1.76979317995731e-02 , -1.63096075137775e-02 , -1.12738072092257e-02 , -4.09333242371338e-03 , 4.95876082069397e-03 , -1.35699155635357e-02 , -8.68152857719622e-03 , -6.56737454138995e-03 , -1.94123960773835e-03 ) 3.81001871240511e-01 + 17 ( 3.02809415710879e+00 , 4.50166506104922e+00 , 5.20168811881594e+00 , 6.16800533349194e+00 , 2.49758857964583e+00 , 3.89558236005592e+00 , 4.58626174925325e+00 , 5.36177010617776e+00 , 1.36949463578708e+00 , 2.49265415188493e+00 , 3.12778059652950e+00 , 3.84655116097139e+00 , 2.21854897895857e+00 , 2.74441563397565e+00 , 2.92505081205027e+00 , 3.29493032180216e+00 ) ( -5.33207795486475e-03 , 1.19238375475688e-02 , 1.69470627883182e-02 , 1.90332731864346e-02 , -1.12416911796005e-02 , 5.55523293564110e-03 , 1.26732473366659e-02 , 1.76965367632408e-02 , -1.63227936088094e-02 , -1.12884863427824e-02 , -4.08612201263206e-03 , 4.97341853049439e-03 , -1.35763317145022e-02 , -8.68411432067984e-03 , -6.58877216935854e-03 , -1.95630818933365e-03 ) 3.81341269972205e-01 + 18 ( 3.03363892679024e+00 , 4.50047208564501e+00 , 5.19744285787811e+00 , 6.16669911720665e+00 , 2.49741999764829e+00 , 3.88744865212165e+00 , 4.57759477230416e+00 , 5.35501860432485e+00 , 1.36962096542427e+00 , 2.48802587288390e+00 , 3.12692927006197e+00 , 3.84712592421505e+00 , 2.21895140215167e+00 , 2.74189783528608e+00 , 2.92274822946829e+00 , 3.29309909618837e+00 ) ( -5.24483234477642e-03 , 1.19472351637181e-02 , 1.69537131714762e-02 , 1.90469452610655e-02 , -1.12359373173825e-02 , 5.49144095224124e-03 , 1.26321668666295e-02 , 1.76946183386180e-02 , -1.63335559240562e-02 , -1.13250482267429e-02 , -4.07634438280624e-03 , 5.01204954188020e-03 , -1.35716288069538e-02 , -8.69964479496807e-03 , -6.60008084392255e-03 , -1.95609218069161e-03 ) 3.81662024543382e-01 + 19 ( 3.03980638894298e+00 , 4.49791396519392e+00 , 5.19293926689468e+00 , 6.16622192395595e+00 , 2.49723246064096e+00 , 3.87679761673723e+00 , 4.56785187518058e+00 , 5.34795393847889e+00 , 1.36827142975610e+00 , 2.48051460680503e+00 , 3.12549701697292e+00 , 3.84866874555677e+00 , 2.22005841870842e+00 , 2.73764013703583e+00 , 2.92061396081615e+00 , 3.29178674652695e+00 ) ( -5.14186565350286e-03 , 1.19631117657520e-02 , 1.69604787022727e-02 , 1.90573528747551e-02 , -1.12237144458926e-02 , 5.40445708215642e-03 , 1.25859420489657e-02 , 1.76919640598146e-02 , -1.63416796397032e-02 , -1.13821966932441e-02 , -4.06622804407803e-03 , 5.06938813317521e-03 , -1.35560499546531e-02 , -8.72742264746697e-03 , -6.60191447225295e-03 , -1.94150498632643e-03 ) 3.81954197447530e-01 + 20 ( 3.04650863844542e+00 , 4.49435411373106e+00 , 5.18841527687423e+00 , 6.16645837246753e+00 , 2.49717925475228e+00 , 3.86424835988508e+00 , 4.55750848670402e+00 , 5.34080670712767e+00 , 1.36568581550375e+00 , 2.47047097074510e+00 , 3.12336009876006e+00 , 3.85074280234761e+00 , 2.22178524374518e+00 , 2.73185149420872e+00 , 2.91864419945045e+00 , 3.29101397434784e+00 ) ( -5.02542975155399e-03 , 1.19730728144022e-02 , 1.69673824743050e-02 , 1.90642123572900e-02 , -1.12042672923401e-02 , 5.29965572198335e-03 , 1.25370495930876e-02 , 1.76884949742769e-02 , -1.63470133946114e-02 , -1.14570941785658e-02 , -4.05868153495528e-03 , 5.13846947648582e-03 , -1.35305636182661e-02 , -8.76608365782640e-03 , -6.59544443037070e-03 , -1.91369494736973e-03 ) 3.82208090962526e-01 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat index 1a12c5a95..03221b542 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat @@ -1,10 +1,10 @@ # one p(one ) - 2.00000000000000 0.09030392971801 - 4.00000000000000 0.19798865118667 - 6.00000000000000 0.14853769410362 - 8.00000000000000 0.04657771650417 - 10.00000000000000 0.00481731602070 - 12.00000000000000 0.00011856440783 + 2.00000000000000 0.09030392972369 + 4.00000000000000 0.19798865120683 + 6.00000000000000 0.14853769410307 + 8.00000000000000 0.04657771648442 + 10.00000000000000 0.00481731601539 + 12.00000000000000 0.00011856440761 14.00000000000000 0.00000057948069 16.00000000000000 0.00000000051553 18.00000000000000 0.00000000000008 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out index c7b2aef1d..852f8a3ae 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -120,20 +124,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - distancePairs colvar component: +colvars: - histogramRestraint colvar bias implementation: +colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 3.04651 , 4.49435 , 5.18842 , 6.16646 , 2.49718 , 3.86425 , 4.55751 , 5.34081 , 1.36569 , 2.47047 , 3.12336 , 3.85074 , 2.22179 , 2.73185 , 2.91864 , 3.29101 ) colvars: Restarting histogramrestraint bias "hr" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped index 0ecc9386e..7bec45097 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.03953158726547e+00 , 4.51209497961311e+00 , 5.09894673434180e+00 , 6.16578599928733e+00 , 2.46957015850689e+00 , 3.86055335115988e+00 , 4.47595360418285e+00 , 5.36499714940424e+00 , 1.33944926924420e+00 , 2.47813660080028e+00 , 3.01476283660714e+00 , 3.86080601707240e+00 , 2.22155937101033e+00 , 2.76529935945446e+00 , 2.86078736535835e+00 , 3.36901381632414e+00 ) + x ( 3.03953158571266e+00 , 4.51209497787138e+00 , 5.09894673253801e+00 , 6.16578599788259e+00 , 2.46957015768712e+00 , 3.86055335003907e+00 , 4.47595360314062e+00 , 5.36499714872809e+00 , 1.33944926913138e+00 , 2.47813660022930e+00 , 3.01476283614106e+00 , 3.86080601681174e+00 , 2.22155937137345e+00 , 2.76529935955117e+00 , 2.86078736612033e+00 , 3.36901381742548e+00 ) } histogramrestraint { diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj index 2c3a7993e..c3e1e1b2e 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hr - 20 ( 3.04650863884945e+00 , 4.49435411437724e+00 , 5.18841527762764e+00 , 6.16645837340779e+00 , 2.49717925480425e+00 , 3.86424836018692e+00 , 4.55750848697779e+00 , 5.34080670765490e+00 , 1.36568581546352e+00 , 2.47047097097987e+00 , 3.12336009885461e+00 , 3.85074280281206e+00 , 2.22178524357949e+00 , 2.73185149414085e+00 , 2.91864419906098e+00 , 3.29101397431997e+00 ) ( -5.02542974750439e-03 , 1.19730728164444e-02 , 1.69673824742426e-02 , 1.90642123537368e-02 , -1.12042672914772e-02 , 5.29965572263668e-03 , 1.25370495916030e-02 , 1.76884949726336e-02 , -1.63470133927038e-02 , -1.14570941759426e-02 , -4.05868153495143e-03 , 5.13846947912402e-03 , -1.35305636185385e-02 , -8.76608365877139e-03 , -6.59544443572543e-03 , -1.91369494935530e-03 ) 3.82208090906906e-01 - 21 ( 3.05358451430521e+00 , 4.49021607894136e+00 , 5.18408103579128e+00 , 6.16725452682985e+00 , 2.49739586887847e+00 , 3.85055803176977e+00 , 4.54707448765203e+00 , 5.33385181877346e+00 , 1.36217943428986e+00 , 2.45839729727885e+00 , 3.12037538162696e+00 , 3.85284349947326e+00 , 2.22398282791541e+00 , 2.72481510484303e+00 , 2.91680739868595e+00 , 3.29080759705819e+00 ) ( -4.89897222229807e-03 , 1.19791313915530e-02 , 1.69742633770421e-02 , 1.90673755260435e-02 , -1.11771991089292e-02 , 5.18394936500707e-03 , 1.24881958008396e-02 , 1.76843138062651e-02 , -1.63494863600467e-02 , -1.15455916046476e-02 , -4.05710100264393e-03 , 5.21127646149069e-03 , -1.34967807334349e-02 , -8.81361359484131e-03 , -6.58240414833905e-03 , -1.87397588842609e-03 ) 3.82415073616570e-01 - 22 ( 3.06080810208345e+00 , 4.48595132812722e+00 , 5.18009807804700e+00 , 6.16843183990917e+00 , 2.49798391786306e+00 , 3.83656952252473e+00 , 4.53705219502262e+00 , 5.32739339769826e+00 , 1.35810535030362e+00 , 2.44491630862121e+00 , 3.11639519256500e+00 , 3.85445062174997e+00 , 2.22645629766064e+00 , 2.71687952037979e+00 , 2.91504287466697e+00 , 3.29119674274122e+00 ) ( -4.76696535200487e-03 , 1.19835479453930e-02 , 1.69807629789190e-02 , 1.90668703403292e-02 , -1.11425894926847e-02 , 5.06534159173061e-03 , 1.24420691523186e-02 , 1.76797272289167e-02 , -1.63491285179391e-02 , -1.16425743073302e-02 , -4.06508397889694e-03 , 5.27951326763638e-03 , -1.34568327363580e-02 , -8.86739837135399e-03 , -6.56503633790696e-03 , -1.82377839347999e-03 ) 3.82568429497945e-01 - 23 ( 3.06790414004814e+00 , 4.48200450135334e+00 , 5.17656382793119e+00 , 6.16980237078029e+00 , 2.49899682565506e+00 , 3.82315020180593e+00 , 4.52789434465689e+00 , 5.32174323381354e+00 , 1.35381897115236e+00 , 2.43073302861496e+00 , 3.11128737638165e+00 , 3.85508563485620e+00 , 2.22898609562760e+00 , 2.70844682598514e+00 , 2.91326470539741e+00 , 3.29220745957774e+00 ) ( -4.63463283228587e-03 , 1.19886381037132e-02 , 1.69863384514790e-02 , 1.90629238539922e-02 , -1.11010960454939e-02 , 4.95233310232833e-03 , 1.24010752251076e-02 , 1.76752321475924e-02 , -1.63460880163246e-02 , -1.17423776630453e-02 , -4.08607045606707e-03 , 5.33543540685033e-03 , -1.34132176179305e-02 , -8.92431330478125e-03 , -6.54597178922480e-03 , -1.76461825305729e-03 ) 3.82664136113375e-01 - 24 ( 3.07456896251547e+00 , 4.47877932788847e+00 , 5.17350292421948e+00 , 6.17118403235812e+00 , 2.50042929771976e+00 , 3.81112677848175e+00 , 4.51996576479011e+00 , 5.31719422129534e+00 , 1.34964937406132e+00 , 2.41659320693017e+00 , 3.10495847674859e+00 , 3.85436854050369e+00 , 2.23134970982392e+00 , 2.69995765863871e+00 , 2.91137078684994e+00 , 3.29385683019661e+00 ) ( -4.50759627415720e-03 , 1.19965650781519e-02 , 1.69902999513099e-02 , 1.90559636458943e-02 , -1.10540221239449e-02 , 4.85322332287748e-03 , 1.23670789588916e-02 , 1.76714640580619e-02 , -1.63406409705032e-02 , -1.18392197113602e-02 , -4.12294937333665e-03 , 5.37265037507770e-03 , -1.33686231655847e-02 , -8.98085589562544e-03 , -6.52804679567177e-03 , -1.69807765323451e-03 ) 3.82701469800512e-01 - 25 ( 3.08049503112063e+00 , 4.47660862669065e+00 , 5.17086621218778e+00 , 6.17241473807144e+00 , 2.50221287184003e+00 , 3.80122270064462e+00 , 4.51351282067087e+00 , 5.31399204919024e+00 , 1.34587887725366e+00 , 2.40324136997555e+00 , 3.09737705599232e+00 , 3.85206778284383e+00 , 2.23334232009805e+00 , 2.69187293445037e+00 , 2.90925556205525e+00 , 3.29614768324761e+00 ) ( -4.39147560687099e-03 , 1.20091384967429e-02 , 1.69918666392056e-02 , 1.90465983705643e-02 , -1.10033293342962e-02 , 4.77538069742523e-03 , 1.23411865313985e-02 , 1.76691155082667e-02 , -1.63331907110018e-02 , -1.19276016500482e-02 , -4.17768182170728e-03 , 5.38679797880718e-03 , -1.33257388623057e-02 , -9.03332249848839e-03 , -6.51408373611267e-03 , -1.62579454590789e-03 ) 3.82683339776474e-01 - 26 ( 3.08539660358762e+00 , 4.47573108499616e+00 , 5.16853739700106e+00 , 6.17336434836052e+00 , 2.50421915077741e+00 , 3.79400439259247e+00 , 4.50864423698743e+00 , 5.31230947973394e+00 , 1.34272952084209e+00 , 2.39138079579576e+00 , 3.08859350101493e+00 , 3.84813653919452e+00 , 2.23479506256020e+00 , 2.68465243778064e+00 , 2.90682401269869e+00 , 3.29906482208583e+00 ) ( -4.29148411013601e-03 , 1.20276418302263e-02 , 1.69902333323270e-02 , 1.90355816605932e-02 , -1.09515770435773e-02 , 4.72457054302800e-03 , 1.23236006618263e-02 , 1.76688416325359e-02 , -1.63242548543774e-02 , -1.20026405094288e-02 , -4.25099682919303e-03 , 5.37602868959405e-03 , -1.32870692584683e-02 , -9.07802146377075e-03 , -6.50666849324502e-03 , -1.54945341877789e-03 ) 3.82616280373843e-01 - 27 ( 3.08903403490314e+00 , 4.47627640362272e+00 , 5.16634667961830e+00 , 6.17394349940788e+00 , 2.50627068489644e+00 , 3.78984102102476e+00 , 4.50532543312949e+00 , 5.31222723709983e+00 , 1.34035363316288e+00 , 2.38163676682551e+00 , 3.07875275681351e+00 , 3.84272979910075e+00 , 2.23558983263006e+00 , 2.67873088548860e+00 , 2.90400432155214e+00 , 3.30257333764965e+00 ) ( -4.21205604684754e-03 , 1.20527080314771e-02 , 1.69846407373501e-02 , 1.90237651417156e-02 , -1.09017840031264e-02 , 4.70442294145814e-03 , 1.23135748673525e-02 , 1.76711728196835e-02 , -1.63144400065064e-02 , -1.20603163377734e-02 , -4.34220656291962e-03 , 5.34122227195625e-03 , -1.32547619866681e-02 , -9.11150666826031e-03 , -6.50795643781969e-03 , -1.47076879862291e-03 ) 3.82510078836494e-01 - 28 ( 3.09123423008446e+00 , 4.47825901549156e+00 , 5.16409003548264e+00 , 6.17410853479198e+00 , 2.50815760716265e+00 , 3.78888026455344e+00 , 4.50338660037037e+00 , 5.31372412214171e+00 , 1.33882620808478e+00 , 2.37452389490195e+00 , 3.06809741626824e+00 , 3.83619894809814e+00 , 2.23566954486208e+00 , 2.67449273808684e+00 , 2.90075730651259e+00 , 3.30661925613651e+00 ) ( -4.15653936805056e-03 , 1.20842556462065e-02 , 1.69744443920294e-02 , 1.90120465097577e-02 , -1.08572245295259e-02 , 4.71610016367071e-03 , 1.23094771128419e-02 , 1.76764515717399e-02 , -1.63044061220960e-02 , -1.20976332878248e-02 , -4.44916678119855e-03 , 5.28592246238156e-03 , -1.32304641411155e-02 , -9.13080846091652e-03 , -6.51952626171290e-03 , -1.39145151742301e-03 ) 3.82377079846062e-01 - 29 ( 3.09190509514426e+00 , 4.48157956515127e+00 , 5.16155211481890e+00 , 6.17386201170314e+00 , 2.50965699808364e+00 , 3.79104075110282e+00 , 4.50254293510334e+00 , 5.31667718843253e+00 , 1.33813889024149e+00 , 2.37041835828804e+00 , 3.05696001593096e+00 , 3.82906376058536e+00 , 2.23504287460586e+00 , 2.67224775251169e+00 , 2.89708163035411e+00 , 3.31113228120092e+00 ) ( -4.12697759527618e-03 , 1.21214889699991e-02 , 1.69591787212609e-02 , 1.90013176216806e-02 , -1.08211849977542e-02 , 4.75819485630298e-03 , 1.23089551811130e-02 , 1.76848031256508e-02 , -1.62948248972696e-02 , -1.21127058757935e-02 , -4.56838460793265e-03 , 5.21600003506868e-03 , -1.32152197152968e-02 , -9.13363622096200e-03 , -6.54228804860898e-03 , -1.31315220707965e-03 ) 3.82231264774811e-01 - 30 ( 3.09104253787141e+00 , 4.48603307941766e+00 , 5.15853060586121e+00 , 6.17324867964149e+00 , 2.51055204409471e+00 , 3.79602095804537e+00 , 4.50242469654790e+00 , 5.32087138951799e+00 , 1.33819822708635e+00 , 2.36953676692819e+00 , 3.04574554895833e+00 , 3.82196513077521e+00 , 2.23378273934522e+00 , 2.67220981841834e+00 , 2.89301507521361e+00 , 3.31603006984730e+00 ) ( -4.12399774225813e-03 , 1.21629569276891e-02 , 1.69386135412590e-02 , 1.89924164868352e-02 , -1.07967128751336e-02 , 4.82686270700478e-03 , 1.23091825418685e-02 , 1.76961399114859e-02 , -1.62863384430780e-02 , -1.21047856613801e-02 , -4.69525042041774e-03 , 5.13908728081744e-03 , -1.32094206833609e-02 , -9.11853167669410e-03 , -6.57644051145824e-03 , -1.23738605942613e-03 ) 3.82087235527624e-01 - 31 ( 3.08872930139670e+00 , 4.49132289037063e+00 , 5.15485959514491e+00 , 6.17234728900319e+00 , 2.51064913021942e+00 , 3.80332415613268e+00 , 4.50261440870123e+00 , 5.32601736328046e+00 , 1.33883231980242e+00 , 2.37192384301024e+00 , 3.03490626643892e+00 , 3.81560419596028e+00 , 2.23201834747819e+00 , 2.67448174853771e+00 , 2.88863286904395e+00 , 3.32122334496031e+00 ) ( -4.14681388778250e-03 , 1.22066593960987e-02 , 1.69127991492826e-02 , 1.89860855651968e-02 , -1.07863857398542e-02 , 4.91617372307837e-03 , 1.23071555307691e-02 , 1.77101930888175e-02 , 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3.08045463729672e+00 , 4.50288519704754e+00 , 5.14520390095076e+00 , 6.17009473576804e+00 , 2.50787564727135e+00 , 3.82219055541500e+00 , 4.50226214069664e+00 , 5.33778558393846e+00 , 1.34086920757905e+00 , 2.38582693292515e+00 , 3.01621801902235e+00 , 3.80779720627924e+00 , 2.22768857394173e+00 , 2.68577746719359e+00 , 2.87938997939690e+00 , 3.33213575260088e+00 ) ( -4.26045164162495e-03 , 1.22908700889301e-02 , 1.68471856059909e-02 , 1.89834261003156e-02 , -1.08150192757933e-02 , 5.12591079664833e-03 , 1.22853421663085e-02 , 1.77447558673838e-02 , -1.62727379913271e-02 , -1.19520165161674e-02 , -5.06601412162525e-03 , 4.95319659363923e-03 , -1.32435252234106e-02 , -8.96495735337770e-03 , -6.73869468915883e-03 , -1.03675679717580e-03 ) 3.81801393160747e-01 - 34 ( 3.07497912152090e+00 , 4.50829914516339e+00 , 5.13922512793544e+00 , 6.16896017434785e+00 , 2.50485309388411e+00 , 3.83220702803533e+00 , 4.50102851775461e+00 , 5.34369563021521e+00 , 1.34176277961509e+00 , 2.39661859744123e+00 , 3.00923587756392e+00 , 3.80745750931824e+00 , 2.22552072975963e+00 , 2.69443239804884e+00 , 2.87483587628920e+00 , 3.33768680793807e+00 ) ( -4.34421639088351e-03 , 1.23259510241342e-02 , 1.68090579824887e-02 , 1.89878261554619e-02 , -1.08552901253035e-02 , 5.22942992615502e-03 , 1.22614659002049e-02 , 1.77642609644918e-02 , -1.62733896651479e-02 , -1.18660435400099e-02 , -5.16722789780436e-03 , 4.93281774142251e-03 , -1.32680512214032e-02 , -8.88197830087080e-03 , -6.80664460996510e-03 , -9.80979867201091e-04 ) 3.81791215679719e-01 - 35 ( 3.06898072962898e+00 , 4.51288823912276e+00 , 5.13261898082506e+00 , 6.16794500639919e+00 , 2.50074653307297e+00 , 3.84158061569010e+00 , 4.49879685556613e+00 , 5.34919353467269e+00 , 1.34229502312659e+00 , 2.40928100931996e+00 , 3.00430451716382e+00 , 3.80996140448631e+00 , 2.22360417014956e+00 , 2.70468750472754e+00 , 2.87057086891121e+00 , 3.34320509035869e+00 ) ( -4.44031489768969e-03 , 1.23527234730989e-02 , 1.67689785306207e-02 , 1.89962130825891e-02 , -1.09121854056437e-02 , 5.32120212595859e-03 , 1.22276539265459e-02 , 1.77845576836149e-02 , -1.62769366896918e-02 , -1.17686217438871e-02 , -5.24875745421665e-03 , 4.94273803761624e-03 , -1.32965365863000e-02 , -8.78720894526610e-03 , -6.87713386725385e-03 , -9.30987612841641e-04 ) 3.81835385411921e-01 - 36 ( 3.06273532976632e+00 , 4.51625453815810e+00 , 5.12558688042565e+00 , 6.16711285602853e+00 , 2.49564990035453e+00 , 3.84963128856745e+00 , 4.49551609176305e+00 , 5.35403199682776e+00 , 1.34235952065396e+00 , 2.42319130987960e+00 , 3.00166756478992e+00 , 3.81540250086734e+00 , 2.22209336131761e+00 , 2.71615108183038e+00 , 2.86679976339768e+00 , 3.34863558008665e+00 ) ( -4.54435366709869e-03 , 1.23686805003577e-02 , 1.67284311239753e-02 , 1.90084516063127e-02 , -1.09840196246657e-02 , 5.39437686141032e-03 , 1.21842739540751e-02 , 1.78051583051095e-02 , -1.62833596505170e-02 , -1.16643470034764e-02 , -5.30682059170320e-03 , 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6.16609340606711e+00 , 2.48321341779800e+00 , 3.85977678566920e+00 , 4.48635217426398e+00 , 5.36117618517027e+00 , 1.34120085894772e+00 , 2.45209075220292e+00 , 3.00367159478445e+00 , 3.83435311427914e+00 , 2.22068007489778e+00 , 2.74095124957973e+00 , 2.86158715690625e+00 , 3.35910007102331e+00 ) ( -4.76019161860031e-03 , 1.23598714103535e-02 , 1.66524680422709e-02 , 1.90428744652835e-02 , -1.11615338051583e-02 , 5.46602270595950e-03 , 1.20759997193952e-02 , 1.78455990014566e-02 , -1.63041248925182e-02 , -1.14552422050043e-02 , -5.34375549291192e-03 , 5.16264172214884e-03 , -1.33903719358613e-02 , -8.46711508758403e-03 , -7.07047589577285e-03 , -8.10789030101033e-04 ) 3.82300990349005e-01 - 39 ( 3.04477330671893e+00 , 4.51608052429989e+00 , 5.10475536430945e+00 , 6.16587487803593e+00 , 2.47638766281039e+00 , 3.86134206645524e+00 , 4.48108638405379e+00 , 5.36344937487428e+00 , 1.34028312454434e+00 , 2.46576763106795e+00 , 3.00819152136954e+00 , 3.84697007402470e+00 , 2.22084607799930e+00 , 2.75339260853697e+00 , 2.86054956534452e+00 , 3.36411702201955e+00 ) ( -4.86543042629372e-03 , 1.23321843437552e-02 , 1.66202988314624e-02 , 1.90637594048100e-02 , -1.12600574737574e-02 , 5.46010859232420e-03 , 1.20173150929056e-02 , 1.78648032607835e-02 , -1.63178447949989e-02 , -1.13604904168987e-02 , -5.32184447456055e-03 , 5.28870221068816e-03 , -1.34202591870486e-02 , -8.36109248159763e-03 , -7.11733591924846e-03 , -7.77701464928409e-04 ) 3.82552280801419e-01 - 40 ( 3.03953158726547e+00 , 4.51209497961311e+00 , 5.09894673434180e+00 , 6.16578599928733e+00 , 2.46957015850689e+00 , 3.86055335115988e+00 , 4.47595360418285e+00 , 5.36499714940424e+00 , 1.33944926924420e+00 , 2.47813660080028e+00 , 3.01476283660714e+00 , 3.86080601707240e+00 , 2.22155937101033e+00 , 2.76529935945446e+00 , 2.86078736535835e+00 , 3.36901381632414e+00 ) ( -4.96580057965820e-03 , 1.22880424192736e-02 , 1.65938976558053e-02 , 1.90859603220539e-02 , -1.13596279851453e-02 , 5.42702341268680e-03 , 1.19610688394556e-02 , 1.78830800496280e-02 , -1.63332290120811e-02 , -1.12784800729915e-02 , -5.27503313459921e-03 , 5.43003603855418e-03 , -1.34479399657521e-02 , -8.26149951976874e-03 , -7.15005911976767e-03 , -7.46119909351650e-04 ) 3.82835834324984e-01 + 20 ( 3.04650863844542e+00 , 4.49435411373106e+00 , 5.18841527687423e+00 , 6.16645837246753e+00 , 2.49717925475228e+00 , 3.86424835988508e+00 , 4.55750848670402e+00 , 5.34080670712767e+00 , 1.36568581550375e+00 , 2.47047097074510e+00 , 3.12336009876006e+00 , 3.85074280234761e+00 , 2.22178524374518e+00 , 2.73185149420872e+00 , 2.91864419945045e+00 , 3.29101397434784e+00 ) ( -5.02542975155399e-03 , 1.19730728144022e-02 , 1.69673824743050e-02 , 1.90642123572900e-02 , -1.12042672923401e-02 , 5.29965572198335e-03 , 1.25370495930876e-02 , 1.76884949742769e-02 , -1.63470133946114e-02 , -1.14570941785658e-02 , -4.05868153495528e-03 , 5.13846947648582e-03 , -1.35305636182661e-02 , -8.76608365782640e-03 , -6.59544443037070e-03 , -1.91369494736973e-03 ) 3.82208090962526e-01 + 21 ( 3.05358451385306e+00 , 4.49021607823814e+00 , 5.18408103497026e+00 , 6.16725452583661e+00 , 2.49739586880410e+00 , 3.85055803143711e+00 , 4.54707448734276e+00 , 5.33385181822192e+00 , 1.36217943433076e+00 , 2.45839729703337e+00 , 3.12037538151779e+00 , 3.85284349899673e+00 , 2.22398282808873e+00 , 2.72481510491786e+00 , 2.91680739909571e+00 , 3.29080759711060e+00 ) ( -4.89897222682100e-03 , 1.19791313892808e-02 , 1.69742633770304e-02 , 1.90673755298261e-02 , -1.11771991099852e-02 , 5.18394936419736e-03 , 1.24881958022913e-02 , 1.76843138080640e-02 , -1.63494863620738e-02 , -1.15455916073648e-02 , -4.05710100270291e-03 , 5.21127645896876e-03 , -1.34967807331177e-02 , -8.81361359377299e-03 , -6.58240414263767e-03 , -1.87397588595395e-03 ) 3.82415073675832e-01 + 22 ( 3.06080810157937e+00 , 4.48595132736801e+00 , 5.18009807716127e+00 , 6.16843183886407e+00 , 2.49798391776076e+00 , 3.83656952216095e+00 , 4.53705219467757e+00 , 5.32739339712202e+00 , 1.35810535034214e+00 , 2.44491630836693e+00 , 3.11639519244157e+00 , 3.85445062126223e+00 , 2.22645629784030e+00 , 2.71687952046412e+00 , 2.91504287509639e+00 , 3.29119674282126e+00 ) ( -4.76696535704344e-03 , 1.19835479428934e-02 , 1.69807629788419e-02 , 1.90668703443345e-02 , -1.11425894939780e-02 , 5.06534159075236e-03 , 1.24420691537260e-02 , 1.76797272308617e-02 , -1.63491285200756e-02 , -1.16425743101174e-02 , -4.06508397900589e-03 , 5.27951326523871e-03 , -1.34568327359927e-02 , -8.86739837013206e-03 , -6.56503633186065e-03 , -1.82377839047625e-03 ) 3.82568429560664e-01 + 23 ( 3.06790413948872e+00 , 4.48200450053951e+00 , 5.17656382698377e+00 , 6.16980236968489e+00 , 2.49899682551938e+00 , 3.82315020141056e+00 , 4.52789434427541e+00 , 5.32174323321216e+00 , 1.35381897118564e+00 , 2.43073302835376e+00 , 3.11128737624436e+00 , 3.85508563435849e+00 , 2.22898609581243e+00 , 2.70844682608125e+00 , 2.91326470584562e+00 , 3.29220745968855e+00 ) ( -4.63463283787862e-03 , 1.19886381009935e-02 , 1.69863384513460e-02 , 1.90629238582122e-02 , -1.11010960470692e-02 , 4.95233310116970e-03 , 1.24010752264571e-02 , 1.76752321496742e-02 , -1.63460880185607e-02 , -1.17423776658788e-02 , -4.08607045622158e-03 , 5.33543540458643e-03 , -1.34132176175144e-02 , -8.92431330337852e-03 , -6.54597178283978e-03 , -1.76461824947690e-03 ) 3.82664136179363e-01 + 24 ( 3.07456896189780e+00 , 4.47877932702159e+00 , 5.17350292321320e+00 , 6.17118403121453e+00 , 2.50042929754554e+00 , 3.81112677805404e+00 , 4.51996576437108e+00 , 5.31719422066849e+00 , 1.34964937408689e+00 , 2.41659320666385e+00 , 3.10495847659781e+00 , 3.85436853999778e+00 , 2.23134971001298e+00 , 2.69995765874844e+00 , 2.91137078731589e+00 , 3.29385683034138e+00 ) ( -4.50759628033739e-03 , 1.19965650752233e-02 , 1.69902999511294e-02 , 1.90559636503187e-02 , -1.10540221258452e-02 , 4.85322332152704e-03 , 1.23670789601672e-02 , 1.76714640602726e-02 , -1.63406409728297e-02 , -1.18392197142181e-02 , -4.12294937353427e-03 , 5.37265037296092e-03 , -1.33686231651157e-02 , -8.98085589401957e-03 , -6.52804678895842e-03 , -1.69807764903222e-03 ) 3.82701469869588e-01 + 25 ( 3.08049503044240e+00 , 4.47660862577235e+00 , 5.17086621112506e+00 , 6.17241473688239e+00 , 2.50221287162265e+00 , 3.80122270018355e+00 , 4.51351282021268e+00 , 5.31399204853792e+00 , 1.34587887726960e+00 , 2.40324136970565e+00 , 3.09737705582823e+00 , 3.85206778233211e+00 , 2.23334232029070e+00 , 2.69187293457495e+00 , 2.90925556253781e+00 , 3.29614768342963e+00 ) ( -4.39147561366562e-03 , 1.20091384936196e-02 , 1.69918666389837e-02 , 1.90465983751812e-02 , -1.10033293365613e-02 , 4.77538069587196e-03 , 1.23411865325813e-02 , 1.76691155106009e-02 , -1.63331907134106e-02 , -1.19276016529115e-02 , -4.17768182194874e-03 , 5.38679797685642e-03 , -1.33257388617823e-02 , -9.03332249666318e-03 , -6.51408372908440e-03 , -1.62579454103830e-03 ) 3.82683339848463e-01 + 26 ( 3.08539660284712e+00 , 4.47573108402803e+00 , 5.16853739588371e+00 , 6.17336434712941e+00 , 2.50421915051295e+00 , 3.79400439209675e+00 , 4.50864423648805e+00 , 5.31230947905661e+00 , 1.34272952084715e+00 , 2.39138079552345e+00 , 3.08859350083748e+00 , 3.84813653868004e+00 , 2.23479506275618e+00 , 2.68465243792059e+00 , 2.90682401319677e+00 , 3.29906482230846e+00 ) ( -4.29148411756531e-03 , 1.20276418269237e-02 , 1.69902333320655e-02 , 1.90355816653891e-02 , -1.09515770462413e-02 , 4.72457054126106e-03 , 1.23236006628952e-02 , 1.76688416349909e-02 , -1.63242548568613e-02 , -1.20026405122825e-02 , -4.25099682948340e-03 , 5.37602868783482e-03 , -1.32870692578888e-02 , -9.07802146171702e-03 , -6.50666848591685e-03 , -1.54945341319546e-03 ) 3.82616280448582e-01 + 27 ( 3.08903403409934e+00 , 4.47627640260616e+00 , 5.16634667844742e+00 , 6.17394349813873e+00 , 2.50627068458191e+00 , 3.78984102049283e+00 , 4.50532543258662e+00 , 5.31222723639859e+00 , 1.34035363315651e+00 , 2.38163676655146e+00 , 3.07875275662228e+00 , 3.84272979858715e+00 , 2.23558983282953e+00 , 2.67873088564368e+00 , 2.90400432206480e+00 , 3.30257333791634e+00 ) ( -4.21205605492461e-03 , 1.20527080280103e-02 , 1.69846407370455e-02 , 1.90237651466753e-02 , -1.09017840062163e-02 , 4.70442293946673e-03 , 1.23135748682848e-02 , 1.76711728222598e-02 , -1.63144400090597e-02 , -1.20603163406075e-02 , -4.34220656326890e-03 , 5.34122227042115e-03 , -1.32547619860300e-02 , -9.11150666597606e-03 , -6.50795643020656e-03 , -1.47076879228184e-03 ) 3.82510078913831e-01 + 28 ( 3.09123422921692e+00 , 4.47825901442763e+00 , 5.16409003425862e+00 , 6.17410853348936e+00 , 2.50815760679602e+00 , 3.78888026398353e+00 , 4.50338659978164e+00 , 5.31372412141838e+00 , 1.33882620806712e+00 , 2.37452389462613e+00 , 3.06809741606238e+00 , 3.83619894758952e+00 , 2.23566954506562e+00 , 2.67449273825598e+00 , 2.90075730703912e+00 , 3.30661925645080e+00 ) ( -4.15653937678158e-03 , 1.20842556425878e-02 , 1.69744443916726e-02 , 1.90120465148651e-02 , -1.08572245330596e-02 , 4.71610016144383e-03 , 1.23094771136140e-02 , 1.76764515744409e-02 , -1.63044061247141e-02 , -1.20976332906350e-02 , -4.44916678162194e-03 , 5.28592246110960e-03 , -1.32304641404146e-02 , -9.13080845840673e-03 , -6.51952625382809e-03 , -1.39145151027727e-03 ) 3.82377079925851e-01 + 29 ( 3.09190509421309e+00 , 4.48157956404059e+00 , 5.16155211354150e+00 , 6.17386201037197e+00 , 2.50965699766396e+00 , 3.79104075049304e+00 , 4.50254293446649e+00 , 5.31667718768969e+00 , 1.33813889021320e+00 , 2.37041835800957e+00 , 3.05696001570915e+00 , 3.82906376008603e+00 , 2.23504287481449e+00 , 2.67224775269306e+00 , 2.89708163089409e+00 , 3.31113228156639e+00 ) ( -4.12697760466075e-03 , 1.21214889662362e-02 , 1.69591787208369e-02 , 1.90013176269185e-02 , -1.08211850017392e-02 , 4.75819485382931e-03 , 1.23089551817022e-02 , 1.76848031284823e-02 , -1.62948248999482e-02 , -1.21127058785823e-02 , -4.56838460845013e-03 , 5.21600003410379e-03 , -1.32152197145269e-02 , -9.13363621823788e-03 , -6.54228804046270e-03 , -1.31315219908283e-03 ) 3.82231264856908e-01 + 30 ( 3.09104253687721e+00 , 4.48603307826026e+00 , 5.15853060452976e+00 , 6.17324867828692e+00 , 2.51055204362215e+00 , 3.79602095739377e+00 , 4.50242469586112e+00 , 5.32087138875897e+00 , 1.33819822704847e+00 , 2.36953676664519e+00 , 3.04574554871881e+00 , 3.82196513028943e+00 , 2.23378273956030e+00 , 2.67220981860937e+00 , 2.89301507576693e+00 , 3.31603007026754e+00 ) ( -4.12399775228976e-03 , 1.21629569237827e-02 , 1.69386135407473e-02 , 1.89924164921859e-02 , -1.07967128795658e-02 , 4.82686270427262e-03 , 1.23091825422540e-02 , 1.76961399144551e-02 , -1.62863384458131e-02 , -1.21047856641569e-02 , -4.69525042105293e-03 , 5.13908728020596e-03 , -1.32094206825129e-02 , -9.11853167377214e-03 , -6.57644050305645e-03 , -1.23738605053167e-03 ) 3.82087235611880e-01 + 31 ( 3.08872930034045e+00 , 4.49132288916588e+00 , 5.15485959375857e+00 , 6.17234728763030e+00 , 2.51064912969521e+00 , 3.80332415543735e+00 , 4.50261440796340e+00 , 5.32601736250928e+00 , 1.33883231975609e+00 , 2.37192384271979e+00 , 3.03490626617957e+00 , 3.81560419549194e+00 , 2.23201834770136e+00 , 2.67448174873522e+00 , 2.88863286961083e+00 , 3.32122334543885e+00 ) ( -4.14681389844940e-03 , 1.22066593920410e-02 , 1.69127991486588e-02 , 1.89860855706422e-02 , -1.07863857447177e-02 , 4.91617372007565e-03 , 1.23071555309342e-02 , 1.77101930919321e-02 , -1.62795237560133e-02 , -1.20742429299629e-02 , -4.82436126980393e-03 , 5.06384588223362e-03 , -1.32128196421779e-02 , -9.08495906809948e-03 , -6.62146792223792e-03 , -1.16545021409847e-03 ) 3.81959230272477e-01 + 32 ( 3.08512587407585e+00 , 4.49707969992627e+00 , 5.15042982483635e+00 , 6.17125913901907e+00 , 2.50979233827432e+00 , 3.81229855394099e+00 , 4.50268874982513e+00 , 5.33177568452012e+00 , 1.33980944632461e+00 , 2.37745103512446e+00 , 3.02491187404977e+00 , 3.81067490080305e+00 , 2.22992148435915e+00 , 2.67904816565005e+00 , 2.88404450587321e+00 , 3.32662115516356e+00 ) ( -4.19334740738677e-03 , 1.22501856597967e-02 , 1.68820961190666e-02 , 1.89829372788785e-02 , -1.07921188400013e-02 , 5.01864637029710e-03 , 1.23000120215299e-02 , 1.77265599742085e-02 , -1.62748657233307e-02 , -1.20225135633812e-02 , -4.94989687037609e-03 , 4.99914062134037e-03 , -1.32246045788317e-02 , -9.03332860324969e-03 , -6.67616648316557e-03 , -1.09835120335049e-03 ) 3.81860258406506e-01 + 33 ( 3.08045463612035e+00 , 4.50288519574339e+00 , 5.14520389945312e+00 , 6.17009473437244e+00 , 2.50787564665153e+00 , 3.82219055462722e+00 , 4.50226213985759e+00 , 5.33778558315697e+00 , 1.34086920751867e+00 , 2.38582693260688e+00 , 3.01621801871649e+00 , 3.80779720585457e+00 , 2.22768857418667e+00 , 2.68577746739276e+00 , 2.87938997999308e+00 , 3.33213575320596e+00 ) ( -4.26045165351063e-03 , 1.22908700845057e-02 , 1.68471856050619e-02 , 1.89834261058958e-02 , -1.08150192814251e-02 , 5.12591079306563e-03 , 1.22853421660068e-02 , 1.77447558708082e-02 , -1.62727379942027e-02 , -1.19520165190434e-02 , -5.06601412276133e-03 , 4.95319659434038e-03 , -1.32435252222438e-02 , -8.96495734999776e-03 , -6.73869467996829e-03 , -1.03675678531612e-03 ) 3.81801393250440e-01 + 34 ( 3.07497912028674e+00 , 4.50829914380588e+00 , 5.13922512638278e+00 , 6.16896017294668e+00 , 2.50485309322197e+00 , 3.83220702719942e+00 , 4.50102851686806e+00 , 5.34369562943610e+00 , 1.34176277954839e+00 , 2.39661859710098e+00 , 3.00923587723178e+00 , 3.80745750891794e+00 , 2.22552073001822e+00 , 2.69443239824280e+00 , 2.87483587690196e+00 , 3.33768680861078e+00 ) ( -4.34421640334799e-03 , 1.23259510194731e-02 , 1.68090579813687e-02 , 1.89878261610829e-02 , -1.08552901312531e-02 , 5.22942992226076e-03 , 1.22614658996729e-02 , 1.77642609680764e-02 , -1.62733896680575e-02 , -1.18660435429885e-02 , -5.16722789914439e-03 , 4.93281774262076e-03 , -1.32680512200940e-02 , -8.88197829739069e-03 , -6.80664460048118e-03 , -9.80979854271153e-04 ) 3.81791215770808e-01 + 35 ( 3.06898072833861e+00 , 4.51288823770881e+00 , 5.13261897921919e+00 , 6.16794500499526e+00 , 2.50074653237299e+00 , 3.84158061480535e+00 , 4.49879685463616e+00 , 5.34919353390091e+00 , 1.34229502305346e+00 , 2.40928100895182e+00 , 3.00430451680425e+00 , 3.80996140411077e+00 , 2.22360417042348e+00 , 2.70468750491233e+00 , 2.87057086954244e+00 , 3.34320509110129e+00 ) ( -4.44031491071235e-03 , 1.23527234681521e-02 , 1.67689785292895e-02 , 1.89962130882339e-02 , -1.09121854118585e-02 , 5.32120212173631e-03 , 1.22276539257989e-02 , 1.77845576873594e-02 , -1.62769366926278e-02 , -1.17686217470126e-02 , -5.24875745576491e-03 , 4.94273803932348e-03 , -1.32965365848290e-02 , -8.78720894171396e-03 , -6.87713385744937e-03 , -9.30987598810157e-04 ) 3.81835385504166e-01 + 36 ( 3.06273532842122e+00 , 4.51625453668437e+00 , 5.12558687876965e+00 , 6.16711285462378e+00 , 2.49564989962145e+00 , 3.84963128763360e+00 , 4.49551609079525e+00 , 5.35403199606795e+00 , 1.34235952057393e+00 , 2.42319130947787e+00 , 3.00166756440291e+00 , 3.81540250051618e+00 , 2.22209336160822e+00 , 2.71615108200234e+00 , 2.86679976404971e+00 , 3.34863558090078e+00 ) ( -4.54435368066141e-03 , 1.23686804950677e-02 , 1.67284311224198e-02 , 1.90084516119658e-02 , -1.09840196310911e-02 , 5.39437685684171e-03 , 1.21842739531386e-02 , 1.78051583090107e-02 , -1.62833596534709e-02 , -1.16643470067951e-02 , -5.30682059345081e-03 , 4.98516473295461e-03 , -1.33273660427321e-02 , -8.68399148739366e-03 , -6.94692018851069e-03 , -8.86427786439946e-04 ) 3.81936327036083e-01 + 37 ( 3.05649192132167e+00 , 4.51806131059166e+00 , 5.11839243202510e+00 , 6.16649586507377e+00 , 2.48972865327600e+00 , 3.85581806466917e+00 , 4.49128596625538e+00 , 5.35804830483488e+00 , 1.34195825281763e+00 , 2.43768478118170e+00 , 3.00145507450914e+00 , 3.82364960560225e+00 , 2.22109872744306e+00 , 2.72838935969239e+00 , 2.86373525953246e+00 , 3.35394019899047e+00 ) ( -4.65218982014911e-03 , 1.23716418558672e-02 , 1.66890397155335e-02 , 1.90241913089743e-02 , -1.10682357362770e-02 , 5.44373642248271e-03 , 1.21328465988092e-02 , 1.78256268057558e-02 , -1.62925100639911e-02 , -1.15581857866223e-02 , -5.33886828047797e-03 , 5.05955490104775e-03 , -1.33590658100595e-02 , -8.57601333848149e-03 , -7.01254065783080e-03 , -8.46660146239399e-04 ) 3.82093031722223e-01 + 38 ( 3.05045519889590e+00 , 4.51805473611829e+00 , 5.11134114887472e+00 , 6.16609340466301e+00 , 2.48321341701307e+00 , 3.85977678463866e+00 , 4.48635217324219e+00 , 5.36117618444632e+00 , 1.34120085885188e+00 , 2.45209075172033e+00 , 3.00367159434843e+00 , 3.83435311397414e+00 , 2.22068007522442e+00 , 2.74095124971729e+00 , 2.86158715760799e+00 , 3.35910007198241e+00 ) ( -4.76019163320950e-03 , 1.23598714041820e-02 , 1.66524680402616e-02 , 1.90428744709146e-02 , -1.11615338118528e-02 , 5.46602270063782e-03 , 1.20759997181952e-02 , 1.78455990056507e-02 , -1.63041248954833e-02 , -1.14552422088381e-02 , -5.34375549496949e-03 , 5.16264172534908e-03 , -1.33903719338111e-02 , -8.46711508398639e-03 , -7.07047588479804e-03 , -8.10789012685766e-04 ) 3.82300990443223e-01 + 39 ( 3.04477330521684e+00 , 4.51608052262827e+00 , 5.10475536253321e+00 , 6.16587487663191e+00 , 2.47638766200614e+00 , 3.86134206537838e+00 , 4.48108638301749e+00 , 5.36344937417303e+00 , 1.34028312443992e+00 , 2.46576763054109e+00 , 3.00819152091531e+00 , 3.84697007374176e+00 , 2.22084607834437e+00 , 2.75339260865446e+00 , 2.86054956607522e+00 , 3.36411702305049e+00 ) ( -4.86543044142400e-03 , 1.23321843370416e-02 , 1.66202988292410e-02 , 1.90637594104161e-02 , -1.12600574805245e-02 , 5.46010858659612e-03 , 1.20173150916460e-02 , 1.78648032651105e-02 , -1.63178447979581e-02 , -1.13604904210382e-02 , -5.32184447669693e-03 , 5.28870221435157e-03 , -1.34202591847899e-02 , -8.36109247803980e-03 , -7.11733590781375e-03 , -7.77701446405796e-04 ) 3.82552280895823e-01 + 40 ( 3.03953158571266e+00 , 4.51209497787138e+00 , 5.09894673253801e+00 , 6.16578599788259e+00 , 2.46957015768712e+00 , 3.86055335003907e+00 , 4.47595360314062e+00 , 5.36499714872809e+00 , 1.33944926913138e+00 , 2.47813660022930e+00 , 3.01476283614106e+00 , 3.86080601681174e+00 , 2.22155937137345e+00 , 2.76529935955117e+00 , 2.86078736612033e+00 , 3.36901381742548e+00 ) ( -4.96580059531963e-03 , 1.22880424119538e-02 , 1.65938976533907e-02 , 1.90859603276296e-02 , -1.13596279919568e-02 , 5.42702340653616e-03 , 1.19610688381882e-02 , 1.78830800540778e-02 , -1.63332290150278e-02 , -1.12784800774510e-02 , -5.27503313674526e-03 , 5.43003604266082e-03 , -1.34479399632883e-02 , -8.26149951627528e-03 , -7.15005910784782e-03 , -7.46119889758067e-04 ) 3.82835834419373e-01 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat index ead9fed19..83bec1298 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat @@ -1,10 +1,10 @@ # one p(one ) - 2.00000000000000 0.09106555928620 - 4.00000000000000 0.19841141655022 - 6.00000000000000 0.14791554502557 - 8.00000000000000 0.04585062006277 - 10.00000000000000 0.00473153263289 - 12.00000000000000 0.00011711012711 + 2.00000000000000 0.09106555930578 + 4.00000000000000 0.19841141658836 + 6.00000000000000 0.14791554501384 + 8.00000000000000 0.04585062002305 + 10.00000000000000 0.00473153262406 + 12.00000000000000 0.00011711012676 14.00000000000000 0.00000057531671 16.00000000000000 0.00000000051315 18.00000000000000 0.00000000000008 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt b/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt index 655c0f78c..157cac038 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2019-04-11". -colvars: Using NAMD interface, version "2019-02-12". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out index 43bcebeb7..3c82fd483 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -109,6 +113,7 @@ colvars: # centers = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 colvars: # targetCenters = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,15 +124,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - distancePairs colvar component: +colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped index 416f80c08..f4aa065ec 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.04629582333038e+00 , 4.49408974940565e+00 , 5.18802765078345e+00 , 6.16600456517094e+00 , 2.49712681746392e+00 , 3.86413458751360e+00 , 4.55726429607857e+00 , 5.34046966422931e+00 , 1.36572415578523e+00 , 2.47043282453162e+00 , 3.12318599155152e+00 , 3.85046871369096e+00 , 2.22191835508463e+00 , 2.73196623727117e+00 , 2.91861957005182e+00 , 3.29084860717030e+00 ) + x ( 3.04629582292620e+00 , 4.49408974875934e+00 , 5.18802765002996e+00 , 6.16600456423064e+00 , 2.49712681741192e+00 , 3.86413458721172e+00 , 4.55726429580482e+00 , 5.34046966370213e+00 , 1.36572415582545e+00 , 2.47043282429680e+00 , 3.12318599145701e+00 , 3.85046871322657e+00 , 2.22191835525029e+00 , 2.73196623733898e+00 , 2.91861957044130e+00 , 3.29084860719824e+00 ) } restraint { diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj index a7fca080e..6323d1e0e 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 ( 2.95543971137580e+00 , 4.40149446295507e+00 , 5.19438956774262e+00 , 6.22241603343745e+00 , 2.46985074910253e+00 , 3.82984200895935e+00 , 4.58947829164686e+00 , 5.41000980054028e+00 , 1.34023744154865e+00 , 2.42537620134385e+00 , 3.12639105039661e+00 , 3.90388793384236e+00 , 2.19602098164167e+00 , 2.66815420835178e+00 , 2.96116058328487e+00 , 3.36815290626777e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 1 ( 2.95875682371316e+00 , 4.40108078803418e+00 , 5.19334659297206e+00 , 6.22376901215925e+00 , 2.46917670614539e+00 , 3.82473558076875e+00 , 4.58659203732274e+00 , 5.40932438791416e+00 , 1.33333853625689e+00 , 2.41676042305356e+00 , 3.12170808828207e+00 , 3.90418242702588e+00 , 2.19936646916485e+00 , 2.66448925154473e+00 , 2.96000447713324e+00 , 3.36551061363074e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 2 ( 2.96294067406756e+00 , 4.40226515812014e+00 , 5.19285541585647e+00 , 6.22442847369399e+00 , 2.46935508867291e+00 , 3.82150643041097e+00 , 4.58422435394613e+00 , 5.40817951632150e+00 , 1.32707961474259e+00 , 2.41052202223200e+00 , 3.11822168290579e+00 , 3.90473111481326e+00 , 2.20349997298783e+00 , 2.66304540103031e+00 , 2.95871452979490e+00 , 3.36219422430751e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 3 ( 2.96775064185415e+00 , 4.40516130340127e+00 , 5.19307524761086e+00 , 6.22425430972040e+00 , 2.47031615576421e+00 , 3.82048584858698e+00 , 4.58270515959109e+00 , 5.40667289710545e+00 , 1.32192370926728e+00 , 2.40699266424479e+00 , 3.11597471297945e+00 , 3.90507282359922e+00 , 2.20807442664992e+00 , 2.66384581354508e+00 , 2.95730110417465e+00 , 3.35823523824198e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 4 ( 2.97293010491750e+00 , 4.40978768836142e+00 , 5.19406903505459e+00 , 6.22314788326388e+00 , 2.47196007304746e+00 , 3.82187612851750e+00 , 4.58226353675987e+00 , 5.40491259100367e+00 , 1.31825265739247e+00 , 2.40633740938353e+00 , 3.11490651575148e+00 , 3.90476431060501e+00 , 2.21272370239864e+00 , 2.66680267300434e+00 , 2.95575856580222e+00 , 3.35370432606659e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 5 ( 2.97823333786876e+00 , 4.41606221703738e+00 , 5.19580203467820e+00 , 6.22106315771777e+00 , 2.47416553032147e+00 , 3.82572100741006e+00 , 4.58300378561067e+00 , 5.40299835193009e+00 , 1.31633344997262e+00 , 2.40854582464716e+00 , 3.11487200507897e+00 , 3.90343726017080e+00 , 2.21709388500464e+00 , 2.67171937531972e+00 , 2.95407275175201e+00 , 3.34870361991155e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 6 ( 2.98344814010494e+00 , 4.42380327996886e+00 , 5.19814908071112e+00 , 6.21801314907934e+00 , 2.47679801686823e+00 , 3.83188876567758e+00 , 4.58489251308149e+00 , 5.40100490583954e+00 , 1.31630005549211e+00 , 2.41343716542307e+00 , 3.11566727600534e+00 , 3.90084606620602e+00 , 2.22087489888148e+00 , 2.67830168764624e+00 , 2.95222915701853e+00 , 3.34335752627100e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 7 ( 2.98841232078424e+00 , 4.43273687426315e+00 , 5.20090974397531e+00 , 6.21407143163464e+00 , 2.47971573108845e+00 , 3.84006896947682e+00 , 4.58775771850319e+00 , 5.39896919272286e+00 , 1.31814854769203e+00 , 2.42067606925974e+00 , 3.11705824330467e+00 , 3.89690002594713e+00 , 2.22382854108974e+00 , 2.68617638138061e+00 , 2.95021953228176e+00 , 3.33780297993749e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 8 ( 2.99302343356408e+00 , 4.44250962515450e+00 , 5.20382996327586e+00 , 6.20936877721994e+00 , 2.48277289806301e+00 , 3.84978342368457e+00 , 4.59130044217903e+00 , 5.39688319381903e+00 , 1.32174181291561e+00 , 2.42979485534901e+00 , 3.11880839063538e+00 , 3.89167562021842e+00 , 2.22580927850425e+00 , 2.69491484659868e+00 , 2.94804551633442e+00 , 3.33217989345794e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 9 ( 2.99724215297088e+00 , 4.45270758695142e+00 , 5.20662810065605e+00 , 6.20408528397123e+00 , 2.48582223191489e+00 , 3.86041172949691e+00 , 4.59511907153488e+00 , 5.39469356936545e+00 , 1.32682097132025e+00 , 2.44021975217169e+00 , 3.12070201377177e+00 , 3.88540749241064e+00 , 2.22677520657858e+00 , 2.70405886573605e+00 , 2.94571912723301e+00 , 3.32662241630005e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 10 ( 3.00109029649387e+00 , 4.46288053096414e+00 , 5.20902297741288e+00 , 6.19843864704866e+00 , 2.48871914762448e+00 , 3.87123105742002e+00 , 4.59874530583182e+00 , 5.39230854017706e+00 , 1.33302269914505e+00 , 2.45130012843502e+00 , 3.12256033871251e+00 , 3.87845986454653e+00 , 2.22678798490271e+00 , 2.71314602610314e+00 , 2.94326100418863e+00 , 3.32125154369191e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 11 ( 3.00464453588942e+00 , 4.47257069558543e+00 , 5.21076119638848e+00 , 6.19266941370346e+00 , 2.49132961385451e+00 , 3.88146798331951e+00 , 4.60168898224801e+00 , 5.38961117979994e+00 , 1.33990328901335e+00 , 2.46234094539705e+00 , 3.12424927277303e+00 , 3.87128278227091e+00 , 2.22600197549542e+00 , 2.72173288748063e+00 , 2.94069782584860e+00 , 3.31616954666578e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 12 ( 3.00802660466872e+00 , 4.48134406067423e+00 , 5.21164113891315e+00 , 6.18702434833565e+00 , 2.49354148220516e+00 , 3.89035788116353e+00 , 4.60348694964941e+00 , 5.38647692484132e+00 , 1.34697040085023e+00 , 2.47263868606845e+00 , 3.12567895935487e+00 , 3.86435935223959e+00 , 2.22464401788052e+00 , 2.72941476960870e+00 , 2.93806020605167e+00 , 3.31145665762186e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 13 ( 3.01139044165349e+00 , 4.48882134512637e+00 , 5.21153128241426e+00 , 6.18173913371892e+00 , 2.49527712738787e+00 , 3.89720566631697e+00 , 4.60374994484304e+00 , 5.38279228320668e+00 , 1.35372197426113e+00 , 2.48152014333316e+00 , 3.12679646629641e+00 , 3.85815073776481e+00 , 2.22298622217618e+00 , 2.73584170506168e+00 , 2.93538174058148e+00 , 3.30717032254531e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 14 ( 3.01490659498393e+00 , 4.49470568819819e+00 , 5.21038109514539e+00 , 6.17702179178737e+00 , 2.49650403390072e+00 , 3.90144127859289e+00 , 4.60220148662660e+00 , 5.37847180935563e+00 , 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5.37347142007190e+00 , 1.36448009941829e+00 , 2.49273019177650e+00 , 3.12799274184721e+00 , 3.84931652407039e+00 , 2.21989896809341e+00 , 2.74387407753706e+00 , 2.93005166831867e+00 , 3.30000695732958e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 16 ( 3.02305313422210e+00 , 4.50104303428906e+00 , 5.20516981146437e+00 , 6.16990178998942e+00 , 2.49755349804038e+00 , 3.90067603022659e+00 , 4.59327213516205e+00 , 5.36779747424164e+00 , 1.36781305326681e+00 , 2.49421050402841e+00 , 3.12803142010965e+00 , 3.84709461346751e+00 , 2.21896204077532e+00 , 2.74514610281301e+00 , 2.92748124565960e+00 , 3.29715922038007e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 17 ( 3.02794278865083e+00 , 4.50147045542482e+00 , 5.20139488461765e+00 , 6.16766577616433e+00 , 2.49755330820884e+00 , 3.89549330636628e+00 , 4.58606702332089e+00 , 5.36151205301774e+00 , 1.36954253123774e+00 , 2.49263619462458e+00 , 3.12765036944035e+00 , 3.84635143602295e+00 , 2.21866044078389e+00 , 2.74450537661546e+00 , 2.92502790937371e+00 , 3.29480918127726e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 18 ( 3.03346785763668e+00 , 4.50025537416632e+00 , 5.19711906880713e+00 , 6.16632276459286e+00 , 2.49737930804475e+00 , 3.88735195236461e+00 , 4.57738383523341e+00 , 5.35473517680542e+00 , 1.36966557265781e+00 , 2.48800127012076e+00 , 3.12678413125048e+00 , 3.84690184520457e+00 , 2.21907037563427e+00 , 2.74199613759987e+00 , 2.92272466405630e+00 , 3.29296402715817e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 19 ( 3.03961480026791e+00 , 4.49767398513431e+00 , 5.19258399588939e+00 , 6.16580745437566e+00 , 2.49718604907339e+00 , 3.87669270155849e+00 , 4.56762447380043e+00 , 5.34764418793476e+00 , 1.36831274921341e+00 , 2.48048318958123e+00 , 3.12533717881288e+00 , 3.84841979353987e+00 , 2.22018461777402e+00 , 2.73774680021871e+00 , 2.92058985532802e+00 , 3.29163694658328e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 20 ( 3.04629582292620e+00 , 4.49408974875934e+00 , 5.18802765002996e+00 , 6.16600456423064e+00 , 2.49712681741192e+00 , 3.86413458721172e+00 , 4.55726429580482e+00 , 5.34046966370213e+00 , 1.36572415582545e+00 , 2.47043282429680e+00 , 3.12318599145701e+00 , 3.85046871322657e+00 , 2.22191835525029e+00 , 2.73196623733898e+00 , 2.91861957044130e+00 , 3.29084860719824e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out index a84b20ece..ffd401600 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,27 +59,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -109,6 +113,7 @@ colvars: # centers = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 colvars: # targetCenters = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,20 +124,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - distancePairs colvar component: +colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 3.0463 , 4.49409 , 5.18803 , 6.166 , 2.49713 , 3.86413 , 4.55726 , 5.34047 , 1.36572 , 2.47043 , 3.12319 , 3.85047 , 2.22192 , 2.73197 , 2.91862 , 3.29085 ) colvars: Restarting linear bias "linear1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped index 0d4ecbc07..aebc65c59 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.03877998958173e+00 , 4.51126454876777e+00 , 5.09780825855294e+00 , 6.16443491538328e+00 , 2.46931564842291e+00 , 3.86026518301130e+00 , 4.47534635855439e+00 , 5.36404748356174e+00 , 1.33947834856915e+00 , 2.47810087633114e+00 , 3.01439850098518e+00 , 3.86006418873543e+00 , 2.22172886207939e+00 , 2.76552022640159e+00 , 2.86065452105383e+00 , 3.36835466726488e+00 ) + x ( 3.03877998802839e+00 , 4.51126454702547e+00 , 5.09780825674884e+00 , 6.16443491397830e+00 , 2.46931564760306e+00 , 3.86026518189025e+00 , 4.47534635751221e+00 , 5.36404748288555e+00 , 1.33947834845631e+00 , 2.47810087575991e+00 , 3.01439850051918e+00 , 3.86006418847475e+00 , 2.22172886244241e+00 , 2.76552022649790e+00 , 2.86065452181562e+00 , 3.36835466836590e+00 ) } restraint { diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj index 305b720d8..fd76bbf8c 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( 3.04629582333038e+00 , 4.49408974940565e+00 , 5.18802765078345e+00 , 6.16600456517094e+00 , 2.49712681746392e+00 , 3.86413458751360e+00 , 4.55726429607857e+00 , 5.34046966422931e+00 , 1.36572415578523e+00 , 2.47043282453162e+00 , 3.12318599155152e+00 , 3.85046871369096e+00 , 2.22191835508463e+00 , 2.73196623727117e+00 , 2.91861957005182e+00 , 3.29084860717030e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 21 ( 3.05334985763277e+00 , 4.48992628740912e+00 , 5.18366022464120e+00 , 6.16676026517965e+00 , 2.49733708347282e+00 , 3.85043471993401e+00 , 4.54681310152768e+00 , 5.33348650550615e+00 , 1.36221538955140e+00 , 2.45835277063441e+00 , 3.12018761715455e+00 , 3.85254424646025e+00 , 2.22412250661172e+00 , 2.72493758201792e+00 , 2.91678212298157e+00 , 3.29062579001597e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 22 ( 3.06055105861170e+00 , 4.48563517122715e+00 , 5.17964329347520e+00 , 6.16789612296411e+00 , 2.49791842481391e+00 , 3.83643598993477e+00 , 4.53677312740863e+00 , 5.32699885081340e+00 , 1.35813975608303e+00 , 2.44486600996319e+00 , 3.11619451815838e+00 , 3.85412638414357e+00 , 2.22660216055130e+00 , 2.71700934094722e+00 , 2.91501666418883e+00 , 3.29099758712820e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 23 ( 3.06762420537455e+00 , 4.48166116819623e+00 , 5.17607431665495e+00 , 6.16922431371692e+00 , 2.49892421173471e+00 , 3.82300581067859e+00 , 4.52759703932642e+00 , 5.32131852904925e+00 , 1.35385283877394e+00 , 2.43067780498747e+00 , 3.11107462107622e+00 , 3.85473675543460e+00 , 2.22913771640750e+00 , 2.70858357689142e+00 , 2.91323709510737e+00 , 3.29199001461179e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 24 ( 3.07426564537620e+00 , 4.47840815480823e+00 , 5.17297796853387e+00 , 6.17056286876168e+00 , 2.50034908333503e+00 , 3.81097097869069e+00 , 4.51964961706314e+00 , 5.31673850364178e+00 , 1.34968380478475e+00 , 2.41653410806774e+00 , 3.10473449544999e+00 , 3.85399547491976e+00 , 2.23150661393285e+00 , 2.70010092743619e+00 , 2.91134113937253e+00 , 3.29362013046587e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 25 ( 3.08016782803923e+00 , 4.47620910850743e+00 , 5.17030513374633e+00 , 6.17174981813669e+00 , 2.50212450431453e+00 , 3.80105507006416e+00 , 4.51317721000767e+00 , 5.31350456378877e+00 , 1.34591496237637e+00 , 2.40317959755503e+00 , 3.09714267660166e+00 , 3.85167104572299e+00 , 2.23350398123885e+00 , 2.69202233127222e+00 , 2.90922309099170e+00 , 3.29589074929859e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 26 ( 3.08504497891933e+00 , 4.47530287675982e+00 , 5.16793956294178e+00 , 6.17265513371149e+00 , 2.50412200545517e+00 , 3.79382467057860e+00 , 4.50828856745208e+00 , 5.31178960122026e+00 , 1.34276823545913e+00 , 2.39131763893910e+00 , 3.08834947595422e+00 , 3.84771665003698e+00 , 2.23496090195447e+00 , 2.68480761429074e+00 , 2.90678782238991e+00 , 3.29878667322874e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 27 ( 3.08865740792342e+00 , 4.47581931207440e+00 , 5.16571151113178e+00 , 6.17318955421352e+00 , 2.50616407558748e+00 , 3.78964913255106e+00 , 4.50494918018836e+00 , 5.31167449467097e+00 , 1.34039573489937e+00 , 2.38157352832347e+00 , 3.07849972517651e+00 , 3.84228723328513e+00 , 2.23575922229624e+00 , 2.67889154886125e+00 , 2.90396346127461e+00 , 3.30227300550551e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 28 ( 3.09083197005963e+00 , 4.47777298003410e+00 , 5.16341701691502e+00 , 6.17330951332411e+00 , 2.50804080769953e+00 , 3.78867633383442e+00 , 4.50298936014305e+00 , 5.31313821853742e+00 , 1.33887215233275e+00 , 2.37446181229422e+00 , 3.06783587794908e+00 , 3.83573409537907e+00 , 2.23584181643077e+00 , 2.67465865880345e+00 , 2.90071083364295e+00 , 3.30629579745776e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 29 ( 3.09147652580173e+00 , 4.48106463042456e+00 , 5.16084080206376e+00 , 6.17301764363929e+00 , 2.50952927552444e+00 , 3.79082510429274e+00 , 4.50212447128619e+00 , 5.31605801172195e+00 , 1.33818877025098e+00 , 2.37035852485007e+00 , 3.05669031842525e+00 , 3.82857689434697e+00 , 2.23521733453550e+00 , 2.67241876505723e+00 , 2.89702867542291e+00 , 3.31078478872068e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , 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-2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 30 ( 3.09058694977931e+00 , 4.48548936034949e+00 , 5.15778063240666e+00 , 6.17235875247401e+00 , 2.51041270196689e+00 , 3.79579411480670e+00 , 4.50198498078247e+00 , 5.32021901611626e+00 , 1.33825174758459e+00 , 2.36948006067847e+00 , 3.04546788921847e+00 , 3.82145639023017e+00 , 2.23395869069158e+00 , 2.67238581517616e+00 , 2.89295490314345e+00 , 3.31565768022867e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 31 ( 3.08824597625239e+00 , 4.49075053845246e+00 , 5.15407068114639e+00 , 6.17141163619470e+00 , 2.51049756105646e+00 , 3.80308681405192e+00 , 4.50215365271137e+00 , 5.32533205627038e+00 , 1.33888880659581e+00 , 2.37187086964207e+00 , 3.03462070382300e+00 , 3.81507358119468e+00 , 2.23219511591932e+00 , 2.67466266655001e+00 , 2.88856492653725e+00 , 3.32082524147622e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 32 ( 3.08461411097271e+00 , 4.49647886423009e+00 , 5.14960177736290e+00 , 6.17027762362695e+00 , 2.50962807667604e+00 , 3.81205156126135e+00 , 4.50220741948503e+00 , 5.33105788079286e+00 , 1.33986789053847e+00 , 2.37740208949063e+00 , 3.02461835056944e+00 , 3.81012227680463e+00 , 2.23009844809748e+00 , 2.67923396951857e+00 , 2.88396845444278e+00 , 3.32619656883699e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 33 ( 3.07991378221424e+00 , 4.50225598774368e+00 , 5.14433661074996e+00 , 6.16906723638448e+00 , 2.50769841868323e+00 , 3.82193487530121e+00 , 4.50176095190848e+00 , 5.33703587344653e+00 , 1.34092834047650e+00 , 2.38578198626423e+00 , 3.01591638646605e+00 , 3.80722231814434e+00 , 2.22786519374588e+00 , 2.68596812945528e+00 , 2.87930570927184e+00 , 3.33168396197019e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 34 ( 3.07440860931254e+00 , 4.50764161547249e+00 , 5.13831857639857e+00 , 6.16788658820268e+00 , 2.50466285985335e+00 , 3.83194370405047e+00 , 4.50050842022841e+00 , 5.34291473611270e+00 , 1.34182117051647e+00 , 2.39657731482946e+00 , 3.00892592878546e+00 , 3.80686000972107e+00 , 2.22569657351854e+00 , 2.69462787716750e+00 , 2.87474349267268e+00 , 3.33720713274434e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 35 ( 3.06838011503852e+00 , 4.51220236445887e+00 , 5.13167322979288e+00 , 6.16682524216936e+00 , 2.50054351728456e+00 , 3.84131072638630e+00 , 4.49825898981490e+00 , 5.34838227913630e+00 , 1.34235119113145e+00 , 2.40924279123168e+00 , 3.00398601326731e+00 , 3.80934088105348e+00 , 2.22377893326655e+00 , 2.70488772649367e+00 , 2.87047066148171e+00 , 3.34269688957208e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 36 ( 3.06210432223467e+00 , 4.51554021275385e+00 , 5.12460206898545e+00 , 6.16594684094431e+00 , 2.49543460132950e+00 , 3.84935590471168e+00 , 4.49496173590441e+00 , 5.35319126883816e+00 , 1.34241205405189e+00 , 2.42315536036212e+00 , 3.00134026458716e+00 , 3.81475851235681e+00 , 2.22226687749169e+00 , 2.71635592301934e+00 , 2.86669215483321e+00 , 3.34809824928536e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 37 ( 3.05583041439362e+00 , 4.51731835465463e+00 , 5.11736876890563e+00 , 6.16528355389606e+00 , 2.48950183931279e+00 , 3.85553820821008e+00 , 4.49071646908266e+00 , 5.35717902456251e+00 , 1.34200592541559e+00 , 2.43765019134095e+00 , 3.00111875540504e+00 , 3.82298171413422e+00 , 2.22127096979832e+00 , 2.72859863700022e+00 , 2.86362073690828e+00 , 3.35337316881309e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 38 ( 3.04976328528447e+00 , 4.51728290588255e+00 , 5.11027889606649e+00 , 6.16483478441171e+00 , 2.48297610040051e+00 , 3.85949338837732e+00 , 4.48576887736932e+00 , 5.36027926392764e+00 , 1.34124273650271e+00 , 2.45205659072561e+00 , 3.00332606664353e+00 , 3.83366091163511e+00 , 2.22085114911933e+00 , 2.74116471592353e+00 , 2.86146619741768e+00 , 3.35850281186161e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 39 ( 3.04405129091709e+00 , 4.51527953755738e+00 , 5.10365482819136e+00 , 6.16456998082301e+00 , 2.47614106192518e+00 , 3.86105594513486e+00 , 4.48049055341963e+00 , 5.36252568367002e+00 , 1.34031865516537e+00 , 2.46573303944144e+00 , 3.00783663869423e+00 , 3.84625320453851e+00 , 2.22101620416641e+00 , 2.75360995509687e+00 , 2.86042255327991e+00 , 3.36348904181343e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 40 ( 3.03877998802839e+00 , 4.51126454702547e+00 , 5.09780825674884e+00 , 6.16443491397830e+00 , 2.46931564760306e+00 , 3.86026518189025e+00 , 4.47534635751221e+00 , 5.36404748288555e+00 , 1.33947834845631e+00 , 2.47810087575991e+00 , 3.01439850051918e+00 , 3.86006418847475e+00 , 2.22172886244241e+00 , 2.76552022649790e+00 , 2.86065452181562e+00 , 3.36835466836590e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt b/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt index afda7aab6..157cac038 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-09-12. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out index aecf18686..8f7a57a73 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -87,25 +91,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -148,6 +152,7 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -158,15 +163,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceVec colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped index 572603c28..13ed1c8c9 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -1.02062769591997e+00 , -6.08213500496868e-03 , 3.05064351583999e+00 ) + x ( -1.02062769534156e+00 , -6.08213499811239e-03 , 3.05064351584125e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj index 8bd23f911..193c60552 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -1.08926570435185e+00 , 2.48645332384094e-02 , 3.01469929653834e+00 ) ( 4.35706281740739e-03 , -9.94581329536377e-05 , -1.20587971861534e-02 ) - 1 ( -1.08757103024997e+00 , 2.23275217747934e-02 , 3.01408140364135e+00 ) ( 4.35028412099990e-03 , -8.93100870991734e-05 , -1.20563256145654e-02 ) - 2 ( -1.08562847089983e+00 , 2.01398180516252e-02 , 3.01423212068838e+00 ) ( 4.34251388359932e-03 , -8.05592722065010e-05 , -1.20569284827535e-02 ) - 3 ( -1.08340349194734e+00 , 1.83171614284610e-02 , 3.01517854061388e+00 ) ( 4.33361396778937e-03 , -7.32686457138438e-05 , -1.20607141624555e-02 ) - 4 ( -1.08086495662244e+00 , 1.68568843161550e-02 , 3.01690562336324e+00 ) ( 4.32345982648975e-03 , -6.74275372646198e-05 , -1.20676224934530e-02 ) - 5 ( -1.07799014212969e+00 , 1.57362299159951e-02 , 3.01935667906087e+00 ) ( 4.31196056851875e-03 , -6.29449196639804e-05 , -1.20774267162435e-02 ) - 6 ( -1.07476840349588e+00 , 1.49116811517320e-02 , 3.02243644260053e+00 ) ( 4.29907361398352e-03 , -5.96467246069281e-05 , -1.20897457704021e-02 ) - 7 ( -1.07120346043007e+00 , 1.43200030669788e-02 , 3.02601615449288e+00 ) ( 4.28481384172026e-03 , -5.72800122679151e-05 , -1.21040646179715e-02 ) - 8 ( -1.06731460026733e+00 , 1.38814843394630e-02 , 3.02994023637554e+00 ) ( 4.26925840106931e-03 , -5.55259373578521e-05 , -1.21197609455021e-02 ) - 9 ( -1.06313721632696e+00 , 1.35053849341971e-02 , 3.03403440487335e+00 ) ( 4.25254886530783e-03 , -5.40215397367883e-05 , -1.21361376194934e-02 ) - 10 ( -1.05872297673822e+00 , 1.30969846539595e-02 , 3.03811518640717e+00 ) ( 4.23489190695288e-03 , -5.23879386158379e-05 , -1.21524607456287e-02 ) - 11 ( -1.05413959121528e+00 , 1.25651405718566e-02 , 3.04200058108683e+00 ) ( 4.21655836486113e-03 , -5.02605622874266e-05 , -1.21680023243473e-02 ) - 12 ( -1.04946980454194e+00 , 1.18290706584114e-02 , 3.04552119759417e+00 ) ( 4.19787921816777e-03 , -4.73162826336457e-05 , -1.21820847903767e-02 ) - 13 ( -1.04480903909869e+00 , 1.08232101954363e-02 , 3.04853081100414e+00 ) ( 4.17923615639474e-03 , -4.32928407817452e-05 , -1.21941232440166e-02 ) - 14 ( -1.04026127402952e+00 , 9.49942100347867e-03 , 3.05091517281576e+00 ) ( 4.16104509611809e-03 , -3.79976840139147e-05 , -1.22036606912630e-02 ) - 15 ( -1.03593320400088e+00 , 7.82645299533791e-03 , 3.05259815158109e+00 ) ( 4.14373281600352e-03 , -3.13058119813516e-05 , -1.22103926063244e-02 ) - 16 ( -1.03192718312749e+00 , 5.78719766133096e-03 , 3.05354476806524e+00 ) ( 4.12770873250994e-03 , -2.31487906453238e-05 , -1.22141790722609e-02 ) - 17 ( -1.02833380809396e+00 , 3.37481068267376e-03 , 3.05376123026148e+00 ) ( 4.11333523237583e-03 , -1.34992427306950e-05 , -1.22150449210459e-02 ) - 18 ( -1.02522512552484e+00 , 5.89042585372512e-04 , 3.05329243259600e+00 ) ( 4.10090050209936e-03 , -2.35617034149005e-06 , -1.22131697303840e-02 ) - 19 ( -1.02264934677565e+00 , -2.56602063071965e-03 , 3.05221745999499e+00 ) ( 4.09059738710258e-03 , 1.02640825228786e-05 , -1.22088698399800e-02 ) - 20 ( -1.02062769591997e+00 , -6.08213500496868e-03 , 3.05064351583999e+00 ) ( 4.08251078367986e-03 , 2.43285400198747e-05 , -1.22025740633599e-02 ) + 0 ( -1.08926570435186e+00 , 2.48645332384574e-02 , 3.01469929653834e+00 ) ( 4.35706281740742e-03 , -9.94581329538296e-05 , -1.20587971861533e-02 ) + 1 ( -1.08757103024838e+00 , 2.23275217750993e-02 , 3.01408140364127e+00 ) ( 4.35028412099354e-03 , -8.93100871003973e-05 , -1.20563256145651e-02 ) + 2 ( -1.08562847072074e+00 , 2.01398180220937e-02 , 3.01423212069547e+00 ) ( 4.34251388288294e-03 , -8.05592720883750e-05 , -1.20569284827819e-02 ) + 3 ( -1.08340349189933e+00 , 1.83171614296354e-02 , 3.01517854062312e+00 ) ( 4.33361396759732e-03 , -7.32686457185414e-05 , -1.20607141624925e-02 ) + 4 ( -1.08086495647312e+00 , 1.68568842988528e-02 , 3.01690562336607e+00 ) ( 4.32345982589247e-03 , -6.74275371954112e-05 , -1.20676224934643e-02 ) + 5 ( -1.07799014209397e+00 , 1.57362299347954e-02 , 3.01935667906812e+00 ) ( 4.31196056837589e-03 , -6.29449197391816e-05 , -1.20774267162725e-02 ) + 6 ( -1.07476840344796e+00 , 1.49116811703516e-02 , 3.02243644259714e+00 ) ( 4.29907361379183e-03 , -5.96467246814063e-05 , -1.20897457703886e-02 ) + 7 ( -1.07120346036405e+00 , 1.43200030870987e-02 , 3.02601615447875e+00 ) ( 4.28481384145619e-03 , -5.72800123483947e-05 , -1.21040646179150e-02 ) + 8 ( -1.06731460018291e+00 , 1.38814843649557e-02 , 3.02994023634960e+00 ) ( 4.26925840073163e-03 , -5.55259374598229e-05 , -1.21197609453984e-02 ) + 9 ( -1.06313721621703e+00 , 1.35053849628509e-02 , 3.03403440483742e+00 ) ( 4.25254886486811e-03 , -5.40215398514037e-05 , -1.21361376193497e-02 ) + 10 ( -1.05872297659907e+00 , 1.30969846845709e-02 , 3.03811518636264e+00 ) ( 4.23489190639626e-03 , -5.23879387382835e-05 , -1.21524607454506e-02 ) + 11 ( -1.05413959104298e+00 , 1.25651406036256e-02 , 3.04200058103587e+00 ) ( 4.21655836417193e-03 , -5.02605624145023e-05 , -1.21680023241435e-02 ) + 12 ( -1.04946980433283e+00 , 1.18290706904701e-02 , 3.04552119753946e+00 ) ( 4.19787921733132e-03 , -4.73162827618805e-05 , -1.21820847901579e-02 ) + 13 ( -1.04480903884802e+00 , 1.08232102376193e-02 , 3.04853081094912e+00 ) ( 4.17923615539206e-03 , -4.32928409504774e-05 , -1.21941232437965e-02 ) + 14 ( -1.04026127373743e+00 , 9.49942103360235e-03 , 3.05091517276253e+00 ) ( 4.16104509494973e-03 , -3.79976841344094e-05 , -1.22036606910501e-02 ) + 15 ( -1.03593320366363e+00 , 7.82645303080387e-03 , 3.05259815153299e+00 ) ( 4.14373281465451e-03 , -3.13058121232155e-05 , -1.22103926061320e-02 ) + 16 ( -1.03192718274189e+00 , 5.78719768553504e-03 , 3.05354476802529e+00 ) ( 4.12770873096756e-03 , -2.31487907421402e-05 , -1.22141790721012e-02 ) + 17 ( -1.02833380767736e+00 , 3.37481068352563e-03 , 3.05376123022586e+00 ) ( 4.11333523070946e-03 , -1.34992427341025e-05 , -1.22150449209035e-02 ) + 18 ( -1.02522512504349e+00 , 5.89042613610813e-04 , 3.05329243257632e+00 ) ( 4.10090050017395e-03 , -2.35617045444325e-06 , -1.22131697303053e-02 ) + 19 ( -1.02264934622731e+00 , -2.56602061946254e-03 , 3.05221745998716e+00 ) ( 4.09059738490925e-03 , 1.02640824778502e-05 , -1.22088698399486e-02 ) + 20 ( -1.02062769534156e+00 , -6.08213499811239e-03 , 3.05064351584125e+00 ) ( 4.08251078136622e-03 , 2.43285399924496e-05 , -1.22025740633650e-02 ) diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out index 39d87c2b9..cfa942a30 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -87,25 +91,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -148,6 +152,7 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -158,20 +163,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceVec colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -1.02063 , -0.00608213 , 3.05064 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped index 57ad6cdde..fa080941c 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -1.00146958058144e+00 , -7.86134845943720e-02 , 3.05294498811922e+00 ) + x ( -1.00146957910752e+00 , -7.86134846594192e-02 , 3.05294498810129e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj index 411da6154..a8901e5cb 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -1.02062769591997e+00 , -6.08213500496868e-03 , 3.05064351583999e+00 ) ( 4.08251078367986e-03 , 2.43285400198747e-05 , -1.22025740633599e-02 ) - 21 ( -1.01915363052765e+00 , -9.94509780830111e-03 , 3.04869855745494e+00 ) ( 4.07661452211062e-03 , 3.97803912332044e-05 , -1.21947942298198e-02 ) - 22 ( -1.01819426535002e+00 , -1.41317848404291e-02 , 3.04652291622540e+00 ) ( 4.07277706140009e-03 , 5.65271393617164e-05 , -1.21860916649016e-02 ) - 23 ( -1.01769353644663e+00 , -1.86072292938941e-02 , 3.04426035188961e+00 ) ( 4.07077414578651e-03 , 7.44289171755765e-05 , -1.21770414075584e-02 ) - 24 ( -1.01757652378195e+00 , -2.33228912103368e-02 , 3.04204924924129e+00 ) ( 4.07030609512782e-03 , 9.32915648413473e-05 , -1.21681969969652e-02 ) - 25 ( -1.01775441505923e+00 , -2.82168582418595e-02 , 3.04001482316877e+00 ) ( 4.07101766023693e-03 , 1.12867432967438e-04 , -1.21600592926751e-02 ) - 26 ( -1.01812972634717e+00 , -3.32161441348876e-02 , 3.03826306321224e+00 ) ( 4.07251890538870e-03 , 1.32864576539550e-04 , -1.21530522528490e-02 ) - 27 ( -1.01860146171764e+00 , -3.82407265273962e-02 , 3.03687681894353e+00 ) ( 4.07440584687057e-03 , 1.52962906109585e-04 , -1.21475072757741e-02 ) - 28 ( -1.01906991022665e+00 , -4.32085185057993e-02 , 3.03591402639455e+00 ) ( 4.07627964090659e-03 , 1.72834074023197e-04 , -1.21436561055782e-02 ) - 29 ( -1.01944079190354e+00 , -4.80403042958217e-02 , 3.03540770557534e+00 ) ( 4.07776316761414e-03 , 1.92161217183287e-04 , -1.21416308223013e-02 ) - 30 ( -1.01962854805362e+00 , -5.26637606618744e-02 , 3.03536739032252e+00 ) ( 4.07851419221450e-03 , 2.10655042647498e-04 , -1.21414695612901e-02 ) - 31 ( -1.01955870015183e+00 , -5.70160615084173e-02 , 3.03578166765498e+00 ) ( 4.07823480060733e-03 , 2.28064246033669e-04 , -1.21431266706199e-02 ) - 32 ( -1.01916935065016e+00 , -6.10450112208311e-02 , 3.03662168656281e+00 ) ( 4.07667740260063e-03 , 2.44180044883324e-04 , -1.21464867462512e-02 ) - 33 ( -1.01841199712945e+00 , -6.47090593651689e-02 , 3.03784542787964e+00 ) ( 4.07364798851779e-03 , 2.58836237460676e-04 , -1.21513817115186e-02 ) - 34 ( -1.01725181024562e+00 , -6.79766893212266e-02 , 3.03940247265176e+00 ) ( 4.06900724098247e-03 , 2.71906757284906e-04 , -1.21576098906070e-02 ) - 35 ( -1.01566747454107e+00 , -7.08256322924462e-02 , 3.04123879386186e+00 ) ( 4.06266989816427e-03 , 2.83302529169785e-04 , -1.21649551754474e-02 ) - 36 ( -1.01365053534415e+00 , -7.32422528716987e-02 , 3.04330111214608e+00 ) ( 4.05460214137660e-03 , 2.92969011486795e-04 , -1.21732044485843e-02 ) - 37 ( -1.01120429173592e+00 , -7.52213163683270e-02 , 3.04554044995591e+00 ) ( 4.04481716694370e-03 , 3.00885265473308e-04 , -1.21821617998237e-02 ) - 38 ( -1.00834238124957e+00 , -7.67661954318190e-02 , 3.04791477760370e+00 ) ( 4.03336952499827e-03 , 3.07064781727276e-04 , -1.21916591104148e-02 ) - 39 ( -1.00508734978189e+00 , -7.78894401522693e-02 , 3.05039080324243e+00 ) ( 4.02034939912757e-03 , 3.11557760609077e-04 , -1.22015632129697e-02 ) - 40 ( -1.00146958058144e+00 , -7.86134845943720e-02 , 3.05294498811922e+00 ) ( 4.00587832232574e-03 , 3.14453938377488e-04 , -1.22117799524769e-02 ) + 20 ( -1.02062769534156e+00 , -6.08213499811239e-03 , 3.05064351584125e+00 ) ( 4.08251078136622e-03 , 2.43285399924496e-05 , -1.22025740633650e-02 ) + 21 ( -1.01915362990077e+00 , -9.94509781004160e-03 , 3.04869855746548e+00 ) ( 4.07661451960309e-03 , 3.97803912401664e-05 , -1.21947942298619e-02 ) + 22 ( -1.01819426467457e+00 , -1.41317848486685e-02 , 3.04652291624334e+00 ) ( 4.07277705869829e-03 , 5.65271393946740e-05 , -1.21860916649734e-02 ) + 23 ( -1.01769353572269e+00 , -1.86072293092575e-02 , 3.04426035191247e+00 ) ( 4.07077414289074e-03 , 7.44289172370300e-05 , -1.21770414076499e-02 ) + 24 ( -1.01757652300947e+00 , -2.33228912331954e-02 , 3.04204924926634e+00 ) ( 4.07030609203789e-03 , 9.32915649327817e-05 , -1.21681969970653e-02 ) + 25 ( -1.01775441423944e+00 , -2.82168582658865e-02 , 3.04001482319277e+00 ) ( 4.07101765695776e-03 , 1.12867433063546e-04 , -1.21600592927711e-02 ) + 26 ( -1.01812972547680e+00 , -3.32161441751850e-02 , 3.03826306323336e+00 ) ( 4.07251890190722e-03 , 1.32864576700740e-04 , -1.21530522529335e-02 ) + 27 ( -1.01860146079953e+00 , -3.82407265723690e-02 , 3.03687681895852e+00 ) ( 4.07440584319812e-03 , 1.52962906289476e-04 , -1.21475072758341e-02 ) + 28 ( -1.01906990926088e+00 , -4.32085185509670e-02 , 3.03591402640151e+00 ) ( 4.07627963704352e-03 , 1.72834074203868e-04 , -1.21436561056061e-02 ) + 29 ( -1.01944079088857e+00 , -4.80403043559997e-02 , 3.03540770557330e+00 ) ( 4.07776316355427e-03 , 1.92161217423999e-04 , -1.21416308222932e-02 ) + 30 ( -1.01962854699229e+00 , -5.26637607211525e-02 , 3.03536739031026e+00 ) ( 4.07851418796916e-03 , 2.10655042884610e-04 , -1.21414695612410e-02 ) + 31 ( -1.01955869904214e+00 , -5.70160615819230e-02 , 3.03578166763320e+00 ) ( 4.07823479616858e-03 , 2.28064246327692e-04 , -1.21431266705328e-02 ) + 32 ( -1.01916934949446e+00 , -6.10450112992021e-02 , 3.03662168653196e+00 ) ( 4.07667739797783e-03 , 2.44180045196809e-04 , -1.21464867461279e-02 ) + 33 ( -1.01841199592886e+00 , -6.47090594473295e-02 , 3.03784542784121e+00 ) ( 4.07364798371542e-03 , 2.58836237789318e-04 , -1.21513817113648e-02 ) + 34 ( -1.01725180900141e+00 , -6.79766894059315e-02 , 3.03940247260780e+00 ) ( 4.06900723600566e-03 , 2.71906757623726e-04 , -1.21576098904312e-02 ) + 35 ( -1.01566747325464e+00 , -7.08256323783010e-02 , 3.04123879381492e+00 ) ( 4.06266989301856e-03 , 2.83302529513204e-04 , -1.21649551752597e-02 ) + 36 ( -1.01365053401866e+00 , -7.32422529508256e-02 , 3.04330111209864e+00 ) ( 4.05460213607464e-03 , 2.92969011803303e-04 , -1.21732044483946e-02 ) + 37 ( -1.01120429036970e+00 , -7.52213164514461e-02 , 3.04554044991178e+00 ) ( 4.04481716147881e-03 , 3.00885265805785e-04 , -1.21821617996471e-02 ) + 38 ( -1.00834237984516e+00 , -7.67661955129212e-02 , 3.04791477756569e+00 ) ( 4.03336951938062e-03 , 3.07064782051685e-04 , -1.21916591102628e-02 ) + 39 ( -1.00508734834212e+00 , -7.78894402311651e-02 , 3.05039080321297e+00 ) ( 4.02034939336848e-03 , 3.11557760924660e-04 , -1.22015632128519e-02 ) + 40 ( -1.00146957910752e+00 , -7.86134846594192e-02 , 3.05294498810129e+00 ) ( 4.00587831643010e-03 , 3.14453938637677e-04 , -1.22117799524052e-02 ) diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out index 049f980a2..d5a9ba71d 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -113,6 +117,7 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -123,15 +128,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceVec colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped index 4798692a9..9da6963c4 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -1.00012595362068e+00 , 6.81665091863780e-01 , 2.98047387611607e+00 ) + x ( -1.00012595304074e+00 , 6.81665091817865e-01 , 2.98047387612439e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj index 2c4dc1d5b..0460e926b 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -1.06103618343284e+00 , 6.89338769329276e-01 , 2.94525790836472e+00 ) ( 4.24414473373135e-03 , -2.75735507731710e-03 , -1.17810316334589e-02 ) - 1 ( -1.05984233192469e+00 , 6.87788139043584e-01 , 2.94477124393315e+00 ) ( 4.23936932769878e-03 , -2.75115255617434e-03 , -1.17790849757326e-02 ) - 2 ( -1.05834139784456e+00 , 6.86747097242960e-01 , 2.94497571747643e+00 ) ( 4.23336559137826e-03 , -2.74698838897184e-03 , -1.17799028699057e-02 ) - 3 ( -1.05650257672870e+00 , 6.86210421249889e-01 , 2.94589847749012e+00 ) ( 4.22601030691479e-03 , -2.74484168499956e-03 , -1.17835939099605e-02 ) - 4 ( -1.05430079785211e+00 , 6.86147780883707e-01 , 2.94752842220746e+00 ) ( 4.21720319140842e-03 , -2.74459112353483e-03 , -1.17901136888298e-02 ) - 5 ( -1.05172167280505e+00 , 6.86504075687213e-01 , 2.94981674140398e+00 ) ( 4.20688669122020e-03 , -2.74601630274885e-03 , -1.17992669656159e-02 ) - 6 ( -1.04876508127498e+00 , 6.87201123703198e-01 , 2.95267979110959e+00 ) ( 4.19506032509991e-03 , -2.74880449481279e-03 , -1.18107191644384e-02 ) - 7 ( -1.04544721833213e+00 , 6.88141185021492e-01 , 2.95600363777447e+00 ) ( 4.18178887332851e-03 , -2.75256474008597e-03 , -1.18240145510979e-02 ) - 8 ( -1.04180123385309e+00 , 6.89212570623204e-01 , 2.95964984570740e+00 ) ( 4.16720493541237e-03 , -2.75685028249282e-03 , -1.18385993828296e-02 ) - 9 ( -1.03787678384604e+00 , 6.90297113521857e-01 , 2.96346243146993e+00 ) ( 4.15150713538415e-03 , -2.76118845408743e-03 , -1.18538497258797e-02 ) - 10 ( -1.03373882413909e+00 , 6.91278691937061e-01 , 2.96727611992879e+00 ) ( 4.13495529655637e-03 , -2.76511476774824e-03 , -1.18691044797152e-02 ) - 11 ( -1.02946582298704e+00 , 6.92051560776091e-01 , 2.97092585777341e+00 ) ( 4.11786329194816e-03 , -2.76820624310436e-03 , -1.18837034310937e-02 ) - 12 ( -1.02514737820470e+00 , 6.92527153624911e-01 , 2.97425707648239e+00 ) ( 4.10058951281881e-03 , -2.77010861449964e-03 , -1.18970283059295e-02 ) - 13 ( -1.02088104360310e+00 , 6.92638311697926e-01 , 2.97713574424865e+00 ) ( 4.08352417441239e-03 , -2.77055324679170e-03 , -1.19085429769946e-02 ) - 14 ( -1.01676819370524e+00 , 6.92340498834602e-01 , 2.97945703491512e+00 ) ( 4.06707277482098e-03 , -2.76936199533841e-03 , -1.19178281396605e-02 ) - 15 ( -1.01290896048165e+00 , 6.91610275887974e-01 , 2.98115162237959e+00 ) ( 4.05163584192661e-03 , -2.76644110355190e-03 , -1.19246064895184e-02 ) - 16 ( -1.00939651136992e+00 , 6.90441852803797e-01 , 2.98218905910471e+00 ) ( 4.03758604547969e-03 , -2.76176741121519e-03 , -1.19287562364189e-02 ) - 17 ( -1.00631118564907e+00 , 6.88842837429205e-01 , 2.98257821433475e+00 ) ( 4.02524474259627e-03 , -2.75537134971682e-03 , -1.19303128573390e-02 ) - 18 ( -1.00371516509773e+00 , 6.86830298565906e-01 , 2.98236510042806e+00 ) ( 4.01486066039091e-03 , -2.74732119426362e-03 , -1.19294604017122e-02 ) - 19 ( -1.00164834896320e+00 , 6.84427986320491e-01 , 2.98162851652942e+00 ) ( 4.00659339585280e-03 , -2.73771194528196e-03 , -1.19265140661177e-02 ) - 20 ( -1.00012595362068e+00 , 6.81665091863780e-01 , 2.98047387611607e+00 ) ( 4.00050381448271e-03 , -2.72666036745512e-03 , -1.19218955044643e-02 ) + 0 ( -1.06103618343284e+00 , 6.89338769329275e-01 , 2.94525790836472e+00 ) ( 4.24414473373135e-03 , -2.75735507731710e-03 , -1.17810316334589e-02 ) + 1 ( -1.05984233192313e+00 , 6.87788139043843e-01 , 2.94477124393299e+00 ) ( 4.23936932769251e-03 , -2.75115255617537e-03 , -1.17790849757320e-02 ) + 2 ( -1.05834139767053e+00 , 6.86747097207406e-01 , 2.94497571748830e+00 ) ( 4.23336559068213e-03 , -2.74698838882962e-03 , -1.17799028699532e-02 ) + 3 ( -1.05650257668221e+00 , 6.86210421251529e-01 , 2.94589847749821e+00 ) ( 4.22601030672886e-03 , -2.74484168500611e-03 , -1.17835939099928e-02 ) + 4 ( -1.05430079770892e+00 , 6.86147780863856e-01 , 2.94752842221134e+00 ) ( 4.21720319083568e-03 , -2.74459112345542e-03 , -1.17901136888454e-02 ) + 5 ( -1.05172167277253e+00 , 6.86504075704956e-01 , 2.94981674140592e+00 ) ( 4.20688669109011e-03 , -2.74601630281983e-03 , -1.17992669656237e-02 ) + 6 ( -1.04876508122907e+00 , 6.87201123721589e-01 , 2.95267979110080e+00 ) ( 4.19506032491627e-03 , -2.74880449488636e-03 , -1.18107191644032e-02 ) + 7 ( -1.04544721826884e+00 , 6.88141185039855e-01 , 2.95600363775429e+00 ) ( 4.18178887307535e-03 , -2.75256474015942e-03 , -1.18240145510172e-02 ) + 8 ( -1.04180123376858e+00 , 6.89212570640885e-01 , 2.95964984567615e+00 ) ( 4.16720493507430e-03 , -2.75685028256354e-03 , -1.18385993827046e-02 ) + 9 ( -1.03787678373610e+00 , 6.90297113537972e-01 , 2.96346243142858e+00 ) ( 4.15150713494440e-03 , -2.76118845415189e-03 , -1.18538497257143e-02 ) + 10 ( -1.03373882399961e+00 , 6.91278691950712e-01 , 2.96727611987909e+00 ) ( 4.13495529599842e-03 , -2.76511476780285e-03 , -1.18691044795164e-02 ) + 11 ( -1.02946582281404e+00 , 6.92051560786413e-01 , 2.97092585771778e+00 ) ( 4.11786329125617e-03 , -2.76820624314565e-03 , -1.18837034308711e-02 ) + 12 ( -1.02514737799452e+00 , 6.92527153631102e-01 , 2.97425707642372e+00 ) ( 4.10058951197807e-03 , -2.77010861452441e-03 , -1.18970283056949e-02 ) + 13 ( -1.02088104335244e+00 , 6.92638311699283e-01 , 2.97713574419012e+00 ) ( 4.08352417340977e-03 , -2.77055324679713e-03 , -1.19085429767605e-02 ) + 14 ( -1.01676819341134e+00 , 6.92340498830537e-01 , 2.97945703485996e+00 ) ( 4.06707277364537e-03 , -2.76936199532215e-03 , -1.19178281394398e-02 ) + 15 ( -1.01290896014230e+00 , 6.91610275878003e-01 , 2.98115162233085e+00 ) ( 4.05163584056920e-03 , -2.76644110351201e-03 , -1.19246064893234e-02 ) + 16 ( -1.00939651098372e+00 , 6.90441852787200e-01 , 2.98218905906499e+00 ) ( 4.03758604393490e-03 , -2.76176741114880e-03 , -1.19287562362600e-02 ) + 17 ( -1.00631118523086e+00 , 6.88842837382683e-01 , 2.98257821430650e+00 ) ( 4.02524474092344e-03 , -2.75537134953073e-03 , -1.19303128572260e-02 ) + 18 ( -1.00371516461503e+00 , 6.86830298535374e-01 , 2.98236510041194e+00 ) ( 4.01486065846013e-03 , -2.74732119414150e-03 , -1.19294604016477e-02 ) + 19 ( -1.00164834841389e+00 , 6.84427986279444e-01 , 2.98162851652728e+00 ) ( 4.00659339365556e-03 , -2.73771194511777e-03 , -1.19265140661091e-02 ) + 20 ( -1.00012595304074e+00 , 6.81665091817865e-01 , 2.98047387612439e+00 ) ( 4.00050381216295e-03 , -2.72666036727146e-03 , -1.19218955044975e-02 ) diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out index 33501e601..0678a53ba 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -113,6 +117,7 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -123,20 +128,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceVec colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -1.00013 , 0.681665 , 2.98047 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped index a98e88769..91a4697ed 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -9.91441715714853e-01 , 6.28848618963486e-01 , 2.99185347903944e+00 ) + x ( -9.91441714242838e-01 , 6.28848618783027e-01 , 2.99185347905522e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj index 03b7dd3c1..620786d60 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -1.00012595362068e+00 , 6.81665091863780e-01 , 2.98047387611607e+00 ) ( 4.00050381448271e-03 , -2.72666036745512e-03 , -1.19218955044643e-02 ) - 21 ( -9.99138074893485e-01 , 6.78576393089195e-01 , 2.97902552991010e+00 ) ( 3.99655229957394e-03 , -2.71430557235678e-03 , -1.19161021196404e-02 ) - 22 ( -9.98651128006031e-01 , 6.75203199276404e-01 , 2.97741796069013e+00 ) ( 3.99460451202413e-03 , -2.70081279710561e-03 , -1.19096718427605e-02 ) - 23 ( -9.98610825708839e-01 , 6.71594275118549e-01 , 2.97578645094022e+00 ) ( 3.99444330283536e-03 , -2.68637710047419e-03 , -1.19031458037609e-02 ) - 24 ( -9.98946204647680e-01 , 6.67806005306121e-01 , 2.97425809124110e+00 ) ( 3.99578481859072e-03 , -2.67122402122448e-03 , -1.18970323649644e-02 ) - 25 ( -9.99574199242226e-01 , 6.63901368166392e-01 , 2.97294412310483e+00 ) ( 3.99829679696891e-03 , -2.65560547266557e-03 , -1.18917764924193e-02 ) - 26 ( -1.00040433184298e+00 , 6.59947725601624e-01 , 2.97193439791086e+00 ) ( 4.00161732737193e-03 , -2.63979090240649e-03 , -1.18877375916435e-02 ) - 27 ( -1.00134314986632e+00 , 6.56013782607379e-01 , 2.97129431690302e+00 ) ( 4.00537259946528e-03 , -2.62405513042951e-03 , -1.18851772676121e-02 ) - 28 ( -1.00229812026062e+00 , 6.52166332643251e-01 , 2.97106411683570e+00 ) ( 4.00919248104249e-03 , -2.60866533057301e-03 , -1.18842564673428e-02 ) - 29 ( -1.00318079820382e+00 , 6.48467421471618e-01 , 2.97125993940365e+00 ) ( 4.01272319281527e-03 , -2.59386968588647e-03 , -1.18850397576146e-02 ) - 30 ( -1.00390922101371e+00 , 6.44972467521952e-01 , 2.97187614715496e+00 ) ( 4.01563688405484e-03 , -2.57988987008781e-03 , -1.18875045886199e-02 ) - 31 ( -1.00440959005691e+00 , 6.41729568368808e-01 , 2.97288843458314e+00 ) ( 4.01763836022764e-03 , -2.56691827347523e-03 , -1.18915537383326e-02 ) - 32 ( -1.00461738044422e+00 , 6.38779886606265e-01 , 2.97425757145878e+00 ) ( 4.01846952177690e-03 , -2.55511954642506e-03 , -1.18970302858351e-02 ) - 33 ( -1.00447805084808e+00 , 6.36158624654867e-01 , 2.97593366048238e+00 ) ( 4.01791220339232e-03 , -2.54463449861947e-03 , -1.19037346419295e-02 ) - 34 ( -1.00394748630005e+00 , 6.33895972963095e-01 , 2.97786077691918e+00 ) ( 4.01578994520019e-03 , -2.53558389185238e-03 , -1.19114431076767e-02 ) - 35 ( -1.00299228530624e+00 , 6.32017486547197e-01 , 2.97998162119086e+00 ) ( 4.01196914122495e-03 , -2.52806994618879e-03 , -1.19199264847635e-02 ) - 36 ( -1.00158989063031e+00 , 6.30543620217316e-01 , 2.98224176226361e+00 ) ( 4.00635956252122e-03 , -2.52217448086926e-03 , -1.19289670490544e-02 ) - 37 ( -9.99728647879413e-01 , 6.29488492575348e-01 , 2.98459308226489e+00 ) ( 3.99891459151765e-03 , -2.51795397030139e-03 , -1.19383723290595e-02 ) - 38 ( -9.97407895568871e-01 , 6.28858255745633e-01 , 2.98699626416867e+00 ) ( 3.98963158227548e-03 , -2.51543302298253e-03 , -1.19479850566747e-02 ) - 39 ( -9.94638189030939e-01 , 6.28649565358814e-01 , 2.98942235138835e+00 ) ( 3.97855275612376e-03 , -2.51459826143525e-03 , -1.19576894055534e-02 ) - 40 ( -9.91441715714853e-01 , 6.28848618963486e-01 , 2.99185347903944e+00 ) ( 3.96576686285941e-03 , -2.51539447585394e-03 , -1.19674139161578e-02 ) + 20 ( -1.00012595304074e+00 , 6.81665091817865e-01 , 2.98047387612439e+00 ) ( 4.00050381216295e-03 , -2.72666036727146e-03 , -1.19218955044975e-02 ) + 21 ( -9.99138074265429e-01 , 6.78576393035151e-01 , 2.97902552992938e+00 ) ( 3.99655229706172e-03 , -2.71430557214061e-03 , -1.19161021197175e-02 ) + 22 ( -9.98651127330001e-01 , 6.75203199213713e-01 , 2.97741796071850e+00 ) ( 3.99460450932001e-03 , -2.70081279685485e-03 , -1.19096718428740e-02 ) + 23 ( -9.98610824984928e-01 , 6.71594275046680e-01 , 2.97578645097527e+00 ) ( 3.99444329993971e-03 , -2.68637710018672e-03 , -1.19031458039011e-02 ) + 24 ( -9.98946203875902e-01 , 6.67806005224566e-01 , 2.97425809128013e+00 ) ( 3.99578481550361e-03 , -2.67122402089826e-03 , -1.18970323651205e-02 ) + 25 ( -9.99574198422540e-01 , 6.63901368074702e-01 , 2.97294412314502e+00 ) ( 3.99829679369016e-03 , -2.65560547229881e-03 , -1.18917764925801e-02 ) + 26 ( -1.00040433097533e+00 , 6.59947725499445e-01 , 2.97193439794950e+00 ) ( 4.00161732390132e-03 , -2.63979090199778e-03 , -1.18877375917980e-02 ) + 27 ( -1.00134314895068e+00 , 6.56013782494476e-01 , 2.97129431693768e+00 ) ( 4.00537259580271e-03 , -2.62405512997790e-03 , -1.18851772677507e-02 ) + 28 ( -1.00229811929707e+00 , 6.52166332519549e-01 , 2.97106411686442e+00 ) ( 4.00919247718828e-03 , -2.60866533007820e-03 , -1.18842564674577e-02 ) + 29 ( -1.00318079719258e+00 , 6.48467421337220e-01 , 2.97125993942505e+00 ) ( 4.01272318877031e-03 , -2.59386968534888e-03 , -1.18850397577002e-02 ) + 30 ( -1.00390921995519e+00 , 6.44972467377165e-01 , 2.97187614716835e+00 ) ( 4.01563687982076e-03 , -2.57988986950866e-03 , -1.18875045886734e-02 ) + 31 ( -1.00440958895174e+00 , 6.41729568214161e-01 , 2.97288843458850e+00 ) ( 4.01763835580695e-03 , -2.56691827285664e-03 , -1.18915537383540e-02 ) + 32 ( -1.00461737929322e+00 , 6.38779886442533e-01 , 2.97425757145681e+00 ) ( 4.01846951717287e-03 , -2.55511954577013e-03 , -1.18970302858273e-02 ) + 33 ( -1.00447804965225e+00 , 6.36158624483086e-01 , 2.97593366047442e+00 ) ( 4.01791219860901e-03 , -2.54463449793234e-03 , -1.19037346418977e-02 ) + 34 ( -1.00394748506057e+00 , 6.33895972784570e-01 , 2.97786077690709e+00 ) ( 4.01578994024229e-03 , -2.53558389113828e-03 , -1.19114431076284e-02 ) + 35 ( -1.00299228402442e+00 , 6.32017486363480e-01 , 2.97998162117694e+00 ) ( 4.01196913609766e-03 , -2.52806994545392e-03 , -1.19199264847078e-02 ) + 36 ( -1.00158988930755e+00 , 6.30543620030167e-01 , 2.98224176225043e+00 ) ( 4.00635955723021e-03 , -2.52217448012067e-03 , -1.19289670490017e-02 ) + 37 ( -9.99728646517214e-01 , 6.29488492386688e-01 , 2.98459308225513e+00 ) ( 3.99891458606886e-03 , -2.51795396954675e-03 , -1.19383723290205e-02 ) + 38 ( -9.97407894168705e-01 , 6.28858255557523e-01 , 2.98699626416501e+00 ) ( 3.98963157667482e-03 , -2.51543302223009e-03 , -1.19479850566600e-02 ) + 39 ( -9.94638187594213e-01 , 6.28649565173414e-01 , 2.98942235139329e+00 ) ( 3.97855275037685e-03 , -2.51459826069366e-03 , -1.19576894055732e-02 ) + 40 ( -9.91441714242838e-01 , 6.28848618783027e-01 , 2.99185347905522e+00 ) ( 3.96576685697135e-03 , -2.51539447513211e-03 , -1.19674139162209e-02 ) diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out index 402d5433b..c28a9ea83 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: Reading legacy options lowerWall and lowerWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). colvars: # lowerWall = 0.1 colvars: Reading legacy options upperWall and upperWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). @@ -113,6 +117,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -126,6 +131,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -141,15 +147,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped index e53a1f4de..c116ac47b 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491539556e+00 + x 3.21685491521323e+00 } restraint { diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj index 222aa6880..d5d525eb6 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095464e+00 -1.20174855638185e-02 - 2 3.20383991847368e+00 -1.20153596738947e-02 - 3 3.20396638983244e+00 -1.20158655593298e-02 - 4 3.20472672282330e+00 -1.20189068912932e-02 - 5 3.20606083670688e+00 -1.20242433468275e-02 - 6 3.20787669545864e+00 -1.20315067818346e-02 - 7 3.21005568759325e+00 -1.20402227503730e-02 - 8 3.21245908147994e+00 -1.20498363259198e-02 - 9 3.21493559056115e+00 -1.20597423622446e-02 - 10 3.21733015649727e+00 -1.20693206259891e-02 - 11 3.21949374134263e+00 -1.20779749653705e-02 - 12 3.22129339473872e+00 -1.20851735789549e-02 - 13 3.22262143332763e+00 -1.20904857333105e-02 - 14 3.22340249788422e+00 -1.20936099915369e-02 - 15 3.22359762744577e+00 -1.20943905097831e-02 - 16 3.22320508670988e+00 -1.20928203468395e-02 - 17 3.22225829351165e+00 -1.20890331740466e-02 - 18 3.22082156091933e+00 -1.20832862436773e-02 - 19 3.21898439805351e+00 -1.20759375922140e-02 - 20 3.21685491539556e+00 -1.20674196615823e-02 +# step one fa_one + 0 3.20554673468334e+00 -1.20221869387334e-02 + 1 3.20437139095402e+00 -1.20174855638161e-02 + 2 3.20383991841948e+00 -1.20153596736779e-02 + 3 3.20396638982490e+00 -1.20158655592996e-02 + 4 3.20472672277551e+00 -1.20189068911021e-02 + 5 3.20606083670179e+00 -1.20242433468072e-02 + 6 3.20787669543948e+00 -1.20315067817579e-02 + 7 3.21005568755800e+00 -1.20402227502320e-02 + 8 3.21245908142754e+00 -1.20498363257101e-02 + 9 3.21493559049101e+00 -1.20597423619640e-02 + 10 3.21733015640955e+00 -1.20693206256382e-02 + 11 3.21949374123820e+00 -1.20779749649528e-02 + 12 3.22129339461899e+00 -1.20851735784760e-02 + 13 3.22262143319445e+00 -1.20904857327778e-02 + 14 3.22340249773966e+00 -1.20936099909586e-02 + 15 3.22359762729192e+00 -1.20943905091677e-02 + 16 3.22320508654863e+00 -1.20928203461945e-02 + 17 3.22225829334495e+00 -1.20890331733798e-02 + 18 3.22082156074746e+00 -1.20832862429898e-02 + 19 3.21898439787187e+00 -1.20759375914875e-02 + 20 3.21685491521323e+00 -1.20674196608529e-02 diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out index 2340e1d34..2607e31b0 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: Reading legacy options lowerWall and lowerWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). colvars: # lowerWall = 0.1 colvars: Reading legacy options upperWall and upperWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). @@ -113,6 +117,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -126,6 +131,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -141,20 +147,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "onew" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped index c542b2a71..1b9898933 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397364247543e+00 + x 3.21397364200070e+00 } restraint { diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj index 1b5a859eb..8b5e494a7 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 20 3.21685491539556e+00 -1.20674196615823e-02 - 21 3.21455264092142e+00 -1.20582105636857e-02 - 22 3.21220094123025e+00 -1.20488037649210e-02 - 23 3.20991934305299e+00 -1.20396773722120e-02 - 24 3.20781628584511e+00 -1.20312651433804e-02 - 25 3.20598302316673e+00 -1.20239320926669e-02 - 26 3.20448930640296e+00 -1.20179572256119e-02 - 27 3.20338117914512e+00 -1.20135247165805e-02 - 28 3.20268080963872e+00 -1.20107232385549e-02 - 29 3.20238791174576e+00 -1.20095516469830e-02 - 30 3.20248233501992e+00 -1.20099293400797e-02 - 31 3.20292744751448e+00 -1.20117097900579e-02 - 32 3.20367415744996e+00 -1.20146966297998e-02 - 33 3.20466540029747e+00 -1.20186616011899e-02 - 34 3.20584087625286e+00 -1.20233635050114e-02 - 35 3.20714161882697e+00 -1.20285664753079e-02 - 36 3.20851394967362e+00 -1.20340557986945e-02 - 37 3.20991249848372e+00 -1.20396499939349e-02 - 38 3.21130224478748e+00 -1.20452089791499e-02 - 39 3.21265973116748e+00 -1.20506389246699e-02 - 40 3.21397364247543e+00 -1.20558945699017e-02 +# step one fa_one + 20 3.21685491521323e+00 -1.20674196608529e-02 + 21 3.21455264073267e+00 -1.20582105629307e-02 + 22 3.21220094103318e+00 -1.20488037641327e-02 + 23 3.20991934284523e+00 -1.20396773713809e-02 + 24 3.20781628562398e+00 -1.20312651424959e-02 + 25 3.20598302292944e+00 -1.20239320917178e-02 + 26 3.20448930614687e+00 -1.20179572245875e-02 + 27 3.20338117886792e+00 -1.20135247154717e-02 + 28 3.20268080933861e+00 -1.20107232373544e-02 + 29 3.20238791142161e+00 -1.20095516456865e-02 + 30 3.20248233467135e+00 -1.20099293386854e-02 + 31 3.20292744714189e+00 -1.20117097885676e-02 + 32 3.20367415705454e+00 -1.20146966282182e-02 + 33 3.20466539988114e+00 -1.20186615995246e-02 + 34 3.20584087581816e+00 -1.20233635032726e-02 + 35 3.20714161837695e+00 -1.20285664735078e-02 + 36 3.20851394921166e+00 -1.20340557968466e-02 + 37 3.20991249801338e+00 -1.20396499920535e-02 + 38 3.21130224431234e+00 -1.20452089772494e-02 + 39 3.21265973069097e+00 -1.20506389227639e-02 + 40 3.21397364200070e+00 -1.20558945680028e-02 diff --git a/namd/tests/library/000_distancewalls-compatible/namd-version.txt b/namd/tests/library/000_distancewalls-compatible/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distancewalls-compatible/namd-version.txt +++ b/namd/tests/library/000_distancewalls-compatible/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out index 104a466ca..5da428bfa 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,6 +116,7 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -127,15 +132,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped index ed4ff587f..a0bbaca3d 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491541898e+00 + x 3.21685491521323e+00 } restraint { diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj index 222aa6880..d5d525eb6 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095464e+00 -1.20174855638185e-02 - 2 3.20383991847368e+00 -1.20153596738947e-02 - 3 3.20396638983244e+00 -1.20158655593298e-02 - 4 3.20472672282330e+00 -1.20189068912932e-02 - 5 3.20606083670688e+00 -1.20242433468275e-02 - 6 3.20787669545864e+00 -1.20315067818346e-02 - 7 3.21005568759325e+00 -1.20402227503730e-02 - 8 3.21245908147994e+00 -1.20498363259198e-02 - 9 3.21493559056115e+00 -1.20597423622446e-02 - 10 3.21733015649727e+00 -1.20693206259891e-02 - 11 3.21949374134263e+00 -1.20779749653705e-02 - 12 3.22129339473872e+00 -1.20851735789549e-02 - 13 3.22262143332763e+00 -1.20904857333105e-02 - 14 3.22340249788422e+00 -1.20936099915369e-02 - 15 3.22359762744577e+00 -1.20943905097831e-02 - 16 3.22320508670988e+00 -1.20928203468395e-02 - 17 3.22225829351165e+00 -1.20890331740466e-02 - 18 3.22082156091933e+00 -1.20832862436773e-02 - 19 3.21898439805351e+00 -1.20759375922140e-02 - 20 3.21685491539556e+00 -1.20674196615823e-02 +# step one fa_one + 0 3.20554673468334e+00 -1.20221869387334e-02 + 1 3.20437139095402e+00 -1.20174855638161e-02 + 2 3.20383991841948e+00 -1.20153596736779e-02 + 3 3.20396638982490e+00 -1.20158655592996e-02 + 4 3.20472672277551e+00 -1.20189068911021e-02 + 5 3.20606083670179e+00 -1.20242433468072e-02 + 6 3.20787669543948e+00 -1.20315067817579e-02 + 7 3.21005568755800e+00 -1.20402227502320e-02 + 8 3.21245908142754e+00 -1.20498363257101e-02 + 9 3.21493559049101e+00 -1.20597423619640e-02 + 10 3.21733015640955e+00 -1.20693206256382e-02 + 11 3.21949374123820e+00 -1.20779749649528e-02 + 12 3.22129339461899e+00 -1.20851735784760e-02 + 13 3.22262143319445e+00 -1.20904857327778e-02 + 14 3.22340249773966e+00 -1.20936099909586e-02 + 15 3.22359762729192e+00 -1.20943905091677e-02 + 16 3.22320508654863e+00 -1.20928203461945e-02 + 17 3.22225829334495e+00 -1.20890331733798e-02 + 18 3.22082156074746e+00 -1.20832862429898e-02 + 19 3.21898439787187e+00 -1.20759375914875e-02 + 20 3.21685491521323e+00 -1.20674196608529e-02 diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out index 442f83cc6..abfe2c323 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,6 +116,7 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -127,20 +132,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped index 6869425e6..24da413b3 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21397364247543e+00 + x 3.21397364200070e+00 } diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj index 744ca6324..8b5e494a7 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 20 3.21685491539556e+00 -1.20674196615823e-02 - 21 3.21455264092142e+00 -1.20582105636857e-02 - 22 3.21220094123025e+00 -1.20488037649210e-02 - 23 3.20991934305299e+00 -1.20396773722120e-02 - 24 3.20781628584511e+00 -1.20312651433804e-02 - 25 3.20598302316673e+00 -1.20239320926669e-02 - 26 3.20448930640296e+00 -1.20179572256119e-02 - 27 3.20338117914513e+00 -1.20135247165805e-02 - 28 3.20268080963872e+00 -1.20107232385549e-02 - 29 3.20238791174576e+00 -1.20095516469830e-02 - 30 3.20248233501992e+00 -1.20099293400797e-02 - 31 3.20292744751448e+00 -1.20117097900579e-02 - 32 3.20367415744996e+00 -1.20146966297998e-02 - 33 3.20466540029747e+00 -1.20186616011899e-02 - 34 3.20584087625286e+00 -1.20233635050114e-02 - 35 3.20714161882697e+00 -1.20285664753079e-02 - 36 3.20851394967362e+00 -1.20340557986945e-02 - 37 3.20991249848372e+00 -1.20396499939349e-02 - 38 3.21130224478748e+00 -1.20452089791499e-02 - 39 3.21265973116748e+00 -1.20506389246699e-02 - 40 3.21397364247543e+00 -1.20558945699017e-02 +# step one fa_one + 20 3.21685491521323e+00 -1.20674196608529e-02 + 21 3.21455264073267e+00 -1.20582105629307e-02 + 22 3.21220094103318e+00 -1.20488037641327e-02 + 23 3.20991934284523e+00 -1.20396773713809e-02 + 24 3.20781628562398e+00 -1.20312651424959e-02 + 25 3.20598302292944e+00 -1.20239320917178e-02 + 26 3.20448930614687e+00 -1.20179572245875e-02 + 27 3.20338117886792e+00 -1.20135247154717e-02 + 28 3.20268080933861e+00 -1.20107232373544e-02 + 29 3.20238791142161e+00 -1.20095516456865e-02 + 30 3.20248233467135e+00 -1.20099293386854e-02 + 31 3.20292744714189e+00 -1.20117097885676e-02 + 32 3.20367415705454e+00 -1.20146966282182e-02 + 33 3.20466539988114e+00 -1.20186615995246e-02 + 34 3.20584087581816e+00 -1.20233635032726e-02 + 35 3.20714161837695e+00 -1.20285664735078e-02 + 36 3.20851394921166e+00 -1.20340557968466e-02 + 37 3.20991249801338e+00 -1.20396499920535e-02 + 38 3.21130224431234e+00 -1.20452089772494e-02 + 39 3.21265973069097e+00 -1.20506389227639e-02 + 40 3.21397364200070e+00 -1.20558945680028e-02 diff --git a/namd/tests/library/000_distancewalls/namd-version.txt b/namd/tests/library/000_distancewalls/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distancewalls/namd-version.txt +++ b/namd/tests/library/000_distancewalls/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out index 6050e7b8b..77591e0dc 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -89,7 +93,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -117,6 +121,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,15 +132,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distanceXY colvar component (derived from distanceZ): +colvars: - distanceZ colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped index e4b21622a..c8670d81f 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.10714243551413e+00 + x 6.10714243532007e+00 } restraint { diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj index f720fa8df..53d38880d 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 6.28105056411478e+00 -2.47242022564591e-02 - 1 6.27348215345519e+00 -2.46939286138208e-02 - 2 6.26560937402416e+00 -2.46624374960966e-02 - 3 6.25746867772978e+00 -2.46298747109191e-02 - 4 6.24910164339331e+00 -2.45964065735732e-02 - 5 6.24055013199026e+00 -2.45622005279610e-02 - 6 6.23185200440414e+00 -2.45274080176166e-02 - 7 6.22303839597047e+00 -2.44921535838819e-02 - 8 6.21413319113433e+00 -2.44565327645373e-02 - 9 6.20515473557225e+00 -2.44206189422890e-02 - 10 6.19611912784920e+00 -2.43844765113968e-02 - 11 6.18704379226119e+00 -2.43481751690448e-02 - 12 6.17794986560366e+00 -2.43117994624146e-02 - 13 6.16886233380139e+00 -2.42754493352055e-02 - 14 6.15980779747392e+00 -2.42392311898957e-02 - 15 6.15081082225229e+00 -2.42032432890092e-02 - 16 6.14189045993828e+00 -2.41675618397531e-02 - 17 6.13305851999790e+00 -2.41322340799916e-02 - 18 6.12432059012462e+00 -2.40972823604985e-02 - 19 6.11567981090937e+00 -2.40627192436375e-02 - 20 6.10714243551413e+00 -2.40285697420565e-02 + 1 6.27348215345428e+00 -2.46939286138171e-02 + 2 6.26560937402036e+00 -2.46624374960814e-02 + 3 6.25746867772245e+00 -2.46298747108898e-02 + 4 6.24910164328359e+00 -2.45964065731343e-02 + 5 6.24055013191846e+00 -2.45622005276738e-02 + 6 6.23185200432364e+00 -2.45274080172946e-02 + 7 6.22303839583394e+00 -2.44921535833358e-02 + 8 6.21413319108828e+00 -2.44565327643531e-02 + 9 6.20515473551492e+00 -2.44206189420597e-02 + 10 6.19611912777932e+00 -2.43844765111173e-02 + 11 6.18704379217786e+00 -2.43481751687115e-02 + 12 6.17794986550634e+00 -2.43117994620254e-02 + 13 6.16886233368985e+00 -2.42754493347594e-02 + 14 6.15980779734801e+00 -2.42392311893920e-02 + 15 6.15081082211236e+00 -2.42032432884494e-02 + 16 6.14189045972150e+00 -2.41675618388860e-02 + 17 6.13305851983281e+00 -2.41322340793312e-02 + 18 6.12432058994875e+00 -2.40972823597950e-02 + 19 6.11567981072365e+00 -2.40627192428946e-02 + 20 6.10714243532007e+00 -2.40285697412803e-02 diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out index 41e804f09..075f0e20f 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -89,7 +93,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -117,6 +121,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,20 +132,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distanceXY colvar component (derived from distanceZ): +colvars: - distanceZ colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 6.10714 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 7dee8d34e..4c3a90cc1 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.98331278931269e+00 + x 5.98331278916950e+00 } restraint { diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 32bba6125..911bdd5e5 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 6.10714243551413e+00 -2.40285697420565e-02 - 21 6.09872341362206e+00 -2.39948936544883e-02 - 22 6.09045001163983e+00 -2.39618000465593e-02 - 23 6.08236193493661e+00 -2.39294477397464e-02 - 24 6.07450749060677e+00 -2.38980299624271e-02 - 25 6.06693661289397e+00 -2.38677464515759e-02 - 26 6.05969250641318e+00 -2.38387700256527e-02 - 27 6.05280395356655e+00 -2.38112158142662e-02 - 28 6.04628004904281e+00 -2.37851201961713e-02 - 29 6.04010849202162e+00 -2.37604339680865e-02 - 30 6.03425782329929e+00 -2.37370312931972e-02 - 31 6.02868299629071e+00 -2.37147319851628e-02 - 32 6.02333268372630e+00 -2.36933307349052e-02 - 33 6.01815611235053e+00 -2.36726244494021e-02 - 34 6.01310736877805e+00 -2.36524294751122e-02 - 35 6.00814619534536e+00 -2.36325847813815e-02 - 36 6.00323573491681e+00 -2.36129429396672e-02 - 37 5.99833888991827e+00 -2.35933555596731e-02 - 38 5.99341543896732e+00 -2.35736617558693e-02 - 39 5.98842160580047e+00 -2.35536864232019e-02 - 40 5.98331278931269e+00 -2.35332511572508e-02 + 20 6.10714243532007e+00 -2.40285697412803e-02 + 21 6.09872341342112e+00 -2.39948936536845e-02 + 22 6.09045001143359e+00 -2.39618000457344e-02 + 23 6.08236193472670e+00 -2.39294477389068e-02 + 24 6.07450749039471e+00 -2.38980299615788e-02 + 25 6.06693661268103e+00 -2.38677464507241e-02 + 26 6.05969250620041e+00 -2.38387700248016e-02 + 27 6.05280395335489e+00 -2.38112158134196e-02 + 28 6.04628004883300e+00 -2.37851201953320e-02 + 29 6.04010849181403e+00 -2.37604339672561e-02 + 30 6.03425782309445e+00 -2.37370312923778e-02 + 31 6.02868299608911e+00 -2.37147319843564e-02 + 32 6.02333268352863e+00 -2.36933307341145e-02 + 33 6.01815611215759e+00 -2.36726244486304e-02 + 34 6.01310736859049e+00 -2.36524294743619e-02 + 35 6.00814619516367e+00 -2.36325847806547e-02 + 36 6.00323573477869e+00 -2.36129429391148e-02 + 37 5.99833888974827e+00 -2.35933555589931e-02 + 38 5.99341543880525e+00 -2.35736617552210e-02 + 39 5.98842160564732e+00 -2.35536864225893e-02 + 40 5.98331278916950e+00 -2.35332511566780e-02 diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 47628ecd0..2c3cfb574 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -87,25 +91,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -124,7 +128,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -152,6 +156,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -162,15 +167,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distanceZ colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 176efa019..72f369787 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -8.59990198173114e-01 + x -8.59990180563031e-01 } restraint { diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 70fa4a67c..4c2bf9e40 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 -8.26433309912938e-01 3.70573323965175e-03 - 1 -8.30798422653703e-01 3.72319369061481e-03 - 2 -8.34843463959367e-01 3.73937385583747e-03 - 3 -8.38485395966467e-01 3.75394158386587e-03 - 4 -8.41661118716793e-01 3.76664447486717e-03 - 5 -8.44330037532375e-01 3.77732015012950e-03 - 6 -8.46475942328684e-01 3.78590376931474e-03 - 7 -8.48108713604438e-01 3.79243485441775e-03 - 8 -8.49265847455379e-01 3.79706338982152e-03 - 9 -8.50013088506371e-01 3.80005235402549e-03 - 10 -8.50442888427590e-01 3.80177155371036e-03 - 11 -8.50669520082139e-01 3.80267808032856e-03 - 12 -8.50820434143500e-01 3.80328173657400e-03 - 13 -8.51024571667568e-01 3.80409828667027e-03 - 14 -8.51399360397394e-01 3.80559744158957e-03 - 15 -8.52038565660105e-01 3.80815426264042e-03 - 16 -8.53002882142410e-01 3.81201152856964e-03 - 17 -8.54314507410905e-01 3.81725802964362e-03 - 18 -8.55956235278788e-01 3.82382494111515e-03 - 19 -8.57875108259331e-01 3.83150043303732e-03 - 20 -8.59990198173114e-01 3.83996079269246e-03 + 0 -8.26433309912956e-01 3.70573323965182e-03 + 1 -8.30798422481479e-01 3.72319368992592e-03 + 2 -8.34843463278505e-01 3.73937385311402e-03 + 3 -8.38485394485613e-01 3.75394157794245e-03 + 4 -8.41661116098088e-01 3.76664446439235e-03 + 5 -8.44330033670842e-01 3.77732013468337e-03 + 6 -8.46475937017231e-01 3.78590374806892e-03 + 7 -8.48108706693449e-01 3.79243482677379e-03 + 8 -8.49265839004939e-01 3.79706335601975e-03 + 9 -8.50013078434704e-01 3.80005231373882e-03 + 10 -8.50442876788669e-01 3.80177150715468e-03 + 11 -8.50669506981126e-01 3.80267802792450e-03 + 12 -8.50820419731476e-01 3.80328167892590e-03 + 13 -8.51024556129912e-01 3.80409822451965e-03 + 14 -8.51399343953497e-01 3.80559737581399e-03 + 15 -8.52038548534679e-01 3.80815419413872e-03 + 16 -8.53002864518614e-01 3.81201145807446e-03 + 17 -8.54314489576230e-01 3.81725795830492e-03 + 18 -8.55956217377252e-01 3.82382486950901e-03 + 19 -8.57875090444802e-01 3.83150036177921e-03 + 20 -8.59990180563031e-01 3.83996072225212e-03 diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index f5cc9bea4..c538704bb 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -87,25 +91,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -124,7 +128,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -152,6 +156,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -162,20 +167,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distanceZ colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -0.85999 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 45102536d..e14a8519c 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -8.73679344015558e-01 + x -8.73679341988515e-01 } restraint { diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 3deea24fd..196573273 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -8.59990198173114e-01 3.83996079269246e-03 - 21 -8.62203472237901e-01 3.84881388895160e-03 - 22 -8.64411983661211e-01 3.85764793464484e-03 - 23 -8.66519200121738e-01 3.86607680048695e-03 - 24 -8.68443542236674e-01 3.87377416894670e-03 - 25 -8.70123161439966e-01 3.88049264575987e-03 - 26 -8.71517313394698e-01 3.88606925357879e-03 - 27 -8.72605605560332e-01 3.89042242224133e-03 - 28 -8.73386599791250e-01 3.89354639916500e-03 - 29 -8.73876670619764e-01 3.89550668247906e-03 - 30 -8.74108987877203e-01 3.89643595150881e-03 - 31 -8.74131751029475e-01 3.89652700411790e-03 - 32 -8.74004684295612e-01 3.89601873718245e-03 - 33 -8.73793453194366e-01 3.89517381277746e-03 - 34 -8.73562594705087e-01 3.89425037882035e-03 - 35 -8.73368255487214e-01 3.89347302194886e-03 - 36 -8.73251953225498e-01 3.89300781290199e-03 - 37 -8.73236016855329e-01 3.89294406742132e-03 - 38 -8.73320784989416e-01 3.89328313995766e-03 - 39 -8.73483522192930e-01 3.89393408877172e-03 - 40 -8.73679344015558e-01 3.89471737606223e-03 + 20 -8.59990180563031e-01 3.83996072225212e-03 + 21 -8.62203454907955e-01 3.84881381963182e-03 + 22 -8.64411966660376e-01 3.85764786664150e-03 + 23 -8.66519183472681e-01 3.86607673389073e-03 + 24 -8.68443525944736e-01 3.87377410377894e-03 + 25 -8.70123145503911e-01 3.88049258201564e-03 + 26 -8.71517297801704e-01 3.88606919120682e-03 + 27 -8.72605590311192e-01 3.89042236124477e-03 + 28 -8.73386584894720e-01 3.89354633957888e-03 + 29 -8.73876656083864e-01 3.89550662433546e-03 + 30 -8.74108973746083e-01 3.89643589498433e-03 + 31 -8.74131737353112e-01 3.89652694941245e-03 + 32 -8.74004671163881e-01 3.89601868465552e-03 + 33 -8.73793440724393e-01 3.89517376289757e-03 + 34 -8.73562583048199e-01 3.89425033219280e-03 + 35 -8.73368244828915e-01 3.89347297931566e-03 + 36 -8.73251943874718e-01 3.89300777549887e-03 + 37 -8.73236008871937e-01 3.89294403548775e-03 + 38 -8.73320778720346e-01 3.89328311488138e-03 + 39 -8.73483517910175e-01 3.89393407164070e-03 + 40 -8.73679341988515e-01 3.89471736795406e-03 diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out index f979e078c..2e51c81a1 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -89,7 +93,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -117,6 +121,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,15 +132,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distanceZ colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 315e08bfa..743d82299 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.36084906835146e+00 + x -1.36084906819583e+00 } restraint { diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj index 5a45e7f71..04f28cf76 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 -1.30811322832419e+00 5.63245291329675e-03 - 1 -1.31312967389554e+00 5.65251869558218e-03 - 2 -1.31783653970528e+00 5.67134615882111e-03 - 3 -1.32215424606121e+00 5.68861698424484e-03 - 4 -1.32602357044897e+00 5.70409428179589e-03 - 5 -1.32940837601300e+00 5.71763350405199e-03 - 6 -1.33229787222417e+00 5.72919148889668e-03 - 7 -1.33470872956429e+00 5.73883491825714e-03 - 8 -1.33668672330288e+00 5.74674689321152e-03 - 9 -1.33830687028298e+00 5.75322748113191e-03 - 10 -1.33967061046305e+00 5.75868244185221e-03 - 11 -1.34089899820229e+00 5.76359599280915e-03 - 12 -1.34212195007558e+00 5.76848780030233e-03 - 13 -1.34346488796592e+00 5.77385955186369e-03 - 14 -1.34503502478640e+00 5.78014009914560e-03 - 15 -1.34690966835284e+00 5.78763867341137e-03 - 16 -1.34912827135129e+00 5.79651308540518e-03 - 17 -1.35168908903116e+00 5.80675635612465e-03 - 18 -1.35455056718115e+00 5.81820226872460e-03 - 19 -1.35763717574320e+00 5.83054870297280e-03 - 20 -1.36084906835146e+00 5.84339627340585e-03 + 1 -1.31312967389517e+00 5.65251869558068e-03 + 2 -1.31783653970327e+00 5.67134615881307e-03 + 3 -1.32215424605829e+00 5.68861698423318e-03 + 4 -1.32602357036953e+00 5.70409428147812e-03 + 5 -1.32940837597080e+00 5.71763350388318e-03 + 6 -1.33229787218032e+00 5.72919148872128e-03 + 7 -1.33470872947835e+00 5.73883491791339e-03 + 8 -1.33668672329647e+00 5.74674689318588e-03 + 9 -1.33830687027260e+00 5.75322748109041e-03 + 10 -1.33967061044650e+00 5.75868244178601e-03 + 11 -1.34089899817730e+00 5.76359599270922e-03 + 12 -1.34212195003997e+00 5.76848780015989e-03 + 13 -1.34346488791768e+00 5.77385955167074e-03 + 14 -1.34503502472400e+00 5.78014009889602e-03 + 15 -1.34690966827500e+00 5.78763867309998e-03 + 16 -1.34912827121975e+00 5.79651308487899e-03 + 17 -1.35168908892136e+00 5.80675635568542e-03 + 18 -1.35455056705533e+00 5.81820226822131e-03 + 19 -1.35763717560197e+00 5.83054870240789e-03 + 20 -1.36084906819583e+00 5.84339627278333e-03 diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out index 485b39b01..a23ca29bd 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -89,7 +93,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -117,6 +121,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,20 +132,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distanceZ colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -1.36085 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 412aeb991..136c16382 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.39034316080283e+00 + x -1.39034316039439e+00 } restraint { diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj index befbe002b..a4c9b3a4c 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -1.36084906835146e+00 5.84339627340585e-03 - 21 -1.36407445408937e+00 5.85629781635750e-03 - 22 -1.36720290826447e+00 5.86881163305788e-03 - 23 -1.37013738761253e+00 5.88054955045011e-03 - 24 -1.37280289923745e+00 5.89121159694979e-03 - 25 -1.37515071174335e+00 5.90060284697339e-03 - 26 -1.37715842596968e+00 5.90863370387872e-03 - 27 -1.37882731773524e+00 5.91530927094096e-03 - 28 -1.38017874381549e+00 5.92071497526196e-03 - 29 -1.38125089796176e+00 5.92500359184703e-03 - 30 -1.38209611869660e+00 5.92838447478640e-03 - 31 -1.38277799996508e+00 5.93111199986032e-03 - 32 -1.38336718498411e+00 5.93346873993646e-03 - 33 -1.38393522986837e+00 5.93574091947349e-03 - 34 -1.38454693867054e+00 5.93818775468217e-03 - 35 -1.38525254071746e+00 5.94101016286982e-03 - 36 -1.38608129820739e+00 5.94432519282957e-03 - 37 -1.38703765754614e+00 5.94815063018456e-03 - 38 -1.38810029519008e+00 5.95240118076033e-03 - 39 -1.38922386337907e+00 5.95689545351630e-03 - 40 -1.39034316080283e+00 5.96137264321130e-03 + 20 -1.36084906819583e+00 5.84339627278333e-03 + 21 -1.36407445392026e+00 5.85629781568104e-03 + 22 -1.36720290808304e+00 5.86881163233218e-03 + 23 -1.37013738742009e+00 5.88054954968036e-03 + 24 -1.37280289903525e+00 5.89121159614099e-03 + 25 -1.37515071153241e+00 5.90060284612964e-03 + 26 -1.37715842575073e+00 5.90863370300290e-03 + 27 -1.37882731750845e+00 5.91530927003381e-03 + 28 -1.38017874358088e+00 5.92071497432353e-03 + 29 -1.38125089771898e+00 5.92500359087591e-03 + 30 -1.38209611844487e+00 5.92838447377948e-03 + 31 -1.38277799970331e+00 5.93111199881324e-03 + 32 -1.38336718471100e+00 5.93346873884401e-03 + 33 -1.38393522958249e+00 5.93574091832994e-03 + 34 -1.38454693837034e+00 5.93818775348136e-03 + 35 -1.38525254040143e+00 5.94101016160571e-03 + 36 -1.38608129795618e+00 5.94432519182472e-03 + 37 -1.38703765719641e+00 5.94815062878565e-03 + 38 -1.38810029482091e+00 5.95240117928366e-03 + 39 -1.38922386299017e+00 5.95689545196067e-03 + 40 -1.39034316039439e+00 5.96137264157755e-03 diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 6a560e3a5..c0a1e5523 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -87,25 +91,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -118,25 +122,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "ref" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "ref2". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "ref2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -154,7 +158,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -182,6 +186,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -192,16 +197,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distanceZ colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 2e49c4c9e..d5eed6ce9 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.08397176799240e+00 + x -1.08397176151429e+00 } restraint { diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 65f7e07c6..f93b97049 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 -9.80249904624397e-01 4.32099961849759e-03 - 1 -9.84212417045979e-01 4.33684966818392e-03 - 2 -9.88661109800629e-01 4.35464443920252e-03 - 3 -9.93533514516252e-01 4.37413405806501e-03 - 4 -9.98748277164812e-01 4.39499310865925e-03 - 5 -1.00421405344078e+00 4.41685621376314e-03 - 6 -1.00983863188372e+00 4.43935452753490e-03 - 7 -1.01553670554762e+00 4.46214682219049e-03 - 8 -1.02123525515648e+00 4.48494102062594e-03 - 9 -1.02687633794460e+00 4.50750535177839e-03 - 10 -1.03241787380232e+00 4.52967149520928e-03 - 11 -1.03783351318359e+00 4.55133405273438e-03 - 12 -1.04311257148085e+00 4.57245028592339e-03 - 13 -1.04826043942746e+00 4.59304175770984e-03 - 14 -1.05329903554539e+00 4.61319614218156e-03 - 15 -1.05826630725091e+00 4.63306522900363e-03 - 16 -1.06321376214922e+00 4.65285504859689e-03 - 17 -1.06820150020073e+00 4.67280600080292e-03 - 18 -1.07329085842513e+00 4.69316343370051e-03 - 19 -1.07853544110981e+00 4.71414176443922e-03 - 20 -1.08397176799240e+00 4.73588707196959e-03 + 1 -9.84212417024538e-01 4.33684966809815e-03 + 2 -9.88661109713663e-01 4.35464443885465e-03 + 3 -9.93533514317858e-01 4.37413405727143e-03 + 4 -9.98748276916619e-01 4.39499310766648e-03 + 5 -1.00421405294110e+00 4.41685621176441e-03 + 6 -1.00983863113832e+00 4.43935452455326e-03 + 7 -1.01553670456534e+00 4.46214681826137e-03 + 8 -1.02123525373971e+00 4.48494101495885e-03 + 9 -1.02687633616795e+00 4.50750534467179e-03 + 10 -1.03241787163978e+00 4.52967148655913e-03 + 11 -1.03783351061600e+00 4.55133404246400e-03 + 12 -1.04311256849593e+00 4.57245027398371e-03 + 13 -1.04826043601893e+00 4.59304174407571e-03 + 14 -1.05329903171149e+00 4.61319612684598e-03 + 15 -1.05826630299168e+00 4.63306521196671e-03 + 16 -1.06321375752698e+00 4.65285503010794e-03 + 17 -1.06820149508569e+00 4.67280598034278e-03 + 18 -1.07329085286143e+00 4.69316341144574e-03 + 19 -1.07853543510507e+00 4.71414174042029e-03 + 20 -1.08397176151429e+00 4.73588704605716e-03 diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index ba5525f63..061d003d9 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -87,25 +91,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -118,25 +122,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "ref" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "ref2". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "ref2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -154,7 +158,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -182,6 +186,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -192,21 +197,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distanceZ colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -1.08397 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index d4af65402..fe4b2733e 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.16407038814966e+00 + x -1.16407036445456e+00 } restraint { diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 6b3544c2b..e130970be 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -1.08397176799240e+00 4.73588707196959e-03 - 21 -1.08961114576828e+00 4.75844458307313e-03 - 22 -1.09543448832272e+00 4.78173795329088e-03 - 23 -1.10139153184823e+00 4.80556612739293e-03 - 24 -1.10740502975272e+00 4.82962011901087e-03 - 25 -1.11337932964347e+00 4.85351731857390e-03 - 26 -1.11921162447008e+00 4.87684649788032e-03 - 27 -1.12480357468871e+00 4.89921429875483e-03 - 28 -1.13007106417501e+00 4.92028425670005e-03 - 29 -1.13495046407338e+00 4.93980185629353e-03 - 30 -1.13940078663755e+00 4.95760314655019e-03 - 31 -1.14340232558319e+00 4.97360930233275e-03 - 32 -1.14695343921062e+00 4.98781375684249e-03 - 33 -1.15006760088067e+00 5.00027040352269e-03 - 34 -1.15277236622642e+00 5.01108946490570e-03 - 35 -1.15511062701432e+00 5.02044250805728e-03 - 36 -1.15714308092986e+00 5.02857232371945e-03 - 37 -1.15895000141084e+00 5.03580000564338e-03 - 38 -1.16063040046971e+00 5.04252160187884e-03 - 39 -1.16229748017487e+00 5.04918992069947e-03 - 40 -1.16407038814966e+00 5.05628155259863e-03 + 20 -1.08397176151429e+00 4.73588704605716e-03 + 21 -1.08961113878614e+00 4.75844455514457e-03 + 22 -1.09543448080392e+00 4.78173792321566e-03 + 23 -1.10139152374815e+00 4.80556609499262e-03 + 24 -1.10740502102334e+00 4.82962008409337e-03 + 25 -1.11337932023318e+00 4.85351728093272e-03 + 26 -1.11921161432554e+00 4.87684645730215e-03 + 27 -1.12480356375684e+00 4.89921425502736e-03 + 28 -1.13007105240499e+00 4.92028420961995e-03 + 29 -1.13495045141868e+00 4.93980180567474e-03 + 30 -1.13940077305703e+00 4.95760309222813e-03 + 31 -1.14340231104241e+00 4.97360924416963e-03 + 32 -1.14695342368223e+00 4.98781369472891e-03 + 33 -1.15006758434473e+00 5.00027033737893e-03 + 34 -1.15277234867027e+00 5.01108939468107e-03 + 35 -1.15511060843172e+00 5.02044243372689e-03 + 36 -1.15714306128669e+00 5.02857224514677e-03 + 37 -1.15894998077622e+00 5.03579992310487e-03 + 38 -1.16063037878806e+00 5.04252151515225e-03 + 39 -1.16229745749708e+00 5.04918982998831e-03 + 40 -1.16407036445456e+00 5.05628145781825e-03 diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out index d0a584bcb..39a4e5160 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,104 +1,123 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: http://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is available. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. +colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": +colvars: # units = "" [default] colvars: # indexFile = "index.ndx" -colvars: The following index groups were read from the index file "index.ndx": -colvars: Protein (104 atoms). -colvars: Protein_noH (51 atoms). -colvars: Protein_Backbone (40 atoms). -colvars: Protein_C-alpha (10 atoms). -colvars: RMSD_atoms (10 atoms). -colvars: Protein_C-alpha_1_2 (2 atoms). -colvars: Protein_C-alpha_9_10 (2 atoms). -colvars: Protein_C-alpha_1 (1 atoms). -colvars: group1 (4 atoms). -colvars: Protein_C-alpha_2 (1 atoms). -colvars: group2 (4 atoms). -colvars: Protein_C-alpha_3 (1 atoms). -colvars: group3 (4 atoms). -colvars: Protein_C-alpha_4 (1 atoms). -colvars: group4 (4 atoms). -colvars: Protein_C-alpha_5 (1 atoms). -colvars: group5 (4 atoms). -colvars: Protein_C-alpha_6 (1 atoms). -colvars: group6 (4 atoms). -colvars: Protein_C-alpha_7 (1 atoms). -colvars: group7 (4 atoms). -colvars: Protein_C-alpha_8 (1 atoms). -colvars: group8 (4 atoms). -colvars: Protein_C-alpha_9 (1 atoms). -colvars: group9 (4 atoms). -colvars: Protein_C-alpha_10 (1 atoms). -colvars: group10 (4 atoms). -colvars: heavy_atoms (51 atoms). +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) colvars: # smp = on [default] -colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 -colvars: # colvarsTrajAppend = off [default] colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = on [default] +colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" colvars: Initializing a new "eigenvector" component. +colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "atoms" defined, 10 atoms initialized: total mass = 120.11, total charge = 0.53. +colvars: # printAtomIDs = off [default] +colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_refpos2.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( -0.0422 , 0.1463 , 0.0241 ) colvars: # differenceVector = on -colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = v - x0. -colvars: "differenceVector" is on: normalizing the vector. +colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = x_vec - x_ref. +colvars: # normalizeVector = off [default] +colvars: Normalizing the vector so that the norm of the projection |v ⋅ (x_vec - x_ref)| = 1. colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] +colvars: # upperBoundary = 0.5 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] -colvars: # timeStepFactor = 1 [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = on colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } +colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] -colvars: # forceConstant = 0.001 +colvars: # outputFreq = 10 [default] +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] -colvars: # targetForceConstant = 0 [default] colvars: # outputCenters = off [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. +colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] +colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -107,15 +126,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - eigenvector colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group one:0/0. 10 atoms: total mass = 120.11. +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Writing to colvar trajectory file "test.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Writing the state file "test.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Writing the state file "test.tmp.colvars.state". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 76e206e36..394993cd3 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -3.60947829208825e-02 + x -3.60947829036805e-02 } restraint { diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj index 4a835eab3..9598d462c 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 -3.63490056109622e-02 5.45396022443849e-04 - 1 -3.61854039791939e-02 5.44741615916776e-04 - 2 -3.60399977707408e-02 5.44159991082963e-04 - 3 -3.59299659186929e-02 5.43719863674771e-04 - 4 -3.58694335574107e-02 5.43477734229643e-04 - 5 -3.58677544007612e-02 5.43471017603045e-04 - 6 -3.59283042420775e-02 5.43713216968310e-04 - 7 -3.60479478851721e-02 5.44191791540688e-04 - 8 -3.62172258845634e-02 5.44868903538253e-04 - 9 -3.64212097912740e-02 5.45684839165096e-04 - 10 -3.66409048811813e-02 5.46563619524725e-04 - 11 -3.68550253132438e-02 5.47420101252975e-04 - 12 -3.70419376920114e-02 5.48167750768046e-04 - 13 -3.71815653295922e-02 5.48726261318369e-04 - 14 -3.72570812908718e-02 5.49028325163487e-04 - 15 -3.72562760947929e-02 5.49025104379172e-04 - 16 -3.71725450821299e-02 5.48690180328520e-04 - 17 -3.70054820597152e-02 5.48021928238861e-04 - 18 -3.67610840935948e-02 5.47044336374379e-04 - 19 -3.64515682570253e-02 5.45806273028101e-04 - 20 -3.60947829208825e-02 5.44379131683530e-04 + 0 -3.63490056109624e-02 5.45396022443850e-04 + 1 -3.61854039791530e-02 5.44741615916612e-04 + 2 -3.60399977705685e-02 5.44159991082274e-04 + 3 -3.59299659182762e-02 5.43719863673105e-04 + 4 -3.58694335566139e-02 5.43477734226456e-04 + 5 -3.58677543994292e-02 5.43471017597717e-04 + 6 -3.59283042400466e-02 5.43713216960186e-04 + 7 -3.60479478822797e-02 5.44191791529119e-04 + 8 -3.62172258806581e-02 5.44868903522632e-04 + 9 -3.64212097862254e-02 5.45684839144902e-04 + 10 -3.66409048748858e-02 5.46563619499543e-04 + 11 -3.68550253056277e-02 5.47420101222511e-04 + 12 -3.70419376830354e-02 5.48167750732142e-04 + 13 -3.71815653192522e-02 5.48726261277009e-04 + 14 -3.72570812792000e-02 5.49028325116800e-04 + 15 -3.72562760818578e-02 5.49025104327431e-04 + 16 -3.71725450680349e-02 5.48690180272139e-04 + 17 -3.70054820445949e-02 5.48021928178380e-04 + 18 -3.67610840776074e-02 5.47044336310430e-04 + 19 -3.64515682403436e-02 5.45806272961374e-04 + 20 -3.60947829036805e-02 5.44379131614722e-04 diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out index 2ea9819fd..dbec86827 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,104 +1,123 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: http://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is available. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. +colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": +colvars: # units = "" [default] colvars: # indexFile = "index.ndx" -colvars: The following index groups were read from the index file "index.ndx": -colvars: Protein (104 atoms). -colvars: Protein_noH (51 atoms). -colvars: Protein_Backbone (40 atoms). -colvars: Protein_C-alpha (10 atoms). -colvars: RMSD_atoms (10 atoms). -colvars: Protein_C-alpha_1_2 (2 atoms). -colvars: Protein_C-alpha_9_10 (2 atoms). -colvars: Protein_C-alpha_1 (1 atoms). -colvars: group1 (4 atoms). -colvars: Protein_C-alpha_2 (1 atoms). -colvars: group2 (4 atoms). -colvars: Protein_C-alpha_3 (1 atoms). -colvars: group3 (4 atoms). -colvars: Protein_C-alpha_4 (1 atoms). -colvars: group4 (4 atoms). -colvars: Protein_C-alpha_5 (1 atoms). -colvars: group5 (4 atoms). -colvars: Protein_C-alpha_6 (1 atoms). -colvars: group6 (4 atoms). -colvars: Protein_C-alpha_7 (1 atoms). -colvars: group7 (4 atoms). -colvars: Protein_C-alpha_8 (1 atoms). -colvars: group8 (4 atoms). -colvars: Protein_C-alpha_9 (1 atoms). -colvars: group9 (4 atoms). -colvars: Protein_C-alpha_10 (1 atoms). -colvars: group10 (4 atoms). -colvars: heavy_atoms (51 atoms). +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) colvars: # smp = on [default] -colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 -colvars: # colvarsTrajAppend = off [default] colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = on [default] +colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" colvars: Initializing a new "eigenvector" component. +colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "atoms" defined, 10 atoms initialized: total mass = 120.11, total charge = 0.53. +colvars: # printAtomIDs = off [default] +colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_refpos2.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( -0.0422 , 0.1463 , 0.0241 ) colvars: # differenceVector = on -colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = v - x0. -colvars: "differenceVector" is on: normalizing the vector. +colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = x_vec - x_ref. +colvars: # normalizeVector = off [default] +colvars: Normalizing the vector so that the norm of the projection |v ⋅ (x_vec - x_ref)| = 1. colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] +colvars: # upperBoundary = 0.5 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] -colvars: # timeStepFactor = 1 [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = on colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } +colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] -colvars: # forceConstant = 0.001 +colvars: # outputFreq = 10 [default] +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] -colvars: # targetForceConstant = 0 [default] colvars: # outputCenters = off [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. +colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] +colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -107,20 +126,37 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - eigenvector colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -0.0360948 -colvars: Restarting restraint bias "harmonic1". +colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group one:0/0. 10 atoms: total mass = 120.11. +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Writing to colvar trajectory file "test.restart.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Writing the state file "test.restart.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Writing the state file "test.restart.tmp.colvars.state". +colvars: Saving collective variables state to "test.restart.tmp.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "test.restart.tmp.colvars.state". colvars: Saving collective variables state to "test.restart.colvars.state". diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 1fe5f317a..4076dc85b 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -3.91331067913926e-02 + x -3.91331067677280e-02 } restraint { diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 4abf779ac..4d83b139d 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -3.60947829208825e-02 5.44379131683530e-04 - 21 -3.57131824308181e-02 5.42852729723272e-04 - 22 -3.53323468338979e-02 5.41329387335592e-04 - 23 -3.49790898890280e-02 5.39916359556112e-04 - 24 -3.46792961060943e-02 5.38717184424377e-04 - 25 -3.44557302134239e-02 5.37822920853696e-04 - 26 -3.43261260365440e-02 5.37304504146176e-04 - 27 -3.43018371828071e-02 5.37207348731229e-04 - 28 -3.43872193204467e-02 5.37548877281787e-04 - 29 -3.45797526720018e-02 5.38319010688007e-04 - 30 -3.48707654295545e-02 5.39483061718218e-04 - 31 -3.52465332702127e-02 5.40986133080851e-04 - 32 -3.56895209481391e-02 5.42758083792556e-04 - 33 -3.61795835230441e-02 5.44718334092176e-04 - 34 -3.66950291055903e-02 5.46780116422361e-04 - 35 -3.72135323361536e-02 5.48854129344615e-04 - 36 -3.77129610513006e-02 5.50851844205202e-04 - 37 -3.81722113307229e-02 5.52688845322892e-04 - 38 -3.85721257652529e-02 5.54288503061011e-04 - 39 -3.88965020851454e-02 5.55586008340582e-04 - 40 -3.91331067913926e-02 5.56532427165571e-04 + 20 -3.60947829036805e-02 5.44379131614722e-04 + 21 -3.57131824132596e-02 5.42852729653038e-04 + 22 -3.53323468161238e-02 5.41329387264495e-04 + 23 -3.49790898711468e-02 5.39916359484587e-04 + 24 -3.46792960881774e-02 5.38717184352710e-04 + 25 -3.44557301955042e-02 5.37822920782017e-04 + 26 -3.43261260186189e-02 5.37304504074476e-04 + 27 -3.43018371648415e-02 5.37207348659366e-04 + 28 -3.43872193023786e-02 5.37548877209514e-04 + 29 -3.45797526537476e-02 5.38319010614990e-04 + 30 -3.48707654110141e-02 5.39483061644056e-04 + 31 -3.52465332512768e-02 5.40986133005107e-04 + 32 -3.56895209286986e-02 5.42758083714794e-04 + 33 -3.61795835030006e-02 5.44718334012002e-04 + 34 -3.66950290848698e-02 5.46780116339479e-04 + 35 -3.72135323147184e-02 5.48854129258874e-04 + 36 -3.77129610291621e-02 5.50851844116648e-04 + 37 -3.81722113079504e-02 5.52688845231802e-04 + 38 -3.85721257419771e-02 5.54288502967908e-04 + 39 -3.88965020615558e-02 5.55586008246223e-04 + 40 -3.91331067677280e-02 5.56532427070912e-04 diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt index fc4f9e327..157cac038 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. -colvars: Using NAMD interface, version 2016-11-23. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out index 4e6b96f89..49596f239 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out @@ -7,7 +7,6 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -116,6 +115,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -140,10 +140,12 @@ colvars: colvars: - NAMD engine: colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped index b33e34fce..496bf49f0 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.24500295670889e-01 + x 4.24500295778074e-01 } restraint { diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj index 7342a9653..70125860e 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 3.02535061282783e-01 -8.10140245131131e-04 - 1 3.02349470333696e-01 -8.09397881334783e-04 - 2 3.02228609120613e-01 -8.08914436482450e-04 - 3 3.02455495418290e-01 -8.09821981673159e-04 - 4 3.03339070526050e-01 -8.13356282104201e-04 - 5 3.05186413715613e-01 -8.20745654862452e-04 - 6 3.08272259770955e-01 -8.33089039083821e-04 - 7 3.12808407683237e-01 -8.51233630732947e-04 - 8 3.18915879042108e-01 -8.75663516168431e-04 - 9 3.26602899373167e-01 -9.06411597492667e-04 - 10 3.35751830571806e-01 -9.43007322287224e-04 - 11 3.46117928865759e-01 -9.84471715463035e-04 - 12 3.57341831542918e-01 -1.02936732617167e-03 - 13 3.68975854268464e-01 -1.07590341707386e-03 - 14 3.80521732650089e-01 -1.12208693060036e-03 - 15 3.91475201665008e-01 -1.16590080666003e-03 - 16 4.01371580224434e-01 -1.20548632089774e-03 - 17 4.09826708672045e-01 -1.23930683468818e-03 - 18 4.16568901921835e-01 -1.26627560768734e-03 - 19 4.21459383017533e-01 -1.28583753207013e-03 - 20 4.24500295670889e-01 -1.29800118268356e-03 + 0 3.02535061282782e-01 -8.10140245131129e-04 + 1 3.02349470333834e-01 -8.09397881335335e-04 + 2 3.02228609121183e-01 -8.08914436484731e-04 + 3 3.02455495419550e-01 -8.09821981678201e-04 + 4 3.03339070528187e-01 -8.13356282112746e-04 + 5 3.05186413718739e-01 -8.20745654874956e-04 + 6 3.08272259775151e-01 -8.33089039100606e-04 + 7 3.12808407688626e-01 -8.51233630754504e-04 + 8 3.18915879048982e-01 -8.75663516195929e-04 + 9 3.26602899382103e-01 -9.06411597528411e-04 + 10 3.35751830583773e-01 -9.43007322335093e-04 + 11 3.46117928882162e-01 -9.84471715528649e-04 + 12 3.57341831565545e-01 -1.02936732626218e-03 + 13 3.68975854299315e-01 -1.07590341719726e-03 + 14 3.80521732691115e-01 -1.12208693076446e-03 + 15 3.91475201717795e-01 -1.16590080687118e-03 + 16 4.01371580289910e-01 -1.20548632115964e-03 + 17 4.09826708750263e-01 -1.23930683500105e-03 + 18 4.16568902011881e-01 -1.26627560804752e-03 + 19 4.21459383117517e-01 -1.28583753247007e-03 + 20 4.24500295778074e-01 -1.29800118311230e-03 diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out index db684e80d..61612ef51 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -7,7 +7,6 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -116,6 +115,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -140,6 +140,7 @@ colvars: colvars: - NAMD engine: colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.4245 @@ -149,6 +150,7 @@ colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index d9441d73e..f4f671fdc 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.37434841805229e-01 + x 4.37434841876234e-01 } restraint { diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 6dd2653f7..2f8530fb3 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 4.24500295670889e-01 -1.29800118268356e-03 - 21 4.25830516013726e-01 -1.30332206405490e-03 - 22 4.25710168880892e-01 -1.30284067552357e-03 - 23 4.24495296829610e-01 -1.29798118731844e-03 - 24 4.22604814515337e-01 -1.29041925806135e-03 - 25 4.20482665079664e-01 -1.28193066031866e-03 - 26 4.18558612398180e-01 -1.27423444959272e-03 - 27 4.17211123833643e-01 -1.26884449533457e-03 - 28 4.16735269426941e-01 -1.26694107770777e-03 - 29 4.17317729237757e-01 -1.26927091695103e-03 - 30 4.19020232671458e-01 -1.27608093068583e-03 - 31 4.21772286281203e-01 -1.28708914512481e-03 - 32 4.25373865465361e-01 -1.30149546186144e-03 - 33 4.29508654241388e-01 -1.31803461696555e-03 - 34 4.33768111249166e-01 -1.33507244499666e-03 - 35 4.37685869093343e-01 -1.35074347637337e-03 - 36 4.40780679733648e-01 -1.36312271893459e-03 - 37 4.42604459067608e-01 -1.37041783627043e-03 - 38 4.42790500277900e-01 -1.37116200111160e-03 - 39 4.41096173869207e-01 -1.36438469547683e-03 - 40 4.37434841805229e-01 -1.34973936722092e-03 + 20 4.24500295778074e-01 -1.29800118311230e-03 + 21 4.25830516124699e-01 -1.30332206449880e-03 + 22 4.25710168991809e-01 -1.30284067596723e-03 + 23 4.24495296936454e-01 -1.29798118774582e-03 + 24 4.22604814614221e-01 -1.29041925845688e-03 + 25 4.20482665167116e-01 -1.28193066066846e-03 + 26 4.18558612471422e-01 -1.27423444988569e-03 + 27 4.17211123890820e-01 -1.26884449556328e-03 + 28 4.16735269467297e-01 -1.26694107786919e-03 + 29 4.17317729261698e-01 -1.26927091704679e-03 + 30 4.19020232680582e-01 -1.27608093072233e-03 + 31 4.21772286278215e-01 -1.28708914511286e-03 + 32 4.25373865453946e-01 -1.30149546181578e-03 + 33 4.29508654225993e-01 -1.31803461690397e-03 + 34 4.33768111234715e-01 -1.33507244493886e-03 + 35 4.37685869084879e-01 -1.35074347633952e-03 + 36 4.40780679735902e-01 -1.36312271894361e-03 + 37 4.42604459084554e-01 -1.37041783633822e-03 + 38 4.42790500312300e-01 -1.37116200124920e-03 + 39 4.41096173922242e-01 -1.36438469568897e-03 + 40 4.37434841876234e-01 -1.34973936750494e-03 diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt index 017b69b3a..157cac038 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2022-04-14. -colvars: Using NAMD interface, version "2022-04-06". +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out index 99840490b..479a448a6 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,19 +74,20 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_random.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( 2.23122 , -1.11745 , -1.91143 ) colvars: # differenceVector = off [default] colvars: Centering the provided vector to zero. -colvars: The norm of the vector is |v| = 0.00180118. +colvars: # normalizeVector = off [default] +colvars: The norm of the vector is |v| = 23.5625. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -110,6 +115,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -120,14 +126,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - eigenvector colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 81e913df1..98d60150c 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.96593083012934e+00 + x 9.96593083265021e+00 } restraint { diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj index 57c3f5382..4010095ee 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 7.12848384426398e+00 -2.81139353770559e-02 - 1 7.12389036856418e+00 -2.80955614742567e-02 - 2 7.12039004726484e+00 -2.80815601890594e-02 - 3 7.12467766711354e+00 -2.80987106684541e-02 - 4 7.14407407726102e+00 -2.81762963090441e-02 - 5 7.18586833879461e+00 -2.83434733551784e-02 - 6 7.25659559553746e+00 -2.86263823821498e-02 - 7 7.36131202489437e+00 -2.90452480995775e-02 - 8 7.50293456608652e+00 -2.96117382643461e-02 - 9 7.68171812012824e+00 -3.03268724805129e-02 - 10 7.89494414888129e+00 -3.11797765955252e-02 - 11 8.13688859798339e+00 -3.21475543919336e-02 - 12 8.39911418317517e+00 -3.31964567327007e-02 - 13 8.67108915452401e+00 -3.42843566180960e-02 - 14 8.94107690127196e+00 -3.53643076050878e-02 - 15 9.19718784273722e+00 -3.63887513709489e-02 - 16 9.42845596982786e+00 -3.73138238793115e-02 - 17 9.62580650703617e+00 -3.81032260281447e-02 - 18 9.78281209617585e+00 -3.87312483847034e-02 - 19 9.89617742502377e+00 -3.91847097000951e-02 - 20 9.96593083012934e+00 -3.94637233205174e-02 + 0 7.12848384426395e+00 -2.81139353770558e-02 + 1 7.12389036856740e+00 -2.80955614742696e-02 + 2 7.12039004727828e+00 -2.80815601891131e-02 + 3 7.12467766714325e+00 -2.80987106685730e-02 + 4 7.14407407731135e+00 -2.81762963092454e-02 + 5 7.18586833886829e+00 -2.83434733554732e-02 + 6 7.25659559563629e+00 -2.86263823825451e-02 + 7 7.36131202502140e+00 -2.90452481000856e-02 + 8 7.50293456624851e+00 -2.96117382649940e-02 + 9 7.68171812033882e+00 -3.03268724813553e-02 + 10 7.89494414916322e+00 -3.11797765966529e-02 + 11 8.13688859836978e+00 -3.21475543934791e-02 + 12 8.39911418370808e+00 -3.31964567348323e-02 + 13 8.67108915525047e+00 -3.42843566210019e-02 + 14 8.94107690223794e+00 -3.53643076089518e-02 + 15 9.19718784397990e+00 -3.63887513759196e-02 + 16 9.42845597136909e+00 -3.73138238854764e-02 + 17 9.62580650887713e+00 -3.81032260355085e-02 + 18 9.78281209829472e+00 -3.87312483931789e-02 + 19 9.89617742737599e+00 -3.91847097095039e-02 + 20 9.96593083265021e+00 -3.94637233306008e-02 diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out index f758c6696..ea096f39d 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,19 +74,20 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_random.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( 2.23122 , -1.11745 , -1.91143 ) colvars: # differenceVector = off [default] colvars: Centering the provided vector to zero. -colvars: The norm of the vector is |v| = 0.00180118. +colvars: # normalizeVector = off [default] +colvars: The norm of the vector is |v| = 23.5625. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -110,6 +115,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -120,19 +126,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - eigenvector colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 9.96593 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 5b5148d25..d228f8399 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.02340499653749e+01 + x 1.02340499670145e+01 } restraint { diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj index eb7bf1ecb..977dc1547 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.96593083012934e+00 -3.94637233205174e-02 - 21 9.99532793060757e+00 -3.95813117224303e-02 - 22 9.99048850012704e+00 -3.95619540005082e-02 - 23 9.95980058552870e+00 -3.94392023421148e-02 - 24 9.91314195129389e+00 -3.92525678051756e-02 - 25 9.86098750530072e+00 -3.90439500212029e-02 - 26 9.81348370336466e+00 -3.88539348134586e-02 - 27 9.77957160942564e+00 -3.87182864377026e-02 - 28 9.76622794832969e+00 -3.86649117933188e-02 - 29 9.77787383900133e+00 -3.87114953560053e-02 - 30 9.81598266564158e+00 -3.88639306625663e-02 - 31 9.87890737166341e+00 -3.91156294866536e-02 - 32 9.96194305284228e+00 -3.94477722113691e-02 - 33 1.00576385226328e+01 -3.98305540905312e-02 - 34 1.01563633556180e+01 -4.02254534224719e-02 - 35 1.02471188264620e+01 -4.05884753058479e-02 - 36 1.03185507061678e+01 -4.08742028246714e-02 - 37 1.03600827313353e+01 -4.10403309253412e-02 - 38 1.03630544975746e+01 -4.10522179902983e-02 - 39 1.03217296667927e+01 -4.08869186671706e-02 - 40 1.02340499653749e+01 -4.05361998614995e-02 + 20 9.96593083265021e+00 -3.94637233306008e-02 + 21 9.99532793321660e+00 -3.95813117328664e-02 + 22 9.99048850273347e+00 -3.95619540109339e-02 + 23 9.95980058803785e+00 -3.94392023521514e-02 + 24 9.91314195361405e+00 -3.92525678144562e-02 + 25 9.86098750735006e+00 -3.90439500294002e-02 + 26 9.81348370507768e+00 -3.88539348203107e-02 + 27 9.77957161075872e+00 -3.87182864430349e-02 + 28 9.76622794926487e+00 -3.86649117970595e-02 + 29 9.77787383954832e+00 -3.87114953581933e-02 + 30 9.81598266583797e+00 -3.88639306633519e-02 + 31 9.87890737157304e+00 -3.91156294862921e-02 + 32 9.96194305255191e+00 -3.94477722102076e-02 + 33 1.00576385222471e+01 -3.98305540889885e-02 + 34 1.01563633552530e+01 -4.02254534210120e-02 + 35 1.02471188262364e+01 -4.05884753049457e-02 + 36 1.03185507061932e+01 -4.08742028247726e-02 + 37 1.03600827317051e+01 -4.10403309268204e-02 + 38 1.03630544983541e+01 -4.10522179934165e-02 + 39 1.03217296680099e+01 -4.08869186720396e-02 + 40 1.02340499670145e+01 -4.05361998680579e-02 diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt b/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt index fc4f9e327..157cac038 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. -colvars: Using NAMD interface, version 2016-11-23. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out index cabed47f2..ac4d45dde 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "eulerTheta" @@ -55,8 +59,9 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -69,15 +74,15 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -100,8 +105,9 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -113,15 +119,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -144,8 +150,9 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -157,15 +164,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -191,6 +198,7 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPsi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -207,6 +215,7 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPhi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -223,6 +232,7 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerTheta" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -234,17 +244,30 @@ colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - eulerPhi colvar component (derived from orientation): +colvars: - eulerPsi colvar component (derived from orientation): +colvars: - eulerTheta colvar component (derived from orientation): +colvars: Fu2017 https://doi.org/10.1021/acs.jctc.7b00791 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped index 9fed64568..9750dbd1a 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name eulerTheta - x 7.42926968363034e-01 + x 7.42926968363036e-01 } colvar { @@ -15,7 +15,7 @@ colvar { colvar { name eulerPsi - x -4.93710444441010e+00 + x -4.93710444441009e+00 } restraint { diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj index d0984ff5d..1109293ce 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step eulerTheta fa_eulerTheta eulerPhi fa_eulerPhi eulerPsi fa_eulerPsi E_harmonic1 E_harmonic2 E_harmonic3 - 0 1.12335897633009e+00 -1.12335897633009e-01 -9.19929987926340e+00 9.19929987926340e-01 -5.23950348243898e+00 5.23950348243898e-01 1.37261983712451e+00 4.23135591343078e+00 6.30967694850690e-02 - 1 1.10359290098423e+00 -1.10359290098423e-01 -9.22565834570168e+00 9.22565834570168e-01 -5.25149538780149e+00 5.25149538780149e-01 1.37891019040502e+00 4.25563859558075e+00 6.08958645551397e-02 - 2 1.08440461653865e+00 -1.08440461653865e-01 -9.25678498979173e+00 9.25678498979173e-01 -5.25779637281105e+00 5.25779637281106e-01 1.38222113489725e+00 4.28440341736168e+00 5.87966686185170e-02 - 3 1.06529304335568e+00 -1.06529304335568e-01 -9.29208424764168e+00 9.29208424764168e-01 -5.25763403749821e+00 5.25763403749821e-01 1.38213578361299e+00 4.31714148326353e+00 5.67424634110999e-02 - 4 1.04571544240957e+00 -1.04571544240957e-01 -9.33104631969663e+00 9.33104631969663e-01 -5.25046695843814e+00 5.25046695843814e-01 1.37837016408253e+00 4.35342127101620e+00 5.46760393246926e-02 + 0 1.12335897633008e+00 -1.12335897633008e-01 -9.19929987926339e+00 9.19929987926340e-01 -5.23950348243898e+00 5.23950348243898e-01 1.37261983712451e+00 4.23135591343078e+00 6.30967694850688e-02 + 1 1.10359290098423e+00 -1.10359290098423e-01 -9.22565834570168e+00 9.22565834570168e-01 -5.25149538780149e+00 5.25149538780149e-01 1.37891019040501e+00 4.25563859558075e+00 6.08958645551400e-02 + 2 1.08440461653865e+00 -1.08440461653865e-01 -9.25678498979173e+00 9.25678498979173e-01 -5.25779637281106e+00 5.25779637281106e-01 1.38222113489726e+00 4.28440341736168e+00 5.87966686185170e-02 + 3 1.06529304335568e+00 -1.06529304335568e-01 -9.29208424764168e+00 9.29208424764168e-01 -5.25763403749821e+00 5.25763403749821e-01 1.38213578361299e+00 4.31714148326353e+00 5.67424634111001e-02 + 4 1.04571544240957e+00 -1.04571544240957e-01 -9.33104631969662e+00 9.33104631969662e-01 -5.25046695843815e+00 5.25046695843815e-01 1.37837016408254e+00 4.35342127101619e+00 5.46760393246926e-02 5 1.02517685434404e+00 -1.02517685434404e-01 -9.37327661318995e+00 9.37327661318995e-01 -5.23607026451037e+00 5.23607026451037e-01 1.37082159074448e+00 4.39291572336868e+00 5.25493791341371e-02 6 1.00330582597764e+00 -1.00330582597764e-01 -9.41848339102013e+00 9.41848339102013e-01 -5.21460973558002e+00 5.21460973558002e-01 1.35960773472030e+00 4.43539146934610e+00 5.03311290220341e-02 - 7 9.79907540363569e-01 -9.79907540363569e-02 -9.46643852313838e+00 9.46643852313838e-01 -5.18668671653799e+00 5.18668671653799e-01 1.34508595477558e+00 4.48067291561792e+00 4.80109393830689e-02 - 8 9.54992420449583e-01 -9.54992420449583e-02 -9.51692832794413e+00 9.51692832794413e-01 -5.15334195139500e+00 5.15334195139500e-01 1.32784666340038e+00 4.52859623996127e+00 4.56005261558077e-02 - 9 9.28783692054884e-01 -9.28783692054884e-02 -9.56970831738819e+00 9.56970831738819e-01 -5.11601429466744e+00 5.11601429466744e-01 1.30868011316208e+00 4.57896586399444e+00 4.31319573313551e-02 - 10 9.01709043906520e-01 -9.01709043906520e-02 -9.62447028619222e+00 9.62447028619222e-01 -5.07645787560575e+00 5.07645787560575e-01 1.28852122813998e+00 4.63152141448985e+00 4.06539599931406e-02 - 11 8.74379467191583e-01 -8.74379467191583e-02 -9.68082504780323e+00 9.68082504780323e-01 -5.03662790099944e+00 5.03662790099944e-01 1.26838103065630e+00 4.68591868030872e+00 3.82269726323119e-02 + 7 9.79907540363570e-01 -9.79907540363570e-02 -9.46643852313838e+00 9.46643852313838e-01 -5.18668671653799e+00 5.18668671653799e-01 1.34508595477558e+00 4.48067291561792e+00 4.80109393830691e-02 + 8 9.54992420449578e-01 -9.54992420449578e-02 -9.51692832794413e+00 9.51692832794413e-01 -5.15334195139500e+00 5.15334195139500e-01 1.32784666340038e+00 4.52859623996127e+00 4.56005261558072e-02 + 9 9.28783692054886e-01 -9.28783692054886e-02 -9.56970831738818e+00 9.56970831738818e-01 -5.11601429466745e+00 5.11601429466745e-01 1.30868011316208e+00 4.57896586399443e+00 4.31319573313553e-02 + 10 9.01709043906521e-01 -9.01709043906521e-02 -9.62447028619222e+00 9.62447028619222e-01 -5.07645787560575e+00 5.07645787560575e-01 1.28852122813998e+00 4.63152141448985e+00 4.06539599931406e-02 + 11 8.74379467191584e-01 -8.74379467191584e-02 -9.68082504780323e+00 9.68082504780323e-01 -5.03662790099944e+00 5.03662790099944e-01 1.26838103065630e+00 4.68591868030872e+00 3.82269726323119e-02 12 8.47554676237916e-01 -8.47554676237916e-02 -9.73829978053727e+00 9.73829978053727e-01 -4.99855008771719e+00 4.99855008771719e-01 1.24927514897088e+00 4.74172413078062e+00 3.59174464606379e-02 - 13 8.22093180764618e-01 -8.22093180764618e-02 -9.79634420282249e+00 9.79634420282249e-01 -4.96419034641283e+00 4.96419034641283e-01 1.23215928977092e+00 4.79841798700869e+00 3.37918598929844e-02 + 13 8.22093180764617e-01 -8.22093180764617e-02 -9.79634420282249e+00 9.79634420282249e-01 -4.96419034641283e+00 4.96419034641283e-01 1.23215928977092e+00 4.79841798700869e+00 3.37918598929842e-02 14 7.98887326318826e-01 -7.98887326318826e-02 -9.85433604587600e+00 9.85433604587600e-01 -4.93533870265480e+00 4.93533870265480e-01 1.21787840549612e+00 4.85539694525255e+00 3.19110480076421e-02 - 15 7.78788129749855e-01 -7.78788129749855e-02 -9.91157703203216e+00 9.91157703203216e-01 -4.91351570715390e+00 4.91351570715390e-01 1.20713183022241e+00 4.91196796309537e+00 3.03255475519638e-02 - 16 7.62528356252240e-01 -7.62528356252240e-02 -9.96727776858340e+00 9.96727776858340e-01 -4.89990324848287e+00 4.89990324848287e-01 1.20045259222465e+00 4.96733130580484e+00 2.90724747044372e-02 - 17 7.50652833132860e-01 -7.50652833132860e-02 -1.00205407738012e+01 1.00205407738012e+00 -4.89529691190416e+00 4.89529691190416e-01 1.19819659278492e+00 5.02056186997061e+00 2.81739837945194e-02 + 15 7.78788129749853e-01 -7.78788129749853e-02 -9.91157703203216e+00 9.91157703203216e-01 -4.91351570715390e+00 4.91351570715390e-01 1.20713183022241e+00 4.91196796309537e+00 3.03255475519637e-02 + 16 7.62528356252244e-01 -7.62528356252244e-02 -9.96727776858339e+00 9.96727776858339e-01 -4.89990324848287e+00 4.89990324848287e-01 1.20045259222465e+00 4.96733130580484e+00 2.90724747044375e-02 + 17 7.50652833132862e-01 -7.50652833132862e-02 -1.00205407738012e+01 1.00205407738012e+00 -4.89529691190416e+00 4.89529691190416e-01 1.19819659278492e+00 5.02056186997061e+00 2.81739837945196e-02 18 7.43463015261251e-01 -7.43463015261251e-02 -1.00703584090617e+01 1.00703584090617e+00 -4.90007484689111e+00 4.90007484689111e-01 1.20053667525675e+00 5.07060592434798e+00 2.76368627530676e-02 - 19 7.40979904753968e-01 -7.40979904753968e-02 -1.01156425246949e+01 1.01156425246949e+00 -4.91417861741104e+00 4.91417861741104e-01 1.20745757419099e+00 5.11631118437075e+00 2.74525609624599e-02 - 20 7.42926968363034e-01 -7.42926968363034e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441010e+00 4.93710444441010e-01 1.21875001475070e+00 5.15650108652104e+00 2.75970240160544e-02 + 19 7.40979904753968e-01 -7.40979904753968e-02 -1.01156425246949e+01 1.01156425246949e+00 -4.91417861741104e+00 4.91417861741104e-01 1.20745757419099e+00 5.11631118437074e+00 2.74525609624600e-02 + 20 7.42926968363036e-01 -7.42926968363036e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441009e+00 4.93710444441009e-01 1.21875001475069e+00 5.15650108652104e+00 2.75970240160545e-02 diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out index 17479fe12..7ec5027d5 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "eulerTheta" @@ -55,8 +59,9 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -69,15 +74,15 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -100,8 +105,9 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -113,15 +119,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -144,8 +150,9 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -157,15 +164,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -191,6 +198,7 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPsi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -207,6 +215,7 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPhi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -223,6 +232,7 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerTheta" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -234,9 +244,25 @@ colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - eulerPhi colvar component (derived from orientation): +colvars: - eulerPsi colvar component (derived from orientation): +colvars: - eulerTheta colvar component (derived from orientation): +colvars: Fu2017 https://doi.org/10.1021/acs.jctc.7b00791 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "eulerTheta" from value: 0.742927 @@ -246,14 +272,11 @@ colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: Restarting harmonic bias "harmonic2" from step number 20. colvars: Restarting harmonic bias "harmonic3" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped index 0abbdad76..2c39b1548 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name eulerTheta - x 4.92888911241022e-01 + x 4.92888911241030e-01 } colvar { @@ -15,7 +15,7 @@ colvar { colvar { name eulerPsi - x -5.16556439137704e+00 + x -5.16556439137703e+00 } restraint { diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj index b66de304b..3f2d8e1ad 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step eulerTheta fa_eulerTheta eulerPhi fa_eulerPhi eulerPsi fa_eulerPsi E_harmonic1 E_harmonic2 E_harmonic3 - 20 7.42926968363034e-01 -7.42926968363034e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441010e+00 4.93710444441010e-01 1.21875001475070e+00 5.15650108652104e+00 2.75970240160544e-02 - 21 7.48733320101764e-01 -7.48733320101764e-02 -1.01883183460673e+01 1.01883183460673e+00 -4.96790750263877e+00 4.96790750263877e-01 1.23400524773873e+00 5.19009153604059e+00 2.80300792315305e-02 - 22 7.57557122198820e-01 -7.57557122198820e-02 -1.02139454102856e+01 1.02139454102856e+00 -5.00522572559092e+00 5.00522572559092e-01 1.25261422820586e+00 5.21623404221472e+00 2.86946396697079e-02 - 23 7.68329051637896e-01 -7.68329051637896e-02 -1.02317713436666e+01 1.02317713436666e+00 -5.04733083960333e+00 5.04733083960333e-01 1.27377743022054e+00 5.23445724145384e+00 2.95164765795395e-02 - 24 7.79814875676108e-01 -7.79814875676108e-02 -1.02418490445600e+01 1.02418490445600e+00 -5.09221216535160e+00 5.09221216535160e-01 1.29653123684774e+00 5.24477359257777e+00 3.04055620162872e-02 - 25 7.90694011146758e-01 -7.90694011146758e-02 -1.02447281510328e+01 1.02447281510328e+00 -5.13769297452897e+00 5.13769297452897e-01 1.31979445502622e+00 5.24772274442817e+00 3.12598509631674e-02 - 26 7.99647836011618e-01 -7.99647836011618e-02 -1.02414229458545e+01 1.02414229458545e+00 -5.18157169207901e+00 5.18157169207901e-01 1.34243426000773e+00 5.24433719779373e+00 3.19718330819032e-02 - 27 8.05448995815154e-01 -8.05448995815154e-02 -1.02333134884667e+01 1.02333134884667e+00 -5.22177344695617e+00 5.22177344695617e-01 1.36334589656682e+00 5.23603524766172e+00 3.24374042429820e-02 - 28 8.07042333855100e-01 -8.07042333855101e-02 -1.02219996119655e+01 1.02219996119655e+00 -5.25649361343075e+00 5.25649361343075e-01 1.38153625540191e+00 5.22446380335109e+00 3.25658664317144e-02 - 29 8.03610000016902e-01 -8.03610000016902e-02 -1.02091368712812e+01 1.02091368712812e+00 -5.28431542925356e+00 5.28431542925356e-01 1.39619947779236e+00 5.21132378282767e+00 3.22894516063583e-02 - 30 7.94616975119385e-01 -7.94616975119385e-02 -1.01962849681356e+01 1.01962849681356e+00 -5.30428814909504e+00 5.30428814909504e-01 1.40677363843151e+00 5.19821135757144e+00 3.15708068573941e-02 - 31 7.79837159581490e-01 -7.79837159581490e-02 -1.01847936556627e+01 1.01847936556627e+00 -5.31595928178051e+00 5.31595928178051e-01 1.41297115427742e+00 5.18650109042140e+00 3.04072997732063e-02 - 32 7.59362971789398e-01 -7.59362971789398e-02 -1.01757407630825e+01 1.01757407630825e+00 -5.31936241154539e+00 5.31936241154539e-01 1.41478082326810e+00 5.17728500387295e+00 2.88316061462413e-02 - 33 7.33602066496012e-01 -7.33602066496012e-02 -1.01699237742566e+01 1.01699237742566e+00 -5.31496943853745e+00 5.31496943853745e-01 1.41244500662935e+00 5.17136747870945e+00 2.69085995983609e-02 - 34 7.03263342872243e-01 -7.03263342872243e-02 -1.01678925721792e+01 1.01678925721792e+00 -5.30362109991434e+00 5.30362109991434e-01 1.40641983857283e+00 5.16930196796882e+00 2.47289664713921e-02 - 35 6.69331542581688e-01 -6.69331542581688e-02 -1.01700001127700e+01 1.01700001127700e+00 -5.28645108127908e+00 5.28645108127908e-01 1.39732825173784e+00 5.17144511468705e+00 2.24002356947391e-02 - 36 6.33027051643073e-01 -6.33027051643073e-02 -1.01764433502072e+01 1.01764433502072e+00 -5.26481622337318e+00 5.26481622337318e-01 1.38591449329467e+00 5.17799996299882e+00 2.00361624055961e-02 - 37 5.95746809302784e-01 -5.95746809302784e-02 -1.01872719611055e+01 1.01872719611055e+00 -5.24023891452942e+00 5.24023891452942e-01 1.37300519406743e+00 5.18902550047632e+00 1.77457130397224e-02 - 38 5.58984709726027e-01 -5.58984709726027e-02 -1.02023564051939e+01 1.02023564051939e+00 -5.21435969588688e+00 5.21435969588688e-01 1.35947735190448e+00 5.20440381093004e+00 1.56231952853745e-02 - 39 5.24235101803488e-01 -5.24235101803488e-02 -1.02213251856666e+01 1.02213251856666e+00 -5.18889149341550e+00 5.18889149341550e-01 1.34622974652199e+00 5.22377442755711e+00 1.37411220981457e-02 - 40 4.92888911241022e-01 -4.92888911241022e-02 -1.02434969074251e+01 1.02434969074251e+00 -5.16556439137704e+00 5.16556439137704e-01 1.33415277407312e+00 5.24646144462136e+00 1.21469739412180e-02 + 20 7.42926968363036e-01 -7.42926968363036e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441009e+00 4.93710444441009e-01 1.21875001475069e+00 5.15650108652104e+00 2.75970240160545e-02 + 21 7.48733320101761e-01 -7.48733320101761e-02 -1.01883183460673e+01 1.01883183460673e+00 -4.96790750263877e+00 4.96790750263877e-01 1.23400524773873e+00 5.19009153604058e+00 2.80300792315303e-02 + 22 7.57557122198821e-01 -7.57557122198821e-02 -1.02139454102856e+01 1.02139454102856e+00 -5.00522572559092e+00 5.00522572559092e-01 1.25261422820586e+00 5.21623404221472e+00 2.86946396697080e-02 + 23 7.68329051637894e-01 -7.68329051637894e-02 -1.02317713436666e+01 1.02317713436666e+00 -5.04733083960333e+00 5.04733083960333e-01 1.27377743022054e+00 5.23445724145382e+00 2.95164765795393e-02 + 24 7.79814875676107e-01 -7.79814875676107e-02 -1.02418490445600e+01 1.02418490445600e+00 -5.09221216535160e+00 5.09221216535160e-01 1.29653123684774e+00 5.24477359257776e+00 3.04055620162871e-02 + 25 7.90694011146757e-01 -7.90694011146757e-02 -1.02447281510328e+01 1.02447281510328e+00 -5.13769297452897e+00 5.13769297452897e-01 1.31979445502622e+00 5.24772274442816e+00 3.12598509631674e-02 + 26 7.99647836011620e-01 -7.99647836011620e-02 -1.02414229458545e+01 1.02414229458545e+00 -5.18157169207901e+00 5.18157169207901e-01 1.34243426000773e+00 5.24433719779371e+00 3.19718330819034e-02 + 27 8.05448995815155e-01 -8.05448995815155e-02 -1.02333134884667e+01 1.02333134884667e+00 -5.22177344695617e+00 5.22177344695617e-01 1.36334589656683e+00 5.23603524766171e+00 3.24374042429820e-02 + 28 8.07042333855102e-01 -8.07042333855102e-02 -1.02219996119654e+01 1.02219996119654e+00 -5.25649361343075e+00 5.25649361343075e-01 1.38153625540191e+00 5.22446380335108e+00 3.25658664317145e-02 + 29 8.03610000016903e-01 -8.03610000016903e-02 -1.02091368712812e+01 1.02091368712812e+00 -5.28431542925356e+00 5.28431542925356e-01 1.39619947779236e+00 5.21132378282767e+00 3.22894516063584e-02 + 30 7.94616975119391e-01 -7.94616975119391e-02 -1.01962849681356e+01 1.01962849681356e+00 -5.30428814909504e+00 5.30428814909504e-01 1.40677363843150e+00 5.19821135757143e+00 3.15708068573945e-02 + 31 7.79837159581488e-01 -7.79837159581488e-02 -1.01847936556627e+01 1.01847936556627e+00 -5.31595928178051e+00 5.31595928178051e-01 1.41297115427742e+00 5.18650109042138e+00 3.04072997732061e-02 + 32 7.59362971789403e-01 -7.59362971789403e-02 -1.01757407630825e+01 1.01757407630825e+00 -5.31936241154539e+00 5.31936241154539e-01 1.41478082326810e+00 5.17728500387294e+00 2.88316061462417e-02 + 33 7.33602066496011e-01 -7.33602066496011e-02 -1.01699237742566e+01 1.01699237742566e+00 -5.31496943853745e+00 5.31496943853745e-01 1.41244500662936e+00 5.17136747870943e+00 2.69085995983609e-02 + 34 7.03263342872247e-01 -7.03263342872247e-02 -1.01678925721792e+01 1.01678925721792e+00 -5.30362109991434e+00 5.30362109991434e-01 1.40641983857283e+00 5.16930196796881e+00 2.47289664713924e-02 + 35 6.69331542581692e-01 -6.69331542581692e-02 -1.01700001127699e+01 1.01700001127699e+00 -5.28645108127907e+00 5.28645108127907e-01 1.39732825173783e+00 5.17144511468704e+00 2.24002356947393e-02 + 36 6.33027051643078e-01 -6.33027051643078e-02 -1.01764433502072e+01 1.01764433502072e+00 -5.26481622337318e+00 5.26481622337318e-01 1.38591449329467e+00 5.17799996299881e+00 2.00361624055964e-02 + 37 5.95746809302786e-01 -5.95746809302786e-02 -1.01872719611055e+01 1.01872719611055e+00 -5.24023891452942e+00 5.24023891452942e-01 1.37300519406742e+00 5.18902550047631e+00 1.77457130397225e-02 + 38 5.58984709726032e-01 -5.58984709726032e-02 -1.02023564051939e+01 1.02023564051939e+00 -5.21435969588687e+00 5.21435969588687e-01 1.35947735190447e+00 5.20440381093002e+00 1.56231952853748e-02 + 39 5.24235101803498e-01 -5.24235101803498e-02 -1.02213251856666e+01 1.02213251856666e+00 -5.18889149341549e+00 5.18889149341549e-01 1.34622974652198e+00 5.22377442755710e+00 1.37411220981462e-02 + 40 4.92888911241030e-01 -4.92888911241030e-02 -1.02434969074251e+01 1.02434969074251e+00 -5.16556439137703e+00 5.16556439137703e-01 1.33415277407312e+00 5.24646144462135e+00 1.21469739412184e-02 diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt index 3226d7191..157cac038 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-11-09". -colvars: Using NAMD interface, version "2020-10-26". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out index 92061cd24..346415abf 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -118,6 +122,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,15 +133,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - groupCoord colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped index bb2a2b55a..f285fde00 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.19072319783456e-06 + x 3.19072319981190e-06 } restraint { diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj index 194c5d94f..3bfd80daf 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.17405979638661e-06 3.99987303760814e-04 - 1 3.18134448325853e-06 3.99987274622067e-04 - 2 3.18580682147849e-06 3.99987256772714e-04 - 3 3.18739100894646e-06 3.99987250435964e-04 - 4 3.18623907575867e-06 3.99987255043697e-04 - 5 3.18267103050743e-06 3.99987269315878e-04 - 6 3.17715514839544e-06 3.99987291379406e-04 - 7 3.17027321023885e-06 3.99987318907159e-04 - 8 3.16268340695069e-06 3.99987349266372e-04 - 9 3.15508117666781e-06 3.99987379675293e-04 - 10 3.14815708769336e-06 3.99987407371649e-04 - 11 3.14255208070990e-06 3.99987429791677e-04 - 12 3.13881288773027e-06 3.99987444748449e-04 - 13 3.13735264362211e-06 3.99987450589426e-04 - 14 3.13842207775938e-06 3.99987446311689e-04 - 15 3.14209485884323e-06 3.99987431620565e-04 - 16 3.14826794436374e-06 3.99987406928223e-04 - 17 3.15667507858251e-06 3.99987373299686e-04 - 18 3.16691009065201e-06 3.99987332359637e-04 - 19 3.17845677143355e-06 3.99987286172914e-04 - 20 3.19072319783456e-06 3.99987237107209e-04 + 1 3.18134448326459e-06 3.99987274622067e-04 + 2 3.18580682150308e-06 3.99987256772714e-04 + 3 3.18739100900219e-06 3.99987250435964e-04 + 4 3.18623907585806e-06 3.99987255043697e-04 + 5 3.18267103066260e-06 3.99987269315877e-04 + 6 3.17715514861791e-06 3.99987291379406e-04 + 7 3.17027321053934e-06 3.99987318907158e-04 + 8 3.16268340733906e-06 3.99987349266371e-04 + 9 3.15508117715307e-06 3.99987379675291e-04 + 10 3.14815708828368e-06 3.99987407371647e-04 + 11 3.14255208141271e-06 3.99987429791674e-04 + 12 3.13881288855239e-06 3.99987444748446e-04 + 13 3.13735264456987e-06 3.99987450589422e-04 + 14 3.13842207883868e-06 3.99987446311685e-04 + 15 3.14209486005973e-06 3.99987431620560e-04 + 16 3.14826794572284e-06 3.99987406928217e-04 + 17 3.15667508008936e-06 3.99987373299680e-04 + 18 3.16691009231148e-06 3.99987332359631e-04 + 19 3.17845677325003e-06 3.99987286172907e-04 + 20 3.19072319981190e-06 3.99987237107201e-04 diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out index d73e8c3c6..da182042c 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -118,6 +122,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,20 +133,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - groupCoord colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.19072e-06 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 2617a40e7..6e6309f87 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.18473697725417e-06 + x 3.18473698183816e-06 } restraint { diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj index e995df08f..d3a79e359 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.19072319783456e-06 3.99987237107209e-04 - 21 3.20307949922131e-06 3.99987187682003e-04 - 22 3.21489837978856e-06 3.99987140406481e-04 - 23 3.22559674927215e-06 3.99987097613003e-04 - 24 3.23467512783040e-06 3.99987061299489e-04 - 25 3.24175014727985e-06 3.99987032999411e-04 - 26 3.24657591182937e-06 3.99987013696353e-04 - 27 3.24905199791042e-06 3.99987003792008e-04 - 28 3.24921865580300e-06 3.99987003125377e-04 - 29 3.24724234180586e-06 3.99987011030633e-04 - 30 3.24339473001463e-06 3.99987026421080e-04 - 31 3.23802801085701e-06 3.99987047887957e-04 - 32 3.23154776239895e-06 3.99987073808950e-04 - 33 3.22438445838087e-06 3.99987102462166e-04 - 34 3.21696474844672e-06 3.99987132141006e-04 - 35 3.20968466708086e-06 3.99987161261332e-04 - 36 3.20288713141188e-06 3.99987188451474e-04 - 37 3.19684522486685e-06 3.99987212619101e-04 - 38 3.19175120648019e-06 3.99987232995174e-04 - 39 3.18771014833031e-06 3.99987249159407e-04 - 40 3.18473697725417e-06 3.99987261052091e-04 + 20 3.19072319981190e-06 3.99987237107201e-04 + 21 3.20307950136251e-06 3.99987187681995e-04 + 22 3.21489838209560e-06 3.99987140406472e-04 + 23 3.22559675174575e-06 3.99987097612993e-04 + 24 3.23467513046995e-06 3.99987061299478e-04 + 25 3.24175015008330e-06 3.99987032999400e-04 + 26 3.24657591479334e-06 3.99987013696341e-04 + 27 3.24905200103034e-06 3.99987003791996e-04 + 28 3.24921865907333e-06 3.99987003125364e-04 + 29 3.24724234522045e-06 3.99987011030619e-04 + 30 3.24339473356695e-06 3.99987026421066e-04 + 31 3.23802801454050e-06 3.99987047887942e-04 + 32 3.23154776620721e-06 3.99987073808935e-04 + 33 3.22438446230774e-06 3.99987102462151e-04 + 34 3.21696475248629e-06 3.99987132140990e-04 + 35 3.20968467122739e-06 3.99987161261315e-04 + 36 3.20288713565953e-06 3.99987188451457e-04 + 37 3.19684522920946e-06 3.99987212619083e-04 + 38 3.19175121091107e-06 3.99987232995156e-04 + 39 3.18771015284195e-06 3.99987249159389e-04 + 40 3.18473698183816e-06 3.99987261052073e-04 diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt index 9e5d53306..157cac038 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-12-21. -colvars: Using NAMD interface, version 2018-12-20. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out index 92061cd24..346415abf 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -118,6 +122,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,15 +133,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - groupCoord colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 79a79deb8..a61c41a68 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 7.87058667403396e-01 + x 7.87058667467717e-01 } restraint { diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj index 9c2fb8adc..5a74dc300 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 7.90587472610727e-01 -2.76234989044291e-03 - 1 7.90951498267062e-01 -2.76380599306825e-03 - 2 7.91115918557351e-01 -2.76446367422940e-03 - 3 7.91076626155406e-01 -2.76430650462163e-03 - 4 7.90841020774526e-01 -2.76336408309811e-03 - 5 7.90427382727841e-01 -2.76170953091136e-03 - 6 7.89863736332951e-01 -2.75945494533180e-03 - 7 7.89186342099336e-01 -2.75674536839735e-03 - 8 7.88437860255107e-01 -2.75375144102043e-03 - 9 7.87665135250171e-01 -2.75066054100068e-03 - 10 7.86916534919116e-01 -2.74766613967646e-03 - 11 7.86238889926666e-01 -2.74495555970666e-03 - 12 7.85674262852968e-01 -2.74269705141187e-03 - 13 7.85256932782819e-01 -2.74102773113128e-03 - 14 7.85011021455946e-01 -2.74004408582379e-03 - 15 7.84949075501872e-01 -2.73979630200749e-03 - 16 7.85071723363813e-01 -2.74028689345525e-03 - 17 7.85368315131961e-01 -2.74147326052785e-03 - 18 7.85818317014519e-01 -2.74327326805808e-03 - 19 7.86393206458784e-01 -2.74557282583514e-03 - 20 7.87058667403396e-01 -2.74823466961359e-03 + 1 7.90951498267255e-01 -2.76380599306902e-03 + 2 7.91115918558132e-01 -2.76446367423253e-03 + 3 7.91076626157176e-01 -2.76430650462870e-03 + 4 7.90841020777686e-01 -2.76336408311074e-03 + 5 7.90427382732787e-01 -2.76170953093115e-03 + 6 7.89863736340070e-01 -2.75945494536028e-03 + 7 7.89186342108997e-01 -2.75674536843599e-03 + 8 7.88437860267658e-01 -2.75375144107063e-03 + 9 7.87665135265936e-01 -2.75066054106374e-03 + 10 7.86916534938388e-01 -2.74766613975355e-03 + 11 7.86238889949708e-01 -2.74495555979883e-03 + 12 7.85674262880010e-01 -2.74269705152004e-03 + 13 7.85256932814059e-01 -2.74102773125624e-03 + 14 7.85011021491553e-01 -2.74004408596621e-03 + 15 7.84949075541991e-01 -2.73979630216797e-03 + 16 7.85071723408572e-01 -2.74028689363429e-03 + 17 7.85368315181469e-01 -2.74147326072588e-03 + 18 7.85818317068877e-01 -2.74327326827551e-03 + 19 7.86393206518082e-01 -2.74557282607233e-03 + 20 7.87058667467717e-01 -2.74823466987087e-03 diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out index 0cd0f727b..1fe205c90 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -118,6 +122,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,20 +133,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - groupCoord colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.787059 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 5187120c9..e43a36e68 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 7.87942474735044e-01 + x 7.87942474885153e-01 } restraint { diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 93a7f33a7..ec60b338f 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 7.87058667403396e-01 -2.74823466961359e-03 - 21 7.87776958908072e-01 -2.75110783563229e-03 - 22 7.88509370009168e-01 -2.75403748003667e-03 - 23 7.89218651378568e-01 -2.75687460551427e-03 - 24 7.89871253667991e-01 -2.75948501467196e-03 - 25 7.90439158345860e-01 -2.76175663338344e-03 - 26 7.90901124405813e-01 -2.76360449762325e-03 - 27 7.91243274223110e-01 -2.76497309689244e-03 - 28 7.91459063543128e-01 -2.76583625417251e-03 - 29 7.91548789307309e-01 -2.76619515722924e-03 - 30 7.91518769812477e-01 -2.76607507924991e-03 - 31 7.91380310101543e-01 -2.76552124040617e-03 - 32 7.91148491170643e-01 -2.76459396468257e-03 - 33 7.90840824982783e-01 -2.76336329993113e-03 - 34 7.90475830187182e-01 -2.76190332074873e-03 - 35 7.90071649196610e-01 -2.76028659678644e-03 - 36 7.89644839776708e-01 -2.75857935910683e-03 - 37 7.89209440521591e-01 -2.75683776208636e-03 - 38 7.88776327186739e-01 -2.75510530874696e-03 - 39 7.88352818361151e-01 -2.75341127344460e-03 - 40 7.87942474735044e-01 -2.75176989894018e-03 + 20 7.87058667467717e-01 -2.74823466987087e-03 + 21 7.87776958977482e-01 -2.75110783590993e-03 + 22 7.88509370083721e-01 -2.75403748033489e-03 + 23 7.89218651458299e-01 -2.75687460583319e-03 + 24 7.89871253752910e-01 -2.75948501501164e-03 + 25 7.90439158435954e-01 -2.76175663374382e-03 + 26 7.90901124501041e-01 -2.76360449800416e-03 + 27 7.91243274323407e-01 -2.76497309729363e-03 + 28 7.91459063648406e-01 -2.76583625459362e-03 + 29 7.91548789417463e-01 -2.76619515766985e-03 + 30 7.91518769927385e-01 -2.76607507970954e-03 + 31 7.91380310221072e-01 -2.76552124088429e-03 + 32 7.91148491294645e-01 -2.76459396517858e-03 + 33 7.90840825111090e-01 -2.76336330044436e-03 + 34 7.90475830319600e-01 -2.76190332127840e-03 + 35 7.90071649332906e-01 -2.76028659733162e-03 + 36 7.89644839916602e-01 -2.75857935966641e-03 + 37 7.89209440664736e-01 -2.75683776265894e-03 + 38 7.88776327332720e-01 -2.75510530933088e-03 + 39 7.88352818509478e-01 -2.75341127403791e-03 + 40 7.87942474885153e-01 -2.75176989954061e-03 diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt b/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt index 9e5d53306..157cac038 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-12-21. -colvars: Using NAMD interface, version 2018-12-20. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out index 722ed98b3..74de50e14 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -98,6 +102,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -108,14 +113,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - gyration colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 390d537cf..36d404925 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.00485448897596e+00 + x 5.00485448890467e+00 } restraint { diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj index cbea421ce..023e68dee 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 5.03768855197214e+00 -1.97507542078886e-02 - 1 5.03744876419419e+00 -1.97497950567768e-02 - 2 5.03694642879595e+00 -1.97477857151838e-02 - 3 5.03620505705716e+00 -1.97448202282286e-02 - 4 5.03525398207157e+00 -1.97410159282863e-02 - 5 5.03412335568541e+00 -1.97364934227416e-02 - 6 5.03284080257023e+00 -1.97313632102809e-02 - 7 5.03142972215521e+00 -1.97257188886209e-02 - 8 5.02990878553720e+00 -1.97196351421488e-02 - 9 5.02829203785433e+00 -1.97131681514173e-02 - 10 5.02658916663561e+00 -1.97063566665424e-02 - 11 5.02480574441698e+00 -1.96992229776679e-02 - 12 5.02294349120610e+00 -1.96917739648244e-02 - 13 5.02100072380662e+00 -1.96840028952265e-02 - 14 5.01897316908046e+00 -1.96758926763219e-02 - 15 5.01685523480251e+00 -1.96674209392100e-02 - 16 5.01464172191010e+00 -1.96585668876404e-02 - 17 5.01232984706209e+00 -1.96493193882483e-02 - 18 5.00992134545152e+00 -1.96396853818061e-02 - 19 5.00742432922767e+00 -1.96296973169107e-02 - 20 5.00485448897596e+00 -1.96194179559038e-02 + 0 5.03768855197227e+00 -1.97507542078891e-02 + 1 5.03744876419417e+00 -1.97497950567767e-02 + 2 5.03694642879576e+00 -1.97477857151830e-02 + 3 5.03620505705731e+00 -1.97448202282292e-02 + 4 5.03525398207188e+00 -1.97410159282875e-02 + 5 5.03412335571070e+00 -1.97364934228428e-02 + 6 5.03284080256979e+00 -1.97313632102792e-02 + 7 5.03142972215272e+00 -1.97257188886109e-02 + 8 5.02990878553163e+00 -1.97196351421265e-02 + 9 5.02829203784451e+00 -1.97131681513781e-02 + 10 5.02658916662064e+00 -1.97063566664825e-02 + 11 5.02480574439595e+00 -1.96992229775838e-02 + 12 5.02294349117820e+00 -1.96917739647128e-02 + 13 5.02100072378728e+00 -1.96840028951491e-02 + 14 5.01897316903736e+00 -1.96758926761494e-02 + 15 5.01685523476086e+00 -1.96674209390434e-02 + 16 5.01464172185107e+00 -1.96585668874043e-02 + 17 5.01232984699556e+00 -1.96493193879822e-02 + 18 5.00992134539975e+00 -1.96396853815990e-02 + 19 5.00742432915842e+00 -1.96296973166337e-02 + 20 5.00485448890467e+00 -1.96194179556187e-02 diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out index c40533751..42156fb61 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -98,6 +102,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -108,19 +113,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - gyration colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 5.00485 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 9d22ab655..ab515bb61 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.96897275199397e+00 + x 4.96897275206382e+00 } restraint { diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 12760b2af..a61b26a78 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.00485448897596e+00 -1.96194179559038e-02 - 21 5.00223519413610e+00 -1.96089407765444e-02 - 22 4.99959613497035e+00 -1.95983845398814e-02 - 23 4.99697045876934e+00 -1.95878818350774e-02 - 24 4.99439079640308e+00 -1.95775631856123e-02 - 25 4.99188501584048e+00 -1.95675400633619e-02 - 26 4.98947279563574e+00 -1.95578911825430e-02 - 27 4.98716399834319e+00 -1.95486559933728e-02 - 28 4.98495936493070e+00 -1.95398374597228e-02 - 29 4.98285340663966e+00 -1.95314136265587e-02 - 30 4.98083878784580e+00 -1.95233551513832e-02 - 31 4.97891115935444e+00 -1.95156446374178e-02 - 32 4.97707338941302e+00 -1.95082935576521e-02 - 33 4.97533838441641e+00 -1.95013535376657e-02 - 34 4.97373007474449e+00 -1.94949202989780e-02 - 35 4.97228253698659e+00 -1.94891301479464e-02 - 36 4.97103753049164e+00 -1.94841501219666e-02 - 37 4.97004091939466e+00 -1.94801636775786e-02 - 38 4.96933848303369e+00 -1.94773539321348e-02 - 39 4.96897154880133e+00 -1.94758861952053e-02 - 40 4.96897275199397e+00 -1.94758910079759e-02 + 20 5.00485448890467e+00 -1.96194179556187e-02 + 21 5.00223519406431e+00 -1.96089407762573e-02 + 22 4.99959613490376e+00 -1.95983845396151e-02 + 23 4.99697045871106e+00 -1.95878818348442e-02 + 24 4.99439079635605e+00 -1.95775631854242e-02 + 25 4.99188501582648e+00 -1.95675400633059e-02 + 26 4.98947279561833e+00 -1.95578911824733e-02 + 27 4.98716399834632e+00 -1.95486559933853e-02 + 28 4.98495936495158e+00 -1.95398374598063e-02 + 29 4.98285340667393e+00 -1.95314136266957e-02 + 30 4.98083878791299e+00 -1.95233551516520e-02 + 31 4.97891115941913e+00 -1.95156446376765e-02 + 32 4.97707338948989e+00 -1.95082935579595e-02 + 33 4.97533838450258e+00 -1.95013535380103e-02 + 34 4.97373007483673e+00 -1.94949202993469e-02 + 35 4.97228253708149e+00 -1.94891301483260e-02 + 36 4.97103753059614e+00 -1.94841501223846e-02 + 37 4.97004091948501e+00 -1.94801636779400e-02 + 38 4.96933848311783e+00 -1.94773539324713e-02 + 39 4.96897154887735e+00 -1.94758861955094e-02 + 40 4.96897275206382e+00 -1.94758910082553e-02 diff --git a/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt b/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out index 2331c1a41..62fe7a40c 100644 --- a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -90,6 +94,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -100,14 +105,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - hBond colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out index 07423f3dd..293e9d354 100644 --- a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -90,6 +94,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -100,19 +105,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - hBond colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.999923 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt b/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt index 9e5d53306..157cac038 100644 --- a/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-12-21. -colvars: Using NAMD interface, version 2018-12-20. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out index 1c304f72b..9b7934c0b 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -98,6 +102,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -108,14 +113,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - gyration colvar component: +colvars: - inertia colvar component (derived from gyration): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped index d529f420f..b526c1a3b 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.47943794577146e+02 + x 2.47943794570369e+02 } restraint { diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj index 9c2662344..54b38db6c 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 2.53783059466712e+02 -1.01473223786685e+00 + 0 2.53783059466725e+02 -1.01473223786690e+00 1 2.53741340236853e+02 -1.01456536094741e+00 - 2 2.53638721286758e+02 -1.01415488514703e+00 - 3 2.53479585453019e+02 -1.01351834181208e+00 - 4 2.53270136271656e+02 -1.01268054508662e+00 - 5 2.53017700001829e+02 -1.01167080000732e+00 - 6 2.52730128240095e+02 -1.01052051296038e+00 - 7 2.52415319839252e+02 -1.00926127935701e+00 - 8 2.52080840138888e+02 -1.00792336055555e+00 - 9 2.51733604629136e+02 -1.00653441851654e+00 - 10 2.51379609096128e+02 -1.00511843638451e+00 - 11 2.51023709840432e+02 -1.00369483936173e+00 - 12 2.50669473383116e+02 -1.00227789353246e+00 - 13 2.50319117866126e+02 -1.00087647146451e+00 - 14 2.49973559962786e+02 -9.99494239851145e-01 - 15 2.49632568526903e+02 -9.98130274107611e-01 - 16 2.49295013002611e+02 -9.96780052010444e-01 - 17 2.48959183660263e+02 -9.95436734641053e-01 - 18 2.48623152213820e+02 -9.94092608855281e-01 - 19 2.48285132616888e+02 -9.92740530467554e-01 - 20 2.47943794577146e+02 -9.91375178308586e-01 + 2 2.53638721286741e+02 -1.01415488514697e+00 + 3 2.53479585453035e+02 -1.01351834181214e+00 + 4 2.53270136271682e+02 -1.01268054508673e+00 + 5 2.53017700005431e+02 -1.01167080002172e+00 + 6 2.52730128240016e+02 -1.01052051296007e+00 + 7 2.52415319838942e+02 -1.00926127935577e+00 + 8 2.52080840138270e+02 -1.00792336055308e+00 + 9 2.51733604628119e+02 -1.00653441851248e+00 + 10 2.51379609094601e+02 -1.00511843637841e+00 + 11 2.51023709838303e+02 -1.00369483935321e+00 + 12 2.50669473380297e+02 -1.00227789352119e+00 + 13 2.50319117864268e+02 -1.00087647145707e+00 + 14 2.49973559958431e+02 -9.99494239833723e-01 + 15 2.49632568521358e+02 -9.98130274085430e-01 + 16 2.49295012996826e+02 -9.96780051987302e-01 + 17 2.48959183654063e+02 -9.95436734616253e-01 + 18 2.48623152206619e+02 -9.94092608826476e-01 + 19 2.48285132610319e+02 -9.92740530441276e-01 + 20 2.47943794570369e+02 -9.91375178281476e-01 diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out index 33f101cd0..c94891992 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -98,6 +102,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -108,19 +113,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - gyration colvar component: +colvars: - inertia colvar component (derived from gyration): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 247.944 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 1d4d73e13..9096628e7 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.41656580632151e+02 + x 2.41656580638813e+02 } restraint { diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 72dbacfd9..270b72c1a 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.47943794577146e+02 -9.91375178308586e-01 - 21 2.47598477046097e+02 -9.89993908184388e-01 - 22 2.47249255874236e+02 -9.88597023496945e-01 - 23 2.46896846075395e+02 -9.87187384301580e-01 - 24 2.46542363784743e+02 -9.85769455138973e-01 - 25 2.46187019172168e+02 -9.84348076688674e-01 - 26 2.45831840554944e+02 -9.82927362219775e-01 - 27 2.45477524529089e+02 -9.81510098116355e-01 - 28 2.45124466797313e+02 -9.80097867189253e-01 - 29 2.44772967363848e+02 -9.78691869455392e-01 - 30 2.44423548274181e+02 -9.77294193096724e-01 - 31 2.44077290776696e+02 -9.75909163106782e-01 - 32 2.43736099721675e+02 -9.74544398886700e-01 - 33 2.43402829965980e+02 -9.73211319863919e-01 - 34 2.43081248673642e+02 -9.71924994694569e-01 - 35 2.42775844774184e+02 -9.70703379096737e-01 - 36 2.42491523384140e+02 -9.69566093536562e-01 - 37 2.42233234214778e+02 -9.68532936859112e-01 - 38 2.42005579213859e+02 -9.67622316855437e-01 - 39 2.41812431250163e+02 -9.66849725000653e-01 - 40 2.41656580632151e+02 -9.66226322528602e-01 + 20 2.47943794570369e+02 -9.91375178281476e-01 + 21 2.47598477040393e+02 -9.89993908161571e-01 + 22 2.47249255867815e+02 -9.88597023471262e-01 + 23 2.46896846069752e+02 -9.87187384279007e-01 + 24 2.46542363780136e+02 -9.85769455120543e-01 + 25 2.46187019170014e+02 -9.84348076680055e-01 + 26 2.45831840553059e+02 -9.82927362212236e-01 + 27 2.45477524529067e+02 -9.81510098116269e-01 + 28 2.45124466798686e+02 -9.80097867194745e-01 + 29 2.44772967366842e+02 -9.78691869467368e-01 + 30 2.44423548281158e+02 -9.77294193124631e-01 + 31 2.44077290782282e+02 -9.75909163129130e-01 + 32 2.43736099728340e+02 -9.74544398913360e-01 + 33 2.43402829973457e+02 -9.73211319893828e-01 + 34 2.43081248681633e+02 -9.71924994726533e-01 + 35 2.42775844782379e+02 -9.70703379129517e-01 + 36 2.42491523393473e+02 -9.69566093573892e-01 + 37 2.42233234222450e+02 -9.68532936889801e-01 + 38 2.42005579220911e+02 -9.67622316883644e-01 + 39 2.41812431256466e+02 -9.66849725025865e-01 + 40 2.41656580638813e+02 -9.66226322555252e-01 diff --git a/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt b/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out index bb024e575..71d0dcbba 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,7 +76,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -100,6 +104,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -110,14 +115,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - gyration colvar component: +colvars: - inertia colvar component (derived from gyration): +colvars: - inertiaZ colvar component (derived from inertia): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 3f0ca8ee3..179a7851f 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.75096079010709e+01 + x 2.75096078961602e+01 } restraint { diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj index 208c352c5..bdcc58815 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 2.74164641878528e+01 -1.09265856751411e-01 - 1 2.74002934369697e+01 -1.09201173747879e-01 - 2 2.73891905423028e+01 -1.09156762169211e-01 - 3 2.73840806711159e+01 -1.09136322684464e-01 - 4 2.73853106963141e+01 -1.09141242785257e-01 - 5 2.73926707769495e+01 -1.09170683107798e-01 - 6 2.74054700020936e+01 -1.09221880008374e-01 - 7 2.74226468649512e+01 -1.09290587459805e-01 - 8 2.74428938162688e+01 -1.09371575265075e-01 - 9 2.74647792832602e+01 -1.09459117133041e-01 - 10 2.74868564357227e+01 -1.09547425742891e-01 - 11 2.75077518065206e+01 -1.09631007226083e-01 - 12 2.75262294388280e+01 -1.09704917755312e-01 - 13 2.75412308252314e+01 -1.09764923300926e-01 - 14 2.75518987145933e+01 -1.09807594858373e-01 - 15 2.75575987160543e+01 -1.09830394864217e-01 - 16 2.75579511825093e+01 -1.09831804730037e-01 - 17 2.75528755165223e+01 -1.09811502066089e-01 - 18 2.75426367051080e+01 -1.09770546820432e-01 - 19 2.75278759473936e+01 -1.09711503789574e-01 - 20 2.75096079010709e+01 -1.09638431604284e-01 + 0 2.74164641878496e+01 -1.09265856751398e-01 + 1 2.74002934369676e+01 -1.09201173747870e-01 + 2 2.73891905422880e+01 -1.09156762169152e-01 + 3 2.73840806710794e+01 -1.09136322684318e-01 + 4 2.73853106962415e+01 -1.09141242784966e-01 + 5 2.73926707772583e+01 -1.09170683109033e-01 + 6 2.74054700019287e+01 -1.09221880007715e-01 + 7 2.74226468646496e+01 -1.09290587458598e-01 + 8 2.74428938157855e+01 -1.09371575263142e-01 + 9 2.74647792825400e+01 -1.09459117130160e-01 + 10 2.74868564347115e+01 -1.09547425738846e-01 + 11 2.75077518051641e+01 -1.09631007220656e-01 + 12 2.75262294370741e+01 -1.09704917748296e-01 + 13 2.75412308249068e+01 -1.09764923299627e-01 + 14 2.75518987119582e+01 -1.09807594847833e-01 + 15 2.75575987144433e+01 -1.09830394857773e-01 + 16 2.75579511788616e+01 -1.09831804715446e-01 + 17 2.75528755131993e+01 -1.09811502052797e-01 + 18 2.75426367029528e+01 -1.09770546811811e-01 + 19 2.75278759428108e+01 -1.09711503771243e-01 + 20 2.75096078961602e+01 -1.09638431584641e-01 diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out index 297ae52c8..938486ff2 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,7 +76,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -100,6 +104,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -110,19 +115,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - gyration colvar component: +colvars: - inertia colvar component (derived from gyration): +colvars: - inertiaZ colvar component (derived from inertia): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 27.5096 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 8f94c73f0..f8c9a41c7 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.83560354929576e+01 + x 2.83560354842176e+01 } restraint { diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 88f514f27..060386c56 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.75096079010709e+01 -1.09638431604284e-01 - 21 2.74891754936655e+01 -1.09556701974662e-01 - 22 2.74681653074554e+01 -1.09472661229822e-01 - 23 2.74482979871198e+01 -1.09393191948479e-01 - 24 2.74313142900221e+01 -1.09325257160089e-01 - 25 2.74188770369929e+01 -1.09275508147972e-01 - 26 2.74125030784876e+01 -1.09250012313950e-01 - 27 2.74135301010474e+01 -1.09254120404190e-01 - 28 2.74231135227322e+01 -1.09292454090929e-01 - 29 2.74422414999913e+01 -1.09368965999965e-01 - 30 2.74717522279309e+01 -1.09487008911723e-01 - 31 2.75123380832048e+01 -1.09649352332819e-01 - 32 2.75645249083534e+01 -1.09858099633413e-01 - 33 2.76286215104829e+01 -1.10114486041931e-01 - 34 2.77046429965729e+01 -1.10418571986291e-01 - 35 2.77922201200098e+01 -1.10768880480039e-01 - 36 2.78905144368573e+01 -1.11162057747429e-01 - 37 2.79981625060488e+01 -1.11592650024195e-01 - 38 2.81132700916190e+01 -1.12053080366476e-01 - 39 2.82334689436511e+01 -1.12533875774604e-01 - 40 2.83560354929576e+01 -1.13024141971830e-01 + 20 2.75096078961602e+01 -1.09638431584641e-01 + 21 2.74891754878350e+01 -1.09556701951340e-01 + 22 2.74681653014033e+01 -1.09472661205613e-01 + 23 2.74482979809375e+01 -1.09393191923750e-01 + 24 2.74313142837939e+01 -1.09325257135176e-01 + 25 2.74188770303968e+01 -1.09275508121587e-01 + 26 2.74125030723945e+01 -1.09250012289578e-01 + 27 2.74135300949930e+01 -1.09254120379972e-01 + 28 2.74231135180919e+01 -1.09292454072368e-01 + 29 2.74422414944483e+01 -1.09368965977793e-01 + 30 2.74717522224079e+01 -1.09487008889632e-01 + 31 2.75123380776605e+01 -1.09649352310642e-01 + 32 2.75645249027809e+01 -1.09858099611124e-01 + 33 2.76286215047991e+01 -1.10114486019196e-01 + 34 2.77046429906839e+01 -1.10418571962736e-01 + 35 2.77922201138172e+01 -1.10768880455269e-01 + 36 2.78905144303044e+01 -1.11162057721218e-01 + 37 2.79981624989707e+01 -1.11592649995883e-01 + 38 2.81132700839839e+01 -1.12053080335936e-01 + 39 2.82334689354104e+01 -1.12533875741642e-01 + 40 2.83560354842176e+01 -1.13024141936871e-01 diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt b/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out index 7a60e0951..6906658ec 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,7 +92,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -120,6 +124,7 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,14 +135,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped index 1fc7844e2..fc86e531f 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99760693961651e-01 , 1.39216433541339e-02 , 1.19362778078050e-02 , -1.19276119878887e-02 ) + x ( 9.99760693961232e-01 , 1.39216433781234e-02 , 1.19362778059823e-02 , -1.19276119968650e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj index 0b4deda96..6b248bf72 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( 9.99574098859266e-01 , 2.06195455609807e-02 , 1.42967532305094e-02 , -1.49016132553015e-02 ) ( 3.40696724955871e-06 , -8.24547608833287e-05 , -5.71707735043578e-05 , 5.95895265542064e-05 ) - 1 ( 9.99574091957315e-01 , 2.05772012682538e-02 , 1.42218162872588e-02 , -1.50317469765650e-02 ) ( 3.40702245733137e-06 , -8.22854314316960e-05 , -5.68711105890215e-05 , 6.01099133460393e-05 ) - 2 ( 9.99576136464277e-01 , 2.04824081529012e-02 , 1.41395609284123e-02 , -1.51026879779233e-02 ) ( 3.39066871841008e-06 , -8.19064783447229e-05 , -5.65422596962969e-05 , 6.03936791307258e-05 ) - 3 ( 9.99580389456449e-01 , 2.03360832367537e-02 , 1.40447201596166e-02 , -1.51074342070060e-02 ) ( 3.35664956469004e-06 , -8.13215747888733e-05 , -5.61631631594061e-05 , 6.04128300631967e-05 ) - 4 ( 9.99586941288897e-01 , 2.01392187847421e-02 , 1.39321349524241e-02 , -1.50417514643484e-02 ) ( 3.30424218003071e-06 , -8.05346892436429e-05 , -5.57131918018609e-05 , 6.01504354667014e-05 ) - 5 ( 9.99595790783300e-01 , 1.98928875282193e-02 , 1.37976726208478e-02 , -1.49047745486655e-02 ) ( 3.23345586919841e-06 , -7.95501051430208e-05 , -5.51758162891334e-05 , 5.96030305201998e-05 ) - 6 ( 9.99606822686883e-01 , 1.95985462834746e-02 , 1.36390185710864e-02 , -1.46994623652575e-02 ) ( 3.14521237086393e-06 , -7.83736341663858e-05 , -5.45417724568780e-05 , 5.87824356558856e-05 ) - 7 ( 9.99619795207068e-01 , 1.92585009929308e-02 , 1.34562172673074e-02 , -1.44327885919656e-02 ) ( 3.04144558788717e-06 , -7.70144759459075e-05 , -5.38112245307334e-05 , 5.77165195908192e-05 ) - 8 ( 9.99634343041421e-01 , 1.88763707892861e-02 , 1.32519032639492e-02 , -1.41155905953322e-02 ) ( 2.92507738224423e-06 , -7.54870750675527e-05 , -5.29946899030751e-05 , 5.64485969674567e-05 ) - 9 ( 9.99649997284929e-01 , 1.84574075526462e-02 , 1.30312276086889e-02 , -1.37620544137684e-02 ) ( 2.79985837326511e-06 , -7.38124013541386e-05 , -5.21127465840553e-05 , 5.50353716224322e-05 ) - 10 ( 9.99666219499819e-01 , 1.80085725929327e-02 , 1.28015269423414e-02 , -1.33888689608095e-02 ) ( 2.67009544563575e-06 , -7.20182596721535e-05 , -5.11947122280763e-05 , 5.35435574674263e-05 ) - 11 ( 9.99682444082219e-01 , 1.75383327400058e-02 , 1.25717990452909e-02 , -1.30141364395225e-02 ) ( 2.54031287802513e-06 , -7.01384778080426e-05 , -5.02765491690069e-05 , 5.20455241319585e-05 ) - 12 ( 9.99698121444904e-01 , 1.70562079144180e-02 , 1.23520473382012e-02 , -1.26561715247952e-02 ) ( 2.41490692588102e-06 , -6.82111000049856e-05 , -4.93982449369732e-05 , 5.06144968383214e-05 ) - 13 ( 9.99712754470511e-01 , 1.65721860535352e-02 , 1.21525545431810e-02 , -1.23323402672332e-02 ) ( 2.29785421626925e-06 , -6.62760490231703e-05 , -4.86009086585655e-05 , 4.93199138291843e-05 ) - 14 ( 9.99725922506467e-01 , 1.60961851402786e-02 , 1.19831437097085e-02 , -1.20580661532487e-02 ) ( 2.19251978481122e-06 , -6.43729753215068e-05 , -4.79238159586543e-05 , 4.82234509694974e-05 ) - 15 ( 9.99737290704757e-01 , 1.56377365465832e-02 , 1.18524811149563e-02 , -1.18460736715164e-02 ) ( 2.10158233554066e-06 , -6.25399901795148e-05 , -4.74016204534546e-05 , 4.73759951688351e-05 ) - 16 ( 9.99746606872466e-01 , 1.52059608462364e-02 , 1.17674662844455e-02 , -1.17058762584516e-02 ) ( 2.02705940516384e-06 , -6.08135677078579e-05 , -4.70619130797105e-05 , 4.68155945962039e-05 ) - 17 ( 9.99753691559363e-01 , 1.48097478197070e-02 , 1.17327398928793e-02 , -1.16434701678110e-02 ) ( 1.97038663064612e-06 , -5.92292631842689e-05 , -4.69232526743774e-05 , 4.65662324128018e-05 ) - 18 ( 9.99758428360226e-01 , 1.44579282082185e-02 , 1.17503257388760e-02 , -1.16611783129527e-02 ) ( 1.93249530528609e-06 , -5.78223984900366e-05 , -4.69937329523329e-05 , 4.66372006807749e-05 ) - 19 ( 9.99760760149993e-01 , 1.41591986268333e-02 , 1.18194125288315e-02 , -1.17575952484608e-02 ) ( 1.91384248212681e-06 , -5.66277606734629e-05 , -4.72701091088012e-05 , 4.70228794279011e-05 ) - 20 ( 9.99760693961651e-01 , 1.39216433541339e-02 , 1.19362778078050e-02 , -1.19276119878887e-02 ) ( 1.91437194663135e-06 , -5.56776886898237e-05 , -4.77374935553765e-05 , 4.77028358061962e-05 ) + 0 ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ) ( 3.40696724956404e-06 , -8.24547608834386e-05 , -5.71707735043921e-05 , 5.95895265542447e-05 ) + 1 ( 9.99574091957316e-01 , 2.05772012681827e-02 , 1.42218162872608e-02 , -1.50317469765464e-02 ) ( 3.40702245731717e-06 , -8.22854314314116e-05 , -5.68711105890293e-05 , 6.01099133459647e-05 ) + 2 ( 9.99576136464269e-01 , 2.04824081529267e-02 , 1.41395609289210e-02 , -1.51026879779696e-02 ) ( 3.39066871847757e-06 , -8.19064783448245e-05 , -5.65422596983307e-05 , 6.03936791309106e-05 ) + 3 ( 9.99580389456459e-01 , 2.03360832362100e-02 , 1.40447201598598e-02 , -1.51074342068980e-02 ) ( 3.35664956461634e-06 , -8.13215747866998e-05 , -5.61631631603791e-05 , 6.04128300627651e-05 ) + 4 ( 9.99586941288893e-01 , 2.01392187843744e-02 , 1.39321349532439e-02 , -1.50417514643494e-02 ) ( 3.30424218006268e-06 , -8.05346892421722e-05 , -5.57131918051387e-05 , 6.01504354667054e-05 ) + 5 ( 9.99595790783329e-01 , 1.98928875288094e-02 , 1.37976726200861e-02 , -1.49047745466495e-02 ) ( 3.23345586896751e-06 , -7.95501051453821e-05 , -5.51758162860883e-05 , 5.96030305121391e-05 ) + 6 ( 9.99606822686916e-01 , 1.95985462816866e-02 , 1.36390185716578e-02 , -1.46994623648640e-02 ) ( 3.14521237059840e-06 , -7.83736341592375e-05 , -5.45417724591643e-05 , 5.87824356543135e-05 ) + 7 ( 9.99619795207092e-01 , 1.92585009913588e-02 , 1.34562172678871e-02 , -1.44327885918466e-02 ) ( 3.04144558769446e-06 , -7.70144759396220e-05 , -5.38112245330522e-05 , 5.77165195903442e-05 ) + 8 ( 9.99634343041458e-01 , 1.88763707874475e-02 , 1.32519032638778e-02 , -1.41155905952574e-02 ) ( 2.92507738195028e-06 , -7.54870750602017e-05 , -5.29946899027906e-05 , 5.64485969671590e-05 ) + 9 ( 9.99649997284953e-01 , 1.84574075512748e-02 , 1.30312276083930e-02 , -1.37620544141233e-02 ) ( 2.79985837307062e-06 , -7.38124013486557e-05 , -5.21127465828725e-05 , 5.50353716238521e-05 ) + 10 ( 9.99666219499820e-01 , 1.80085725925678e-02 , 1.28015269417140e-02 , -1.33888689618389e-02 ) ( 2.67009544562864e-06 , -7.20182596706942e-05 , -5.11947122255672e-05 , 5.35435574715432e-05 ) + 11 ( 9.99682444082188e-01 , 1.75383327410858e-02 , 1.25717990443000e-02 , -1.30141364413955e-02 ) ( 2.54031287827201e-06 , -7.01384778123604e-05 , -5.02765491650432e-05 , 5.20455241394477e-05 ) + 12 ( 9.99698121444835e-01 , 1.70562079173577e-02 , 1.23520473368371e-02 , -1.26561715276433e-02 ) ( 2.41490692643697e-06 , -6.82111000167390e-05 , -4.93982449315156e-05 , 5.06144968497088e-05 ) + 13 ( 9.99712754470273e-01 , 1.65721860651408e-02 , 1.21525545409691e-02 , -1.23323402730933e-02 ) ( 2.29785421817066e-06 , -6.62760490695734e-05 , -4.86009086497119e-05 , 4.93199138526125e-05 ) + 14 ( 9.99725922506310e-01 , 1.60961851478372e-02 , 1.19831437077868e-02 , -1.20580661581261e-02 ) ( 2.19251978606965e-06 , -6.43729753517290e-05 , -4.79238159509638e-05 , 4.82234509889984e-05 ) + 15 ( 9.99737290704466e-01 , 1.56377365616588e-02 , 1.18524811131054e-02 , -1.18460736780739e-02 ) ( 2.10158233787459e-06 , -6.25399902397942e-05 , -4.74016204460428e-05 , 4.73759951950515e-05 ) + 16 ( 9.99746606872211e-01 , 1.52059608592562e-02 , 1.17674662824491e-02 , -1.17058762653601e-02 ) ( 2.02705940720648e-06 , -6.08135677599179e-05 , -4.70619130717184e-05 , 4.68155946238250e-05 ) + 17 ( 9.99753691558999e-01 , 1.48097478384659e-02 , 1.17327398910912e-02 , -1.16434701770315e-02 ) ( 1.97038663356000e-06 , -5.92292632592778e-05 , -4.69232526672145e-05 , 4.65662324496665e-05 ) + 18 ( 9.99758428359742e-01 , 1.44579282356846e-02 , 1.17503257360525e-02 , -1.16611783232732e-02 ) ( 1.93249530916090e-06 , -5.78223985998645e-05 , -4.69937329410254e-05 , 4.66372007220352e-05 ) + 19 ( 9.99760760149601e-01 , 1.41591986489713e-02 , 1.18194125264703e-02 , -1.17575952575529e-02 ) ( 1.91384248526716e-06 , -5.66277607619860e-05 , -4.72701090993454e-05 , 4.70228794642514e-05 ) + 20 ( 9.99760693961232e-01 , 1.39216433781234e-02 , 1.19362778059823e-02 , -1.19276119968650e-02 ) ( 1.91437194998574e-06 , -5.56776887857508e-05 , -4.77374935480734e-05 , 4.77028358420824e-05 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out index d4c3e96c6..69fbc3cc3 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,7 +92,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -120,6 +124,7 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,19 +135,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.999761 , 0.0139216 , 0.0119363 , -0.0119276 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped index a1d021f26..ad9c0da83 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99742652480851e-01 , 1.40902379472968e-02 , 1.15309598520170e-02 , -1.35325891843641e-02 ) + x ( 9.99742652479780e-01 , 1.40902379967357e-02 , 1.15309598522144e-02 , -1.35325892118309e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj index 7507a9c22..326f48b81 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( 9.99760693961651e-01 , 1.39216433541339e-02 , 1.19362778078050e-02 , -1.19276119878887e-02 ) ( 1.91437194663135e-06 , -5.56776886898237e-05 , -4.77374935553765e-05 , 4.77028358061962e-05 ) - 21 ( 9.99758313633772e-01 , 1.37518501706272e-02 , 1.20943629928691e-02 , -1.21625375985983e-02 ) ( 1.93341304299124e-06 , -5.49985370139702e-05 , -4.83696566258740e-05 , 4.86423111072771e-05 ) - 22 ( 9.99753796262334e-01 , 1.36537811661746e-02 , 1.22845204621472e-02 , -1.24503685059100e-02 ) ( 1.96954907564106e-06 , -5.46061597039727e-05 , -4.91300159332110e-05 , 4.97932992137969e-05 ) - 23 ( 9.99747426628399e-01 , 1.36276729060903e-02 , 1.24954569267165e-02 , -1.27762685182456e-02 ) ( 2.02050191076346e-06 , -5.45015122960296e-05 , -4.99734110166082e-05 , 5.10964682336444e-05 ) - 24 ( 9.99739603282506e-01 , 1.36692734713397e-02 , 1.27143797766633e-02 , -1.31233051552796e-02 ) ( 2.08308332664440e-06 , -5.46676013199467e-05 , -5.08486896628677e-05 , 5.24841072009449e-05 ) - 25 ( 9.99730831051754e-01 , 1.37696613185747e-02 , 1.29278128058886e-02 , -1.34734378611172e-02 ) ( 2.15325497820459e-06 , -5.50687608354267e-05 , -5.17019710987588e-05 , 5.38840796471852e-05 ) - 26 ( 9.99721697041131e-01 , 1.39157628525684e-02 , 1.31225011988153e-02 , -1.38086918902498e-02 ) ( 2.22632039515597e-06 , -5.56527230866618e-05 , -5.24802652329812e-05 , 5.52245187057974e-05 ) - 27 ( 9.99712830629568e-01 , 1.40915177545030e-02 , 1.32862957776279e-02 , -1.41123969084309e-02 ) ( 2.29724500214521e-06 , -5.63552790154987e-05 , -5.31350077880288e-05 , 5.64387796408899e-05 ) - 28 ( 9.99704851767985e-01 , 1.42794879373133e-02 , 1.34089105192648e-02 , -1.43703407922426e-02 ) ( 2.36106969928898e-06 , -5.71067119123539e-05 , -5.36250874991995e-05 , 5.74700518189137e-05 ) - 29 ( 9.99698315097026e-01 , 1.44626114126131e-02 , 1.34824839010541e-02 , -1.45716948620744e-02 ) ( 2.41335786476355e-06 , -5.78388095265717e-05 , -5.39190880575035e-05 , 5.82750555595938e-05 ) - 30 ( 9.99693659069529e-01 , 1.46257879511962e-02 , 1.35019242354909e-02 , -1.47096017934521e-02 ) ( 2.45060230974677e-06 , -5.84912027666410e-05 , -5.39966660827548e-05 , 5.88263896610770e-05 ) - 31 ( 9.99691168692650e-01 , 1.47570433195187e-02 , 1.34650605688713e-02 , -1.47813752494873e-02 ) ( 2.47052328190881e-06 , -5.90160189866762e-05 , -5.38491520952702e-05 , 5.91133266661292e-05 ) - 32 ( 9.99690957801472e-01 , 1.48481228167761e-02 , 1.33726419068354e-02 , -1.47883260454137e-02 ) ( 2.47221023758033e-06 , -5.93802536084388e-05 , -5.34795460437290e-05 , 5.91411158068268e-05 ) - 33 ( 9.99692972560360e-01 , 1.48944891406353e-02 , 1.32282283648437e-02 , -1.47352903262270e-02 ) ( 2.45609382160275e-06 , -5.95657607275349e-05 , -5.29020819841198e-05 , 5.89290958243205e-05 ) - 34 ( 9.99697013270129e-01 , 1.48948261332085e-02 , 1.30380054990091e-02 , -1.46299769600688e-02 ) ( 2.42377143026910e-06 , -5.95672689463881e-05 , -5.21414867913377e-05 , 5.85080862620418e-05 ) - 35 ( 9.99702767875741e-01 , 1.48502581444742e-02 , 1.28105336109831e-02 , -1.44822637466295e-02 ) ( 2.37773919115572e-06 , -5.93892609314672e-05 , -5.12319796660980e-05 , 5.79175750454513e-05 ) - 36 ( 9.99709848842744e-01 , 1.47635626439325e-02 , 1.25564244173485e-02 , -1.43035502840116e-02 ) ( 2.32109700127172e-06 , -5.90428264751950e-05 , -5.02159814607548e-05 , 5.72031329948130e-05 ) - 37 ( 9.99717826026293e-01 , 1.46386367524169e-02 , 1.22879235287665e-02 , -1.41062246772189e-02 ) ( 2.25728562079388e-06 , -5.85435310309807e-05 , -4.91424471130407e-05 , 5.64142833849880e-05 ) - 38 ( 9.99726251233621e-01 , 1.44803731319332e-02 , 1.20183761983179e-02 , -1.39032378202861e-02 ) ( 2.18989020771502e-06 , -5.79109210347829e-05 , -4.80647306975977e-05 , 5.56028011296765e-05 ) - 39 ( 9.99734674140845e-01 , 1.42949333257481e-02 , 1.17615680020998e-02 , -1.37077248236990e-02 ) ( 2.12251300450785e-06 , -5.71696183232687e-05 , -4.70379496175808e-05 , 5.48211998190806e-05 ) - 40 ( 9.99742652480851e-01 , 1.40902379472968e-02 , 1.15309598520170e-02 , -1.35325891843641e-02 ) ( 2.05869184498829e-06 , -5.63512814751691e-05 , -4.61159255599756e-05 , 5.41210691450550e-05 ) + 20 ( 9.99760693961232e-01 , 1.39216433781234e-02 , 1.19362778059823e-02 , -1.19276119968650e-02 ) ( 1.91437194998574e-06 , -5.56776887857508e-05 , -4.77374935480734e-05 , 4.77028358420824e-05 ) + 21 ( 9.99758313633365e-01 , 1.37518501939863e-02 , 1.20943629910000e-02 , -1.21625376074929e-02 ) ( 1.93341304624615e-06 , -5.49985371073767e-05 , -4.83696566183854e-05 , 4.86423111428367e-05 ) + 22 ( 9.99753796261908e-01 , 1.36537811906101e-02 , 1.22845204605505e-02 , -1.24503685149034e-02 ) ( 1.96954907904872e-06 , -5.46061598016831e-05 , -4.91300159268110e-05 , 4.97932992497502e-05 ) + 23 ( 9.99747426627959e-01 , 1.36276729311783e-02 , 1.24954569253732e-02 , -1.27762685273114e-02 ) ( 2.02050191429012e-06 , -5.45015123963486e-05 , -4.99734110112214e-05 , 5.10964682698865e-05 ) + 24 ( 9.99739603282054e-01 , 1.36692734966396e-02 , 1.27143797755336e-02 , -1.31233051644571e-02 ) ( 2.08308333026075e-06 , -5.46676014211123e-05 , -5.08486896583343e-05 , 5.24841072376327e-05 ) + 25 ( 9.99730831051212e-01 , 1.37696613473913e-02 , 1.29278128060350e-02 , -1.34734378717380e-02 ) ( 2.15325498254029e-06 , -5.50687609506525e-05 , -5.17019710993255e-05 , 5.38840796896415e-05 ) + 26 ( 9.99721697040658e-01 , 1.39157628774382e-02 , 1.31225011979706e-02 , -1.38086919002263e-02 ) ( 2.22632039893925e-06 , -5.56527231861050e-05 , -5.24802652295864e-05 , 5.52245187456788e-05 ) + 27 ( 9.99712830629082e-01 , 1.40915177790539e-02 , 1.32862957768867e-02 , -1.41123969189936e-02 ) ( 2.29724500602795e-06 , -5.63552791136652e-05 , -5.31350077850472e-05 , 5.64387796831146e-05 ) + 28 ( 9.99704851767406e-01 , 1.42794879664030e-02 , 1.34089105192784e-02 , -1.43703408036104e-02 ) ( 2.36106970392215e-06 , -5.71067120286679e-05 , -5.36250874992332e-05 , 5.74700518643537e-05 ) + 29 ( 9.99698315096535e-01 , 1.44626114353530e-02 , 1.34824838999583e-02 , -1.45716948741664e-02 ) ( 2.41335786868624e-06 , -5.78388096174942e-05 , -5.39190880531035e-05 , 5.82750556079333e-05 ) + 30 ( 9.99693659068928e-01 , 1.46257879779070e-02 , 1.35019242353861e-02 , -1.47096018078657e-02 ) ( 2.45060231455666e-06 , -5.84912028734389e-05 , -5.39966660823142e-05 , 5.88263897186958e-05 ) + 31 ( 9.99691168692138e-01 , 1.47570433407831e-02 , 1.34650605673288e-02 , -1.47813752642869e-02 ) ( 2.47052328600467e-06 , -5.90160190716963e-05 , -5.38491520890833e-05 , 5.91133267252955e-05 ) + 32 ( 9.99690957800930e-01 , 1.48481228383961e-02 , 1.33726419051513e-02 , -1.47883260618358e-02 ) ( 2.47221024191153e-06 , -5.93802536948794e-05 , -5.34795460369745e-05 , 5.91411158724805e-05 ) + 33 ( 9.99692972559779e-01 , 1.48944891632750e-02 , 1.32282283630868e-02 , -1.47352903443807e-02 ) ( 2.45609382625367e-06 , -5.95657608180521e-05 , -5.29020819770730e-05 , 5.89290958968973e-05 ) + 34 ( 9.99697013269497e-01 , 1.48948261575969e-02 , 1.30380054972646e-02 , -1.46299769799956e-02 ) ( 2.42377143532588e-06 , -5.95672690438967e-05 , -5.21414867843392e-05 , 5.85080863417083e-05 ) + 35 ( 9.99702767875048e-01 , 1.48502581713688e-02 , 1.28105336093448e-02 , -1.44822637683003e-02 ) ( 2.37773919669474e-06 , -5.93892610389970e-05 , -5.12319796595224e-05 , 5.79175751320903e-05 ) + 36 ( 9.99709848841837e-01 , 1.47635626794789e-02 , 1.25564244174860e-02 , -1.43035503105882e-02 ) ( 2.32109700852655e-06 , -5.90428266173175e-05 , -5.02159814612746e-05 , 5.72031331010642e-05 ) + 37 ( 9.99717826025458e-01 , 1.46386367865957e-02 , 1.22879235275554e-02 , -1.41062247019792e-02 ) ( 2.25728562747236e-06 , -5.85435311676375e-05 , -4.91424471081696e-05 , 5.64142834839795e-05 ) + 38 ( 9.99726251232708e-01 , 1.44803731708344e-02 , 1.20183761975352e-02 , -1.39032378460851e-02 ) ( 2.18989021501695e-06 , -5.79109211903237e-05 , -4.80647306944381e-05 , 5.56028012328199e-05 ) + 39 ( 9.99734674139844e-01 , 1.42949333703084e-02 , 1.17615680015969e-02 , -1.37077248507170e-02 ) ( 2.12251301251851e-06 , -5.71696185014405e-05 , -4.70379496155383e-05 , 5.48211999270969e-05 ) + 40 ( 9.99742652479780e-01 , 1.40902379967357e-02 , 1.15309598522144e-02 , -1.35325892118309e-02 ) ( 2.05869185355315e-06 , -5.63512816728506e-05 , -4.61159255607322e-05 , 5.41210692548650e-05 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out index 9a2c9b63c..ec40acc6d 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,7 +92,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -123,6 +127,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,14 +138,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped index 01d155e7c..279228b77 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99760693818246e-01 , 1.39216454886428e-02 , 1.19362887828950e-02 , -1.19276105335207e-02 ) + x ( 9.99760693817830e-01 , 1.39216455125237e-02 , 1.19362887805905e-02 , -1.19276105428297e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.27813232055700e-03 + accumulatedWork 2.27813232055650e-03 } } diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj index 7b97e03f8..b339c9cfb 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ) ( 3.40696724956404e-06 , -8.24547608834386e-05 , -5.71707735043921e-05 , 5.95895265542447e-05 ) 1.70372550452894e-06 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 - 1 ( 9.99574091957314e-01 , 2.05772012682737e-02 , 1.42218162872633e-02 , -1.50317469765766e-02 ) ( -2.89857105411844e-06 , -8.20357344753561e-05 , 3.85760678003595e-04 , 5.99275084883605e-05 ) 1.98926088015600e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.24615390673084e-05 - 2 ( 9.99576136464107e-01 , 2.04824081530443e-02 , 1.41395609423345e-02 , -1.51026879759213e-02 ) ( -1.05168657308638e-05 , -8.04517476328365e-05 , 9.23378079065062e-04 , 5.93210345452325e-05 ) 1.07841143774923e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.63130419745423e-04 - 3 ( 9.99580389455804e-01 , 2.03360832361746e-02 , 1.40447202158361e-02 , -1.51074341981852e-02 ) ( -1.95312689951841e-05 , -7.71426869009185e-05 , 1.56340858862312e-03 , 5.73083839543752e-05 ) 3.06732891307857e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.94155785846709e-04 - 4 ( 9.99586941287210e-01 , 2.01392187842197e-02 , 1.39321350986691e-02 , -1.50417514416994e-02 ) ( -2.97615745191412e-05 , -7.14911802684271e-05 , 2.29629026903087e-03 , 5.33959422852095e-05 ) 6.60224608309056e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.47035553394905e-04 - 5 ( 9.99595790779864e-01 , 1.98928875293495e-02 , 1.37976729206519e-02 , -1.49047745000832e-02 ) ( -4.06413192373453e-05 , -6.31016250685387e-05 , 3.08637898561516e-03 , 4.72789830459629e-05 ) 1.19170050962504e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.18350423122495e-03 - 6 ( 9.99606822680701e-01 , 1.95985462853154e-02 , 1.36390191112217e-02 , -1.46994622819746e-02 ) ( -5.12953295471253e-05 , -5.21496651351779e-05 , 3.87653754433995e-03 , 3.91137191765353e-05 ) 1.87930300176401e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.61639198938565e-03 - 7 ( 9.99619795196980e-01 , 1.92585010029931e-02 , 1.34562181455343e-02 , -1.44327884584219e-02 ) ( -6.08644895999444e-05 , -3.94609368010510e-05 , 4.60962560797654e-03 , 2.95729845813135e-05 ) 2.65684805734470e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.95913218474054e-03 - 8 ( 9.99634343026175e-01 , 1.88763708154653e-02 , 1.32519045888371e-02 , -1.41155903961733e-02 ) ( -6.88272478679810e-05 , -2.61706583239472e-05 , 5.24998743935999e-03 , 1.95701968832050e-05 ) 3.44602164993124e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.17342875845418e-03 - 9 ( 9.99649997263176e-01 , 1.84574076082982e-02 , 1.30312294936897e-02 , -1.37620541343428e-02 ) ( -7.50701457830531e-05 , -1.32797169780534e-05 , 5.78803752266541e-03 , 9.90150880444109e-06 ) 4.18841103516628e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.26930643841376e-03 - 10 ( 9.99666219470242e-01 , 1.80085726959886e-02 , 1.28015294976327e-02 , -1.33888685873615e-02 ) ( -7.97587545540024e-05 , -1.43682091237256e-06 , 6.23146712392570e-03 , 1.06823603980643e-06 ) 4.85469339763468e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 11 ( 9.99682444043579e-01 , 1.75383329132778e-02 , 1.25718023724709e-02 , -1.30141359600538e-02 ) ( -7.83400542266416e-05 , -1.37439039732819e-06 , 6.23240419814393e-03 , 1.01985197689343e-06 ) 4.85612527277317e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 12 ( 9.99698121396221e-01 , 1.70562081842655e-02 , 1.23520515143566e-02 , -1.26561709307220e-02 ) ( -7.69825486935338e-05 , -1.31342687254272e-06 , 6.23330027300938e-03 , 9.74598505384046e-07 ) 4.85749516015432e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 13 ( 9.99712754410915e-01 , 1.65721864559041e-02 , 1.21525596192655e-02 , -1.23323395554808e-02 ) ( -7.57498609780799e-05 , -1.25570151485890e-06 , 6.23411347952353e-03 , 9.34441421038598e-07 ) 4.85873892087277e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 14 ( 9.99725922435667e-01 , 1.60961856940404e-02 , 1.19831497127895e-02 , -1.20580653182552e-02 ) ( -7.47028381413507e-05 , -1.20276040423710e-06 , 6.23480386681979e-03 , 9.01018650764673e-07 ) 4.85979525377557e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 15 ( 9.99737290622154e-01 , 1.56377372962370e-02 , 1.18524880466519e-02 , -1.18460727176508e-02 ) ( -7.38952136327416e-05 , -1.15585759286722e-06 , 6.23533622412687e-03 , 8.75598102012420e-07 ) 4.86061005414818e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 16 ( 9.99746606777969e-01 , 1.52059618150989e-02 , 1.17674741247817e-02 , -1.17058751888952e-02 ) ( -7.33697991762876e-05 , -1.11594113657630e-06 , 6.23568254121877e-03 , 8.59075395674407e-07 ) 4.86114023320336e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 17 ( 9.99753691452656e-01 , 1.48097490467918e-02 , 1.17327486042245e-02 , -1.16434689912063e-02 ) ( -7.31554048139585e-05 , -1.08368010638398e-06 , 6.23582398801883e-03 , 8.51992540535477e-07 ) 4.86135680288230e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 18 ( 9.99758428241199e-01 , 1.44579297242938e-02 , 1.17503352677578e-02 , -1.16611770361988e-02 ) ( -7.32645959816383e-05 , -1.05951032775465e-06 , 6.23575235353089e-03 , 8.54557861273005e-07 ) 4.86124712105271e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 19 ( 9.99760760018823e-01 , 1.41592004405267e-02 , 1.18194228146038e-02 , -1.17575938779946e-02 ) ( -7.36923301385327e-05 , -1.04367416194781e-06 , 6.23547092567585e-03 , 8.66651827458857e-07 ) 4.86081625810141e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 20 ( 9.99760693818246e-01 , 1.39216454886428e-02 , 1.19362887828950e-02 , -1.19276105335207e-02 ) ( -7.44154910910036e-05 , -1.03623406304924e-06 , 6.23499480534843e-03 , 8.87811454163381e-07 ) 4.86008746875330e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 1 ( 9.99574091957316e-01 , 2.05772012681827e-02 , 1.42218162872608e-02 , -1.50317469765464e-02 ) ( -2.89857105413568e-06 , -8.20357344749931e-05 , 3.85760678003605e-04 , 5.99275084882400e-05 ) 1.98926088015520e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.24615390673096e-05 + 2 ( 9.99576136464117e-01 , 2.04824081526900e-02 , 1.41395609423227e-02 , -1.51026879758038e-02 ) ( -1.05168657309248e-05 , -8.04517476314451e-05 , 9.23378079065106e-04 , 5.93210345447713e-05 ) 1.07841143774898e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.63130419745432e-04 + 3 ( 9.99580389455824e-01 , 2.03360832354197e-02 , 1.40447202158084e-02 , -1.51074341979379e-02 ) ( -1.95312689952873e-05 , -7.71426868980550e-05 , 1.56340858862322e-03 , 5.73083839534375e-05 ) 3.06732891307828e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.94155785846739e-04 + 4 ( 9.99586941287241e-01 , 2.01392187829879e-02 , 1.39321350986197e-02 , -1.50417514413077e-02 ) ( -2.97615745192475e-05 , -7.14911802640544e-05 , 2.29629026903105e-03 , 5.33959422838193e-05 ) 6.60224608309061e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.47035553394974e-04 + 5 ( 9.99595790779906e-01 , 1.98928875276492e-02 , 1.37976729205755e-02 , -1.49047744995720e-02 ) ( -4.06413192373749e-05 , -6.31016250631435e-05 , 3.08637898561543e-03 , 4.72789830443403e-05 ) 1.19170050962515e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.18350423122506e-03 + 6 ( 9.99606822680751e-01 , 1.95985462832515e-02 , 1.36390191111118e-02 , -1.46994622814130e-02 ) ( -5.12953295469620e-05 , -5.21496651296818e-05 , 3.87653754434035e-03 , 3.91137191750376e-05 ) 1.87930300176431e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.61639198938578e-03 + 7 ( 9.99619795197032e-01 , 1.92585010007719e-02 , 1.34562181453815e-02 , -1.44327884579218e-02 ) ( -6.08644895994507e-05 , -3.94609367964904e-05 , 4.60962560797712e-03 , 2.95729845802817e-05 ) 2.65684805734531e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.95913218474063e-03 + 8 ( 9.99634343026221e-01 , 1.88763708133848e-02 , 1.32519045886273e-02 , -1.41155903958815e-02 ) ( -6.88272478670076e-05 , -2.61706583210457e-05 , 5.24998743936081e-03 , 1.95701968827877e-05 ) 3.44602164993228e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.17342875845415e-03 + 9 ( 9.99649997263207e-01 , 1.84574076067301e-02 , 1.30312294934032e-02 , -1.37620541344282e-02 ) ( -7.50701457814478e-05 , -1.32797169768971e-05 , 5.78803752266657e-03 , 9.90150880448157e-06 ) 4.18841103516792e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.26930643841353e-03 + 10 ( 9.99666219470249e-01 , 1.80085726953522e-02 , 1.28015294972442e-02 , -1.33888685880002e-02 ) ( -7.97587545516019e-05 , -1.43682091227853e-06 , 6.23146712392729e-03 , 1.06823603982523e-06 ) 4.85469339763710e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 11 ( 9.99682444043555e-01 , 1.75383329140093e-02 , 1.25718023719501e-02 , -1.30141359614126e-02 ) ( -7.83400542234201e-05 , -1.37439039732904e-06 , 6.23240419814605e-03 , 1.01985197695800e-06 ) 4.85612527277641e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 12 ( 9.99698121396159e-01 , 1.70562081867899e-02 , 1.23520515136698e-02 , -1.26561709329443e-02 ) ( -7.69825486892822e-05 , -1.31342687266466e-06 , 6.23330027301218e-03 , 9.74598505501407e-07 ) 4.85749516015860e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 13 ( 9.99712754410809e-01 , 1.65721864606089e-02 , 1.21525596183800e-02 , -1.23323395586735e-02 ) ( -7.57498609725947e-05 , -1.25570151512460e-06 , 6.23411347952713e-03 , 9.34441421212952e-07 ) 4.85873892087829e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 14 ( 9.99725922435513e-01 , 1.60961857012553e-02 , 1.19831497116778e-02 , -1.20580653224807e-02 ) ( -7.47028381344618e-05 , -1.20276040466548e-06 , 6.23480386682432e-03 , 9.01018650997467e-07 ) 4.85979525378250e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 15 ( 9.99737290621952e-01 , 1.56377373062154e-02 , 1.18524880452973e-02 , -1.18460727229225e-02 ) ( -7.38952136243442e-05 , -1.15585759347365e-06 , 6.23533622413239e-03 , 8.75598102302748e-07 ) 4.86061005415662e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 16 ( 9.99746606777718e-01 , 1.52059618280014e-02 , 1.17674741231820e-02 , -1.17058751951783e-02 ) ( -7.33697991663691e-05 , -1.11594113737261e-06 , 6.23568254122528e-03 , 8.59075396019594e-07 ) 4.86114023321333e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 17 ( 9.99753691452358e-01 , 1.48097490626708e-02 , 1.17327486023943e-02 , -1.16434689984246e-02 ) ( -7.31554048026095e-05 , -1.08368010737810e-06 , 6.23582398802628e-03 , 8.51992540931742e-07 ) 4.86135680289371e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 18 ( 9.99758428240858e-01 , 1.44579297430799e-02 , 1.17503352657271e-02 , -1.16611770442436e-02 ) ( -7.32645959690450e-05 , -1.05951032894958e-06 , 6.23575235353917e-03 , 8.54557861715953e-07 ) 4.86124712106538e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 19 ( 9.99760760018442e-01 , 1.41592004620220e-02 , 1.18194228124135e-02 , -1.17575938867382e-02 ) ( -7.36923301249498e-05 , -1.04367416334025e-06 , 6.23547092568478e-03 , 8.66651827943935e-07 ) 4.86081625811507e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 20 ( 9.99760693817830e-01 , 1.39216455125237e-02 , 1.19362887805905e-02 , -1.19276105428297e-02 ) ( -7.44154910767136e-05 , -1.03623406462822e-06 , 6.23499480535782e-03 , 8.87811454686164e-07 ) 4.86008746876767e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out index f89ad9c5b..124c00f20 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,7 +92,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -123,6 +127,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,19 +138,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.999761 , 0.0139216 , 0.0119363 , -0.0119276 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped index cc10dd18f..938849f24 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99742652209286e-01 , 1.40902435879328e-02 , 1.15309792246189e-02 , -1.35325868663831e-02 ) + x ( 9.99742652208198e-01 , 1.40902436380753e-02 , 1.15309792258764e-02 , -1.35325868934950e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.27813232055700e-03 + accumulatedWork 2.27813232055650e-03 } } diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj index 789205d92..f4c99c252 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 ( 9.99760693818246e-01 , 1.39216454886428e-02 , 1.19362887828950e-02 , -1.19276105335207e-02 ) ( -7.44154910910036e-05 , -1.03623406304924e-06 , 6.23499480534843e-03 , 8.87811454163381e-07 ) 4.86008746875330e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 21 ( 9.99758313478268e-01 , 1.37518526317376e-02 , 1.20943745877787e-02 , -1.21625360684149e-02 ) ( -7.53933764660893e-05 , -1.03704924339528e-06 , 6.23435061795005e-03 , 9.17196334580247e-07 ) 4.85910171318368e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 22 ( 9.99753796094871e-01 , 1.36537839555646e-02 , 1.22845326108695e-02 , -1.24503669071325e-02 ) ( -7.65692635273181e-05 , -1.04571764160572e-06 , 6.23357553386989e-03 , 9.53550192505157e-07 ) 4.85791609892022e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 23 ( 9.99747426449245e-01 , 1.36276760151045e-02 , 1.24954695687563e-02 , -1.27762668567522e-02 ) ( -7.78731950371622e-05 , -1.06149877874316e-06 , 6.23271549315738e-03 , 9.95180076948371e-07 ) 4.85660109628904e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 24 ( 9.99739603092028e-01 , 1.36692768838184e-02 , 1.27143928598848e-02 , -1.31233034359725e-02 ) ( -7.92260158564982e-05 , -1.08324442064198e-06 , 6.23182259923561e-03 , 1.03997785312531e-06 ) 4.85523649061308e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 25 ( 9.99730830850349e-01 , 1.37696650158448e-02 , 1.29278262893479e-02 , -1.34734360893895e-02 ) ( -8.05444416230567e-05 , -1.10936858783720e-06 , 6.23095181081672e-03 , 1.08550257036763e-06 ) 4.85390628560139e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 26 ( 9.99721696829550e-01 , 1.39157668005032e-02 , 1.31225150492047e-02 , -1.38086900675579e-02 ) ( -8.17466563544410e-05 , -1.13788408329726e-06 , 6.23015725331999e-03 , 1.12912848169394e-06 ) 4.85269306082901e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 27 ( 9.99712830408440e-01 , 1.40915219271310e-02 , 1.32863099760682e-02 , -1.41123950392548e-02 ) ( -8.27577572531398e-05 , -1.16651773939557e-06 , 6.22948859730489e-03 , 1.16824564754451e-06 ) 4.85167246948734e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 28 ( 9.99704851538043e-01 , 1.42794923087412e-02 , 1.34089250569295e-02 , -1.43703388798510e-02 ) ( -8.35143963095269e-05 , -1.19289526097260e-06 , 6.22898794027442e-03 , 1.20048449746711e-06 ) 4.85090853482966e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 29 ( 9.99698314859356e-01 , 1.44626159417893e-02 , 1.34824987759774e-02 , -1.45716929091923e-02 ) ( -8.39681999132023e-05 , -1.21476630361119e-06 , 6.22868748240004e-03 , 1.22392806418303e-06 ) 4.85045017320758e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 30 ( 9.99693658824898e-01 , 1.46257926205038e-02 , 1.35019394575005e-02 , -1.47095998041003e-02 ) ( -8.40878559230599e-05 , -1.23022841225092e-06 , 6.22860808561504e-03 , 1.23727773812928e-06 ) 4.85032906200261e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 31 ( 9.99691168442251e-01 , 1.47570480953222e-02 , 1.34650761492187e-02 , -1.47813732236213e-02 ) ( -8.38600119325431e-05 , -1.23790853458392e-06 , 6.22875863535765e-03 , 1.23994907031517e-06 ) 4.85055871362938e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 32 ( 9.99690957546167e-01 , 1.48481276856586e-02 , 1.33726578643432e-02 , -1.47883239855450e-02 ) ( -8.32892561630635e-05 , -1.23707181806292e-06 , 6.22913603470891e-03 , 1.23208927254656e-06 ) 4.85113448593648e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 33 ( 9.99692972301071e-01 , 1.48944940900112e-02 , 1.32282447187099e-02 , -1.47352882331596e-02 ) ( -8.23974522868586e-05 , -1.22764528722624e-06 , 6.22972565464919e-03 , 1.21452310135798e-06 ) 4.85203425681462e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 34 ( 9.99697013007692e-01 , 1.48948311570748e-02 , 1.30380222677718e-02 , -1.46299748341174e-02 ) ( -8.12226196305917e-05 , -1.21016386944397e-06 , 6.23050211131118e-03 , 1.18864502513774e-06 ) 4.85321956879579e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 35 ( 9.99702767610873e-01 , 1.48502632434009e-02 , 1.28105508103196e-02 , -1.44822615878513e-02 ) ( -7.98174260893882e-05 , -1.18566220604831e-06 , 6.23143031865448e-03 , 1.15628052791932e-06 ) 4.85463717256666e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 36 ( 9.99709848575880e-01 , 1.47635678298615e-02 , 1.25564420596702e-02 , -1.43035480957163e-02 ) ( -7.82472390297188e-05 , -1.15554370356586e-06 , 6.23246684237558e-03 , 1.11953798235853e-06 ) 4.85622102004666e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 37 ( 9.99717825758149e-01 , 1.46386420259571e-02 , 1.22879416152389e-02 , -1.41062224530848e-02 ) ( -7.65875917949357e-05 , -1.12145478557008e-06 , 6.23356163672723e-03 , 1.08066654326796e-06 ) 4.85789484544943e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 38 ( 9.99726250964308e-01 , 1.44803785129685e-02 , 1.20183947274420e-02 , -1.39032355639129e-02 ) ( -7.49209173989000e-05 , -1.08518030953821e-06 , 6.23466024929299e-03 , 1.04192839015343e-06 ) 4.85957547890113e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 39 ( 9.99734673870441e-01 , 1.42949388301149e-02 , 1.17615869623806e-02 , -1.37077225363170e-02 ) ( -7.33324894756701e-05 , -1.04856166212217e-06 , 6.23570652181050e-03 , 1.00548820092254e-06 ) 4.86117694883134e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 - 40 ( 9.99742652209286e-01 , 1.40902435879328e-02 , 1.15309792246189e-02 , -1.35325868663831e-02 ) ( -7.19056857990176e-05 , -1.01342943209091e-06 , 6.23664570367131e-03 , 9.73320421122090e-07 ) 4.86261525439548e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 20 ( 9.99760693817830e-01 , 1.39216455125237e-02 , 1.19362887805905e-02 , -1.19276105428297e-02 ) ( -7.44154910767136e-05 , -1.03623406462822e-06 , 6.23499480535782e-03 , 8.87811454686164e-07 ) 4.86008746876767e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 21 ( 9.99758313477823e-01 , 1.37518526575684e-02 , 1.20943745854034e-02 , -1.21625360781649e-02 ) ( -7.53933764513610e-05 , -1.03704924514109e-06 , 6.23435061795974e-03 , 9.17196335136740e-07 ) 4.85910171319849e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 22 ( 9.99753796094403e-01 , 1.36537839828244e-02 , 1.22845326084587e-02 , -1.24503669172219e-02 ) ( -7.65692635123717e-05 , -1.04571764348986e-06 , 6.23357553387972e-03 , 9.53550193092197e-07 ) 4.85791609893525e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 23 ( 9.99747426448760e-01 , 1.36276760432249e-02 , 1.24954695663346e-02 , -1.27762668671144e-02 ) ( -7.78731950221508e-05 , -1.06149878072943e-06 , 6.23271549316725e-03 , 9.95180077564155e-07 ) 4.85660109630414e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 24 ( 9.99739603091531e-01 , 1.36692769122303e-02 , 1.27143928574664e-02 , -1.31233034465857e-02 ) ( -7.92260158415096e-05 , -1.08324442268912e-06 , 6.23182259924548e-03 , 1.03997785377014e-06 ) 4.85523649062815e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 25 ( 9.99730830849845e-01 , 1.37696650440250e-02 , 1.29278262869396e-02 , -1.34734361002817e-02 ) ( -8.05444416081335e-05 , -1.10936858990258e-06 , 6.23095181082655e-03 , 1.08550257104459e-06 ) 4.85390628561639e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 26 ( 9.99721696829043e-01 , 1.39157668280219e-02 , 1.31225150468116e-02 , -1.38086900788067e-02 ) ( -8.17466563396149e-05 , -1.13788408534165e-06 , 6.23015725332975e-03 , 1.12912848240953e-06 ) 4.85269306084392e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 27 ( 9.99712830407931e-01 , 1.40915219536903e-02 , 1.32863099736998e-02 , -1.41123950509825e-02 ) ( -8.27577572384685e-05 , -1.16651774138799e-06 , 6.22948859731456e-03 , 1.16824564830883e-06 ) 4.85167246950209e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 28 ( 9.99704851537533e-01 , 1.42794923342033e-02 , 1.34089250546046e-02 , -1.43703388922140e-02 ) ( -8.35143962951262e-05 , -1.19289526289459e-06 , 6.22898794028392e-03 , 1.20048449829351e-06 ) 4.85090853484415e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 29 ( 9.99698314858842e-01 , 1.44626159661916e-02 , 1.34824987737283e-02 , -1.45716929223678e-02 ) ( -8.39681998992706e-05 , -1.21476630545989e-06 , 6.22868748240922e-03 , 1.22392806508725e-06 ) 4.85045017322160e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 30 ( 9.99693658824374e-01 , 1.46257926440631e-02 , 1.35019394553724e-02 , -1.47095998182711e-02 ) ( -8.40878559098745e-05 , -1.23022841404033e-06 , 6.22860808562373e-03 , 1.23727773912788e-06 ) 4.85032906201587e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 31 ( 9.99691168441709e-01 , 1.47570481184252e-02 , 1.34650761472677e-02 , -1.47813732389598e-02 ) ( -8.38600119204497e-05 , -1.23790853634409e-06 , 6.22875863536561e-03 , 1.23994907142371e-06 ) 4.85055871364153e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 32 ( 9.99690957545599e-01 , 1.48481277088428e-02 , 1.33726578626311e-02 , -1.47883240021993e-02 ) ( -8.32892561524428e-05 , -1.23707181983747e-06 , 6.22913603471590e-03 , 1.23208927377770e-06 ) 4.85113448594715e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 33 ( 9.99692972300467e-01 , 1.48944941139382e-02 , 1.32282447172976e-02 , -1.47352882512418e-02 ) ( -8.23974522780850e-05 , -1.22764528906839e-06 , 6.22972565465496e-03 , 1.21452310271978e-06 ) 4.85203425682343e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 34 ( 9.99697013007040e-01 , 1.48948311824960e-02 , 1.30380222667125e-02 , -1.46299748536945e-02 ) ( -8.12226196239937e-05 , -1.21016387141186e-06 , 6.23050211131550e-03 , 1.18864502663254e-06 ) 4.85321956880239e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 35 ( 9.99702767610164e-01 , 1.48502632711203e-02 , 1.28105508096523e-02 , -1.44822616089398e-02 ) ( -7.98174260852071e-05 , -1.18566220820019e-06 , 6.23143031865720e-03 , 1.15628052954330e-06 ) 4.85463717257082e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 36 ( 9.99709848575105e-01 , 1.47635678606929e-02 , 1.25564420594164e-02 , -1.43035481182791e-02 ) ( -7.82472390280891e-05 , -1.15554370595586e-06 , 6.23246684237661e-03 , 1.11953798410207e-06 ) 4.85622102004825e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 37 ( 9.99717825757301e-01 , 1.46386420606817e-02 , 1.22879416154002e-02 , -1.41062224770323e-02 ) ( -7.65875917958683e-05 , -1.12145478824491e-06 , 6.23356163672657e-03 , 1.08066654511663e-06 ) 4.85789484544842e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 38 ( 9.99726250963382e-01 , 1.44803785522926e-02 , 1.20183947280021e-02 , -1.39032355891063e-02 ) ( -7.49209174022956e-05 , -1.08518031253540e-06 , 6.23466024929070e-03 , 1.04192839208965e-06 ) 4.85957547889764e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 39 ( 9.99734673869434e-01 , 1.42949388746288e-02 , 1.17615869633091e-02 , -1.37077225625754e-02 ) ( -7.33324894813423e-05 , -1.04856166546951e-06 , 6.23570652180672e-03 , 1.00548820292743e-06 ) 4.86117694882555e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 40 ( 9.99742652208198e-01 , 1.40902436380753e-02 , 1.15309792258764e-02 , -1.35325868934950e-02 ) ( -7.19056858067241e-05 , -1.01342943580709e-06 , 6.23664570366618e-03 , 9.73320423177462e-07 ) 4.86261525438764e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt index 129300d44..157cac038 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out index 116aff668..ab5aa163d 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -102,6 +106,7 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -112,14 +117,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped index 1f5d27b1f..869052fe0 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.95047582247901e-01 , -8.94218407474711e-02 , 1.03501830154734e-02 , -4.21534953649891e-02 ) + x ( 9.95047582249982e-01 , -8.94218407198434e-02 , 1.03501830123263e-02 , -4.21534953752505e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj index 883efbc35..479a43598 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( 9.95725692918273e-01 , -7.96585470771966e-02 , 1.34264420545491e-02 , -4.47726589977706e-02 ) ( 3.41700762028921e-05 , 3.17725061894297e-04 , -5.35525350301423e-05 , 1.78579654954705e-04 ) - 1 ( 9.95703202497440e-01 , -7.99005029584874e-02 , 1.32741369737811e-02 , -4.48869630396686e-02 ) ( 3.43497422149066e-05 , 3.18685319686154e-04 , -5.29442547720266e-05 , 1.79032867583693e-04 ) - 2 ( 9.95678521556900e-01 , -8.01968009433796e-02 , 1.31263198798460e-02 , -4.49494666834364e-02 ) ( 3.45469057624427e-05 , 3.19861820322023e-04 , -5.23538161311571e-05 , 1.79279199004696e-04 ) - 3 ( 9.95652403679522e-01 , -8.05419873402017e-02 , 1.29777382160836e-02 , -4.49539501409555e-02 ) ( 3.47555464978077e-05 , 3.21232958648346e-04 , -5.17602977203342e-05 , 1.79293941999634e-04 ) - 4 ( 9.95625468036919e-01 , -8.09309980540691e-02 , 1.28228853926206e-02 , -4.48962644375516e-02 ) ( 3.49707179799499e-05 , 3.22778657189527e-04 , -5.11417606089582e-05 , 1.79060635558914e-04 ) - 5 ( 9.95598135270061e-01 , -8.13594233179634e-02 , 1.26568594211301e-02 , -4.47750063510777e-02 ) ( 3.51890598487685e-05 , 3.24481408187548e-04 , -5.04786710710785e-05 , 1.78573747451775e-04 ) - 6 ( 9.95570599011000e-01 , -8.18234325633647e-02 , 1.24760860073947e-02 , -4.45921018383624e-02 ) ( 3.54090252509857e-05 , 3.26325967026764e-04 , -4.97567836440902e-05 , 1.77840996133848e-04 ) - 7 ( 9.95542831967394e-01 , -8.23194900179106e-02 , 1.22788215872136e-02 , -4.43531489520439e-02 ) ( 3.56308321555336e-05 , 3.28298218071023e-04 , -4.89691474791349e-05 , 1.76884717867258e-04 ) - 8 ( 9.95514620286082e-01 , -8.28440052644148e-02 , 1.20654160975387e-02 , -4.40674179275458e-02 ) ( 3.58561887749678e-05 , 3.30383787220305e-04 , -4.81171552723796e-05 , 1.75741870295307e-04 ) - 9 ( 9.95485617186446e-01 , -8.33930320003749e-02 , 1.18383657124410e-02 , -4.37474717665303e-02 ) ( 3.60878650734080e-05 , 3.32566851187595e-04 , -4.72107550685531e-05 , 1.74462525031441e-04 ) - 10 ( 9.95455406148282e-01 , -8.39620802380189e-02 , 1.16022024367708e-02 , -4.34084364021512e-02 ) ( 3.63291879738892e-05 , 3.34829401791962e-04 , -4.62680115876186e-05 , 1.73106963906254e-04 ) - 11 ( 9.95423564349686e-01 , -8.45460630939964e-02 , 1.13632516824820e-02 , -4.30670089961288e-02 ) ( 3.65835345919473e-05 , 3.37151047685463e-04 , -4.53141408323535e-05 , 1.71741730748373e-04 ) - 12 ( 9.95389718653998e-01 , -8.51393630217013e-02 , 1.11292589658322e-02 , -4.27403375869374e-02 ) ( 3.68538850107258e-05 , 3.39509291404714e-04 , -4.43800222511196e-05 , 1.70435169039739e-04 ) - 13 ( 9.95353590493668e-01 , -8.57359613292896e-02 , 1.09088757916328e-02 , -4.24449202528342e-02 ) ( 3.71424637701849e-05 , 3.41880056891084e-04 , -4.35001488108009e-05 , 1.69253036016511e-04 ) - 14 ( 9.95315031422500e-01 , -8.63295419718748e-02 , 1.07110129770663e-02 , -4.21956467939341e-02 ) ( 3.74504559211243e-05 , 3.44238112793326e-04 , -4.27100481377666e-05 , 1.68254684186438e-04 ) - 15 ( 9.95274054250948e-01 , -8.69134880574461e-02 , 1.05441067595788e-02 , -4.20050513773208e-02 ) ( 3.77777583895344e-05 , 3.46557067343460e-04 , -4.20433559626645e-05 , 1.67490084039822e-04 ) - 16 ( 9.95230862599338e-01 , -8.74807544340958e-02 , 1.04153736880360e-02 , -4.18827855372420e-02 ) ( 3.81227440111029e-05 , 3.48808869094348e-04 , -4.15288452965480e-05 , 1.66997725982946e-04 ) - 17 ( 9.95185875294234e-01 , -8.80236982832042e-02 , 1.03301362042927e-02 , -4.18352774748477e-02 ) ( 3.84820667905813e-05 , 3.50963139290033e-04 , -4.11877381007968e-05 , 1.66803265507009e-04 ) - 18 ( 9.95139736351655e-01 , -8.85340181100190e-02 , 1.02912848994442e-02 , -4.18655255117140e-02 ) ( 3.88505823112175e-05 , 3.52986933124393e-04 , -4.10315624673211e-05 , 1.66918702770913e-04 ) - 19 ( 9.95093299815157e-01 , -8.90029543780060e-02 , 1.02989187541513e-02 , -4.19729799688224e-02 ) ( 3.92214689902938e-05 , 3.54845537886740e-04 , -4.10607197312513e-05 , 1.67341913061558e-04 ) - 20 ( 9.95047582247901e-01 , -8.94218407474711e-02 , 1.03501830154734e-02 , -4.21534953649891e-02 ) ( 3.95866076580436e-05 , 3.56504660282400e-04 , -4.12638394484893e-05 , 1.68056454879410e-04 ) + 0 ( 9.95725692918276e-01 , -7.96585470771598e-02 , 1.34264420545571e-02 , -4.47726589977838e-02 ) ( 3.41700762028735e-05 , 3.17725061894150e-04 , -5.35525350301741e-05 , 1.78579654954758e-04 ) + 1 ( 9.95703202497434e-01 , -7.99005029585730e-02 , 1.32741369737813e-02 , -4.48869630396400e-02 ) ( 3.43497422149501e-05 , 3.18685319686495e-04 , -5.29442547720273e-05 , 1.79032867583579e-04 ) + 2 ( 9.95678521556875e-01 , -8.01968009437818e-02 , 1.31263198798365e-02 , -4.49494666832817e-02 ) ( 3.45469057626449e-05 , 3.19861820323622e-04 , -5.23538161311184e-05 , 1.79279199004076e-04 ) + 3 ( 9.95652403679467e-01 , -8.05419873410536e-02 , 1.29777382161078e-02 , -4.49539501406355e-02 ) ( 3.47555464982458e-05 , 3.21232958651731e-04 , -5.17602977204288e-05 , 1.79293941998351e-04 ) + 4 ( 9.95625468036827e-01 , -8.09309980554691e-02 , 1.28228853926643e-02 , -4.48962644370436e-02 ) ( 3.49707179806798e-05 , 3.22778657195090e-04 , -5.11417606091293e-05 , 1.79060635556877e-04 ) + 5 ( 9.95598135270229e-01 , -8.13594233176651e-02 , 1.26568594199537e-02 , -4.47750063482282e-02 ) ( 3.51890598474303e-05 , 3.24481408186395e-04 , -5.04786710663926e-05 , 1.78573747440431e-04 ) + 6 ( 9.95570599010826e-01 , -8.18234325659399e-02 , 1.24760860076073e-02 , -4.45921018374740e-02 ) ( 3.54090252523799e-05 , 3.26325967036996e-04 , -4.97567836449325e-05 , 1.77840996130284e-04 ) + 7 ( 9.95542831967203e-01 , -8.23194900206118e-02 , 1.22788215872927e-02 , -4.43531489512843e-02 ) ( 3.56308321570564e-05 , 3.28298218081753e-04 , -4.89691474794440e-05 , 1.76884717864206e-04 ) + 8 ( 9.95514620285900e-01 , -8.28440052668668e-02 , 1.20654160973878e-02 , -4.40674179270895e-02 ) ( 3.58561887764231e-05 , 3.30383787230043e-04 , -4.81171552717718e-05 , 1.75741870293466e-04 ) + 9 ( 9.95485617186302e-01 , -8.33930320021245e-02 , 1.18383657119753e-02 , -4.37474717666082e-02 ) ( 3.60878650745618e-05 , 3.32566851194540e-04 , -4.72107550666910e-05 , 1.74462525031735e-04 ) + 10 ( 9.95455406148209e-01 , -8.39620802385744e-02 , 1.16022024359213e-02 , -4.34084364029869e-02 ) ( 3.63291879744745e-05 , 3.34829401794161e-04 , -4.62680115842287e-05 , 1.73106963909578e-04 ) + 11 ( 9.95423564349720e-01 , -8.45460630928600e-02 , 1.13632516811963e-02 , -4.30670089979245e-02 ) ( 3.65835345916786e-05 , 3.37151047680939e-04 , -4.53141408272277e-05 , 1.71741730755538e-04 ) + 12 ( 9.95389718654174e-01 , -8.51393630184037e-02 , 1.11292589640790e-02 , -4.27403375898543e-02 ) ( 3.68538850093158e-05 , 3.39509291391604e-04 , -4.43800222441335e-05 , 1.70435169051391e-04 ) + 13 ( 9.95353590494649e-01 , -8.57359613149864e-02 , 1.09088757881713e-02 , -4.24449202596133e-02 ) ( 3.71424637623492e-05 , 3.41880056834273e-04 , -4.35001487970268e-05 , 1.69253036043655e-04 ) + 14 ( 9.95315031423055e-01 , -8.63295419632000e-02 , 1.07110129745439e-02 , -4.21956467992482e-02 ) ( 3.74504559166966e-05 , 3.44238112758864e-04 , -4.27100481277245e-05 , 1.68254684207691e-04 ) + 15 ( 9.95274054252229e-01 , -8.69134880395287e-02 , 1.05441067567461e-02 , -4.20050513847555e-02 ) ( 3.77777583793028e-05 , 3.46557067272315e-04 , -4.20433559514056e-05 , 1.67490084069610e-04 ) + 16 ( 9.95230862600358e-01 , -8.74807544192303e-02 , 1.04153736849348e-02 , -4.18827855448026e-02 ) ( 3.81227440029491e-05 , 3.48808869035314e-04 , -4.15288452842110e-05 , 1.66997726013206e-04 ) + 17 ( 9.95185875295753e-01 , -8.80236982613176e-02 , 1.03301362013300e-02 , -4.18352774854899e-02 ) ( 3.84820667784462e-05 , 3.50963139203125e-04 , -4.11877380890261e-05 , 1.66803265549611e-04 ) + 18 ( 9.95139736354077e-01 , -8.85340180775604e-02 , 1.02912848947750e-02 , -4.18655255239391e-02 ) ( 3.88505822918751e-05 , 3.52986932995553e-04 , -4.10315624487717e-05 , 1.66918702819926e-04 ) + 19 ( 9.95093299817054e-01 , -8.90029543523046e-02 , 1.02989187503535e-02 , -4.19729799792916e-02 ) ( 3.92214689751451e-05 , 3.54845537784723e-04 , -4.10607197161619e-05 , 1.67341913103511e-04 ) + 20 ( 9.95047582249982e-01 , -8.94218407198434e-02 , 1.03501830123263e-02 , -4.21534953752505e-02 ) ( 3.95866076414231e-05 , 3.56504660172752e-04 , -4.12638394360000e-05 , 1.68056454920554e-04 ) diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out index 5914612e6..90fb86396 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -102,6 +106,7 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -112,19 +117,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.995048 , -0.0894218 , 0.0103502 , -0.0421535 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped index ed7e25462..dfd0bab71 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.94724148736992e-01 , -9.22283984220502e-02 , 8.57198032337350e-03 , -4.40943488137254e-02 ) + x ( 9.94724148740762e-01 , -9.22283983670171e-02 , 8.57198031977685e-03 , -4.40943488444842e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj index c0667eff6..726901e4a 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( 9.95047582247901e-01 , -8.94218407474711e-02 , 1.03501830154734e-02 , -4.21534953649891e-02 ) ( 3.95866076580436e-05 , 3.56504660282400e-04 , -4.12638394484893e-05 , 1.68056454879410e-04 ) - 21 ( 9.95003682839837e-01 , -8.97829885242213e-02 , 1.04393119624910e-02 , -4.23993734926744e-02 ) ( 3.99372197271322e-05 , 3.57933932898174e-04 , -4.16179506708815e-05 , 1.69031737037327e-04 ) - 22 ( 9.94962679614012e-01 , -9.00807729701850e-02 , 1.05578791084465e-02 , -4.26995515799716e-02 ) ( 4.02646961578782e-05 , 3.59111217849485e-04 , -4.20894792476610e-05 , 1.70223761008198e-04 ) - 23 ( 9.94925517922001e-01 , -9.03126986794675e-02 , 1.06952529221899e-02 , -4.30400024372660e-02 ) ( 4.05614879036287e-05 , 3.60026823523198e-04 , -4.26360632851805e-05 , 1.71576706138696e-04 ) - 24 ( 9.94892911461449e-01 , -9.04801848414051e-02 , 1.08392438023233e-02 , -4.34043968812029e-02 ) ( 4.08218962640658e-05 , 3.60686606895834e-04 , -4.32091299904993e-05 , 1.73025559827073e-04 ) - 25 ( 9.94865274494471e-01 , -9.05888500412821e-02 , 1.09769033233308e-02 , -4.37750322292276e-02 ) ( 4.10426140153920e-05 , 3.61113088679918e-04 , -4.37570789498096e-05 , 1.74499809724437e-04 ) - 26 ( 9.94842696773042e-01 , -9.06481848174512e-02 , 1.10954059447183e-02 , -4.41339691571599e-02 ) ( 4.12229254801604e-05 , 3.61344139503753e-04 , -4.42287942291727e-05 , 1.75927969656476e-04 ) - 27 ( 9.94824962046056e-01 , -9.06706489146701e-02 , 1.11829212647168e-02 , -4.44642619127326e-02 ) ( 4.13645585949729e-05 , 3.61429385087017e-04 , -4.45771195482112e-05 , 1.77242481815600e-04 ) - 28 ( 9.94811601034407e-01 , -9.06703674988958e-02 , 1.12293836999313e-02 , -4.47511323509693e-02 ) ( 4.14712617792593e-05 , 3.61425022712328e-04 , -4.47619257619370e-05 , 1.78384399142845e-04 ) - 29 ( 9.94801963553301e-01 , -9.06616843507634e-02 , 1.12270902259919e-02 , -4.49829383904157e-02 ) ( 4.15482279543266e-05 , 3.61388073162416e-04 , -4.47524942101701e-05 , 1.79307251420585e-04 ) - 30 ( 9.94795293171562e-01 , -9.06578423239697e-02 , 1.11710965065822e-02 , -4.51518206909619e-02 ) ( 4.16014983432260e-05 , 3.61371140753713e-04 , -4.45290973684036e-05 , 1.79979630354449e-04 ) - 31 ( 9.94790790368376e-01 , -9.06700109952209e-02 , 1.10594218017861e-02 , -4.52539688182038e-02 ) ( 4.16374581484353e-05 , 3.61418554153441e-04 , -4.40838177198993e-05 , 1.80386257820595e-04 ) - 32 ( 9.94787655101548e-01 , -9.07067883426823e-02 , 1.08930998924629e-02 , -4.52895151315648e-02 ) ( 4.16624966490124e-05 , 3.61564391109476e-04 , -4.34207527559406e-05 , 1.80527568679028e-04 ) - 33 ( 9.94785106316866e-01 , -9.07741837073836e-02 , 1.06761181635399e-02 , -4.52621290192839e-02 ) ( 4.16828514352205e-05 , 3.61832415426825e-04 , -4.25557737313109e-05 , 1.80418096880953e-04 ) - 34 ( 9.94782383325423e-01 , -9.08759672251909e-02 , 1.04152699913556e-02 , -4.51784302215533e-02 ) ( 4.17045974305217e-05 , 3.62237469888589e-04 , -4.15159383176215e-05 , 1.80084138377755e-04 ) - 35 ( 9.94778740634731e-01 , -9.10141758273820e-02 , 1.01199150029673e-02 , -4.50473561929485e-02 ) ( 4.17336881757203e-05 , 3.62787491421699e-04 , -4.03385356616366e-05 , 1.79561229883738e-04 ) - 36 ( 9.94773451639091e-01 , -9.11895286402353e-02 , 9.80161261834228e-03 , -4.48795963718487e-02 ) ( 4.17759263472595e-05 , 3.63485167161823e-04 , -3.90696262406339e-05 , 1.78891895074220e-04 ) - 37 ( 9.94765834652613e-01 , -9.14015536948658e-02 , 9.47358561936806e-03 , -4.46871498930807e-02 ) ( 4.18367558332307e-05 , 3.64328445257653e-04 , -3.77619042586746e-05 , 1.78123885047879e-04 ) - 38 ( 9.94755307045228e-01 , -9.16483518244586e-02 , 9.14999203197848e-03 , -4.44829895469045e-02 ) ( 4.19208293709127e-05 , 3.65309606589932e-04 , -3.64717959784524e-05 , 1.77308845034647e-04 ) - 39 ( 9.94741461697262e-01 , -9.19260831338689e-02 , 8.84503297656702e-03 , -4.42807521582896e-02 ) ( 4.20313979540273e-05 , 3.66413236673037e-04 , -3.52559039930375e-05 , 1.76501088347335e-04 ) - 40 ( 9.94724148736992e-01 , -9.22283984220502e-02 , 8.57198032337350e-03 , -4.40943488137254e-02 ) ( 4.21696580758678e-05 , 3.67613980339042e-04 , -3.41671313822781e-05 , 1.75756050795697e-04 ) + 20 ( 9.95047582249982e-01 , -8.94218407198434e-02 , 1.03501830123263e-02 , -4.21534953752505e-02 ) ( 3.95866076414231e-05 , 3.56504660172752e-04 , -4.12638394360000e-05 , 1.68056454920554e-04 ) + 21 ( 9.95003682841854e-01 , -8.97829884973678e-02 , 1.04393119593296e-02 , -4.23993735029785e-02 ) ( 3.99372197110201e-05 , 3.57933932791603e-04 , -4.16179506583343e-05 , 1.69031737078635e-04 ) + 22 ( 9.94962679616141e-01 , -9.00807729420692e-02 , 1.05578791054915e-02 , -4.26995515904153e-02 ) ( 4.02646961408769e-05 , 3.59111217737913e-04 , -4.20894792359408e-05 , 1.70223761050075e-04 ) + 23 ( 9.94925517924194e-01 , -9.03126986506125e-02 , 1.06952529194415e-02 , -4.30400024478075e-02 ) ( 4.05614878861151e-05 , 3.60026823408699e-04 , -4.26360632742869e-05 , 1.71576706180971e-04 ) + 24 ( 9.94892911463656e-01 , -9.04801848123271e-02 , 1.08392437997452e-02 , -4.34043968918623e-02 ) ( 4.08218962464344e-05 , 3.60686606780452e-04 , -4.32091299802860e-05 , 1.73025559869822e-04 ) + 25 ( 9.94865274497008e-01 , -9.05888500075216e-02 , 1.09769033218979e-02 , -4.37750322417940e-02 ) ( 4.10426139951310e-05 , 3.61113088545953e-04 , -4.37570789441720e-05 , 1.74499809774828e-04 ) + 26 ( 9.94842696775133e-01 , -9.06481847893688e-02 , 1.10954059422353e-02 , -4.41339691683329e-02 ) ( 4.12229254634621e-05 , 3.61344139392317e-04 , -4.42287942193370e-05 , 1.75927969701260e-04 ) + 27 ( 9.94824962048116e-01 , -9.06706488864391e-02 , 1.11829212623721e-02 , -4.44642619247934e-02 ) ( 4.13645585785194e-05 , 3.61429384974983e-04 , -4.45771195389264e-05 , 1.77242481863921e-04 ) + 28 ( 9.94811601036927e-01 , -9.06703674651151e-02 , 1.12293836982419e-02 , -4.47511323638196e-02 ) ( 4.14712617591352e-05 , 3.61425022578285e-04 , -4.47619257552785e-05 , 1.78384399194370e-04 ) + 29 ( 9.94801963555091e-01 , -9.06616843247956e-02 , 1.12270902231604e-02 , -4.49829384038806e-02 ) ( 4.15482279400340e-05 , 3.61388073059340e-04 , -4.47524941989370e-05 , 1.79307251474472e-04 ) + 30 ( 9.94795293173688e-01 , -9.06578422928237e-02 , 1.11710965045517e-02 , -4.51518207071648e-02 ) ( 4.16014983262487e-05 , 3.61371140630078e-04 , -4.45290973603736e-05 , 1.79979630419292e-04 ) + 31 ( 9.94790790369875e-01 , -9.06700109711078e-02 , 1.10594217982803e-02 , -4.52539688344244e-02 ) ( 4.16374581364648e-05 , 3.61418554057688e-04 , -4.40838177059692e-05 , 1.80386257885433e-04 ) + 32 ( 9.94787655103003e-01 , -9.07067883182348e-02 , 1.08930998886607e-02 , -4.52895151494764e-02 ) ( 4.16624966373904e-05 , 3.61564391012379e-04 , -4.34207527408272e-05 , 1.80527568750601e-04 ) + 33 ( 9.94785106318339e-01 , -9.07741836818644e-02 , 1.06761181594841e-02 , -4.52621290390331e-02 ) ( 4.16828514234531e-05 , 3.61832415325462e-04 , -4.25557737151859e-05 , 1.80418096959853e-04 ) + 34 ( 9.94782383326987e-01 , -9.08759671977928e-02 , 1.04152699871068e-02 , -4.51784302432211e-02 ) ( 4.17045974180370e-05 , 3.62237469779759e-04 , -4.15159383007289e-05 , 1.80084138464314e-04 ) + 35 ( 9.94778740636462e-01 , -9.10141757972667e-02 , 1.01199149985978e-02 , -4.50473562165450e-02 ) ( 4.17336881618950e-05 , 3.62787491302079e-04 , -4.03385356442665e-05 , 1.79561229978004e-04 ) + 36 ( 9.94773451641488e-01 , -9.11895285998344e-02 , 9.80161261516879e-03 , -4.48795964015018e-02 ) ( 4.17759263281172e-05 , 3.63485167001368e-04 , -3.90696262280471e-05 , 1.78891895192706e-04 ) + 37 ( 9.94765834654937e-01 , -9.14015536567541e-02 , 9.47358561494656e-03 , -4.46871499202457e-02 ) ( 4.18367558146745e-05 , 3.64328445106307e-04 , -3.77619042411093e-05 , 1.78123885156437e-04 ) + 38 ( 9.94755307047952e-01 , -9.16483517814180e-02 , 9.14999202764146e-03 , -4.44829895755552e-02 ) ( 4.19208293491576e-05 , 3.65309606419041e-04 , -3.64717959612317e-05 , 1.77308845149173e-04 ) + 39 ( 9.94741461700454e-01 , -9.19260830853272e-02 , 8.84503297238212e-03 , -4.42807521881895e-02 ) ( 4.20313979285352e-05 , 3.66413236480337e-04 , -3.52559039764323e-05 , 1.76501088466893e-04 ) + 40 ( 9.94724148740762e-01 , -9.22283983670171e-02 , 8.57198031977685e-03 , -4.40943488444842e-02 ) ( 4.21696580457610e-05 , 3.67613980120615e-04 , -3.41671313680286e-05 , 1.75756050918744e-04 ) diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt b/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out index e51e7ce01..913368e3f 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -105,6 +109,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -115,14 +120,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped index 75d556e11..68355e27e 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.95047581772214e-01 , -8.94218449921444e-02 , 1.03501990099413e-02 , -4.21534936621476e-02 ) + x ( 9.95047581774198e-01 , -8.94218449655825e-02 , 1.03501990061269e-02 , -4.21534936725870e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.26088591477312e-03 + accumulatedWork 2.26088591477162e-03 } } diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj index c68dda8dd..509adba31 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 0 ( 9.95725692918276e-01 , -7.96585470771598e-02 , 1.34264420545571e-02 , -4.47726589977838e-02 ) ( 3.41700762028735e-05 , 3.17725061894150e-04 , -5.35525350301742e-05 , 1.78579654954758e-04 ) 1.71094220294084e-05 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 - 1 ( 9.95703202497441e-01 , -7.99005029584633e-02 , 1.32741369737848e-02 , -4.48869630396836e-02 ) ( 2.83367138119876e-05 , 3.17696149303388e-04 , 3.90264420205874e-04 , 1.78477165770087e-04 ) 3.57367786264763e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.25751658795682e-05 - 2 ( 9.95678521556434e-01 , -8.01968009473040e-02 , 1.31263198967912e-02 , -4.49494666818169e-02 ) ( 2.10043163772193e-05 , 3.14124330882618e-04 , 9.28834252114706e-04 , 1.76063396272304e-04 ) 1.24105832995919e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.62928156880146e-04 - 3 ( 9.95652403677545e-01 , -8.05419873570241e-02 , 1.29777382869849e-02 , -4.49539501341403e-02 ) ( 1.18560940371760e-05 , 3.04619185564628e-04 , 1.56985791890452e-03 , 1.70021080024672e-04 ) 3.23286808547484e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.92924287234960e-04 - 4 ( 9.95625468031697e-01 , -8.09309980989665e-02 , 1.28228855772213e-02 , -4.48962644197014e-02 ) ( 7.70725692445905e-07 , 2.86357930583270e-04 , 2.30368856073438e-03 , 1.58856330357171e-04 ) 6.76777222122379e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.43830024565586e-04 - 5 ( 9.95598135259372e-01 , -8.13594234111277e-02 , 1.26568598024581e-02 , -4.47750063116703e-02 ) ( -1.19638357695980e-05 , 2.57128422727014e-04 , 3.09452499115279e-03 , 1.41506985519482e-04 ) 1.20779591337005e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.17743292406597e-03 - 6 ( 9.95570598990892e-01 , -8.18234327398263e-02 , 1.24760866965111e-02 , -4.45921017706951e-02 ) ( -2.55774576567467e-05 , 2.16780943535973e-04 , 3.88503951911439e-03 , 1.18141192228400e-04 ) 1.89439219877529e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.60702762768054e-03 - 7 ( 9.95542831934058e-01 , -8.23194903131902e-02 , 1.22788227120833e-02 , -4.43531488408355e-02 ) ( -3.90575682806717e-05 , 1.67766250714442e-04 , 4.61795501118331e-03 , 9.03912482948679e-05 ) 2.67041875895001e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.94669840769403e-03 - 8 ( 9.95514620234786e-01 , -8.28440057228855e-02 , 1.20654178027640e-02 , -4.40674177575778e-02 ) ( -5.15481325640461e-05 , 1.14015827330549e-04 , 5.25759497784824e-03 , 6.06487222594931e-05 ) 3.45770500468243e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.15860938064247e-03 - 9 ( 9.95485617112086e-01 , -8.33930326705179e-02 , 1.18383681504187e-02 , -4.37474715214257e-02 ) ( -6.25780827768114e-05 , 5.92548196842370e-05 , 5.79445555467360e-03 , 3.10847135981400e-05 ) 4.19801357307588e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.25291457221944e-03 - 10 ( 9.95455406045667e-01 , -8.39620811696408e-02 , 1.16022057599854e-02 , -4.34084360651368e-02 ) ( -7.20363521614028e-05 , 6.07593470346080e-06 , 6.23635565891194e-03 , 3.14126114356596e-06 ) 4.86217099062247e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 11 ( 9.95423564213811e-01 , -8.45460643353971e-02 , 1.13632560365135e-02 , -4.30670085508141e-02 ) ( -7.05611115416490e-05 , 5.99309127335064e-06 , 6.23732857267671e-03 , 3.05282706113075e-06 ) 4.86366147886091e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 12 ( 9.95389718481123e-01 , -8.51393646079810e-02 , 1.11292644694778e-02 , -4.27403370200617e-02 ) ( -6.91159591117955e-05 , 5.91174364552275e-06 , 6.23828095598795e-03 , 2.96772141710540e-06 ) 4.86512125721615e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 13 ( 9.95353590281985e-01 , -8.57359632733491e-02 , 1.09088825344929e-02 , -4.24449195570245e-02 ) ( -6.77542728936322e-05 , 5.83609473973489e-06 , 6.23917763572405e-03 , 2.88924929863384e-06 ) 4.86649632742223e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 14 ( 9.95315031169567e-01 , -8.63295442986035e-02 , 1.07110210249439e-02 , -4.21956459569390e-02 ) ( -6.65310885279126e-05 , 5.77063379376035e-06 , 6.23998242899110e-03 , 2.82053638168687e-06 ) 4.86773104443728e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 15 ( 9.95274053957830e-01 , -8.69134907480067e-02 , 1.05441161484066e-02 , -4.20050503986284e-02 ) ( -6.54985597936450e-05 , 5.71973965160146e-06 , 6.24066111878534e-03 , 2.76433440038838e-06 ) 4.86877270222756e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 16 ( 9.95230862265883e-01 , -8.74807574867389e-02 , 1.04153844320038e-02 , -4.18827844130215e-02 ) ( -6.47013397119858e-05 , 5.68724546536339e-06 , 6.24118446605571e-03 , 2.72285794697030e-06 ) 4.86957619517651e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 17 ( 9.95185874922694e-01 , -8.80237016666293e-02 , 1.03301482988283e-02 , -4.18352762077715e-02 ) ( -6.41723928341247e-05 , 5.67601661599500e-06 , 6.24153092938165e-03 , 2.69765663558857e-06 ) 4.87010824161822e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 18 ( 9.95139735944289e-01 , -8.85340217957036e-02 , 1.02912983231547e-02 , -4.18655241007787e-02 ) ( -6.39296531703027e-05 , 5.68759250860446e-06 , 6.24168882976025e-03 , 2.68952021397884e-06 ) 4.87035075379198e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 19 ( 9.95093299372444e-01 , -8.90029583582581e-02 , 1.02989334803762e-02 , -4.19729784112083e-02 ) ( -6.39737894643545e-05 , 5.72193232866381e-06 , 6.24165779845369e-03 , 2.69841077792800e-06 ) 4.87030309258332e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 20 ( 9.95047581772214e-01 , -8.94218449921444e-02 , 1.03501990099413e-02 , -4.21534936621476e-02 ) ( -6.42872031816166e-05 , 5.77729188351618e-06 , 6.24144943236418e-03 , 2.72341771540914e-06 ) 4.86998308191970e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 0 ( 9.95725692918276e-01 , -7.96585470771598e-02 , 1.34264420545571e-02 , -4.47726589977838e-02 ) ( 3.41700762028735e-05 , 3.17725061894150e-04 , -5.35525350301741e-05 , 1.78579654954758e-04 ) 1.71094220294084e-05 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 + 1 ( 9.95703202497434e-01 , -7.99005029585730e-02 , 1.32741369737813e-02 , -4.48869630396400e-02 ) ( 2.83367138120423e-05 , 3.17696149303822e-04 , 3.90264420205889e-04 , 1.78477165769913e-04 ) 3.57367786265048e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.25751658795693e-05 + 2 ( 9.95678521556407e-01 , -8.01968009477312e-02 , 1.31263198967770e-02 , -4.49494666816481e-02 ) ( 2.10043163774406e-05 , 3.14124330884285e-04 , 9.28834252114772e-04 , 1.76063396271639e-04 ) 1.24105832996037e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.62928156880148e-04 + 3 ( 9.95652403677488e-01 , -8.05419873579345e-02 , 1.29777382869545e-02 , -4.49539501337857e-02 ) ( 1.18560940376575e-05 , 3.04619185568056e-04 , 1.56985791890468e-03 , 1.70021080023323e-04 ) 3.23286808547749e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.92924287234955e-04 + 4 ( 9.95625468031602e-01 , -8.09309981004511e-02 , 1.28228855771687e-02 , -4.48962644191386e-02 ) ( 7.70725693236790e-07 , 2.86357930588497e-04 , 2.30368856073467e-03 , 1.58856330355165e-04 ) 6.76777222122836e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.43830024565543e-04 + 5 ( 9.95598135259239e-01 , -8.13594234131779e-02 , 1.26568598023747e-02 , -4.47750063109274e-02 ) ( -1.19638357685023e-05 , 2.57128422733453e-04 , 3.09452499115324e-03 , 1.41506985517112e-04 ) 1.20779591337073e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.17743292406584e-03 + 6 ( 9.95570598990727e-01 , -8.18234327423189e-02 , 1.24760866963825e-02 , -4.45921017698568e-02 ) ( -2.55774576553760e-05 , 2.16780943542518e-04 , 3.88503951911507e-03 , 1.18141192226147e-04 ) 1.89439219877622e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.60702762768025e-03 + 7 ( 9.95542831933873e-01 , -8.23194903158855e-02 , 1.22788227118873e-02 , -4.43531488400399e-02 ) ( -3.90575682790280e-05 , 1.67766250719849e-04 , 4.61795501118427e-03 , 9.03912482932004e-05 ) 2.67041875895129e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.94669840769354e-03 + 8 ( 9.95514620234602e-01 , -8.28440057254391e-02 , 1.20654178024697e-02 , -4.40674177570056e-02 ) ( -5.15481325620161e-05 , 1.14015827333934e-04 , 5.25759497784956e-03 , 6.06487222586368e-05 ) 3.45770500468423e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.15860938064172e-03 + 9 ( 9.95485617111931e-01 , -8.33930326725034e-02 , 1.18383681499865e-02 , -4.37474715212837e-02 ) ( -6.25780827741211e-05 , 5.92548196854455e-05 , 5.79445555467542e-03 , 3.10847135979329e-05 ) 4.19801357307849e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.25291457221835e-03 + 10 ( 9.95455406045573e-01 , -8.39620811705810e-02 , 1.16022057593680e-02 , -4.34084360656384e-02 ) ( -7.20363521575908e-05 , 6.07593470320788e-06 , 6.23635565891445e-03 , 3.14126114343633e-06 ) 4.86217099062632e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 11 ( 9.95423564213814e-01 , -8.45460643347972e-02 , 1.13632560356581e-02 , -4.30670085521597e-02 ) ( -7.05611115363754e-05 , 5.99309127286019e-06 , 6.23732857268019e-03 , 3.05282706099796e-06 ) 4.86366147886625e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 12 ( 9.95389718481259e-01 , -8.51393646053625e-02 , 1.11292644683300e-02 , -4.27403370224198e-02 ) ( -6.91159591047267e-05 , 5.91174364473551e-06 , 6.23828095599262e-03 , 2.96772141696521e-06 ) 4.86512125722331e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 13 ( 9.95353590282289e-01 , -8.57359632682770e-02 , 1.09088825330022e-02 , -4.24449195605181e-02 ) ( -6.77542728844581e-05 , 5.83609473859762e-06 , 6.23917763573012e-03 , 2.88924929847956e-06 ) 4.86649632743153e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 14 ( 9.95315031170072e-01 , -8.63295442907098e-02 , 1.07110210230709e-02 , -4.21956459616350e-02 ) ( -6.65310885163908e-05 , 5.77063379223042e-06 , 6.23998242899872e-03 , 2.82053638151088e-06 ) 4.86773104444897e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 15 ( 9.95274053958565e-01 , -8.69134907370101e-02 , 1.05441161461300e-02 , -4.20050504045343e-02 ) ( -6.54985597796452e-05 , 5.71973964965100e-06 , 6.24066111879459e-03 , 2.76433440018415e-06 ) 4.86877270224177e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 16 ( 9.95230862266868e-01 , -8.74807574724623e-02 , 1.04153844293258e-02 , -4.18827844200880e-02 ) ( -6.47013396955228e-05 , 5.68724546298252e-06 , 6.24118446606660e-03 , 2.72285794673419e-06 ) 4.86957619519322e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 17 ( 9.95185874923942e-01 , -8.80237016490180e-02 , 1.03301482957764e-02 , -4.18352762159005e-02 ) ( -6.41723928153701e-05 , 5.67601661319342e-06 , 6.24153092939405e-03 , 2.69765663532097e-06 ) 4.87010824163727e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 18 ( 9.95139735945799e-01 , -8.85340217748383e-02 , 1.02912983197793e-02 , -4.18655241098357e-02 ) ( -6.39296531495683e-05 , 5.68759250541073e-06 , 6.24168882977397e-03 , 2.68952021368430e-06 ) 4.87035075381305e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 19 ( 9.95093299374205e-01 , -8.90029583343626e-02 , 1.02989334767443e-02 , -4.19729784210373e-02 ) ( -6.39737894420540e-05 , 5.72193232512286e-06 , 6.24165779846845e-03 , 2.69841077761449e-06 ) 4.87030309260599e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 20 ( 9.95047581774198e-01 , -8.94218449655825e-02 , 1.03501990061269e-02 , -4.21534936725870e-02 ) ( -6.42872031582073e-05 , 5.77729187968484e-06 , 6.24144943237969e-03 , 2.72341771508647e-06 ) 4.86998308194352e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out index 5455bcf82..023407b4d 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -105,6 +109,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -115,19 +120,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.995048 , -0.0894218 , 0.0103502 , -0.0421535 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped index 80ded7bf8..0d834a02a 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.94724147278495e-01 , -9.22284124393750e-02 , 8.57202436227895e-03 , -4.40943438358672e-02 ) + x ( 9.94724147282287e-01 , -9.22284123842412e-02 , 8.57202435943065e-03 , -4.40943438661931e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.26088591477312e-03 + accumulatedWork 2.26088591477162e-03 } } diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj index 545a4a767..a8608cd4b 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 ( 9.95047581772214e-01 , -8.94218449921444e-02 , 1.03501990099413e-02 , -4.21534936621476e-02 ) ( -6.42872031816166e-05 , 5.77729188351618e-06 , 6.24144943236418e-03 , 2.72341771540914e-06 ) 4.86998308191970e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 21 ( 9.95003682332090e-01 , -8.97829930212753e-02 , 1.04393291902568e-02 , -4.23993716437056e-02 ) ( -6.48343047552602e-05 , 5.85024762696099e-06 , 6.24108712856311e-03 , 2.76273729574205e-06 ) 4.86942673643799e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 22 ( 9.94962679074848e-01 , -9.00807777119746e-02 , 1.05578975392661e-02 , -4.26995495825972e-02 ) ( -6.55630800076457e-05 , 5.93587413929206e-06 , 6.24060508568570e-03 , 2.81368743215307e-06 ) 4.86868668804814e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 23 ( 9.94925517351027e-01 , -9.03127036714925e-02 , 1.06952725327247e-02 , -4.30400002879546e-02 ) ( -6.64079281069542e-05 , 6.02806886341535e-06 , 6.24004647488748e-03 , 2.87277509220557e-06 ) 4.86782932651527e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 24 ( 9.94892910857417e-01 , -9.04801901001701e-02 , 1.08392645787803e-02 , -4.34043945757192e-02 ) ( -6.72936746943171e-05 , 6.11999986373752e-06 , 6.23946083146203e-03 , 2.93583477880549e-06 ) 4.86693074744086e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 25 ( 9.94865273855686e-01 , -9.05888555887877e-02 , 1.09769252640617e-02 , -4.37750297648312e-02 ) ( -6.81405121461231e-05 , 6.20463009089469e-06 , 6.23890081875418e-03 , 2.99824813044994e-06 ) 4.86607175532170e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 26 ( 9.94842696096015e-01 , -9.06481906996373e-02 , 1.10954290567160e-02 , -4.41339665262560e-02 ) ( -6.88694319923092e-05 , 6.27525279032860e-06 , 6.23841864349104e-03 , 3.05523799708078e-06 ) 4.86533236042453e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 27 ( 9.94824961327947e-01 , -9.06706551684395e-02 , 1.11829455700586e-02 , -4.44642591139523e-02 ) ( -6.94075830901017e-05 , 6.32596816231558e-06 , 6.23806249525430e-03 , 3.10221081995358e-06 ) 4.86478634360924e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 28 ( 9.94811600272105e-01 , -9.06703741663319e-02 , 1.12294092309447e-02 , -4.47511293814425e-02 ) ( -6.96929861916542e-05 , 6.35204608896586e-06 , 6.23787339221755e-03 , 3.13510602529034e-06 ) 4.86449646837991e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 29 ( 9.94801962741897e-01 , -9.06616914948174e-02 , 1.12271170222758e-02 , -4.49829352481218e-02 ) ( -6.96781856669942e-05 , 6.35015049171011e-06 , 6.23788272161999e-03 , 3.15070680542899e-06 ) 4.86451076870096e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 30 ( 9.94795292308519e-01 , -9.06578499805883e-02 , 1.11711246192723e-02 , -4.51518173770135e-02 ) ( -6.93326642807366e-05 , 6.31843588898705e-06 , 6.23811060335627e-03 , 3.14687435703579e-06 ) 4.86486009293656e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 31 ( 9.94790789449473e-01 , -9.06700192222035e-02 , 1.10594512834366e-02 , -4.52539653295560e-02 ) ( -6.86440920759764e-05 , 6.25655284913111e-06 , 6.23856504118798e-03 , 3.12268408174970e-06 ) 4.86555683501490e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 32 ( 9.94787654124658e-01 , -9.07067971724354e-02 , 1.08931308022897e-02 , -4.52895114701268e-02 ) ( -6.76186433057460e-05 , 6.16560784402434e-06 , 6.23924171411324e-03 , 3.07846132678909e-06 ) 4.86659461746219e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 33 ( 9.94785105280032e-01 , -9.07741931710955e-02 , 1.06761505602423e-02 , -4.52621251859446e-02 ) ( -6.62806416350276e-05 , 6.04811203479819e-06 , 6.24012423797141e-03 , 3.01572941046886e-06 ) 4.86794866288210e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 34 ( 9.94782382227464e-01 , -9.08759773447180e-02 , 1.04153039316759e-02 , -4.51784262176578e-02 ) ( -6.46716868343866e-05 , 5.90792805804091e-06 , 6.24118479329044e-03 , 2.93708964314039e-06 ) 4.86957669764842e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 35 ( 9.94778739475224e-01 , -9.10141866146385e-02 , 1.01199505392699e-02 , -4.50473520203313e-02 ) ( -6.28492246886030e-05 , 5.75019432704345e-06 , 6.24238513755075e-03 , 2.84605112313311e-06 ) 4.87142042441254e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 36 ( 9.94773450418677e-01 , -9.11895400906934e-02 , 9.80164979780012e-03 , -4.48795920370193e-02 ) ( -6.08843396495280e-05 , 5.58118527291748e-06 , 6.24367813619005e-03 , 2.74682071959611e-06 ) 4.87340778322567e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 37 ( 9.94765833371153e-01 , -9.14015658154700e-02 , 9.47362447745856e-03 , -4.46871453903308e-02 ) ( -5.88584935642695e-05 , 5.40806518764580e-06 , 6.24500998009463e-03 , 2.64405749687727e-06 ) 4.87545627649441e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 38 ( 9.94755305704011e-01 , -9.16483645954890e-02 , 9.15003259920000e-03 , -4.44829848832778e-02 ) ( -5.68590654616153e-05 , 5.23851477052131e-06 , 6.24632316887178e-03 , 2.54259608860927e-06 ) 4.87747749876768e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 39 ( 9.94741460297122e-01 , -9.19260965378052e-02 , 8.84507527332342e-03 , -4.42807473365176e-02 ) ( -5.49738529763158e-05 , 5.08024639311451e-06 , 6.24756014034971e-03 , 2.44715173833410e-06 ) 4.87938270365658e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 - 40 ( 9.94724147278495e-01 , -9.22284124393750e-02 , 8.57202436227895e-03 , -4.40943438358672e-02 ) ( -5.32850485171137e-05 , 4.94046057385252e-06 , 6.24866720236290e-03 , 2.36203097818903e-06 ) 4.88108888620278e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 20 ( 9.95047581774198e-01 , -8.94218449655825e-02 , 1.03501990061269e-02 , -4.21534936725870e-02 ) ( -6.42872031582073e-05 , 5.77729187968484e-06 , 6.24144943237969e-03 , 2.72341771508647e-06 ) 4.86998308194352e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 21 ( 9.95003682334260e-01 , -8.97829929925345e-02 , 1.04393291863312e-02 , -4.23993716546049e-02 ) ( -6.48343047311814e-05 , 5.85024762290276e-06 , 6.24108712857907e-03 , 2.76273729542017e-06 ) 4.86942673646249e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 22 ( 9.94962679077155e-01 , -9.00807776816361e-02 , 1.05578975352894e-02 , -4.26995495938328e-02 ) ( -6.55630799832673e-05 , 5.93587413507200e-06 , 6.24060508570187e-03 , 2.81368743184070e-06 ) 4.86868668807296e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 23 ( 9.94925517353414e-01 , -9.03127036401896e-02 , 1.06952725287408e-02 , -4.30400002994432e-02 ) ( -6.64079280825436e-05 , 6.02806885909569e-06 , 6.24004647490369e-03 , 2.87277509190952e-06 ) 4.86782932654013e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 24 ( 9.94892910859826e-01 , -9.04801900685380e-02 , 1.08392645748153e-02 , -4.34043945874284e-02 ) ( -6.72936746700319e-05 , 6.11999985937453e-06 , 6.23946083147816e-03 , 2.93583477853088e-06 ) 4.86693074746560e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 25 ( 9.94865273858061e-01 , -9.05888555574097e-02 , 1.09769252601266e-02 , -4.37750297767849e-02 ) ( -6.81405121220271e-05 , 6.20463008653664e-06 , 6.23890081877020e-03 , 2.99824813020128e-06 ) 4.86607175534625e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 26 ( 9.94842696098306e-01 , -9.06481906689943e-02 , 1.10954290528118e-02 , -4.41339665385350e-02 ) ( -6.88694319684040e-05 , 6.27525278601464e-06 , 6.23841864350692e-03 , 3.05523799686328e-06 ) 4.86533236044889e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 27 ( 9.94824961330116e-01 , -9.06706551388669e-02 , 1.11829455661831e-02 , -4.44642591266877e-02 ) ( -6.94075830663685e-05 , 6.32596815807546e-06 , 6.23806249527008e-03 , 3.10221081977458e-06 ) 4.86478634363342e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 28 ( 9.94811600274131e-01 , -9.06703741379878e-02 , 1.12294092270974e-02 , -4.47511293948060e-02 ) ( -6.96929861680878e-05 , 6.35204608481931e-06 , 6.23787339223321e-03 , 3.13510602516003e-06 ) 4.86449646840391e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 29 ( 9.94801962743773e-01 , -9.06616914676642e-02 , 1.12271170184627e-02 , -4.49829352623114e-02 ) ( -6.96781856436282e-05 , 6.35015048766679e-06 , 6.23788272163551e-03 , 3.15070680536035e-06 ) 4.86451076872475e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 30 ( 9.94795292310257e-01 , -9.06578499543900e-02 , 1.11711246155064e-02 , -4.51518173922375e-02 ) ( -6.93326642576498e-05 , 6.31843588504616e-06 , 6.23811060337159e-03 , 3.14687435704348e-06 ) 4.86486009296005e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 31 ( 9.94790789451105e-01 , -9.06700191965351e-02 , 1.10594512797368e-02 , -4.52539653460176e-02 ) ( -6.86440920532849e-05 , 6.25655284528142e-06 , 6.23856504120304e-03 , 3.12268408184823e-06 ) 4.86555683503798e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 32 ( 9.94787654126230e-01 , -9.07067971467051e-02 , 1.08931307986771e-02 , -4.52895114880088e-02 ) ( -6.76186432835818e-05 , 6.16560784024465e-06 , 6.23924171412794e-03 , 3.07846132699065e-06 ) 4.86659461748473e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 33 ( 9.94785105281604e-01 , -9.07741931445759e-02 , 1.06761505567364e-02 , -4.52621252053962e-02 ) ( -6.62806416135132e-05 , 6.04811203105849e-06 , 6.24012423798566e-03 , 3.01572941078122e-06 ) 4.86794866290398e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 34 ( 9.94782382229110e-01 , -9.08759773165833e-02 , 1.04153039282901e-02 , -4.51784262387849e-02 ) ( -6.46716868136083e-05 , 5.90792805430392e-06 , 6.24118479330421e-03 , 2.93708964356536e-06 ) 4.86957669766956e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 35 ( 9.94778739477024e-01 , -9.10141865840077e-02 , 1.01199505360086e-02 , -4.50473520431876e-02 ) ( -6.28492246685917e-05 , 5.75019432326694e-06 , 6.24238513756400e-03 , 2.84605112366581e-06 ) 4.87142042443290e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 36 ( 9.94773450420717e-01 , -9.11895400566741e-02 , 9.80164979465735e-03 , -4.48795920616019e-02 ) ( -6.08843396302519e-05 , 5.58118526905689e-06 , 6.24367813620281e-03 , 2.74682072022538e-06 ) 4.87340778324529e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 37 ( 9.94765833373519e-01 , -9.14015657772049e-02 , 9.47362447441949e-03 , -4.46871454165775e-02 ) ( -5.88584935456410e-05 , 5.40806518365723e-06 , 6.24500998010697e-03 , 2.64405749758712e-06 ) 4.87545627651339e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 38 ( 9.94755305706783e-01 , -9.16483645522010e-02 , 9.15003259624412e-03 , -4.44829849110689e-02 ) ( -5.68590654435119e-05 , 5.23851476636451e-06 , 6.24632316888377e-03 , 2.54259608938115e-06 ) 4.87747749878614e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 39 ( 9.94741460300375e-01 , -9.19260964888404e-02 , 8.84507527042971e-03 , -4.42807473656820e-02 ) ( -5.49738529586110e-05 , 5.08024638875575e-06 , 6.24756014036145e-03 , 2.44715173914973e-06 ) 4.87938270367466e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 40 ( 9.94724147282287e-01 , -9.22284123842412e-02 , 8.57202435943065e-03 , -4.40943438661931e-02 ) ( -5.32850484997073e-05 , 4.94046056926641e-06 , 6.24866720237444e-03 , 2.36203097903292e-06 ) 4.88108888622058e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt b/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 22567fc90..e9a9f6185 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,7 +92,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -122,6 +126,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,14 +137,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - orientationAngle colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 174f4aa5e..57a7f087b 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.50586699060249e+00 + x 2.50586699278142e+00 } restraint { diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 9e8670803..10296e333 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.34454807259353e+00 -1.29781922903741e-02 - 1 3.34456621006869e+00 -1.29782648402748e-02 - 2 3.33650183434893e+00 -1.29460073373957e-02 - 3 3.31967608173955e+00 -1.28787043269582e-02 - 4 3.29359679364577e+00 -1.27743871745831e-02 - 5 3.25804972949454e+00 -1.26321989179782e-02 - 6 3.21319557916635e+00 -1.24527823166654e-02 - 7 3.15964721770391e+00 -1.22385888708157e-02 - 8 3.09850657690298e+00 -1.19940263076119e-02 - 9 3.03134993712323e+00 -1.17253997484929e-02 - 10 2.96016041313917e+00 -1.14406416525567e-02 - 11 2.88721545954542e+00 -1.11488618381817e-02 - 12 2.81494477251460e+00 -1.08597790900584e-02 - 13 2.74578033330936e+00 -1.05831213332374e-02 - 14 2.68202224548980e+00 -1.03280889819592e-02 - 15 2.62573819506619e+00 -1.01029527802647e-02 - 16 2.57870029809758e+00 -9.91480119239031e-03 - 17 2.54234658587039e+00 -9.76938634348154e-03 - 18 2.51774460747483e+00 -9.67097842989931e-03 - 19 2.50553744033959e+00 -9.62214976135836e-03 - 20 2.50586699060249e+00 -9.62346796240996e-03 + 1 3.34456621005910e+00 -1.29782648402364e-02 + 2 3.33650183431222e+00 -1.29460073372489e-02 + 3 3.31967608166225e+00 -1.28787043266490e-02 + 4 3.29359679352004e+00 -1.27743871740802e-02 + 5 3.25804972932359e+00 -1.26321989172944e-02 + 6 3.21319557896124e+00 -1.24527823158450e-02 + 7 3.15964721748749e+00 -1.22385888699500e-02 + 8 3.09850657670722e+00 -1.19940263068289e-02 + 9 3.03134993698711e+00 -1.17253997479484e-02 + 10 2.96016041310420e+00 -1.14406416524168e-02 + 11 2.88721545965500e+00 -1.11488618386200e-02 + 12 2.81494477280673e+00 -1.08597790912269e-02 + 13 2.74578033381965e+00 -1.05831213352786e-02 + 14 2.68202224624271e+00 -1.03280889849708e-02 + 15 2.62573819607844e+00 -1.01029527843138e-02 + 16 2.57870029937537e+00 -9.91480119750147e-03 + 17 2.54234658740788e+00 -9.76938634963152e-03 + 18 2.51774460925550e+00 -9.67097843702200e-03 + 19 2.50553744233726e+00 -9.62214976934902e-03 + 20 2.50586699278142e+00 -9.62346797112569e-03 diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index 706323615..e3acdcd80 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,7 +92,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -122,6 +126,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,19 +137,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - orientationAngle colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 2.50587 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 92df7f52f..86c2b39dd 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.59806113934628e+00 + x 2.59806114483912e+00 } restraint { diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 08b065f51..64498a7a8 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.50586699060249e+00 -9.62346796240996e-03 - 21 2.51828912444925e+00 -9.67315649779702e-03 - 22 2.54171016390634e+00 -9.76684065562536e-03 - 23 2.57437672068062e+00 -9.89750688272248e-03 - 24 2.61394043953042e+00 -1.00557617581217e-02 - 25 2.65760032461011e+00 -1.02304012984404e-02 - 26 2.70230713425706e+00 -1.04092285370282e-02 - 27 2.74500166558147e+00 -1.05800066623259e-02 - 28 2.78285410144146e+00 -1.07314164057658e-02 - 29 2.81347401811216e+00 -1.08538960724486e-02 - 30 2.83506753488489e+00 -1.09402701395396e-02 - 31 2.84652760030681e+00 -1.09861104012272e-02 - 32 2.84745364001396e+00 -1.09898145600559e-02 - 33 2.83810685678234e+00 -1.09524274271294e-02 - 34 2.81931678845251e+00 -1.08772671538101e-02 - 35 2.79236160334505e+00 -1.07694464133802e-02 - 36 2.75884755937459e+00 -1.06353902374984e-02 - 37 2.72060908633430e+00 -1.04824363453372e-02 - 38 2.67964053899086e+00 -1.03185621559634e-02 - 39 2.63805614546050e+00 -1.01522245818420e-02 - 40 2.59806113934628e+00 -9.99224455738511e-03 + 20 2.50586699278142e+00 -9.62346797112569e-03 + 21 2.51828912676855e+00 -9.67315650707419e-03 + 22 2.54171016632473e+00 -9.76684066529891e-03 + 23 2.57437672315441e+00 -9.89750689261763e-03 + 24 2.61394044202478e+00 -1.00557617680991e-02 + 25 2.65760032709751e+00 -1.02304013083901e-02 + 26 2.70230713671789e+00 -1.04092285468715e-02 + 27 2.74500166801146e+00 -1.05800066720458e-02 + 28 2.78285410384574e+00 -1.07314164153830e-02 + 29 2.81347402051205e+00 -1.08538960820482e-02 + 30 2.83506753731124e+00 -1.09402701492450e-02 + 31 2.84652760280228e+00 -1.09861104112091e-02 + 32 2.84745364262997e+00 -1.09898145705199e-02 + 33 2.83810685957546e+00 -1.09524274383019e-02 + 34 2.81931679148249e+00 -1.08772671659299e-02 + 35 2.79236160667317e+00 -1.07694464266927e-02 + 36 2.75884756305916e+00 -1.06353902522366e-02 + 37 2.72060909042328e+00 -1.04824363616931e-02 + 38 2.67964054352647e+00 -1.03185621741059e-02 + 39 2.63805615046828e+00 -1.01522246018731e-02 + 40 2.59806114483912e+00 -9.99224457935649e-03 diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt index 129300d44..157cac038 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out index 9e25d6b26..23e52329c 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -104,6 +108,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -114,14 +119,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - orientationAngle colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index b775835f5..3794713ae 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.14042525000436e+01 + x 1.14042524977569e+01 } restraint { diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj index 362277f2e..208ef8be6 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.05987658982707e+01 -4.19950635930827e-02 - 1 1.06266098864992e+01 -4.21064395459970e-02 - 2 1.06570380232614e+01 -4.22281520930457e-02 - 3 1.06891026493980e+01 -4.23564105975918e-02 - 4 1.07220322921382e+01 -4.24881291685529e-02 - 5 1.07553082612621e+01 -4.26212330450483e-02 - 6 1.07886956708129e+01 -4.27547826832515e-02 - 7 1.08222315378305e+01 -4.28889261513219e-02 - 8 1.08561787305042e+01 -4.30247149220168e-02 - 9 1.08909573890554e+01 -4.31638295562217e-02 - 10 1.09270659264173e+01 -4.33082637056690e-02 - 11 1.09650029613711e+01 -4.34600118454845e-02 - 12 1.10051994776244e+01 -4.36207979104977e-02 - 13 1.10479655809806e+01 -4.37918623239224e-02 - 14 1.10934497464229e+01 -4.39737989856916e-02 - 15 1.11416047509002e+01 -4.41664190036009e-02 - 16 1.11921570627529e+01 -4.43686282510115e-02 - 17 1.12445838379582e+01 -4.45783353518327e-02 - 18 1.12981079856473e+01 -4.47924319425893e-02 - 19 1.13517227452027e+01 -4.50068909808106e-02 - 20 1.14042525000436e+01 -4.52170100001743e-02 + 1 1.06266098865076e+01 -4.21064395460305e-02 + 2 1.06570380232944e+01 -4.22281520931778e-02 + 3 1.06891026494686e+01 -4.23564105978743e-02 + 4 1.07220322922544e+01 -4.24881291690175e-02 + 5 1.07553082614248e+01 -4.26212330456994e-02 + 6 1.07886956710148e+01 -4.27547826840591e-02 + 7 1.08222315380552e+01 -4.28889261522210e-02 + 8 1.08561787307268e+01 -4.30247149229071e-02 + 9 1.08909573892425e+01 -4.31638295569698e-02 + 10 1.09270659265304e+01 -4.33082637061217e-02 + 11 1.09650029613683e+01 -4.34600118454733e-02 + 12 1.10051994774624e+01 -4.36207979098498e-02 + 13 1.10479655806188e+01 -4.37918623224750e-02 + 14 1.10934497458239e+01 -4.39737989832956e-02 + 15 1.11416047500329e+01 -4.41664190001316e-02 + 16 1.11921570615955e+01 -4.43686282463821e-02 + 17 1.12445838365001e+01 -4.45783353460005e-02 + 18 1.12981079838905e+01 -4.47924319355620e-02 + 19 1.13517227431649e+01 -4.50068909726597e-02 + 20 1.14042524977569e+01 -4.52170099910277e-02 diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 659cdc13a..8a00c0457 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -104,6 +108,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -114,19 +119,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - orientationAngle colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 11.4043 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index a902f9774..d6e8c97ef 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.17634448064811e+01 + x 1.17634448022492e+01 } restraint { diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 9b350dcb7..4da52b8db 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.14042525000436e+01 -4.52170100001743e-02 - 21 1.14544480780461e+01 -4.54177923121844e-02 - 22 1.15011053923729e+01 -4.56044215694917e-02 - 23 1.15431885969782e+01 -4.57727543879128e-02 - 24 1.15799356451165e+01 -4.59197425804660e-02 - 25 1.16109269861924e+01 -4.60437079447695e-02 - 26 1.16361065810996e+01 -4.61444263243983e-02 - 27 1.16557559231474e+01 -4.62230236925897e-02 - 28 1.16704320392906e+01 -4.62817281571624e-02 - 29 1.16808864197082e+01 -4.63235456788327e-02 - 30 1.16879826731775e+01 -4.63519306927099e-02 - 31 1.16926277194411e+01 -4.63705108777642e-02 - 32 1.16957259285228e+01 -4.63829037140912e-02 - 33 1.16981585991540e+01 -4.63926343966159e-02 - 34 1.17007830917475e+01 -4.64031323669901e-02 - 35 1.17044386489778e+01 -4.64177545959111e-02 - 36 1.17099416859060e+01 -4.64397667436240e-02 - 37 1.17180555444153e+01 -4.64722221776613e-02 - 38 1.17294285137575e+01 -4.65177140550300e-02 - 39 1.17445071578377e+01 -4.65780286313510e-02 - 40 1.17634448064811e+01 -4.66537792259242e-02 + 20 1.14042524977569e+01 -4.52170099910277e-02 + 21 1.14544480755564e+01 -4.54177923022257e-02 + 22 1.15011053897376e+01 -4.56044215589506e-02 + 23 1.15431885942609e+01 -4.57727543770436e-02 + 24 1.15799356423833e+01 -4.59197425695332e-02 + 25 1.16109269835055e+01 -4.60437079340218e-02 + 26 1.16361065785131e+01 -4.61444263140523e-02 + 27 1.16557559207023e+01 -4.62230236828094e-02 + 28 1.16704320370109e+01 -4.62817281480436e-02 + 29 1.16808864175993e+01 -4.63235456703971e-02 + 30 1.16879826712242e+01 -4.63519306848966e-02 + 31 1.16926277176089e+01 -4.63705108704357e-02 + 32 1.16957259267591e+01 -4.63829037070363e-02 + 33 1.16981585973899e+01 -4.63926343895594e-02 + 34 1.17007830899012e+01 -4.64031323596047e-02 + 35 1.17044386469586e+01 -4.64177545878343e-02 + 36 1.17099416836191e+01 -4.64397667344764e-02 + 37 1.17180555417655e+01 -4.64722221670619e-02 + 38 1.17294285106548e+01 -4.65177140426191e-02 + 39 1.17445071542025e+01 -4.65780286168101e-02 + 40 1.17634448022492e+01 -4.66537792089967e-02 diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt index 129300d44..157cac038 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 3159c4a1d..e3dd29780 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,7 +92,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -122,6 +126,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,14 +137,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - orientationProj colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 8993379a3..6aab80c05 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.99042890073178e-01 + x 9.99042890071513e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 52560e9b2..6408cd312 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 9.98296758220625e-01 -3.59318703288250e-03 - 1 9.98296730621296e-01 -3.59318692248518e-03 - 2 9.98304905164651e-01 -3.59321962065860e-03 - 3 9.98321909943172e-01 -3.59328763977269e-03 - 4 9.98348106341147e-01 -3.59339242536459e-03 - 5 9.98383489829382e-01 -3.59353395931753e-03 - 6 9.98427599823041e-01 -3.59371039929216e-03 - 7 9.98479469809825e-01 -3.59391787923930e-03 - 8 9.98537639417652e-01 -3.59415055767061e-03 - 9 9.98600233958565e-01 -3.59440093583426e-03 - 10 9.98665100608658e-01 -3.59466040243463e-03 - 11 9.98729977781503e-01 -3.59491991112601e-03 - 12 9.98792667792032e-01 -3.59517067116813e-03 - 13 9.98851182638057e-01 -3.59540473055223e-03 - 14 9.98903839987981e-01 -3.59561535995193e-03 - 15 9.98949300567580e-01 -3.59579720227032e-03 - 16 9.98986555616080e-01 -3.59594622246432e-03 - 17 9.99014887277948e-01 -3.59605954911179e-03 - 18 9.99033829854858e-01 -3.59613531941943e-03 - 19 9.99043154767953e-01 -3.59617261907181e-03 - 20 9.99042890073178e-01 -3.59617156029271e-03 + 1 9.98296730621305e-01 -3.59318692248522e-03 + 2 9.98304905164688e-01 -3.59321962065875e-03 + 3 9.98321909943251e-01 -3.59328763977300e-03 + 4 9.98348106341271e-01 -3.59339242536509e-03 + 5 9.98383489829552e-01 -3.59353395931821e-03 + 6 9.98427599823242e-01 -3.59371039929297e-03 + 7 9.98479469810032e-01 -3.59391787924013e-03 + 8 9.98537639417837e-01 -3.59415055767135e-03 + 9 9.98600233958691e-01 -3.59440093583477e-03 + 10 9.98665100608690e-01 -3.59466040243476e-03 + 11 9.98729977781407e-01 -3.59491991112563e-03 + 12 9.98792667791781e-01 -3.59517067116713e-03 + 13 9.98851182637630e-01 -3.59540473055052e-03 + 14 9.98903839987366e-01 -3.59561535994946e-03 + 15 9.98949300566769e-01 -3.59579720226708e-03 + 16 9.98986555615076e-01 -3.59594622246030e-03 + 17 9.99014887276758e-01 -3.59605954910703e-03 + 18 9.99033829853492e-01 -3.59613531941397e-03 + 19 9.99043154766428e-01 -3.59617261906571e-03 + 20 9.99042890071513e-01 -3.59617156028605e-03 diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index deb021ce1..8798aa21c 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,7 +92,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -122,6 +126,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,19 +137,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - orientationProj colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.999043 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 0f04cd392..8b0add5c8 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.98970741883698e-01 + x 9.98970741879346e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 7997c7579..32cfd70e2 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.99042890073178e-01 -3.59617156029271e-03 - 21 9.99033371045725e-01 -3.59613348418290e-03 - 22 9.99015305960388e-01 -3.59606122384155e-03 - 23 9.98989833769218e-01 -3.59595933507687e-03 - 24 9.98958548400342e-01 -3.59583419360137e-03 - 25 9.98923468754291e-01 -3.59569387501716e-03 - 26 9.98886942697797e-01 -3.59554777079119e-03 - 27 9.98851487061923e-01 -3.59540594824769e-03 - 28 9.98819580889739e-01 -3.59527832355896e-03 - 29 9.98793441990623e-01 -3.59517376796249e-03 - 30 9.98774823524341e-01 -3.59509929409736e-03 - 31 9.98764865064516e-01 -3.59505946025807e-03 - 32 9.98764021745399e-01 -3.59505608698159e-03 - 33 9.98772078285790e-01 -3.59508831314316e-03 - 34 9.98788236185128e-01 -3.59515294474051e-03 - 35 9.98811247692583e-01 -3.59524499077033e-03 - 36 9.98839563237711e-01 -3.59535825295084e-03 - 37 9.98871462840668e-01 -3.59548585136267e-03 - 38 9.98905154304598e-01 -3.59562061721839e-03 - 39 9.98938836857002e-01 -3.59575534742801e-03 - 40 9.98970741883698e-01 -3.59588296753479e-03 + 20 9.99042890071513e-01 -3.59617156028605e-03 + 21 9.99033371043944e-01 -3.59613348417578e-03 + 22 9.99015305958516e-01 -3.59606122383406e-03 + 23 9.98989833767277e-01 -3.59595933506911e-03 + 24 9.98958548398355e-01 -3.59583419359342e-03 + 25 9.98923468752275e-01 -3.59569387500910e-03 + 26 9.98886942695769e-01 -3.59554777078308e-03 + 27 9.98851487059890e-01 -3.59540594823956e-03 + 28 9.98819580887699e-01 -3.59527832355080e-03 + 29 9.98793441988564e-01 -3.59517376795426e-03 + 30 9.98774823522244e-01 -3.59509929408898e-03 + 31 9.98764865062350e-01 -3.59505946024940e-03 + 32 9.98764021743129e-01 -3.59505608697251e-03 + 33 9.98772078283373e-01 -3.59508831313349e-03 + 34 9.98788236182522e-01 -3.59515294473009e-03 + 35 9.98811247689749e-01 -3.59524499075900e-03 + 36 9.98839563234612e-01 -3.59535825293845e-03 + 37 9.98871462837275e-01 -3.59548585134910e-03 + 38 9.98905154300893e-01 -3.59562061720357e-03 + 39 9.98938836852973e-01 -3.59575534741189e-03 + 40 9.98970741879346e-01 -3.59588296751738e-03 diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt index 129300d44..157cac038 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out index 0867faa1d..15ba472df 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -104,6 +108,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -114,14 +119,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - orientationProj colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped index fbbe4454a..dbd322f7c 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.80239375941569e-01 + x 9.80239375949467e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj index 63a14b625..2a3c28388 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 9.82939311075160e-01 -3.53175724430064e-03 - 1 9.82849734901072e-01 -3.53139893960429e-03 - 2 9.82751436474814e-01 -3.53100574589926e-03 - 3 9.82647417671973e-01 -3.53058967068789e-03 - 4 9.82540144797111e-01 -3.53016057918845e-03 - 5 9.82431293276853e-01 -3.52972517310741e-03 - 6 9.82321634340193e-01 -3.52928653736077e-03 - 7 9.82211059380804e-01 -3.52884423752322e-03 - 8 9.82098716904383e-01 -3.52839486761753e-03 - 9 9.81983226206714e-01 -3.52793290482686e-03 - 10 9.81862929059493e-01 -3.52745171623797e-03 - 11 9.81736142358011e-01 -3.52694456943204e-03 - 12 9.81601381064049e-01 -3.52640552425620e-03 - 13 9.81457536904562e-01 -3.52583014761825e-03 - 14 9.81304019861054e-01 -3.52521607944422e-03 - 15 9.81140882068755e-01 -3.52456352827502e-03 - 16 9.80968935305186e-01 -3.52387574122074e-03 - 17 9.80789847964994e-01 -3.52315939185998e-03 - 18 9.80606184557429e-01 -3.52242473822972e-03 - 19 9.80421345121349e-01 -3.52168538048540e-03 - 20 9.80239375941569e-01 -3.52095750376628e-03 + 1 9.82849734901045e-01 -3.53139893960418e-03 + 2 9.82751436474708e-01 -3.53100574589883e-03 + 3 9.82647417671745e-01 -3.53058967068698e-03 + 4 9.82540144796735e-01 -3.53016057918694e-03 + 5 9.82431293276323e-01 -3.52972517310529e-03 + 6 9.82321634339533e-01 -3.52928653735813e-03 + 7 9.82211059380067e-01 -3.52884423752027e-03 + 8 9.82098716903652e-01 -3.52839486761461e-03 + 9 9.81983226206096e-01 -3.52793290482439e-03 + 10 9.81862929059119e-01 -3.52745171623648e-03 + 11 9.81736142358021e-01 -3.52694456943208e-03 + 12 9.81601381064589e-01 -3.52640552425836e-03 + 13 9.81457536905773e-01 -3.52583014762309e-03 + 14 9.81304019863068e-01 -3.52521607945227e-03 + 15 9.81140882071682e-01 -3.52456352828673e-03 + 16 9.80968935309110e-01 -3.52387574123644e-03 + 17 9.80789847969960e-01 -3.52315939187984e-03 + 18 9.80606184563440e-01 -3.52242473825376e-03 + 19 9.80421345128356e-01 -3.52168538051342e-03 + 20 9.80239375949467e-01 -3.52095750379787e-03 diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out index 821e0a8d3..5af1ca243 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -104,6 +108,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -114,19 +119,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - orientationProj colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.980239 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 39341551b..32bda65e7 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.78952248438667e-01 + x 9.78952248453755e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 36e1592b7..f961e9ce6 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.80239375941569e-01 -3.52095750376628e-03 - 21 9.80064651407338e-01 -3.52025860562935e-03 - 22 9.79901460928968e-01 -3.51960584371587e-03 - 23 9.79753565294644e-01 -3.51901426117858e-03 - 24 9.79623802999823e-01 -3.51849521199929e-03 - 25 9.79513820802291e-01 -3.51805528320916e-03 - 26 9.79423974205426e-01 -3.51769589682171e-03 - 27 9.79353401314998e-01 -3.51741360525999e-03 - 28 9.79300233723229e-01 -3.51720093489292e-03 - 29 9.79261883501562e-01 -3.51704753400625e-03 - 30 9.79235340251636e-01 -3.51694136100655e-03 - 31 9.79217422304405e-01 -3.51686968921762e-03 - 32 9.79204946061162e-01 -3.51681978424465e-03 - 33 9.79194803544898e-01 -3.51677921417959e-03 - 34 9.79183967858975e-01 -3.51673587143590e-03 - 35 9.79169472609521e-01 -3.51667789043808e-03 - 36 9.79148426606516e-01 -3.51659370642606e-03 - 37 9.79118117478109e-01 -3.51647246991243e-03 - 38 9.79076227144190e-01 -3.51630490857676e-03 - 39 9.79021136055294e-01 -3.51608454422118e-03 - 40 9.78952248438667e-01 -3.51580899375467e-03 + 20 9.80239375949467e-01 -3.52095750379787e-03 + 21 9.80064651415975e-01 -3.52025860566390e-03 + 22 9.79901460938148e-01 -3.51960584375259e-03 + 23 9.79753565304145e-01 -3.51901426121658e-03 + 24 9.79623803009410e-01 -3.51849521203764e-03 + 25 9.79513820811740e-01 -3.51805528324696e-03 + 26 9.79423974214543e-01 -3.51769589685817e-03 + 27 9.79353401323632e-01 -3.51741360529453e-03 + 28 9.79300233731289e-01 -3.51720093492516e-03 + 29 9.79261883509026e-01 -3.51704753403610e-03 + 30 9.79235340258555e-01 -3.51694136103422e-03 + 31 9.79217422310898e-01 -3.51686968924359e-03 + 32 9.79204946067415e-01 -3.51681978426966e-03 + 33 9.79194803551154e-01 -3.51677921420462e-03 + 34 9.79183967865525e-01 -3.51673587146210e-03 + 35 9.79169472616686e-01 -3.51667789046674e-03 + 36 9.79148426614635e-01 -3.51659370645854e-03 + 37 9.79118117487522e-01 -3.51647246995009e-03 + 38 9.79076227155221e-01 -3.51630490862088e-03 + 39 9.79021136068235e-01 -3.51608454427294e-03 + 40 9.78952248453755e-01 -3.51580899381502e-03 diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt index 129300d44..157cac038 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index e3e2b88a3..188d105ae 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -94,7 +98,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,6 +126,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,14 +137,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index a5b66188c..95457b174 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.51992447935402e-01 + x 6.51992448739790e-01 } restraint { diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 20f9e8ab6..9ff521cd9 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 6.42446480928998e-01 -2.16978592371599e-03 - 1 6.41362151827951e-01 -2.16544860731180e-03 - 2 6.39964191522473e-01 -2.15985676608989e-03 - 3 6.38339929621363e-01 -2.15335971848545e-03 - 4 6.36588007540679e-01 -2.14635203016272e-03 - 5 6.34817335398304e-01 -2.13926934159321e-03 - 6 6.33145320132662e-01 -2.13258128053065e-03 - 7 6.31694089805813e-01 -2.12677635922325e-03 - 8 6.30583853131960e-01 -2.12233541252784e-03 - 9 6.29923415581364e-01 -2.11969366232546e-03 - 10 6.29798996732227e-01 -2.11919598692891e-03 - 11 6.30263471904012e-01 -2.12105388761605e-03 - 12 6.31328581404817e-01 -2.12531432561927e-03 - 13 6.32962276627263e-01 -2.13184910650905e-03 - 14 6.35092221427288e-01 -2.14036888570915e-03 - 15 6.37614970671458e-01 -2.15045988268583e-03 - 16 6.40409021950152e-01 -2.16163608780061e-03 - 17 6.43349209139955e-01 -2.17339683655982e-03 - 18 6.46319867119914e-01 -2.18527946847966e-03 - 19 6.49224737403552e-01 -2.19689894961421e-03 - 20 6.51992447935402e-01 -2.20796979174161e-03 + 0 6.42446480928994e-01 -2.16978592371598e-03 + 1 6.41362151829732e-01 -2.16544860731893e-03 + 2 6.39964191531625e-01 -2.15985676612650e-03 + 3 6.38339929638892e-01 -2.15335971855557e-03 + 4 6.36588007574356e-01 -2.14635203029742e-03 + 5 6.34817335440207e-01 -2.13926934176083e-03 + 6 6.33145320204402e-01 -2.13258128081761e-03 + 7 6.31694089901779e-01 -2.12677635960711e-03 + 8 6.30583853252009e-01 -2.12233541300803e-03 + 9 6.29923415729674e-01 -2.11969366291869e-03 + 10 6.29798996911838e-01 -2.11919598764735e-03 + 11 6.30263472118592e-01 -2.12105388847437e-03 + 12 6.31328581658953e-01 -2.12531432663581e-03 + 13 6.32962276844382e-01 -2.13184910737753e-03 + 14 6.35092221778593e-01 -2.14036888711437e-03 + 15 6.37614971049963e-01 -2.15045988419985e-03 + 16 6.40409022430485e-01 -2.16163608972194e-03 + 17 6.43349209707525e-01 -2.17339683883010e-03 + 18 6.46319867665476e-01 -2.18527947066190e-03 + 19 6.49224738102162e-01 -2.19689895240865e-03 + 20 6.51992448739790e-01 -2.20796979495916e-03 diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index d4194b991..f1030f219 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -94,7 +98,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,6 +126,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,19 +137,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.651992 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 57f5c66cf..2c5997d6d 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.75350774255469e-01 + x 6.75350774458524e-01 } restraint { diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 465a8190b..db5a45ae4 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 6.51992447935402e-01 -2.20796979174161e-03 - 21 6.54577358969536e-01 -2.21830943587814e-03 - 22 6.56956476804603e-01 -2.22782590721841e-03 - 23 6.59123836309169e-01 -2.23649534523667e-03 - 24 6.61084124493515e-01 -2.24433649797406e-03 - 25 6.62847213541526e-01 -2.25138885416610e-03 - 26 6.64424716728470e-01 -2.25769886691388e-03 - 27 6.65828839710307e-01 -2.26331535884123e-03 - 28 6.67072977661715e-01 -2.26829191064686e-03 - 29 6.68172990385695e-01 -2.27269196154278e-03 - 30 6.69147997661702e-01 -2.27659199064681e-03 - 31 6.70019871557500e-01 -2.28007948623000e-03 - 32 6.70811208574338e-01 -2.28324483429735e-03 - 33 6.71542239966417e-01 -2.28616895986567e-03 - 34 6.72227643578755e-01 -2.28891057431502e-03 - 35 6.72874368078643e-01 -2.29149747231457e-03 - 36 6.73481315978386e-01 -2.29392526391354e-03 - 37 6.74041160330857e-01 -2.29616464132343e-03 - 38 6.74543902153436e-01 -2.29817560861374e-03 - 39 6.74981258926052e-01 -2.29992503570421e-03 - 40 6.75350774255469e-01 -2.30140309702188e-03 + 20 6.51992448739790e-01 -2.20796979495916e-03 + 21 6.54577359871602e-01 -2.21830943948641e-03 + 22 6.56956477797988e-01 -2.22782591119195e-03 + 23 6.59123837391726e-01 -2.23649534956690e-03 + 24 6.61084125660818e-01 -2.24433650264327e-03 + 25 6.62847214781938e-01 -2.25138885912775e-03 + 26 6.64424718041335e-01 -2.25769887216534e-03 + 27 6.65828841073339e-01 -2.26331536429336e-03 + 28 6.67072979054150e-01 -2.26829191621660e-03 + 29 6.68172991793991e-01 -2.27269196717596e-03 + 30 6.69147999050168e-01 -2.27659199620067e-03 + 31 6.70019872911646e-01 -2.28007949164658e-03 + 32 6.70811209861948e-01 -2.28324483944779e-03 + 33 6.71542241163152e-01 -2.28616896465261e-03 + 34 6.72227644663412e-01 -2.28891057865365e-03 + 35 6.72874369034013e-01 -2.29149747613605e-03 + 36 6.73481316803640e-01 -2.29392526721456e-03 + 37 6.74041160994404e-01 -2.29616464397762e-03 + 38 6.74543902662182e-01 -2.29817561064873e-03 + 39 6.74981259280343e-01 -2.29992503712137e-03 + 40 6.75350774458524e-01 -2.30140309783410e-03 diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out index 66f42f578..0df5ce6ef 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,13 +74,13 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -104,6 +108,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -114,14 +119,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 5965781f5..59c145889 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.34779999776054e-01 + x 6.34779999706673e-01 } restraint { diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj index 4aec974c6..0de897eb5 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 6.13624515542246e-01 -2.05449806216899e-03 - 1 6.12490538024335e-01 -2.04996215209734e-03 - 2 6.11173746799938e-01 -2.04469498719975e-03 - 3 6.09786235548445e-01 -2.03914494219378e-03 - 4 6.08443934153189e-01 -2.03377573661276e-03 - 5 6.07262363750067e-01 -2.02904945500027e-03 - 6 6.06352646518334e-01 -2.02541058607334e-03 - 7 6.05817100403672e-01 -2.02326840161469e-03 - 8 6.05743803262677e-01 -2.02297521305071e-03 - 9 6.06199958866108e-01 -2.02479983546443e-03 - 10 6.07224667113594e-01 -2.02889866845438e-03 - 11 6.08822487990989e-01 -2.03528995196396e-03 - 12 6.10959603629905e-01 -2.04383841451962e-03 - 13 6.13564160971268e-01 -2.05425664388507e-03 - 14 6.16531504985440e-01 -2.06612601994176e-03 - 15 6.19733849359571e-01 -2.07893539743829e-03 - 16 6.23032907749212e-01 -2.09213163099685e-03 - 17 6.26293468706736e-01 -2.10517387482694e-03 - 18 6.29395874814933e-01 -2.11758349925973e-03 - 19 6.32245759668358e-01 -2.12898303867343e-03 - 20 6.34779999776054e-01 -2.13911999910422e-03 + 0 6.13624515542194e-01 -2.05449806216878e-03 + 1 6.12490538024418e-01 -2.04996215209767e-03 + 2 6.11173746800116e-01 -2.04469498720046e-03 + 3 6.09786235548945e-01 -2.03914494219578e-03 + 4 6.08443934153914e-01 -2.03377573661566e-03 + 5 6.07262363747078e-01 -2.02904945498831e-03 + 6 6.06352646519890e-01 -2.02541058607956e-03 + 7 6.05817100403337e-01 -2.02326840161335e-03 + 8 6.05743803259169e-01 -2.02297521303668e-03 + 9 6.06199958858187e-01 -2.02479983543275e-03 + 10 6.07224667100095e-01 -2.02889866840038e-03 + 11 6.08822487970901e-01 -2.03528995188360e-03 + 12 6.10959603602463e-01 -2.04383841440985e-03 + 13 6.13564160848909e-01 -2.05425664339564e-03 + 14 6.16531504942698e-01 -2.06612601977079e-03 + 15 6.19733849273886e-01 -2.07893539709555e-03 + 16 6.23032907695619e-01 -2.09213163078248e-03 + 17 6.26293468659005e-01 -2.10517387463602e-03 + 18 6.29395874658527e-01 -2.11758349863411e-03 + 19 6.32245759582595e-01 -2.12898303833038e-03 + 20 6.34779999706673e-01 -2.13911999882669e-03 diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out index 46a799d77..c6589b658 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,13 +74,13 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -104,6 +108,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -114,19 +119,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.63478 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 1b15cce3c..c6c8eee84 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.57869102603360e-01 + x 6.57869102539559e-01 } restraint { diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj index b53dc8777..6131bf0e9 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 6.34779999776054e-01 -2.13911999910422e-03 - 21 6.36968499730488e-01 -2.14787399892195e-03 - 22 6.38812086644733e-01 -2.15524834657893e-03 - 23 6.40337357461428e-01 -2.16134942984571e-03 - 24 6.41589727271310e-01 -2.16635890908524e-03 - 25 6.42626037763938e-01 -2.17050415105575e-03 - 26 6.43507870335777e-01 -2.17403148134311e-03 - 27 6.44296238145373e-01 -2.17718495258149e-03 - 28 6.45047779464950e-01 -2.18019111785980e-03 - 29 6.45812131951865e-01 -2.18324852780746e-03 - 30 6.46629949006064e-01 -2.18651979602426e-03 - 31 6.47531080168799e-01 -2.19012432067520e-03 - 32 6.48532731443661e-01 -2.19413092577464e-03 - 33 6.49637836133461e-01 -2.19855134453384e-03 - 34 6.50834212234814e-01 -2.20333684893926e-03 - 35 6.52095178934730e-01 -2.20838071573892e-03 - 36 6.53382073098997e-01 -2.21352829239599e-03 - 37 6.54648626732206e-01 -2.21859450692882e-03 - 38 6.55846616507654e-01 -2.22338646603062e-03 - 39 6.56931804692009e-01 -2.22772721876803e-03 - 40 6.57869102603360e-01 -2.23147641041344e-03 + 20 6.34779999706673e-01 -2.13911999882669e-03 + 21 6.36968499670390e-01 -2.14787399868156e-03 + 22 6.38812086586848e-01 -2.15524834634739e-03 + 23 6.40337357406265e-01 -2.16134942962506e-03 + 24 6.41589727219131e-01 -2.16635890887652e-03 + 25 6.42626037705784e-01 -2.17050415082314e-03 + 26 6.43507870289948e-01 -2.17403148115979e-03 + 27 6.44296238099800e-01 -2.17718495239920e-03 + 28 6.45047779413727e-01 -2.18019111765491e-03 + 29 6.45812131910624e-01 -2.18324852764250e-03 + 30 6.46629948954352e-01 -2.18651979581741e-03 + 31 6.47531080128373e-01 -2.19012432051349e-03 + 32 6.48532731402192e-01 -2.19413092560877e-03 + 33 6.49637836090191e-01 -2.19855134436077e-03 + 34 6.50834212189133e-01 -2.20333684875653e-03 + 35 6.52095178886227e-01 -2.20838071554491e-03 + 36 6.53382073051404e-01 -2.21352829220561e-03 + 37 6.54648626678558e-01 -2.21859450671423e-03 + 38 6.55846616450873e-01 -2.22338646580349e-03 + 39 6.56931804632144e-01 -2.22772721852858e-03 + 40 6.57869102539559e-01 -2.23147641015824e-03 diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt b/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out index 162de8092..61f83bfee 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -103,6 +107,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -113,14 +118,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - selfCoordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped index b757a82d5..699308a19 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.50086992991043e+00 + x 5.50086993007309e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj index 4497991fb..3eabd5c33 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 5.50064408080373e+00 -2.16025763232149e-02 - 1 5.50080703004843e+00 -2.16032281201937e-02 - 2 5.50068939069653e+00 -2.16027575627861e-02 - 3 5.50034727665768e+00 -2.16013891066307e-02 - 4 5.49985543898452e+00 -2.15994217559381e-02 - 5 5.49929900079136e+00 -2.15971960031654e-02 - 6 5.49876326011562e+00 -2.15950530404625e-02 - 7 5.49832342751543e+00 -2.15932937100617e-02 - 8 5.49803620213495e+00 -2.15921448085398e-02 - 9 5.49793456345215e+00 -2.15917382538086e-02 - 10 5.49802625410834e+00 -2.15921050164334e-02 - 11 5.49829556490095e+00 -2.15931822596038e-02 - 12 5.49870744197941e+00 -2.15948297679177e-02 - 13 5.49921283621840e+00 -2.15968513448736e-02 - 14 5.49975442842220e+00 -2.15990177136888e-02 - 15 5.50027220375965e+00 -2.16010888150386e-02 - 16 5.50070878627497e+00 -2.16028351450999e-02 - 17 5.50101460460263e+00 -2.16040584184105e-02 - 18 5.50115288487476e+00 -2.16046115394991e-02 - 19 5.50110418952966e+00 -2.16044167581187e-02 - 20 5.50086992991043e+00 -2.16034797196417e-02 + 1 5.50080703004882e+00 -2.16032281201953e-02 + 2 5.50068939069810e+00 -2.16027575627924e-02 + 3 5.50034727666126e+00 -2.16013891066450e-02 + 4 5.49985543899098e+00 -2.15994217559639e-02 + 5 5.49929900080157e+00 -2.15971960032063e-02 + 6 5.49876326013045e+00 -2.15950530405218e-02 + 7 5.49832342753577e+00 -2.15932937101431e-02 + 8 5.49803620216166e+00 -2.15921448086467e-02 + 9 5.49793456348608e+00 -2.15917382539443e-02 + 10 5.49802625415031e+00 -2.15921050166012e-02 + 11 5.49829556495176e+00 -2.15931822598070e-02 + 12 5.49870744203985e+00 -2.15948297681594e-02 + 13 5.49921283628923e+00 -2.15968513451569e-02 + 14 5.49975442850415e+00 -2.15990177140166e-02 + 15 5.50027220385344e+00 -2.16010888154138e-02 + 16 5.50070878638128e+00 -2.16028351455251e-02 + 17 5.50101460472211e+00 -2.16040584188884e-02 + 18 5.50115288500804e+00 -2.16046115400322e-02 + 19 5.50110418967735e+00 -2.16044167587094e-02 + 20 5.50086993007309e+00 -2.16034797202924e-02 diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out index c7aa828f5..2b29746be 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -103,6 +107,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -113,19 +118,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - selfCoordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 5.50087 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index c26ac3859..4e2699486 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.52672800804253e+00 + x 5.52672800845913e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 2eae1fa46..ae8c62635 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.50086992991043e+00 -2.16034797196417e-02 - 21 5.50047411684707e+00 -2.16018964673883e-02 - 22 5.49996271461392e+00 -2.15998508584557e-02 - 23 5.49940030442948e+00 -2.15976012177179e-02 - 24 5.49886427456701e+00 -2.15954570982680e-02 - 25 5.49843732333905e+00 -2.15937492933562e-02 - 26 5.49819952685563e+00 -2.15927981074225e-02 - 27 5.49822134763710e+00 -2.15928853905484e-02 - 28 5.49855877481886e+00 -2.15942350992754e-02 - 29 5.49925111569040e+00 -2.15970044627616e-02 - 30 5.50032111781463e+00 -2.16012844712585e-02 - 31 5.50177638720568e+00 -2.16071055488227e-02 - 32 5.50361077502124e+00 -2.16144431000850e-02 - 33 5.50580475208785e+00 -2.16232190083514e-02 - 34 5.50832462428283e+00 -2.16332984971313e-02 - 35 5.51112148810689e+00 -2.16444859524276e-02 - 36 5.51413136388995e+00 -2.16565254555598e-02 - 37 5.51727794263797e+00 -2.16691117705519e-02 - 38 5.52047847332390e+00 -2.16819138932956e-02 - 39 5.52365200645431e+00 -2.16946080258172e-02 - 40 5.52672800804253e+00 -2.17069120321701e-02 + 20 5.50086993007309e+00 -2.16034797202924e-02 + 21 5.50047411702526e+00 -2.16018964681010e-02 + 22 5.49996271480815e+00 -2.15998508592326e-02 + 23 5.49940030464023e+00 -2.15976012185609e-02 + 24 5.49886427479469e+00 -2.15954570991788e-02 + 25 5.49843732358400e+00 -2.15937492943360e-02 + 26 5.49819952711805e+00 -2.15927981084722e-02 + 27 5.49822134791709e+00 -2.15928853916683e-02 + 28 5.49855877511631e+00 -2.15942351004652e-02 + 29 5.49925111600498e+00 -2.15970044640199e-02 + 30 5.50032111814578e+00 -2.16012844725831e-02 + 31 5.50177638755253e+00 -2.16071055502101e-02 + 32 5.50361077538265e+00 -2.16144431015306e-02 + 33 5.50580475246237e+00 -2.16232190098495e-02 + 34 5.50832462466879e+00 -2.16332984986752e-02 + 35 5.51112148850244e+00 -2.16444859540097e-02 + 36 5.51413136429316e+00 -2.16565254571726e-02 + 37 5.51727794304695e+00 -2.16691117721878e-02 + 38 5.52047847373687e+00 -2.16819138949475e-02 + 39 5.52365200686973e+00 -2.16946080274789e-02 + 40 5.52672800845913e+00 -2.17069120338365e-02 diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt index b2949c9aa..157cac038 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-05-08. -colvars: Using NAMD interface, version 2018-04-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out index 541860fb0..50bb8b9f3 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -102,6 +106,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -112,14 +117,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - selfCoordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 3d35609cc..f9e22915c 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.50586098356346e+00 + x 5.50586098376003e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj index 85b262a41..429397ed3 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 5.50563763999569e+00 -2.16225505599828e-02 - 1 5.50579895884940e+00 -2.16231958353976e-02 - 2 5.50568249321115e+00 -2.16227299728446e-02 - 3 5.50534379589073e+00 -2.16213751835629e-02 - 4 5.50485687049274e+00 -2.16194274819710e-02 - 5 5.50430598897902e+00 -2.16172239559161e-02 - 6 5.50377559650355e+00 -2.16151023860142e-02 - 7 5.50334015162730e+00 -2.16133606065092e-02 - 8 5.50305578662091e+00 -2.16122231464836e-02 - 9 5.50295515129356e+00 -2.16118206051742e-02 - 10 5.50304591099096e+00 -2.16121836439638e-02 - 11 5.50331251373771e+00 -2.16132500549508e-02 - 12 5.50372025636123e+00 -2.16148810254449e-02 - 13 5.50422058036933e+00 -2.16168823214773e-02 - 14 5.50475673990153e+00 -2.16190269596061e-02 - 15 5.50526932041704e+00 -2.16210772816681e-02 - 16 5.50570151985664e+00 -2.16228060794265e-02 - 17 5.50600426269577e+00 -2.16240170507831e-02 - 18 5.50614114291938e+00 -2.16245645716775e-02 - 19 5.50609291743878e+00 -2.16243716697551e-02 - 20 5.50586098356346e+00 -2.16234439342538e-02 + 0 5.50563763999570e+00 -2.16225505599828e-02 + 1 5.50579895884978e+00 -2.16231958353991e-02 + 2 5.50568249321270e+00 -2.16227299728508e-02 + 3 5.50534379589551e+00 -2.16213751835821e-02 + 4 5.50485687050173e+00 -2.16194274820069e-02 + 5 5.50430598899447e+00 -2.16172239559779e-02 + 6 5.50377559652656e+00 -2.16151023861063e-02 + 7 5.50334015165911e+00 -2.16133606066364e-02 + 8 5.50305578666305e+00 -2.16122231466522e-02 + 9 5.50295515134696e+00 -2.16118206053878e-02 + 10 5.50304591105647e+00 -2.16121836442259e-02 + 11 5.50331251381601e+00 -2.16132500552641e-02 + 12 5.50372025645284e+00 -2.16148810258114e-02 + 13 5.50422058047457e+00 -2.16168823218983e-02 + 14 5.50475674002052e+00 -2.16190269600821e-02 + 15 5.50526932054974e+00 -2.16210772821990e-02 + 16 5.50570152000281e+00 -2.16228060800113e-02 + 17 5.50600426285527e+00 -2.16240170514211e-02 + 18 5.50614114309177e+00 -2.16245645723671e-02 + 19 5.50609291762347e+00 -2.16243716704939e-02 + 20 5.50586098376003e+00 -2.16234439350401e-02 diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out index 6fe484f98..604f12633 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -102,6 +106,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -112,19 +117,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - selfCoordNum colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 5.50586 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 465216db6..2bc07b6b9 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.53146030724717e+00 + x 5.53146030766424e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj index ccbfc7916..536d293f8 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.50586098356346e+00 -2.16234439342538e-02 - 21 5.50546911207949e+00 -2.16218764483180e-02 - 22 5.50496280767144e+00 -2.16198512306858e-02 - 23 5.50440600579367e+00 -2.16176240231747e-02 - 24 5.50387532088709e+00 -2.16155012835484e-02 - 25 5.50345262434073e+00 -2.16138104973629e-02 - 26 5.50321719157780e+00 -2.16128687663112e-02 - 27 5.50323878058562e+00 -2.16129551223425e-02 - 28 5.50357282071772e+00 -2.16142912828709e-02 - 29 5.50425822631558e+00 -2.16170329052623e-02 - 30 5.50531751760189e+00 -2.16212700704076e-02 - 31 5.50675822466860e+00 -2.16270328986744e-02 - 32 5.50857426029279e+00 -2.16342970411712e-02 - 33 5.51074629070554e+00 -2.16429851628222e-02 - 34 5.51324095880821e+00 -2.16529638352328e-02 - 35 5.51600985017893e+00 -2.16640394007157e-02 - 36 5.51898962493855e+00 -2.16759584997542e-02 - 37 5.52210473712539e+00 -2.16884189485016e-02 - 38 5.52527326311583e+00 -2.17010930524633e-02 - 39 5.52841506276376e+00 -2.17136602510550e-02 - 40 5.53146030724717e+00 -2.17258412289887e-02 + 20 5.50586098376003e+00 -2.16234439350401e-02 + 21 5.50546911228746e+00 -2.16218764491499e-02 + 22 5.50496280789046e+00 -2.16198512315618e-02 + 23 5.50440600602358e+00 -2.16176240240943e-02 + 24 5.50387532112795e+00 -2.16155012845118e-02 + 25 5.50345262459281e+00 -2.16138104983712e-02 + 26 5.50321719184149e+00 -2.16128687673660e-02 + 27 5.50323878086140e+00 -2.16129551234456e-02 + 28 5.50357282100607e+00 -2.16142912840243e-02 + 29 5.50425822661691e+00 -2.16170329064677e-02 + 30 5.50531751791649e+00 -2.16212700716660e-02 + 31 5.50675822499661e+00 -2.16270328999864e-02 + 32 5.50857426063415e+00 -2.16342970425366e-02 + 33 5.51074629106000e+00 -2.16429851642400e-02 + 34 5.51324095917529e+00 -2.16529638367011e-02 + 35 5.51600985055786e+00 -2.16640394022315e-02 + 36 5.51898962532829e+00 -2.16759585013131e-02 + 37 5.52210473752456e+00 -2.16884189500983e-02 + 38 5.52527326352281e+00 -2.17010930540912e-02 + 39 5.52841506317671e+00 -2.17136602527069e-02 + 40 5.53146030766424e+00 -2.17258412306570e-02 diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt b/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 97875d855..90d795b91 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,17 +92,17 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -124,6 +128,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -134,14 +139,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - spinAngle colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 2c69fa7d4..7b11d47e8 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.56417643615813e+00 + x -1.56417643630365e+00 } restraint { diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 7fdccd94c..813c43c6c 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 -1.84067203510482e+00 7.76268814041928e-03 - 1 -1.84826917190272e+00 7.79307668761089e-03 - 2 -1.85122278124769e+00 7.80489112499078e-03 - 3 -1.84852747919607e+00 7.79410991678428e-03 - 4 -1.83943263507235e+00 7.75773054028941e-03 - 5 -1.82355826067355e+00 7.69423304269421e-03 - 6 -1.80098250082777e+00 7.60393000331108e-03 - 7 -1.77228476375683e+00 7.48913905502733e-03 - 8 -1.73853720796757e+00 7.35414883187027e-03 - 9 -1.70124617187310e+00 7.20498468749239e-03 - 10 -1.66225195274677e+00 7.04900781098710e-03 - 11 -1.62359992633788e+00 6.89439970535152e-03 - 12 -1.58739844242825e+00 6.74959376971300e-03 - 13 -1.55567854096568e+00 6.62271416386271e-03 - 14 -1.53026683705662e+00 6.52106734822649e-03 - 15 -1.51267765467802e+00 6.45071061871208e-03 - 16 -1.50402646506685e+00 6.41610586026742e-03 - 17 -1.50496521229370e+00 6.41986084917482e-03 - 18 -1.51564034657794e+00 6.46256138631175e-03 - 19 -1.53567491256393e+00 6.54269965025573e-03 - 20 -1.56417643615813e+00 6.65670574463252e-03 + 1 -1.84826917190189e+00 7.79307668760756e-03 + 2 -1.85122278124429e+00 7.80489112497715e-03 + 3 -1.84852747918889e+00 7.79410991675556e-03 + 4 -1.83943263506144e+00 7.75773054024574e-03 + 5 -1.82355826066059e+00 7.69423304264234e-03 + 6 -1.80098250081617e+00 7.60393000326468e-03 + 7 -1.77228476375142e+00 7.48913905500567e-03 + 8 -1.73853720797388e+00 7.35414883189552e-03 + 9 -1.70124617189668e+00 7.20498468758673e-03 + 10 -1.66225195279233e+00 7.04900781116932e-03 + 11 -1.62359992640856e+00 6.89439970563425e-03 + 12 -1.58739844252513e+00 6.74959377010052e-03 + 13 -1.55567854108748e+00 6.62271416434992e-03 + 14 -1.53026683719969e+00 6.52106734879876e-03 + 15 -1.51267765483671e+00 6.45071061934683e-03 + 16 -1.50402646523430e+00 6.41610586093720e-03 + 17 -1.50496521246286e+00 6.41986084985144e-03 + 18 -1.51564034674263e+00 6.46256138697051e-03 + 19 -1.53567491271986e+00 6.54269965087945e-03 + 20 -1.56417643630365e+00 6.65670574521461e-03 diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index ddf8c7f74..b11e0344c 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,17 +92,17 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -124,6 +128,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -134,19 +139,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - spinAngle colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -1.56418 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 6e327970d..00ee63db3 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.67720949787628e+00 + x -1.67720949927313e+00 } restraint { diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 5c8d1aff8..0a68c54fa 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -1.56417643615813e+00 6.65670574463252e-03 - 21 -1.59977280215672e+00 6.79909120862687e-03 - 22 -1.64067849453734e+00 6.96271397814937e-03 - 23 -1.68479233900518e+00 7.13916935602071e-03 - 24 -1.72982439569390e+00 7.31929758277560e-03 - 25 -1.77344385023716e+00 7.49377540094865e-03 - 26 -1.81343393754057e+00 7.65373575016229e-03 - 27 -1.84783676684341e+00 7.79134706737363e-03 - 28 -1.87507204637838e+00 7.90028818551353e-03 - 29 -1.89401880659213e+00 7.97607522636850e-03 - 30 -1.90405601764340e+00 8.01622407057361e-03 - 31 -1.90506463874174e+00 8.02025855496697e-03 - 32 -1.89739864463758e+00 7.98959457855033e-03 - 33 -1.88183530286499e+00 7.92734121145994e-03 - 34 -1.85951507033553e+00 7.83806028134214e-03 - 35 -1.83187885892875e+00 7.72751543571502e-03 - 36 -1.80060563799079e+00 7.60242255196314e-03 - 37 -1.76754822314118e+00 7.47019289256470e-03 - 38 -1.73466169408694e+00 7.33864677634775e-03 - 39 -1.70391870854367e+00 7.21567483417467e-03 - 40 -1.67720949787628e+00 7.10883799150512e-03 + 20 -1.56417643630365e+00 6.65670574521461e-03 + 21 -1.59977280229335e+00 6.79909120917339e-03 + 22 -1.64067849467003e+00 6.96271397868011e-03 + 23 -1.68479233914237e+00 7.13916935656949e-03 + 24 -1.72982439584738e+00 7.31929758338951e-03 + 25 -1.77344385042163e+00 7.49377540168654e-03 + 26 -1.81343393777301e+00 7.65373575109205e-03 + 27 -1.84783676714212e+00 7.79134706856848e-03 + 28 -1.87507204676182e+00 7.90028818704729e-03 + 29 -1.89401880707755e+00 7.97607522831020e-03 + 30 -1.90405601824540e+00 8.01622407298159e-03 + 31 -1.90506463947095e+00 8.02025855788378e-03 + 32 -1.89739864549939e+00 7.98959458199754e-03 + 33 -1.88183530385872e+00 7.92734121543490e-03 + 34 -1.85951507145392e+00 7.83806028581570e-03 + 35 -1.83187886015785e+00 7.72751544063142e-03 + 36 -1.80060563931043e+00 7.60242255724172e-03 + 37 -1.76754822452589e+00 7.47019289810355e-03 + 38 -1.73466169550726e+00 7.33864678202902e-03 + 39 -1.70391870996803e+00 7.21567483987211e-03 + 40 -1.67720949927313e+00 7.10883799709252e-03 diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt index 832c6a06f..157cac038 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-12-14. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out index 38bb57ee5..21561ed31 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,17 +74,17 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 3 -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -106,6 +110,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.000111111 according to the specified width (3). colvars: ---------------------------------------------------------------------- @@ -116,14 +121,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - spinAngle colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 79a2a90e4..448e93eef 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -6.52196175528559e+00 + x -6.52196175536141e+00 } restraint { diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj index b65c4790b..b5f5b8fe8 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 -6.74120349418967e+00 7.60133721576629e-04 - 1 -6.74680409124886e+00 7.60756010138763e-04 - 2 -6.74928398676683e+00 7.61031554085203e-04 - 3 -6.74760118854837e+00 7.60844576505375e-04 - 4 -6.74089237394015e+00 7.60099152660017e-04 - 5 -6.72859795268796e+00 7.58733105854218e-04 - 6 -6.71056189836587e+00 7.56729099818430e-04 - 7 -6.68709018460367e+00 7.54121131622629e-04 - 8 -6.65896053826554e+00 7.50995615362838e-04 - 9 -6.62738484678158e+00 7.47487205197953e-04 - 10 -6.59393151683697e+00 7.43770168537441e-04 - 11 -6.56041836901761e+00 7.40046485446401e-04 - 12 -6.52878782058752e+00 7.36531980065280e-04 - 13 -6.50097576071506e+00 7.33441751190562e-04 - 14 -6.47878371974444e+00 7.30975968860493e-04 - 15 -6.46376168610113e+00 7.29306854011237e-04 - 16 -6.45710716417506e+00 7.28567462686117e-04 - 17 -6.45958482166641e+00 7.28842757962935e-04 - 18 -6.47146995371894e+00 7.30163328190994e-04 - 19 -6.49251798066684e+00 7.32501997851872e-04 - 20 -6.52196175528559e+00 7.35773528365066e-04 + 0 -6.74120349419055e+00 7.60133721576728e-04 + 1 -6.74680409124828e+00 7.60756010138697e-04 + 2 -6.74928398676149e+00 7.61031554084610e-04 + 3 -6.74760118854074e+00 7.60844576504527e-04 + 4 -6.74089237392950e+00 7.60099152658834e-04 + 5 -6.72859795234419e+00 7.58733105816021e-04 + 6 -6.71056189835939e+00 7.56729099817710e-04 + 7 -6.68709018460270e+00 7.54121131622523e-04 + 8 -6.65896053827068e+00 7.50995615363409e-04 + 9 -6.62738484679749e+00 7.47487205199721e-04 + 10 -6.59393151686784e+00 7.43770168540871e-04 + 11 -6.56041836906667e+00 7.40046485451852e-04 + 12 -6.52878782065636e+00 7.36531980072929e-04 + 13 -6.50097576076332e+00 7.33441751195925e-04 + 14 -6.47878371985369e+00 7.30975968872632e-04 + 15 -6.46376168616761e+00 7.29306854018624e-04 + 16 -6.45710716430512e+00 7.28567462700569e-04 + 17 -6.45958482192202e+00 7.28842757991336e-04 + 18 -6.47146995375796e+00 7.30163328195329e-04 + 19 -6.49251798076206e+00 7.32501997862452e-04 + 20 -6.52196175536141e+00 7.35773528373490e-04 diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 62bc7782b..58c424da8 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,17 +74,17 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 3 -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -106,6 +110,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.000111111 according to the specified width (3). colvars: ---------------------------------------------------------------------- @@ -116,19 +121,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - spinAngle colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -6.52196 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index e4d09163e..311efe354 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -6.64191475373326e+00 + x -6.64191475499626e+00 } restraint { diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 59936cd90..e9ee60f48 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -6.52196175528559e+00 7.35773528365066e-04 - 21 -6.55853866126809e+00 7.39837629029787e-04 - 22 -6.60054957179227e+00 7.44505507976919e-04 - 23 -6.64595045358898e+00 7.49550050398775e-04 - 24 -6.69247420100935e+00 7.54719355667705e-04 - 25 -6.73777528436304e+00 7.59752809373671e-04 - 26 -6.77958465029172e+00 7.64398294476858e-04 - 27 -6.81585908038471e+00 7.68428786709412e-04 - 28 -6.84490920631285e+00 7.71656578479206e-04 - 29 -6.86549395828653e+00 7.73943773142947e-04 - 30 -6.87687521003861e+00 7.75208356670957e-04 - 31 -6.87883312782949e+00 7.75425903092165e-04 - 32 -6.87164844151262e+00 7.74627604612513e-04 - 33 -6.85606123010451e+00 7.72895692233834e-04 - 34 -6.83321599913451e+00 7.70357333237168e-04 - 35 -6.80460001891363e+00 7.67177779879293e-04 - 36 -6.77197706280820e+00 7.63553006978689e-04 - 37 -6.73731414535818e+00 7.59701571706465e-04 - 38 -6.70269652174944e+00 7.55855169083271e-04 - 39 -6.67022757425629e+00 7.52247508250699e-04 - 40 -6.64191475373326e+00 7.49101639303696e-04 + 20 -6.52196175536141e+00 7.35773528373490e-04 + 21 -6.55853866136453e+00 7.39837629040503e-04 + 22 -6.60054957188598e+00 7.44505507987332e-04 + 23 -6.64595045368826e+00 7.49550050409807e-04 + 24 -6.69247420112553e+00 7.54719355680614e-04 + 25 -6.73777528462053e+00 7.59752809402281e-04 + 26 -6.77958465048355e+00 7.64398294498173e-04 + 27 -6.81585908066260e+00 7.68428786740289e-04 + 28 -6.84490920657793e+00 7.71656578508659e-04 + 29 -6.86549395871066e+00 7.73943773190073e-04 + 30 -6.87687521064447e+00 7.75208356738274e-04 + 31 -6.87883312849994e+00 7.75425903166660e-04 + 32 -6.87164844230811e+00 7.74627604700902e-04 + 33 -6.85606123102412e+00 7.72895692336013e-04 + 34 -6.83321600017101e+00 7.70357333352334e-04 + 35 -6.80460002005342e+00 7.67177780005936e-04 + 36 -6.77197706433820e+00 7.63553007148689e-04 + 37 -6.73731414663200e+00 7.59701571848000e-04 + 38 -6.70269652304925e+00 7.55855169227695e-04 + 39 -6.67022757555205e+00 7.52247508394672e-04 + 40 -6.64191475499626e+00 7.49101639444029e-04 diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 69afc9ed5..0b71aa10e 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,7 +92,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -124,6 +128,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -134,14 +139,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - tilt colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 1c8f75a13..21771cc4e 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.99415492548698e-01 + x 9.99415492547103e-01 } restraint { diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index a797dc77d..257bb1412 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 9.98812440566840e-01 -3.59524976226736e-03 - 1 9.98816680233352e-01 -3.59526672093341e-03 - 2 9.98826523073460e-01 -3.59530609229384e-03 - 3 9.98842018672504e-01 -3.59536807469002e-03 - 4 9.98863121611482e-01 -3.59545248644593e-03 - 5 9.98889669016271e-01 -3.59555867606508e-03 - 6 9.98921340686809e-01 -3.59568536274724e-03 - 7 9.98957619944074e-01 -3.59583047977630e-03 - 8 9.98997773201637e-01 -3.59599109280655e-03 - 9 9.99040860340198e-01 -3.59616344136079e-03 - 10 9.99085779266763e-01 -3.59634311706705e-03 - 11 9.99131338939470e-01 -3.59652535575788e-03 - 12 9.99176347611108e-01 -3.59670539044443e-03 - 13 9.99219697607536e-01 -3.59687879043014e-03 - 14 9.99260427488563e-01 -3.59704170995425e-03 - 15 9.99297748983282e-01 -3.59719099593313e-03 - 16 9.99331038662066e-01 -3.59732415464826e-03 - 17 9.99359807086426e-01 -3.59743922834570e-03 - 18 9.99383664675241e-01 -3.59753465870096e-03 - 19 9.99402301733660e-01 -3.59760920693464e-03 - 20 9.99415492548698e-01 -3.59766197019479e-03 + 1 9.98816680233361e-01 -3.59526672093344e-03 + 2 9.98826523073495e-01 -3.59530609229398e-03 + 3 9.98842018672579e-01 -3.59536807469031e-03 + 4 9.98863121611601e-01 -3.59545248644640e-03 + 5 9.98889669016434e-01 -3.59555867606574e-03 + 6 9.98921340687004e-01 -3.59568536274802e-03 + 7 9.98957619944279e-01 -3.59583047977712e-03 + 8 9.98997773201826e-01 -3.59599109280730e-03 + 9 9.99040860340336e-01 -3.59616344136134e-03 + 10 9.99085779266818e-01 -3.59634311706727e-03 + 11 9.99131338939409e-01 -3.59652535575764e-03 + 12 9.99176347610903e-01 -3.59670539044361e-03 + 13 9.99219697607167e-01 -3.59687879042867e-03 + 14 9.99260427488015e-01 -3.59704170995206e-03 + 15 9.99297748982546e-01 -3.59719099593018e-03 + 16 9.99331038661138e-01 -3.59732415464455e-03 + 17 9.99359807085313e-01 -3.59743922834125e-03 + 18 9.99383664673950e-01 -3.59753465869580e-03 + 19 9.99402301732208e-01 -3.59760920692883e-03 + 20 9.99415492547103e-01 -3.59766197018841e-03 diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index 0ed6ee7d8..35a5c40ee 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -88,7 +92,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -124,6 +128,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -134,19 +139,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - tilt colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.999415 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 50c49fa3e..71c119b43 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.99399210041976e-01 + x 9.99399210038338e-01 } restraint { diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 86fc22b8b..c3db036ec 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.99415492548698e-01 -3.59766197019479e-03 - 21 9.99423124213315e-01 -3.59769249685326e-03 - 22 9.99425243205266e-01 -3.59770097282107e-03 - 23 9.99422108248105e-01 -3.59768843299242e-03 - 24 9.99414235599357e-01 -3.59765694239743e-03 - 25 9.99402422547979e-01 -3.59760969019192e-03 - 26 9.99387736078806e-01 -3.59755094431523e-03 - 27 9.99371458558828e-01 -3.59748583423531e-03 - 28 9.99354991190644e-01 -3.59741996476258e-03 - 29 9.99339727178734e-01 -3.59735890871494e-03 - 30 9.99326916412614e-01 -3.59730766565046e-03 - 31 9.99317547851597e-01 -3.59727019140639e-03 - 32 9.99312272724061e-01 -3.59724909089624e-03 - 33 9.99311381511187e-01 -3.59724552604475e-03 - 34 9.99314833118093e-01 -3.59725933247237e-03 - 35 9.99322320514697e-01 -3.59728928205879e-03 - 36 9.99333348007473e-01 -3.59733339202989e-03 - 37 9.99347295867101e-01 -3.59738918346840e-03 - 38 9.99363457671199e-01 -3.59745383068479e-03 - 39 9.99381050368662e-01 -3.59752420147465e-03 - 40 9.99399210041976e-01 -3.59759684016791e-03 + 20 9.99415492547103e-01 -3.59766197018841e-03 + 21 9.99423124211601e-01 -3.59769249684640e-03 + 22 9.99425243203459e-01 -3.59770097281383e-03 + 23 9.99422108246234e-01 -3.59768843298494e-03 + 24 9.99414235597450e-01 -3.59765694238980e-03 + 25 9.99402422546063e-01 -3.59760969018425e-03 + 26 9.99387736076906e-01 -3.59755094430763e-03 + 27 9.99371458556963e-01 -3.59748583422785e-03 + 28 9.99354991188822e-01 -3.59741996475529e-03 + 29 9.99339727176955e-01 -3.59735890870782e-03 + 30 9.99326916410865e-01 -3.59730766564346e-03 + 31 9.99317547849854e-01 -3.59727019139942e-03 + 32 9.99312272722288e-01 -3.59724909088915e-03 + 33 9.99311381509340e-01 -3.59724552603736e-03 + 34 9.99314833116121e-01 -3.59725933246448e-03 + 35 9.99322320512548e-01 -3.59728928205019e-03 + 36 9.99333348005097e-01 -3.59733339202039e-03 + 37 9.99347295864453e-01 -3.59738918345781e-03 + 38 9.99363457668243e-01 -3.59745383067297e-03 + 39 9.99381050365372e-01 -3.59752420146149e-03 + 40 9.99399210038338e-01 -3.59759684015335e-03 diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt index 832c6a06f..157cac038 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-12-14. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out index ffac56dd2..466786003 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -106,6 +110,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.4 according to the specified width (0.05). colvars: ---------------------------------------------------------------------- @@ -116,14 +121,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - tilt colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 776f51f15..22e226ed8 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.86667458341471e-01 + x 9.86667458349930e-01 } restraint { diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj index 036a31008..be7100171 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 9.89817622562340e-01 -3.55927049024936e-01 - 1 9.89739193890710e-01 -3.55895677556284e-01 - 2 9.89645626534500e-01 -3.55858250613800e-01 - 3 9.89537793456669e-01 -3.55815117382668e-01 - 4 9.89416411925387e-01 -3.55766564770155e-01 - 5 9.89282053848041e-01 -3.55712821539216e-01 - 6 9.89135240738356e-01 -3.55654096295342e-01 - 7 9.88976581442317e-01 -3.55590632576927e-01 - 8 9.88806911284239e-01 -3.55522764513695e-01 - 9 9.88627402347221e-01 -3.55450960938888e-01 - 10 9.88439627709016e-01 -3.55375851083606e-01 - 11 9.88245572588017e-01 -3.55298229035207e-01 - 12 9.88047593326122e-01 -3.55219037330449e-01 - 13 9.87848337457110e-01 -3.55139334982844e-01 - 14 9.87650651620881e-01 -3.55060260648352e-01 - 15 9.87457507486578e-01 -3.54983002994631e-01 - 16 9.87271960371439e-01 -3.54908784148575e-01 - 17 9.87097125283486e-01 -3.54838850113394e-01 - 18 9.86936130473010e-01 -3.54774452189204e-01 - 19 9.86792003040408e-01 -3.54716801216163e-01 - 20 9.86667458341471e-01 -3.54666983336588e-01 + 0 9.89817622562351e-01 -3.55927049024940e-01 + 1 9.89739193890686e-01 -3.55895677556274e-01 + 2 9.89645626534388e-01 -3.55858250613755e-01 + 3 9.89537793456435e-01 -3.55815117382574e-01 + 4 9.89416411924999e-01 -3.55766564770000e-01 + 5 9.89282053848009e-01 -3.55712821539204e-01 + 6 9.89135240737646e-01 -3.55654096295058e-01 + 7 9.88976581441553e-01 -3.55590632576621e-01 + 8 9.88806911283522e-01 -3.55522764513409e-01 + 9 9.88627402346676e-01 -3.55450960938670e-01 + 10 9.88439627708785e-01 -3.55375851083514e-01 + 11 9.88245572588250e-01 -3.55298229035300e-01 + 12 9.88047593326962e-01 -3.55219037330785e-01 + 13 9.87848337461123e-01 -3.55139334984449e-01 + 14 9.87650651623308e-01 -3.55060260649323e-01 + 15 9.87457507491825e-01 -3.54983002996730e-01 + 16 9.87271960375771e-01 -3.54908784150308e-01 + 17 9.87097125290053e-01 -3.54838850116021e-01 + 18 9.86936130482758e-01 -3.54774452193103e-01 + 19 9.86792003048169e-01 -3.54716801219267e-01 + 20 9.86667458349930e-01 -3.54666983339972e-01 diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out index 8e045427a..790ae8ec1 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,14 +59,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +74,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -106,6 +110,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.4 according to the specified width (0.05). colvars: ---------------------------------------------------------------------- @@ -116,19 +121,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: - tilt colvar component (derived from orientation): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.986667 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 33ffc6902..ffcadedd3 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.85614564513385e-01 + x 9.85614564530977e-01 } restraint { diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj index e9303a790..b5e56c253 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.86667458341471e-01 -3.54666983336588e-01 - 21 9.86564598790534e-01 -3.54625839516214e-01 - 22 9.86484566764204e-01 -3.54593826705681e-01 - 23 9.86427228487669e-01 -3.54570891395068e-01 - 24 9.86390977445951e-01 -3.54556390978380e-01 - 25 9.86372728511522e-01 -3.54549091404609e-01 - 26 9.86368130541750e-01 -3.54547252216700e-01 - 27 9.86371969378090e-01 -3.54548787751236e-01 - 28 9.86378686073627e-01 -3.54551474429451e-01 - 29 9.86382912469260e-01 -3.54553164987704e-01 - 30 9.86379931725049e-01 -3.54551972690020e-01 - 31 9.86365997681395e-01 -3.54546399072558e-01 - 32 9.86338483193996e-01 -3.54535393277598e-01 - 33 9.86295866419978e-01 -3.54518346567991e-01 - 34 9.86237598499642e-01 -3.54495039399857e-01 - 35 9.86163919701783e-01 -3.54465567880713e-01 - 36 9.86075697585368e-01 -3.54430279034147e-01 - 37 9.85974343814067e-01 -3.54389737525627e-01 - 38 9.85861830020574e-01 -3.54344732008230e-01 - 39 9.85740778408907e-01 -3.54296311363563e-01 - 40 9.85614564513385e-01 -3.54245825805354e-01 + 20 9.86667458349930e-01 -3.54666983339972e-01 + 21 9.86564598798781e-01 -3.54625839519512e-01 + 22 9.86484566772892e-01 -3.54593826709157e-01 + 23 9.86427228496625e-01 -3.54570891398650e-01 + 24 9.86390977455002e-01 -3.54556390982001e-01 + 25 9.86372728522180e-01 -3.54549091408872e-01 + 26 9.86368130550494e-01 -3.54547252220198e-01 + 27 9.86371969386892e-01 -3.54548787754757e-01 + 28 9.86378686084241e-01 -3.54551474433696e-01 + 29 9.86382912477289e-01 -3.54553164990916e-01 + 30 9.86379931734801e-01 -3.54551972693920e-01 + 31 9.86365997688778e-01 -3.54546399075511e-01 + 32 9.86338483201464e-01 -3.54535393280585e-01 + 33 9.86295866427772e-01 -3.54518346571109e-01 + 34 9.86237598508030e-01 -3.54495039403212e-01 + 35 9.86163919711047e-01 -3.54465567884419e-01 + 36 9.86075697598078e-01 -3.54430279039231e-01 + 37 9.85974343825943e-01 -3.54389737530377e-01 + 38 9.85861830034088e-01 -3.54344732013635e-01 + 39 9.85740778424268e-01 -3.54296311369707e-01 + 40 9.85614564530977e-01 -3.54245825812391e-01 diff --git a/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt b/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out index bb4bac866..9990cc125 100644 --- a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out +++ b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsdA" @@ -25,14 +27,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 8 atoms requested: total mass = 43.069, total charge = -0.09. @@ -40,7 +42,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -76,14 +78,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] @@ -129,14 +131,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] @@ -181,14 +183,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] @@ -234,14 +236,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off -colvars: # rotateReference = off +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off +colvars: # rotateToReference = off colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 8 atoms requested: total mass = 43.069, total charge = -0.09. @@ -286,6 +288,7 @@ colvars: # centers = { 0, 0, 0, 0, 0 } colvars: # targetCenters = { 0, 0, 0, 0, 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsdA" will be rescaled to 1 according to the specified width (1). colvars: The force constant for colvar "rmsdB" will be rescaled to 1 according to the specified width (1). @@ -300,6 +303,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 5 in total. colvars: ---------------------------------------------------------------------- @@ -313,6 +317,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -331,6 +336,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -349,6 +355,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -367,6 +374,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -385,6 +393,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -400,17 +409,34 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - harmonicWalls colvar bias implementation: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdB":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdC":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdD":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdE":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdB":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdC":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. diff --git a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj index 9c94197c3..266bf3e21 100644 --- a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj +++ b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj @@ -1,2 +1,2 @@ -# step rmsdA ft_rmsdA rmsdB ft_rmsdB rmsdC ft_rmsdC rmsdD ft_rmsdD rmsdE ft_rmsdE - 0 2.61009345658189e-01 0.00000000000000e+00 1.27145912684355e+01 0.00000000000000e+00 6.68502465870546e-01 0.00000000000000e+00 9.31703240469482e-01 0.00000000000000e+00 1.24224459145532e+00 0.00000000000000e+00 +# step rmsdA ft_rmsdA rmsdB ft_rmsdB rmsdC ft_rmsdC rmsdD ft_rmsdD rmsdE ft_rmsdE + 0 2.61009345658189e-01 0.00000000000000e+00 1.27145912684355e+01 0.00000000000000e+00 6.68502465870546e-01 0.00000000000000e+00 9.31703240469482e-01 0.00000000000000e+00 1.24224459145532e+00 0.00000000000000e+00 diff --git a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out index aae270fda..a4dfd6895 100644 --- a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out +++ b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "eigenvector_Ca" @@ -55,14 +57,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,19 +72,20 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "../Common/da.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( 0.9999 , 2 , 3 ) colvars: # differenceVector = on -colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = v - x0. -colvars: "differenceVector" is on: normalizing the vector. +colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = x_vec - x_ref. +colvars: # normalizeVector = off [default] +colvars: Normalizing the vector so that the norm of the projection |v ⋅ (x_vec - x_ref)| = 1. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -110,6 +113,7 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eigenvector_Ca" will be rescaled to 10 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -120,13 +124,28 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - eigenvector colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "eigenvector_Ca":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "eigenvector_Ca":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj index a10b71b97..d319abefa 100644 --- a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj +++ b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj @@ -1,2 +1,2 @@ # step eigenvector_Ca ft_eigenvector_Ca fa_eigenvector_Ca - 0 1.00000000000000e+00 0.00000000000000e+00 -1.00000000000000e+01 + 0 9.99999999999999e-01 0.00000000000000e+00 -9.99999999999999e+00 diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out index 832cffd51..5b4640743 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -55,14 +57,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +72,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -110,6 +112,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd" will be rescaled to 10000 according to the specified width (0.01). colvars: ---------------------------------------------------------------------- @@ -120,6 +123,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -133,6 +137,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -147,14 +152,30 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - harmonicWalls colvar bias implementation: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped index 20535536d..e621f3ff5 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name rmsd - x 1.39198635631904e+00 + x 1.39198635632537e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 1.00000000000000e-01 - accumulatedWork -1.79849880092103e+03 + accumulatedWork -1.79849880092255e+03 } } diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj index 62e3fc7d4..88056a153 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step rmsd ft_rmsd fa_rmsd E_harmonic1 x0_rmsd W_harmonic1 0 2.17249057079325e+00 0.00000000000000e+00 -2.17456306136404e+04 2.35985764009279e+04 0.00000000000000e+00 0.00000000000000e+00 - 1 2.16345956010639e+00 -2.17419903527299e+04 -2.15552301966649e+04 2.31869403850679e+04 1.00000000000000e-02 -2.15345956010639e+02 - 2 2.13583213462437e+00 -2.14389529078606e+04 -2.11786796675899e+04 2.23837281095455e+04 2.00000000000000e-02 -4.26929169473075e+02 - 3 2.09038365006916e+00 -2.07262996389219e+04 -2.06237403371923e+04 2.12259039273616e+04 3.00000000000000e-02 -6.32967534479991e+02 - 4 2.02806882503376e+00 -1.96255637094443e+04 -1.98999689385880e+04 1.97620882653556e+04 4.00000000000000e-02 -8.31774416983368e+02 - 5 1.95030623811151e+00 -1.81667585437567e+04 -1.90215654434962e+04 1.80558189930276e+04 5.00000000000000e-02 -1.02180504079452e+03 - 6 1.85875201230753e+00 -1.63966970220336e+04 -1.80051076431984e+04 1.61775440089019e+04 6.00000000000000e-02 -1.20168024202527e+03 - 7 1.75513110974436e+00 -1.43781737215985e+04 -1.68678624085410e+04 1.41983342851413e+04 7.00000000000000e-02 -1.37019335299971e+03 - 8 1.64142178718173e+00 -1.21888818492009e+04 -1.56296320896891e+04 1.21901899874289e+04 8.00000000000000e-02 -1.52633553171788e+03 - 9 1.51964633571245e+00 -9.89848282440100e+03 -1.43106598204816e+04 1.02194432260802e+04 9.00000000000000e-02 -1.66930016528913e+03 - 10 1.39198635631904e+00 -7.49967017479936e+03 -1.29327834267536e+04 8.34614372457276e+03 1.00000000000000e-01 -1.79849880092103e+03 + 1 2.16345956010640e+00 -2.17419903526924e+04 -2.15552301966651e+04 2.31869403850683e+04 1.00000000000000e-02 -2.15345956010640e+02 + 2 2.13583213462443e+00 -2.14389529078214e+04 -2.11786796675906e+04 2.23837281095469e+04 2.00000000000000e-02 -4.26929169473084e+02 + 3 2.09038365006932e+00 -2.07262996388757e+04 -2.06237403371939e+04 2.12259039273649e+04 3.00000000000000e-02 -6.32967534480016e+02 + 4 2.02806882503406e+00 -1.96255637093855e+04 -1.98999689385910e+04 1.97620882653616e+04 4.00000000000000e-02 -8.31774416983422e+02 + 5 1.95030623811202e+00 -1.81667585436761e+04 -1.90215654435014e+04 1.80558189930374e+04 5.00000000000000e-02 -1.02180504079462e+03 + 6 1.85875201230836e+00 -1.63966970219124e+04 -1.80051076432067e+04 1.61775440089168e+04 6.00000000000000e-02 -1.20168024202546e+03 + 7 1.75513110974568e+00 -1.43781737213953e+04 -1.68678624085543e+04 1.41983342851636e+04 7.00000000000000e-02 -1.37019335300003e+03 + 8 1.64142178718387e+00 -1.21888818488311e+04 -1.56296320897105e+04 1.21901899874623e+04 8.00000000000000e-02 -1.52633553171842e+03 + 9 1.51964633571603e+00 -9.89848282368767e+03 -1.43106598205174e+04 1.02194432261313e+04 9.00000000000000e-02 -1.66930016529002e+03 + 10 1.39198635632537e+00 -7.49967017329654e+03 -1.29327834268169e+04 8.34614372465450e+03 1.00000000000000e-01 -1.79849880092255e+03 diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out index 460e18798..1539c97b7 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -55,14 +57,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +72,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -110,6 +112,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd" will be rescaled to 10000 according to the specified width (0.01). colvars: ---------------------------------------------------------------------- @@ -120,6 +123,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -133,6 +137,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -147,20 +152,36 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - harmonicWalls colvar bias implementation: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "rmsd" from value: 1.39199 colvars: Restarting harmonic bias "harmonic1" from step number 10. colvars: Restarting harmonicwalls bias "rmsdw" from step number 10. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testres.colvars.state". colvars: The final output state file will be "testres.colvars.state". -colvars: Opening trajectory file "testres.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "testres.colvars.state". colvars: The final output state file will be "testres.colvars.state". diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped index 0329bdfbc..e2cb96809 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name rmsd - x 3.58513981358481e-01 + x 3.58513981869359e-01 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -2.38254491346066e+03 + accumulatedWork -2.38254491368653e+03 } } diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj index afd7851c5..cfd59f064 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj @@ -1,12 +1,12 @@ # step rmsd ft_rmsd fa_rmsd E_harmonic1 x0_rmsd W_harmonic1 - 10 1.39198635631904e+00 0.00000000000000e+00 -1.29327834267536e+04 8.34614372457276e+03 1.00000000000000e-01 -1.79849880092103e+03 - 11 1.26066443053330e+00 -5.04906136565955e+03 -1.15182509496383e+04 6.62014315847261e+03 1.10000000000000e-01 -1.91356524397436e+03 - 12 1.12800176082188e+00 -2.47793069731417e+03 -1.00902976258270e+04 5.08033774910002e+03 1.20000000000000e-01 -2.01436542005655e+03 - 13 9.96492050911879e-01 3.15682468320502e+02 -8.67388542962791e+03 3.75404237146737e+03 1.30000000000000e-01 -2.10101462514774e+03 - 14 8.68461409518928e-01 2.99293969889592e+03 -7.29229870928447e+03 2.65328012579152e+03 1.40000000000000e-01 -2.17386076609963e+03 - 15 7.47100495082919e-01 6.43619258679187e+03 -5.97747595578002e+03 1.78264500614134e+03 1.50000000000000e-01 -2.23357081560792e+03 - 16 6.35910082961470e-01 1.00836160673481e+04 -4.76445993044432e+03 1.13245203532197e+03 1.60000000000000e-01 -2.28116182390407e+03 - 17 5.38589381992358e-01 1.33134883328259e+04 -3.69027971374350e+03 6.79290662587542e+02 1.70000000000000e-01 -2.31802076210330e+03 - 18 4.58478967939376e-01 1.57771913740319e+04 -2.78837446907315e+03 3.87752677922900e+02 1.80000000000000e-01 -2.34586865889724e+03 - 19 3.98248564275675e-01 1.64627515062483e+04 -2.08546812839950e+03 2.16837322614399e+02 1.90000000000000e-01 -2.36669351532481e+03 - 20 3.58513981358481e-01 1.49916694678179e+04 -1.58772495339839e+03 1.25633411430584e+02 2.00000000000000e-01 -2.38254491346066e+03 + 10 1.39198635632537e+00 0.00000000000000e+00 -1.29327834268169e+04 8.34614372465450e+03 1.00000000000000e-01 -1.79849880092255e+03 + 11 1.26066443054501e+00 -5.04906136264293e+03 -1.15182509497555e+04 6.62014315860736e+03 1.10000000000000e-01 -1.91356524397705e+03 + 12 1.12800176084383e+00 -2.47793069174467e+03 -1.00902976260468e+04 5.08033774932134e+03 1.20000000000000e-01 -2.01436542006143e+03 + 13 9.96492050953577e-01 3.15682479164454e+02 -8.67388543004531e+03 3.75404237182868e+03 1.30000000000000e-01 -2.10101462515679e+03 + 14 8.68461409598148e-01 2.99293971896176e+03 -7.29229871007746e+03 2.65328012636860e+03 1.40000000000000e-01 -2.17386076611661e+03 + 15 7.47100495226679e-01 6.43619261578947e+03 -5.97747595721906e+03 1.78264500699973e+03 1.50000000000000e-01 -2.23357081563928e+03 + 16 6.35910083193821e-01 1.00836160874306e+04 -4.76445993277015e+03 1.13245203642775e+03 1.60000000000000e-01 -2.28116182395866e+03 + 17 5.38589382317609e-01 1.33134883220103e+04 -3.69027971699926e+03 6.79290663786381e+02 1.70000000000000e-01 -2.31802076219042e+03 + 18 4.58478968346367e-01 1.57771913409965e+04 -2.78837447314713e+03 3.87752679056283e+02 1.80000000000000e-01 -2.34586865902505e+03 + 19 3.98248564745421e-01 1.64627514687814e+04 -2.08546813310166e+03 2.16837323592639e+02 1.90000000000000e-01 -2.36669351549960e+03 + 20 3.58513981869359e-01 1.49916694393498e+04 -1.58772495851228e+03 1.25633412240397e+02 2.00000000000000e-01 -2.38254491368653e+03 diff --git a/namd/tests/library/003_10ala_SMD_restart/namd-version.txt b/namd/tests/library/003_10ala_SMD_restart/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/003_10ala_SMD_restart/namd-version.txt +++ b/namd/tests/library/003_10ala_SMD_restart/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out index 80cd2d40b..24596243b 100644 --- a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out +++ b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -25,56 +27,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.011, total charge = 0.51. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -84,10 +86,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerBoundary = -180 [default] +colvars: # upperBoundary = 180 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = on [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -116,6 +118,7 @@ colvars: # targetNumStages = 36 colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 10 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -126,22 +129,39 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - dihedral colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. colvars: Re-initialized atom group for variable "d":0/3. 1 atoms: total mass = 14.007, total charge = -0.47. colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "previous.colvars.state". +colvars: Loading state from file "previous.colvars.state". +colvars: This state file was generated with version colvars: Restarting collective variable "d" from value: -137.21 colvars: Restarting harmonic bias "harmonic1" from step number 8000. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testr.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. diff --git a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj index 1cecbe504..4ec655cd6 100644 --- a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj +++ b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step d fa_d 8000 -1.37210258611294e+02 2.21025861129385e+01 - 8002 -1.36437406938780e+02 1.43740693877973e+01 - 8004 -1.32448586831588e+02 -2.55141316841204e+01 - 8006 -1.34451844766881e+02 -5.48155233119189e+00 - 8008 -1.37758781619817e+02 2.75878161981655e+01 - 8010 -1.35039285402271e+02 3.92854022709912e-01 - 8012 -1.32417992183434e+02 -2.58200781656637e+01 - 8014 -1.35927148506204e+02 9.27148506203707e+00 - 8016 -1.37371418693973e+02 2.37141869397252e+01 - 8018 -1.33415236151821e+02 -1.58476384817905e+01 - 8020 -1.33332063900607e+02 -1.66793609939288e+01 + 8002 -1.36437406938754e+02 1.43740693875392e+01 + 8004 -1.32448586831542e+02 -2.55141316845757e+01 + 8006 -1.34451844766900e+02 -5.48155233099777e+00 + 8008 -1.37758781619839e+02 2.75878161983877e+01 + 8010 -1.35039285402134e+02 3.92854021337428e-01 + 8012 -1.32417992183404e+02 -2.58200781659573e+01 + 8014 -1.35927148506493e+02 9.27148506492500e+00 + 8016 -1.37371418693785e+02 2.37141869378459e+01 + 8018 -1.33415236151160e+02 -1.58476384884008e+01 + 8020 -1.33332063901251e+02 -1.66793609874881e+01 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out b/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out index f8428a56e..477048315 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out @@ -1,4 +1,4 @@ -TCL: Running Colvars version 2020-04-09 +TCL: Running Colvars version 2023-07-21 TCL: Running cv units real TCL: TCL: d = 0.00000000000000e+00 @@ -13,7 +13,7 @@ TCL: E(harmonic1) = 18000 TCL: Original numsteps 20 will be ignored. TCL: Running for 20 steps TCL: d = 1.28684277602119e+01 -TCL: E(abf1) = 0 +TCL: E(abf1) = 32.885 TCL: E(harmonic1) = 94.2708 TCL: Running cv bias harm2 getconfig TCL: @@ -27,7 +27,7 @@ TCL: TCL: Running cv bias harm2 energy TCL: 17.8166 TCL: Running cv bias harm2 update -TCL: 17.8166 +TCL: 1.78166082981433e+01 TCL: Running for 20 steps TCL: Running cv bias harm2 energy TCL: 13.4817 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out index d3135664a..ca61c96ea 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -25,28 +27,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -104,6 +106,7 @@ colvars: # centers = { 12 } colvars: # targetCenters = { 12 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 250 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -114,17 +117,35 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - ABF colvar bias implementation: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Prepared sample and gradient buffers at step 0. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. -colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". colvars: ---------------------------------------------------------------------- @@ -135,6 +156,7 @@ colvars: # colvarsTrajFrequency = 2 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -151,6 +173,7 @@ colvars: # centers = { 13 } colvars: # targetCenters = { 13 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 25 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -161,271 +184,296 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Saving collective variables state to "test.colvars.state". -colvars: Features of "colvar d" ON/OFF (refcount) -colvars: - active ON (4) -colvars: - awake ON (0) -colvars: - gradient ON (3) -colvars: - collect_gradient OFF (0) -colvars: - velocity_from_finite_differences OFF (0) -colvars: - total_force ON (3) -colvars: - total_force_calculation ON (1) -colvars: - subtract_applied_force_from_total_force ON (0) -colvars: - Jacobian_derivative ON (1) -colvars: - hide_Jacobian_force OFF (0) -colvars: - extended_Lagrangian OFF (0) -colvars: - Langevin_dynamics OFF (0) -colvars: - output_energy OFF (0) -colvars: - output_value ON (0) -colvars: - output_velocity OFF (0) -colvars: - output_applied_force ON (0) -colvars: - output_total_force ON (0) -colvars: - lower_boundary ON (1) -colvars: - upper_boundary ON (1) -colvars: - hard_lower_boundary OFF (0) -colvars: - hard_upper_boundary OFF (0) -colvars: - reflecting_lower_boundary OFF (0) -colvars: - reflecting_upper_boundary OFF (0) -colvars: - grid ON (0) -colvars: - running_average OFF (0) -colvars: - correlation_function OFF (0) -colvars: - scripted OFF (0) -colvars: - custom_function OFF (0) -colvars: - periodic OFF (0) -colvars: - single_component ON (0) -colvars: - scalar ON (6) -colvars: - linear ON (2) -colvars: - homogeneous ON (0) -colvars: - multiple_timestep OFF (0) +colvars: Features of "colvar d" (refcount) +colvars: - ON active (3) +colvars: - awake +colvars: - ON gradient (3) +colvars: - collect_gradient +colvars: - collect_atom_ids +colvars: - velocity_from_finite_differences +colvars: - ON total_force (3) +colvars: - ON total_force_calculation (1) +colvars: - ON subtract_applied_force_from_total_force +colvars: - ON Jacobian_derivative (1) +colvars: - hide_Jacobian_force +colvars: - extended_Lagrangian +colvars: - external +colvars: - Langevin_dynamics +colvars: - output_energy +colvars: - ON output_value +colvars: - output_velocity +colvars: - ON output_applied_force +colvars: - ON output_total_force +colvars: - ON lower_boundary +colvars: - ON upper_boundary +colvars: - hard_lower_boundary +colvars: - hard_upper_boundary +colvars: - reflecting_lower_boundary +colvars: - reflecting_upper_boundary +colvars: - ON grid +colvars: - running_average +colvars: - correlation_function +colvars: - scripted +colvars: - custom_function +colvars: - periodic +colvars: - ON single_component +colvars: - ON scalar (7) +colvars: - ON linear (2) +colvars: - ON homogeneous +colvars: - multiple_timestep colvars: * child 1 -colvars: Features of "cvc distance0001" ON/OFF (refcount) -colvars: - active ON (0) -colvars: - scalar OFF (0) -colvars: - periodic OFF (0) -colvars: - defined_width OFF (0) -colvars: - defined_lower_boundary ON (0) -colvars: - defined_upper_boundary OFF (0) -colvars: - gradient ON (2) -colvars: - explicit_gradient ON (0) -colvars: - inverse_gradient ON (2) -colvars: - Jacobian_derivative ON (1) -colvars: - total_force_from_one_group OFF (0) -colvars: - debug_gradient OFF (0) -colvars: - use_minimum-image_with_PBCs ON (0) -colvars: - function_of_centers_of_mass ON (1) -colvars: - scalable_calculation ON (0) -colvars: - scalable_calculation_of_centers_of_mass ON (1) +colvars: Features of "cvc distance0001" (refcount) +colvars: - ON active +colvars: - scalar +colvars: - periodic +colvars: - defined_width +colvars: - ON defined_lower_boundary +colvars: - defined_upper_boundary +colvars: - ON gradient (2) +colvars: - explicit_gradient +colvars: - ON inverse_gradient (2) +colvars: - ON Jacobian_derivative (1) +colvars: - total_force_from_one_group +colvars: - debug_gradient +colvars: - ON use_minimum-image_with_PBCs +colvars: - ON function_of_centers_of_mass (1) +colvars: - ON scalable_calculation (1) +colvars: - ON scalable_calculation_of_centers_of_mass +colvars: - collect_atom_ids colvars: * child 1 -colvars: Features of "atom group group1" ON/OFF (refcount) -colvars: - active OFF (0) -colvars: - translational_fit OFF (0) -colvars: - rotational_fit OFF (0) -colvars: - fitting_group OFF (0) -colvars: - explicit_atom_gradient ON (1) -colvars: - fit_gradients OFF (0) -colvars: - atomic_forces OFF (0) -colvars: - scalable_group ON (0) -colvars: - scalable_group_center_of_mass ON (1) +colvars: Features of "atom group group1" (refcount) +colvars: - active +colvars: - center_to_reference +colvars: - center_to_origin +colvars: - rotate_to_origin +colvars: - fitting_group +colvars: - explicit_atom_gradient +colvars: - fit_gradients +colvars: - atomic_forces +colvars: - ON scalable_group (1) +colvars: - ON scalable_group_center_of_mass +colvars: - collect_atom_ids colvars: * child 2 -colvars: Features of "atom group group2" ON/OFF (refcount) -colvars: - active OFF (0) -colvars: - translational_fit OFF (0) -colvars: - rotational_fit OFF (0) -colvars: - fitting_group OFF (0) -colvars: - explicit_atom_gradient ON (1) -colvars: - fit_gradients OFF (0) -colvars: - atomic_forces OFF (0) -colvars: - scalable_group ON (0) -colvars: - scalable_group_center_of_mass ON (1) -colvars: Features of "bias harmonic1" ON/OFF (refcount) -colvars: - active ON (1) -colvars: - awake ON (0) -colvars: - step_zero_data OFF (0) -colvars: - apply_force ON (0) -colvars: - bypass_extended_Lagrangian_coordinates OFF (0) -colvars: - obtain_total_force OFF (0) -colvars: - output_accumulated_work OFF (0) -colvars: - history_dependent OFF (0) -colvars: - time_dependent OFF (0) -colvars: - require_scalar_variables OFF (0) -colvars: - calculate_a_PMF OFF (0) -colvars: - calculate_TI_samples OFF (0) -colvars: - write_TI_samples_ OFF (0) -colvars: - write_TI_PMF OFF (0) +colvars: Features of "atom group group2" (refcount) +colvars: - active +colvars: - center_to_reference +colvars: - center_to_origin +colvars: - rotate_to_origin +colvars: - fitting_group +colvars: - explicit_atom_gradient +colvars: - fit_gradients +colvars: - atomic_forces +colvars: - ON scalable_group (1) +colvars: - ON scalable_group_center_of_mass +colvars: - collect_atom_ids +colvars: Features of "bias harmonic1" (refcount) +colvars: - ON active +colvars: - awake +colvars: - step_zero_data +colvars: - ON apply_force +colvars: - bypass_extended_Lagrangian_coordinates +colvars: - obtain_total_force +colvars: - output_accumulated_work +colvars: - history_dependent +colvars: - time_dependent +colvars: - require_scalar_variables +colvars: - calculate_a_PMF +colvars: - calculate_TI_samples +colvars: - write_TI_samples_ +colvars: - write_TI_PMF +colvars: - scale_biasing_force colvars: * child 1 -colvars: Features of "colvar d" ON/OFF (refcount) -colvars: - active ON (4) -colvars: - awake ON (0) -colvars: - gradient ON (3) -colvars: - collect_gradient OFF (0) -colvars: - velocity_from_finite_differences OFF (0) -colvars: - total_force ON (3) -colvars: - total_force_calculation ON (1) -colvars: - subtract_applied_force_from_total_force ON (0) -colvars: - Jacobian_derivative ON (1) -colvars: - hide_Jacobian_force OFF (0) -colvars: - extended_Lagrangian OFF (0) -colvars: - Langevin_dynamics OFF (0) -colvars: - output_energy OFF (0) -colvars: - output_value ON (0) -colvars: - output_velocity OFF (0) -colvars: - output_applied_force ON (0) -colvars: - output_total_force ON (0) -colvars: - lower_boundary ON (1) -colvars: - upper_boundary ON (1) -colvars: - hard_lower_boundary OFF (0) -colvars: - hard_upper_boundary OFF (0) -colvars: - reflecting_lower_boundary OFF (0) -colvars: - reflecting_upper_boundary OFF (0) -colvars: - grid ON (0) -colvars: - running_average OFF (0) -colvars: - correlation_function OFF (0) -colvars: - scripted OFF (0) -colvars: - custom_function OFF (0) -colvars: - periodic OFF (0) -colvars: - single_component ON (0) -colvars: - scalar ON (6) -colvars: - linear ON (2) -colvars: - homogeneous ON (0) -colvars: - multiple_timestep OFF (0) +colvars: Features of "colvar d" (refcount) +colvars: - ON active (3) +colvars: - awake +colvars: - ON gradient (3) +colvars: - collect_gradient +colvars: - collect_atom_ids +colvars: - velocity_from_finite_differences +colvars: - ON total_force (3) +colvars: - ON total_force_calculation (1) +colvars: - ON subtract_applied_force_from_total_force +colvars: - ON Jacobian_derivative (1) +colvars: - hide_Jacobian_force +colvars: - extended_Lagrangian +colvars: - external +colvars: - Langevin_dynamics +colvars: - output_energy +colvars: - ON output_value +colvars: - output_velocity +colvars: - ON output_applied_force +colvars: - ON output_total_force +colvars: - ON lower_boundary +colvars: - ON upper_boundary +colvars: - hard_lower_boundary +colvars: - hard_upper_boundary +colvars: - reflecting_lower_boundary +colvars: - reflecting_upper_boundary +colvars: - ON grid +colvars: - running_average +colvars: - correlation_function +colvars: - scripted +colvars: - custom_function +colvars: - periodic +colvars: - ON single_component +colvars: - ON scalar (7) +colvars: - ON linear (2) +colvars: - ON homogeneous +colvars: - multiple_timestep colvars: * child 1 -colvars: Features of "cvc distance0001" ON/OFF (refcount) -colvars: - active ON (0) -colvars: - scalar OFF (0) -colvars: - periodic OFF (0) -colvars: - defined_width OFF (0) -colvars: - defined_lower_boundary ON (0) -colvars: - defined_upper_boundary OFF (0) -colvars: - gradient ON (2) -colvars: - explicit_gradient ON (0) -colvars: - inverse_gradient ON (2) -colvars: - Jacobian_derivative ON (1) -colvars: - total_force_from_one_group OFF (0) -colvars: - debug_gradient OFF (0) -colvars: - use_minimum-image_with_PBCs ON (0) -colvars: - function_of_centers_of_mass ON (1) -colvars: - scalable_calculation ON (0) -colvars: - scalable_calculation_of_centers_of_mass ON (1) +colvars: Features of "cvc distance0001" (refcount) +colvars: - ON active +colvars: - scalar +colvars: - periodic +colvars: - defined_width +colvars: - ON defined_lower_boundary +colvars: - defined_upper_boundary +colvars: - ON gradient (2) +colvars: - explicit_gradient +colvars: - ON inverse_gradient (2) +colvars: - ON Jacobian_derivative (1) +colvars: - total_force_from_one_group +colvars: - debug_gradient +colvars: - ON use_minimum-image_with_PBCs +colvars: - ON function_of_centers_of_mass (1) +colvars: - ON scalable_calculation (1) +colvars: - ON scalable_calculation_of_centers_of_mass +colvars: - collect_atom_ids colvars: * child 1 -colvars: Features of "atom group group1" ON/OFF (refcount) -colvars: - active OFF (0) -colvars: - translational_fit OFF (0) -colvars: - rotational_fit OFF (0) -colvars: - fitting_group OFF (0) -colvars: - explicit_atom_gradient ON (1) -colvars: - fit_gradients OFF (0) -colvars: - atomic_forces OFF (0) -colvars: - scalable_group ON (0) -colvars: - scalable_group_center_of_mass ON (1) +colvars: Features of "atom group group1" (refcount) +colvars: - active +colvars: - center_to_reference +colvars: - center_to_origin +colvars: - rotate_to_origin +colvars: - fitting_group +colvars: - explicit_atom_gradient +colvars: - fit_gradients +colvars: - atomic_forces +colvars: - ON scalable_group (1) +colvars: - ON scalable_group_center_of_mass +colvars: - collect_atom_ids colvars: * child 2 -colvars: Features of "atom group group2" ON/OFF (refcount) -colvars: - active OFF (0) -colvars: - translational_fit OFF (0) -colvars: - rotational_fit OFF (0) -colvars: - fitting_group OFF (0) -colvars: - explicit_atom_gradient ON (1) -colvars: - fit_gradients OFF (0) -colvars: - atomic_forces OFF (0) -colvars: - scalable_group ON (0) -colvars: - scalable_group_center_of_mass ON (1) +colvars: Features of "atom group group2" (refcount) +colvars: - active +colvars: - center_to_reference +colvars: - center_to_origin +colvars: - rotate_to_origin +colvars: - fitting_group +colvars: - explicit_atom_gradient +colvars: - fit_gradients +colvars: - atomic_forces +colvars: - ON scalable_group (1) +colvars: - ON scalable_group_center_of_mass +colvars: - collect_atom_ids colvars: Saving collective variables state to "test.colvars.state". -colvars: Features of "bias harm2" ON/OFF (refcount) -colvars: - active ON (1) -colvars: - awake ON (0) -colvars: - step_zero_data OFF (0) -colvars: - apply_force ON (0) -colvars: - bypass_extended_Lagrangian_coordinates OFF (0) -colvars: - obtain_total_force OFF (0) -colvars: - output_accumulated_work OFF (0) -colvars: - history_dependent OFF (0) -colvars: - time_dependent OFF (0) -colvars: - require_scalar_variables OFF (0) -colvars: - calculate_a_PMF OFF (0) -colvars: - calculate_TI_samples OFF (0) -colvars: - write_TI_samples_ OFF (0) -colvars: - write_TI_PMF OFF (0) +colvars: Features of "bias harm2" (refcount) +colvars: - ON active +colvars: - awake +colvars: - step_zero_data +colvars: - ON apply_force +colvars: - bypass_extended_Lagrangian_coordinates +colvars: - obtain_total_force +colvars: - output_accumulated_work +colvars: - history_dependent +colvars: - time_dependent +colvars: - require_scalar_variables +colvars: - calculate_a_PMF +colvars: - calculate_TI_samples +colvars: - write_TI_samples_ +colvars: - write_TI_PMF +colvars: - scale_biasing_force colvars: * child 1 -colvars: Features of "colvar d" ON/OFF (refcount) -colvars: - active ON (3) -colvars: - awake ON (0) -colvars: - gradient ON (2) -colvars: - collect_gradient OFF (0) -colvars: - velocity_from_finite_differences OFF (0) -colvars: - total_force ON (3) -colvars: - total_force_calculation ON (1) -colvars: - subtract_applied_force_from_total_force ON (0) -colvars: - Jacobian_derivative ON (1) -colvars: - hide_Jacobian_force OFF (0) -colvars: - extended_Lagrangian OFF (0) -colvars: - Langevin_dynamics OFF (0) -colvars: - output_energy OFF (0) -colvars: - output_value ON (0) -colvars: - output_velocity OFF (0) -colvars: - output_applied_force ON (0) -colvars: - output_total_force ON (0) -colvars: - lower_boundary ON (1) -colvars: - upper_boundary ON (1) -colvars: - hard_lower_boundary OFF (0) -colvars: - hard_upper_boundary OFF (0) -colvars: - reflecting_lower_boundary OFF (0) -colvars: - reflecting_upper_boundary OFF (0) -colvars: - grid ON (0) -colvars: - running_average OFF (0) -colvars: - correlation_function OFF (0) -colvars: - scripted OFF (0) -colvars: - custom_function OFF (0) -colvars: - periodic OFF (0) -colvars: - single_component ON (0) -colvars: - scalar ON (6) -colvars: - linear ON (2) -colvars: - homogeneous ON (0) -colvars: - multiple_timestep OFF (0) +colvars: Features of "colvar d" (refcount) +colvars: - ON active (2) +colvars: - awake +colvars: - ON gradient (2) +colvars: - collect_gradient +colvars: - collect_atom_ids +colvars: - velocity_from_finite_differences +colvars: - ON total_force (3) +colvars: - ON total_force_calculation (1) +colvars: - ON subtract_applied_force_from_total_force +colvars: - ON Jacobian_derivative (1) +colvars: - hide_Jacobian_force +colvars: - extended_Lagrangian +colvars: - external +colvars: - Langevin_dynamics +colvars: - output_energy +colvars: - ON output_value +colvars: - output_velocity +colvars: - ON output_applied_force +colvars: - ON output_total_force +colvars: - ON lower_boundary +colvars: - ON upper_boundary +colvars: - hard_lower_boundary +colvars: - hard_upper_boundary +colvars: - reflecting_lower_boundary +colvars: - reflecting_upper_boundary +colvars: - ON grid +colvars: - running_average +colvars: - correlation_function +colvars: - scripted +colvars: - custom_function +colvars: - periodic +colvars: - ON single_component +colvars: - ON scalar (7) +colvars: - ON linear (2) +colvars: - ON homogeneous +colvars: - multiple_timestep colvars: * child 1 -colvars: Features of "cvc distance0001" ON/OFF (refcount) -colvars: - active ON (0) -colvars: - scalar OFF (0) -colvars: - periodic OFF (0) -colvars: - defined_width OFF (0) -colvars: - defined_lower_boundary ON (0) -colvars: - defined_upper_boundary OFF (0) -colvars: - gradient ON (2) -colvars: - explicit_gradient ON (0) -colvars: - inverse_gradient ON (2) -colvars: - Jacobian_derivative ON (1) -colvars: - total_force_from_one_group OFF (0) -colvars: - debug_gradient OFF (0) -colvars: - use_minimum-image_with_PBCs ON (0) -colvars: - function_of_centers_of_mass ON (1) -colvars: - scalable_calculation ON (0) -colvars: - scalable_calculation_of_centers_of_mass ON (1) +colvars: Features of "cvc distance0001" (refcount) +colvars: - ON active +colvars: - scalar +colvars: - periodic +colvars: - defined_width +colvars: - ON defined_lower_boundary +colvars: - defined_upper_boundary +colvars: - ON gradient (2) +colvars: - explicit_gradient +colvars: - ON inverse_gradient (2) +colvars: - ON Jacobian_derivative (1) +colvars: - total_force_from_one_group +colvars: - debug_gradient +colvars: - ON use_minimum-image_with_PBCs +colvars: - ON function_of_centers_of_mass (1) +colvars: - ON scalable_calculation (1) +colvars: - ON scalable_calculation_of_centers_of_mass +colvars: - collect_atom_ids colvars: * child 1 -colvars: Features of "atom group group1" ON/OFF (refcount) -colvars: - active OFF (0) -colvars: - translational_fit OFF (0) -colvars: - rotational_fit OFF (0) -colvars: - fitting_group OFF (0) -colvars: - explicit_atom_gradient ON (1) -colvars: - fit_gradients OFF (0) -colvars: - atomic_forces OFF (0) -colvars: - scalable_group ON (0) -colvars: - scalable_group_center_of_mass ON (1) +colvars: Features of "atom group group1" (refcount) +colvars: - active +colvars: - center_to_reference +colvars: - center_to_origin +colvars: - rotate_to_origin +colvars: - fitting_group +colvars: - explicit_atom_gradient +colvars: - fit_gradients +colvars: - atomic_forces +colvars: - ON scalable_group (1) +colvars: - ON scalable_group_center_of_mass +colvars: - collect_atom_ids colvars: * child 2 -colvars: Features of "atom group group2" ON/OFF (refcount) -colvars: - active OFF (0) -colvars: - translational_fit OFF (0) -colvars: - rotational_fit OFF (0) -colvars: - fitting_group OFF (0) -colvars: - explicit_atom_gradient ON (1) -colvars: - fit_gradients OFF (0) -colvars: - atomic_forces OFF (0) -colvars: - scalable_group ON (0) -colvars: - scalable_group_center_of_mass ON (1) +colvars: Features of "atom group group2" (refcount) +colvars: - active +colvars: - center_to_reference +colvars: - center_to_origin +colvars: - rotate_to_origin +colvars: - fitting_group +colvars: - explicit_atom_gradient +colvars: - fit_gradients +colvars: - atomic_forces +colvars: - ON scalable_group (1) +colvars: - ON scalable_group_center_of_mass +colvars: - collect_atom_ids colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "d" from value: 11.9615 colvars: Restarting abf bias "abf1" from step number 60. colvars: ---------------------------------------------------------------------- @@ -438,6 +486,7 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -451,32 +500,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. +colvars: Atom group "group1" defined with 1 atoms requested. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. +colvars: Atom group "group2" defined with 1 atoms requested. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. @@ -530,6 +579,7 @@ colvars: # centers = { 12 } colvars: # targetCenters = { 12 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 250 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -540,5 +590,7 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Warning: before deleting colvar d, deleting related bias harmonic1 colvars: Warning: before deleting colvar d, deleting related bias abf1 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj index f029f1ae9..31374c82a 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj @@ -1,38 +1,38 @@ # step d ft_d fa_d E_harmonic1 - 0 0.00000000000000e+00 0.00000000000000e+00 3.00000000000000e+03 1.80000000000000e+04 + 0 0.00000000000000e+00 0.00000000000000e+00 3.00000000000000e+03 1.80000000000000e+04 # step d ft_d fa_d E_harmonic1 - 0 1.42467449615693e+01 0.00000000000000e+00 -5.61686240392322e+02 6.30982865292123e+02 - 2 1.42282559728026e+01 5.32933601891204e+00 -5.59529927203773e+02 6.20640585041317e+02 - 4 1.41727662460744e+01 3.36254334374946e+01 -5.43191561518601e+02 5.90114145010033e+02 - 6 1.40831323320990e+01 8.13697354080271e+01 -5.89087882343440e+02 5.42430039129534e+02 - 8 1.39609835871970e+01 1.43683712693643e+02 -4.90245896799256e+02 4.80682078657013e+02 - 10 1.38136915830229e+01 2.11747525548495e+02 -6.48260269460101e+02 4.11184644791030e+02 - 12 1.36437184346326e+01 2.81640059905252e+02 -6.92569668563411e+02 3.37726286543895e+02 - 14 1.34588898265340e+01 3.45729335512429e+02 -7.10451792145928e+02 2.66044940745548e+02 - 16 1.32645132385777e+01 4.00985013276056e+02 -7.17113322920477e+02 1.99874216317278e+02 - 18 1.30658878095430e+01 4.46271310459046e+02 -7.12743262844788e+02 1.42014602816538e+02 - 20 1.28684277602171e+01 4.80580457979151e+02 -6.97687398033433e+02 9.42708468394674e+01 + 0 1.42467449615693e+01 0.00000000000000e+00 -5.61686240392322e+02 6.30982865292123e+02 + 2 1.42282559728026e+01 5.32933601659170e+00 -5.59529927201590e+02 6.20640585041297e+02 + 4 1.41727662460742e+01 3.36254334328178e+01 -5.43191561518562e+02 5.90114145009947e+02 + 6 1.40831323320984e+01 8.13697353990825e+01 -5.89087882335502e+02 5.42430039129236e+02 + 8 1.39609835871958e+01 1.43683712679872e+02 -4.90245896798950e+02 4.80682078656413e+02 + 10 1.38136915830204e+01 2.11747525531865e+02 -6.48260269443340e+02 4.11184644789902e+02 + 12 1.36437184346286e+01 2.81640059890150e+02 -6.92569668547312e+02 3.37726286542257e+02 + 14 1.34588898265283e+01 3.45729335505761e+02 -7.10451792137843e+02 2.66044940743482e+02 + 16 1.32645132385707e+01 4.00985013285219e+02 -7.17113322927902e+02 1.99874216315080e+02 + 18 1.30658878095359e+01 4.46271310489825e+02 -7.12743262873798e+02 1.42014602814653e+02 + 20 1.28684277602119e+01 4.80580458032557e+02 -6.97687398085530e+02 9.42708468383301e+01 # step d ft_d fa_d E_harmonic1 E_harm2 - 20 1.28684277602171e+01 4.91888943151427e+02 -7.00052334624999e+02 9.42708468394674e+01 2.16390678518517e-01 - 22 1.26751474320475e+01 5.03084201909373e+02 -6.63749745722433e+02 5.69780068750397e+01 1.31911488631676e+00 - 24 1.24888492973110e+01 5.15335038327460e+02 -6.24768595087998e+02 2.98717044351878e+01 3.26593801074265e+00 - 26 1.23139243019631e+01 5.23015189033541e+02 -5.84344372073400e+02 1.23185584203791e+01 5.88374829295988e+00 - 28 1.21466432033769e+01 5.30527139707869e+02 -1.53268809286588e+01 2.68802863708136e+00 9.10272277928461e+00 - 30 1.19993450537562e+01 5.38695710361251e+02 2.51801102170466e+01 5.36193227844337e-05 1.25163790180274e+01 - 32 1.18850444890963e+01 5.34994463383540e+02 5.66127654985307e+01 1.65184618589271e+00 1.55390723911830e+01 - 34 1.18115458381165e+01 5.01682267555293e+02 7.68248945179519e+01 4.43937139139973e+00 1.76552911862265e+01 - 36 1.17769967622096e+01 4.41508793313709e+02 8.63258903923681e+01 6.21630550812685e+00 1.86967114955734e+01 - 38 1.17769542139854e+01 3.61640408006584e+02 8.63375911540067e+01 6.21867783235716e+00 1.86980124336000e+01 - 40 1.18061287066284e+01 2.69866689808628e+02 7.83146056771794e+01 4.69825979919525e+00 1.78166083142086e+01 + 20 1.28684277602119e+01 4.91888943214004e+02 -7.00052334681550e+02 9.42708468383301e+01 2.16390678535748e-01 + 22 1.26751474320465e+01 5.03084201979406e+02 -6.63749745792196e+02 5.69780068748745e+01 1.31911488632471e+00 + 24 1.24888492973171e+01 5.15335038410192e+02 -6.24768595172394e+02 2.98717044359277e+01 3.26593801066529e+00 + 26 1.23139243019797e+01 5.23015189146873e+02 -5.84344372191302e+02 1.23185584216834e+01 5.88374829267482e+00 + 28 1.21466432034073e+01 5.30527139882848e+02 -1.53268809370116e+01 2.68802863819490e+00 9.10272277863661e+00 + 30 1.19993450538088e+01 5.38695710631225e+02 2.51801102025817e+01 5.36193141719397e-05 1.25163790167116e+01 + 32 1.18850444891885e+01 5.34994463767922e+02 5.66127654731507e+01 1.65184618324038e+00 1.55390723886105e+01 + 34 1.18115458382762e+01 5.01682268034594e+02 7.68248944740457e+01 4.43937138387764e+00 1.76552911814828e+01 + 36 1.17769967624676e+01 4.41508793838497e+02 8.63258903213991e+01 6.21630549373929e+00 1.86967114876829e+01 + 38 1.17769542143717e+01 3.61640408513788e+02 8.63375910477925e+01 6.21867781082023e+00 1.86980124217904e+01 + 40 1.18061287071667e+01 2.69866690242884e+02 7.83146055291581e+01 4.69825977310700e+00 1.78166082981433e+01 # step d ft_d fa_d E_harm2 - 40 1.18061287066284e+01 2.21949532217238e+02 2.98467823342890e+01 1.78166083142086e+01 - 42 1.18555777458287e+01 1.74464230745251e+02 2.86105563542814e+01 1.63712786980303e+01 - 44 1.19176677646512e+01 8.22937404700844e+01 2.70583058837192e+01 1.46430383459383e+01 - 46 1.19851813910175e+01 -6.16868563783110e+00 2.53704652245623e+01 1.28732101142145e+01 - 48 1.20415309208210e+01 -8.97664352869559e+01 -3.04621864055419e+02 1.14832871967769e+01 - 50 1.20655400380907e+01 -1.50412424518311e+02 -1.19070572741895e+02 1.09151927551443e+01 - 52 1.20686235841253e+01 -1.88148861003765e+02 -2.70255157752960e+01 1.08432753505955e+01 - 54 1.20571466466005e+01 -2.05067811286631e+02 2.93687990112175e+01 1.11121555752091e+01 - 56 1.20332538278214e+01 -2.00399869950163e+02 6.58114558084562e+01 1.16824770177739e+01 - 58 1.20000609172601e+01 -1.75170570145191e+02 8.83273231404457e+01 1.24984771148846e+01 - 60 1.19614725548519e+01 -1.36757725550194e+02 2.59631861287023e+01 1.34817406790728e+01 + 40 1.18061287071667e+01 2.21949532598602e+02 2.98467823208325e+01 1.78166082981433e+01 + 42 1.18555777465383e+01 1.74464231066044e+02 2.86105563365434e+01 1.63712786777305e+01 + 44 1.19176677655463e+01 8.22937406521174e+01 2.70583058613429e+01 1.46430383217196e+01 + 46 1.19851813921025e+01 -6.16868558833627e+00 2.53704651974387e+01 1.28732100866889e+01 + 48 1.20415309220875e+01 -8.97664353399688e+01 -3.04621864232869e+02 1.14832871664300e+01 + 50 1.20655400395174e+01 -1.50412424652567e+02 -1.19070572819524e+02 1.09151927218147e+01 + 52 1.20686235856919e+01 -1.88148861256361e+02 -2.70255157819366e+01 1.08432753141169e+01 + 54 1.20571466482814e+01 -2.05067811724940e+02 2.93687990810595e+01 1.11121555355867e+01 + 56 1.20332538295850e+01 -2.00399870515217e+02 6.58114559546446e+01 1.16824769751521e+01 + 58 1.20000609190792e+01 -1.75170570569691e+02 8.83273233309201e+01 1.24984770694101e+01 + 60 1.19614725567188e+01 -1.36757725642476e+02 2.59631860820309e+01 1.34817406306033e+01 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.grad b/namd/tests/library/005_Tcl_script/AutoDiff/test.grad index 2a30d2884..09257e021 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.grad +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.grad @@ -1,18 +1,18 @@ # 1 # 1.20000000000000e+01 2.00000000000000e-01 100 0 - 1.21000000000000e+01 6.99836008077528e+01 - 1.23000000000000e+01 -5.26375313396654e+02 - 1.25000000000000e+01 -5.16708951944646e+02 - 1.27000000000000e+01 -5.05977066222890e+02 - 1.29000000000000e+01 -4.88119448094002e+02 - 1.31000000000000e+01 -4.54995001210363e+02 - 1.33000000000000e+01 -4.12314411188385e+02 - 1.35000000000000e+01 -3.59715820941386e+02 - 1.37000000000000e+01 -2.97680997044662e+02 - 1.39000000000000e+01 -2.12126120236132e+02 - 1.41000000000000e+01 -9.78647225049371e+01 - 1.43000000000000e+01 -1.38644228524206e+01 + 1.21000000000000e+01 6.99836010424488e+01 + 1.23000000000000e+01 -5.26375313539263e+02 + 1.25000000000000e+01 -5.16708952033009e+02 + 1.27000000000000e+01 -5.05977066295794e+02 + 1.29000000000000e+01 -4.88119448153522e+02 + 1.31000000000000e+01 -4.54995001246909e+02 + 1.33000000000000e+01 -4.12314411202659e+02 + 1.35000000000000e+01 -3.59715820938218e+02 + 1.37000000000000e+01 -2.97680997031215e+02 + 1.39000000000000e+01 -2.12126120219850e+02 + 1.41000000000000e+01 -9.78647224947473e+01 + 1.43000000000000e+01 -1.38644228493632e+01 1.45000000000000e+01 0.00000000000000e+00 1.47000000000000e+01 0.00000000000000e+00 1.49000000000000e+01 0.00000000000000e+00 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf b/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf index edf8b154a..53f87f0d2 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf @@ -1,18 +1,18 @@ # 1 # 1.19000000000000e+01 2.00000000000000e-01 101 0 - 1.20000000000000e+01 7.63151734965745e+02 - 1.22000000000000e+01 7.77148455127296e+02 - 1.24000000000000e+01 6.71873392447965e+02 - 1.26000000000000e+01 5.68531602059036e+02 - 1.28000000000000e+01 4.67336188814458e+02 - 1.30000000000000e+01 3.69712299195657e+02 - 1.32000000000000e+01 2.78713298953585e+02 - 1.34000000000000e+01 1.96250416715908e+02 - 1.36000000000000e+01 1.24307252527630e+02 - 1.38000000000000e+01 6.47710531186980e+01 - 1.40000000000000e+01 2.23458290714716e+01 - 1.42000000000000e+01 2.77288457048417e+00 + 1.20000000000000e+01 7.63151734992420e+02 + 1.22000000000000e+01 7.77148455200910e+02 + 1.24000000000000e+01 6.71873392493057e+02 + 1.26000000000000e+01 5.68531602086455e+02 + 1.28000000000000e+01 4.67336188827297e+02 + 1.30000000000000e+01 3.69712299196592e+02 + 1.32000000000000e+01 2.78713298947211e+02 + 1.34000000000000e+01 1.96250416706679e+02 + 1.36000000000000e+01 1.24307252519035e+02 + 1.38000000000000e+01 6.47710531127921e+01 + 1.40000000000000e+01 2.23458290688221e+01 + 1.42000000000000e+01 2.77288456987264e+00 1.44000000000000e+01 0.00000000000000e+00 1.46000000000000e+01 0.00000000000000e+00 1.48000000000000e+01 0.00000000000000e+00 diff --git a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out index ed14c521a..dbb4752af 100644 --- a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out +++ b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsdA" @@ -55,14 +57,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -70,7 +72,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -106,21 +108,21 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -159,6 +161,7 @@ colvars: # centers = { 0, 0 } colvars: # targetCenters = { 0, 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsdA" will be rescaled to 1 according to the specified width (1). colvars: The force constant for colvar "rmsdB" will be rescaled to 1 according to the specified width (1). @@ -170,6 +173,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- @@ -183,6 +187,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -201,6 +206,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -216,14 +222,30 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - harmonicWalls colvar bias implementation: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "rmsdB":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "rmsdB":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj index ddcb476b2..c60285dcf 100644 --- a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj +++ b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step rmsdA ft_rmsdA rmsdB ft_rmsdB - 0 4.84870372257743e-01 0.00000000000000e+00 4.84870372257743e-01 0.00000000000000e+00 - 1 4.84397558390947e-01 2.73671250418532e+01 4.84397558390947e-01 2.73671250418532e+01 - 2 4.83907428259583e-01 2.16076115744649e+01 4.83907428259583e-01 2.16076115744649e+01 - 3 4.83522392476985e-01 1.48700273236137e+01 4.83522392476985e-01 1.48700273236137e+01 - 4 4.83083112856857e-01 9.62041732419351e+00 4.83083112856857e-01 9.62041732419351e+00 - 5 4.82621016610959e-01 6.75848678249268e+00 4.82621016610959e-01 6.75848678249268e+00 - 6 4.82181848616375e-01 3.55598526400234e+00 4.82181848616375e-01 3.55598526400234e+00 - 7 4.81645520125956e-01 3.84568147972637e+00 4.81645520125956e-01 3.84568147972637e+00 - 8 4.81136761645330e-01 7.38903466954419e+00 4.81136761645330e-01 7.38903466954419e+00 - 9 4.80598465150393e-01 1.31715075507452e+01 4.80598465150393e-01 1.31715075507452e+01 - 10 4.80094226695461e-01 2.27871464821819e+01 4.80094226695461e-01 2.27871464821819e+01 - 11 4.79704703208599e-01 3.33000067601667e+01 4.79704703208599e-01 3.33000067601667e+01 - 12 4.79506792183813e-01 4.04751300762086e+01 4.79506792183813e-01 4.04751300762086e+01 - 13 4.79327275850325e-01 4.50913690064303e+01 4.79327275850325e-01 4.50913690064303e+01 - 14 4.79314968874545e-01 4.98879889015527e+01 4.79314968874545e-01 4.98879889015527e+01 - 15 4.79397379647665e-01 4.87227324434123e+01 4.79397379647665e-01 4.87227324434123e+01 - 16 4.79394129016958e-01 4.65370310981482e+01 4.79394129016958e-01 4.65370310981482e+01 - 17 4.79404085661514e-01 4.25674542132686e+01 4.79404085661514e-01 4.25674542132686e+01 - 18 4.79306164127760e-01 3.79497993178883e+01 4.79306164127760e-01 3.79497993178883e+01 - 19 4.79258291379496e-01 3.40970491422707e+01 4.79258291379496e-01 3.40970491422707e+01 - 20 4.79299937828241e-01 2.83439957758912e+01 4.79299937828241e-01 2.83439957758912e+01 +# step rmsdA ft_rmsdA rmsdB ft_rmsdB + 0 4.84870372257743e-01 0.00000000000000e+00 4.84870372257743e-01 0.00000000000000e+00 + 1 4.84397558390959e-01 2.73671250705184e+01 4.84397558390959e-01 2.73671250705184e+01 + 2 4.83907428259633e-01 2.16076116033336e+01 4.83907428259633e-01 2.16076116033336e+01 + 3 4.83522392477099e-01 1.48700273529640e+01 4.83522392477099e-01 1.48700273529640e+01 + 4 4.83083112857061e-01 9.62041735404308e+00 4.83083112857061e-01 9.62041735404308e+00 + 5 4.82621016611279e-01 6.75848681260943e+00 4.82621016611279e-01 6.75848681260943e+00 + 6 4.82181848616836e-01 3.55598529366702e+00 4.82181848616836e-01 3.55598529366702e+00 + 7 4.81645520126582e-01 3.84568150780596e+00 4.81645520126582e-01 3.84568150780596e+00 + 8 4.81136761646141e-01 7.38903469459440e+00 4.81136761646141e-01 7.38903469459440e+00 + 9 4.80598465151405e-01 1.31715075709571e+01 4.80598465151405e-01 1.31715075709571e+01 + 10 4.80094226696681e-01 2.27871464954793e+01 4.80094226696681e-01 2.27871464954793e+01 + 11 4.79704703210026e-01 3.33000067642520e+01 4.79704703210026e-01 3.33000067642520e+01 + 12 4.79506792185437e-01 4.04751300688640e+01 4.79506792185437e-01 4.04751300688640e+01 + 13 4.79327275852122e-01 4.50913689853400e+01 4.79327275852122e-01 4.50913689853400e+01 + 14 4.79314968876482e-01 4.98879888654564e+01 4.79314968876482e-01 4.98879888654564e+01 + 15 4.79397379649694e-01 4.87227323912461e+01 4.79397379649694e-01 4.87227323912461e+01 + 16 4.79394129019021e-01 4.65370310291944e+01 4.79394129019021e-01 4.65370310291944e+01 + 17 4.79404085663536e-01 4.25674541281252e+01 4.79404085663536e-01 4.25674541281252e+01 + 18 4.79306164129660e-01 3.79497992181814e+01 4.79306164129660e-01 3.79497992181814e+01 + 19 4.79258291381186e-01 3.40970490306029e+01 4.79258291381186e-01 3.40970490306029e+01 + 20 4.79299937829629e-01 2.83439956536282e+01 4.79299937829629e-01 2.83439956536282e+01 diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out index 0e9b1d0ff..4ffa0e954 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out @@ -4,4 +4,4 @@ TCL: Running for 20 steps TCL: Resetting colvars with scripted config TCL: Reinitializing atom data TCL: Running for 20 steps -TCL: { 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1.} {0.8030419238525889 -0.044335223471426655 -0.5942710294931696 -0.8030419238525889 0.044335223471426655 0.5942710294931696 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.} +TCL: { 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1.} {0.803041923852589 -0.044335223471426634 -0.5942710294931693 -0.803041923852589 0.044335223471426634 0.5942710294931693 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.} diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out index 4169f3a81..7d1128cfc 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "unscripted.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -25,28 +27,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -85,14 +87,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 104 atoms requested: total mass = 727.821, total charge = 6.70552e-08. @@ -100,7 +102,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -1.09169 , -2.08869 , -2.98243 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -132,6 +134,7 @@ colvars: # centers = { 18 } colvars: # targetCenters = { 18 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 500 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 500 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -144,6 +147,7 @@ colvars: # colvarsTrajFrequency = 2 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- @@ -157,6 +161,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -173,15 +178,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (104 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "o":0/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08. colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (104 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "o":0/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08. @@ -196,6 +219,7 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "ds" @@ -209,32 +233,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. +colvars: Atom group "group1" defined with 1 atoms requested. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. +colvars: Atom group "group2" defined with 1 atoms requested. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. @@ -273,17 +297,17 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] -colvars: Atom group "atoms" defined with 2 atoms requested: total mass = 24.022, total charge = -0.03. +colvars: Atom group "atoms" defined with 2 atoms requested. colvars: # useX = on [default] colvars: # useY = on [default] colvars: # useZ = on [default] @@ -297,21 +321,21 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] -colvars: Atom group "atoms" defined with 104 atoms requested: total mass = 727.821, total charge = 6.70552e-08. +colvars: Atom group "atoms" defined with 104 atoms requested. colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -1.09169 , -2.08869 , -2.98243 ); it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: This colvar uses scripted function "vector". @@ -346,6 +370,7 @@ colvars: # colvarsTrajFrequency = 2 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- @@ -359,6 +384,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -375,4 +401,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (104 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - cartesian colvar component: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - Scripted functions (Tcl): +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped index b8c350fb2..f2e2c8800 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name ds - x 1.91635808809730e+01 + x 1.91635808809322e+01 } colvar { name vec - x ( 1.91635808809730e+01 , 9.74600371909626e-01 , 2.12939348547346e-01 , -1.24954463323046e-03 , -6.93497480317003e-02 ) + x ( 1.91635808809322e+01 , 9.74600371905328e-01 , 2.12939348562529e-01 , -1.24954463293996e-03 , -6.93497480454941e-02 ) } restraint { diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj index bc74a2043..219a7e69d 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj @@ -1,24 +1,24 @@ -# step d fa_d o - 0 1.42467449615693e+01 1.87662751921536e+03 ( 9.99999748638998e-01 , 6.84042724576832e-04 , 5.12508171643214e-05 , -1.79390207161565e-04 ) - 2 1.45977275439175e+01 1.70113622804125e+03 ( 9.99985973761768e-01 , 5.11485913744026e-03 , -3.32731800417789e-05 , -1.37455033645004e-03 ) - 4 1.50626713340646e+01 1.46866433296768e+03 ( 9.99843158592016e-01 , 1.70395625507908e-02 , -1.43866916456290e-04 , -4.82605709972753e-03 ) - 6 1.56168085965048e+01 1.19159570174758e+03 ( 9.99321288192724e-01 , 3.53760784411667e-02 , -2.78427047992860e-04 , -1.02673520119492e-02 ) - 8 1.62291266298068e+01 8.85436685096593e+02 ( 9.98133542942867e-01 , 5.85622743061378e-02 , -4.51475701577846e-04 , -1.73114600800356e-02 ) - 10 1.68643388381563e+01 5.67830580921871e+02 ( 9.96054934943978e-01 , 8.49744253292275e-02 , -6.83720355648298e-04 , -2.55625925952464e-02 ) - 12 1.74846635628575e+01 2.57668218571256e+02 ( 9.92972839557288e-01 , 1.13139164123728e-01 , -9.51259111211344e-04 , -3.46924278340861e-02 ) - 14 1.80530624332059e+01 -2.65312166029723e+01 ( 9.88977962066854e-01 , 1.41311479837272e-01 , -1.14108784183725e-03 , -4.41854515743639e-02 ) - 16 1.85372200961765e+01 -2.68610048088240e+02 ( 9.84381327967116e-01 , 1.67770992125046e-01 , -1.20902908935363e-03 , -5.33369815394103e-02 ) - 18 1.89124918771857e+01 -4.56245938592827e+02 ( 9.79545563657221e-01 , 1.91522263357025e-01 , -1.22366955206206e-03 , -6.17107283289307e-02 ) - 20 1.91635808809730e+01 -5.81790440486497e+02 ( 9.74600371909626e-01 , 2.12939348547346e-01 , -1.24954463323043e-03 , -6.93497480317004e-02 ) -# step ds fa_ds vec fa_vec - 20 1.42467449615693e+01 0.00000000000000e+00 ( 1.42467449615693e+01 , 9.99999748638998e-01 , 6.84042724576832e-04 , 5.12508171643214e-05 , -1.79390207161565e-04 ) ( 1.87662751921535e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 22 1.45977275439175e+01 0.00000000000000e+00 ( 1.45977275439175e+01 , 9.99985973761768e-01 , 5.11485913744027e-03 , -3.32731800417788e-05 , -1.37455033645004e-03 ) ( 1.70113622804125e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 24 1.50626713340646e+01 0.00000000000000e+00 ( 1.50626713340647e+01 , 9.99843158592016e-01 , 1.70395625507908e-02 , -1.43866916456290e-04 , -4.82605709972753e-03 ) ( 1.46866433296765e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 26 1.56168085965049e+01 0.00000000000000e+00 ( 1.56168085965048e+01 , 9.99321288192724e-01 , 3.53760784411667e-02 , -2.78427047992838e-04 , -1.02673520119492e-02 ) ( 1.19159570174760e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 28 1.62291266298068e+01 0.00000000000000e+00 ( 1.62291266298068e+01 , 9.98133542942867e-01 , 5.85622743061378e-02 , -4.51475701577845e-04 , -1.73114600800356e-02 ) ( 8.85436685096600e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 30 1.68643388381563e+01 0.00000000000000e+00 ( 1.68643388381563e+01 , 9.96054934943978e-01 , 8.49744253292276e-02 , -6.83720355648297e-04 , -2.55625925952464e-02 ) ( 5.67830580921850e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 32 1.74846635628575e+01 0.00000000000000e+00 ( 1.74846635628575e+01 , 9.92972839557288e-01 , 1.13139164123728e-01 , -9.51259111211365e-04 , -3.46924278340861e-02 ) ( 2.57668218571251e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 34 1.80530624332059e+01 0.00000000000000e+00 ( 1.80530624332059e+01 , 9.88977962066854e-01 , 1.41311479837272e-01 , -1.14108784183723e-03 , -4.41854515743639e-02 ) ( -2.65312166029492e+01 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 36 1.85372200961765e+01 0.00000000000000e+00 ( 1.85372200961765e+01 , 9.84381327967116e-01 , 1.67770992125046e-01 , -1.20902908935363e-03 , -5.33369815394102e-02 ) ( -2.68610048088250e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 38 1.89124918771856e+01 0.00000000000000e+00 ( 1.89124918771856e+01 , 9.79545563657221e-01 , 1.91522263357025e-01 , -1.22366955206212e-03 , -6.17107283289307e-02 ) ( -4.56245938592801e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 40 1.91635808809730e+01 0.00000000000000e+00 ( 1.91635808809730e+01 , 9.74600371909626e-01 , 2.12939348547346e-01 , -1.24954463323041e-03 , -6.93497480317004e-02 ) ( -5.81790440486500e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) +# step d fa_d o + 0 1.42467449615693e+01 1.87662751921536e+03 ( 9.99999748638998e-01 , 6.84042724576856e-04 , 5.12508171642993e-05 , -1.79390207161577e-04 ) + 2 1.45977275439174e+01 1.70113622804129e+03 ( 9.99985973761768e-01 , 5.11485913752449e-03 , -3.32731800435062e-05 , -1.37455033649980e-03 ) + 4 1.50626713340642e+01 1.46866433296788e+03 ( 9.99843158592009e-01 , 1.70395625511364e-02 , -1.43866916458119e-04 , -4.82605709994617e-03 ) + 6 1.56168085965040e+01 1.19159570174801e+03 ( 9.99321288192689e-01 , 3.53760784420164e-02 , -2.78427047982270e-04 , -1.02673520124943e-02 ) + 8 1.62291266298058e+01 8.85436685097112e+02 ( 9.98133542942750e-01 , 5.85622743078173e-02 , -4.51475701501585e-04 , -1.73114600811307e-02 ) + 10 1.68643388381556e+01 5.67830580922218e+02 ( 9.96054934943680e-01 , 8.49744253320995e-02 , -6.83720355286896e-04 , -2.55625925973094e-02 ) + 12 1.74846635628564e+01 2.57668218571810e+02 ( 9.92972839556575e-01 , 1.13139164128729e-01 , -9.51259109789660e-04 , -3.46924278382252e-02 ) + 14 1.80530624332013e+01 -2.65312166006630e+01 ( 9.88977962065000e-01 , 1.41311479847713e-01 , -1.14108783882053e-03 , -4.41854515825400e-02 ) + 16 1.85372200961635e+01 -2.68610048081769e+02 ( 9.84381327963322e-01 , 1.67770992143166e-01 , -1.20902908627445e-03 , -5.33369815525160e-02 ) + 18 1.89124918771599e+01 -4.56245938579931e+02 ( 9.79545563652526e-01 , 1.91522263376275e-01 , -1.22366955068550e-03 , -6.17107283437381e-02 ) + 20 1.91635808809322e+01 -5.81790440466119e+02 ( 9.74600371905327e-01 , 2.12939348562529e-01 , -1.24954463293998e-03 , -6.93497480454941e-02 ) +# step ds fa_ds vec fa_vec + 20 1.42467449615693e+01 0.00000000000000e+00 ( 1.42467449615693e+01 , 9.99999748638998e-01 , 6.84042724576856e-04 , 5.12508171642993e-05 , -1.79390207161577e-04 ) ( 1.87662751921535e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 22 1.45977275439174e+01 0.00000000000000e+00 ( 1.45977275439174e+01 , 9.99985973761768e-01 , 5.11485913752449e-03 , -3.32731800435062e-05 , -1.37455033649980e-03 ) ( 1.70113622804130e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 24 1.50626713340642e+01 0.00000000000000e+00 ( 1.50626713340642e+01 , 9.99843158592009e-01 , 1.70395625511364e-02 , -1.43866916458118e-04 , -4.82605709994616e-03 ) ( 1.46866433296790e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 26 1.56168085965040e+01 0.00000000000000e+00 ( 1.56168085965040e+01 , 9.99321288192689e-01 , 3.53760784420164e-02 , -2.78427047982271e-04 , -1.02673520124943e-02 ) ( 1.19159570174800e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 28 1.62291266298058e+01 0.00000000000000e+00 ( 1.62291266298058e+01 , 9.98133542942750e-01 , 5.85622743078173e-02 , -4.51475701501585e-04 , -1.73114600811307e-02 ) ( 8.85436685097099e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 30 1.68643388381556e+01 0.00000000000000e+00 ( 1.68643388381556e+01 , 9.96054934943680e-01 , 8.49744253320995e-02 , -6.83720355286896e-04 , -2.55625925973094e-02 ) ( 5.67830580922200e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 32 1.74846635628564e+01 0.00000000000000e+00 ( 1.74846635628564e+01 , 9.92972839556575e-01 , 1.13139164128729e-01 , -9.51259109789661e-04 , -3.46924278382252e-02 ) ( 2.57668218571800e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 34 1.80530624332013e+01 0.00000000000000e+00 ( 1.80530624332013e+01 , 9.88977962065000e-01 , 1.41311479847713e-01 , -1.14108783882053e-03 , -4.41854515825400e-02 ) ( -2.65312166006506e+01 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 36 1.85372200961635e+01 0.00000000000000e+00 ( 1.85372200961635e+01 , 9.84381327963322e-01 , 1.67770992143166e-01 , -1.20902908627445e-03 , -5.33369815525160e-02 ) ( -2.68610048081751e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 38 1.89124918771599e+01 0.00000000000000e+00 ( 1.89124918771599e+01 , 9.79545563652526e-01 , 1.91522263376275e-01 , -1.22366955068550e-03 , -6.17107283437381e-02 ) ( -4.56245938579951e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 40 1.91635808809322e+01 0.00000000000000e+00 ( 1.91635808809322e+01 , 9.74600371905328e-01 , 2.12939348562529e-01 , -1.24954463293996e-03 , -6.93497480454941e-02 ) ( -5.81790440466101e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/namd/tests/library/007_scripted_cv_biases/namd-version.txt b/namd/tests/library/007_scripted_cv_biases/namd-version.txt index 3851f0163..157cac038 100644 --- a/namd/tests/library/007_scripted_cv_biases/namd-version.txt +++ b/namd/tests/library/007_scripted_cv_biases/namd-version.txt @@ -1,5 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. -colvars: Using NAMD interface, version 2016-11-23. - -Wall-compatible restart information added later. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out index bc3b30e0e..6a9e4c603 100644 --- a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out +++ b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "dmat" @@ -55,27 +57,27 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1_2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 2 atoms requested: total mass = 24.022, total charge = -0.03. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_9_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 2 atoms requested: total mass = 24.022, total charge = 0.14. @@ -112,6 +114,7 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = on colvars: # forceConstant = 1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "dmat" will be rescaled to 25 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -122,14 +125,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - distancePairs colvar component: +colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "dmat":0/0. 2 atoms: total mass = 24.022, total charge = -0.03. colvars: Re-initialized atom group for variable "dmat":0/1. 2 atoms: total mass = 24.022, total charge = 0.14. colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "dmat":0/0. 2 atoms: total mass = 24.022, total charge = -0.03. colvars: Re-initialized atom group for variable "dmat":0/1. 2 atoms: total mass = 24.022, total charge = 0.14. colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj index 4da3a5ad0..82cfa8cb8 100644 --- a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj +++ b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step dmat fa_dmat x0_dmat 0 ( 1.21777809554943e+01 , 1.42467449615693e+01 , 1.04037423074584e+01 , 1.19921066122679e+01 ) ( -4.44452388735783e+00 , -6.16862403923228e+00 , -1.00935576864602e+01 , 1.97334693301965e-01 ) ( 1.20000000000000e+01 , 1.40000000000000e+01 , 1.00000000000000e+01 , 1.20000000000000e+01 ) - 1 ( 1.21756207147491e+01 , 1.42470238788079e+01 , 1.04051155961944e+01 , 1.19946270847732e+01 ) ( -4.56551786872841e+00 , -6.40059697019852e+00 , -1.02528899048611e+01 , -4.06771193293132e-02 ) ( 1.19930000000000e+01 , 1.39910000000000e+01 , 9.99500000000000e+00 , 1.19930000000000e+01 ) - 2 ( 1.21730460027225e+01 , 1.42474017558769e+01 , 1.04061807237121e+01 , 1.19973140354256e+01 ) ( -4.67615006806308e+00 , -6.63504389692182e+00 , -1.04045180928033e+01 , -2.82850885641173e-01 ) ( 1.19860000000000e+01 , 1.39820000000000e+01 , 9.99000000000000e+00 , 1.19860000000000e+01 ) - 3 ( 1.21706185978868e+01 , 1.42476454576845e+01 , 1.04071659086201e+01 , 1.19998189022154e+01 ) ( -4.79046494716990e+00 , -6.86613644211285e+00 , -1.05541477155027e+01 , -5.20472555385387e-01 ) ( 1.19790000000000e+01 , 1.39730000000000e+01 , 9.98500000000000e+00 , 1.19790000000000e+01 ) - 4 ( 1.21683952007756e+01 , 1.42481001273692e+01 , 1.04075924776310e+01 , 1.20018588027657e+01 ) ( -4.90988001939003e+00 , -7.10250318422965e+00 , -1.06898119407748e+01 , -7.46470069142058e-01 ) ( 1.19720000000000e+01 , 1.39640000000000e+01 , 9.98000000000000e+00 , 1.19720000000000e+01 ) - 5 ( 1.21663636501515e+01 , 1.42484947491521e+01 , 1.04077166779268e+01 , 1.20033662039911e+01 ) ( -5.03409125378686e+00 , -7.33736872880351e+00 , -1.08179169481691e+01 , -9.59155099778552e-01 ) ( 1.19650000000000e+01 , 1.39550000000000e+01 , 9.97500000000000e+00 , 1.19650000000000e+01 ) - 6 ( 1.21637914428210e+01 , 1.42488413632153e+01 , 1.04074400269777e+01 , 1.20048328024051e+01 ) ( -5.14478607052502e+00 , -7.57103408038215e+00 , -1.09360006744432e+01 , -1.17082006012863e+00 ) ( 1.19580000000000e+01 , 1.39460000000000e+01 , 9.97000000000000e+00 , 1.19580000000000e+01 ) - 7 ( 1.21606504826571e+01 , 1.42491108211564e+01 , 1.04064186711883e+01 , 1.20059438853600e+01 ) ( -5.24126206642750e+00 , -7.80277052890939e+00 , -1.10354667797074e+01 , -1.37359713399947e+00 ) ( 1.19510000000000e+01 , 1.39370000000000e+01 , 9.96499999999999e+00 , 1.19510000000000e+01 ) - 8 ( 1.21578350901344e+01 , 1.42493400866701e+01 , 1.04052750916562e+01 , 1.20066641446713e+01 ) ( -5.34587725336086e+00 , -8.03350216675169e+00 , -1.11318772914041e+01 , -1.56660361678274e+00 ) ( 1.19440000000000e+01 , 1.39280000000000e+01 , 9.95999999999999e+00 , 1.19440000000000e+01 ) - 9 ( 1.21551529536135e+01 , 1.42495154307479e+01 , 1.04038460769379e+01 , 1.20069492651880e+01 ) ( -5.45382384033828e+00 , -8.26288576869678e+00 , -1.12211519234485e+01 , -1.74873162970037e+00 ) ( 1.19370000000000e+01 , 1.39190000000000e+01 , 9.95499999999999e+00 , 1.19370000000000e+01 ) - 10 ( 1.21523782650667e+01 , 1.42496785499723e+01 , 1.04020777830222e+01 , 1.20068009867465e+01 ) ( -5.55945662666826e+00 , -8.49196374930874e+00 , -1.13019445755558e+01 , -1.92002466866330e+00 ) ( 1.19300000000000e+01 , 1.39100000000000e+01 , 9.94999999999999e+00 , 1.19300000000000e+01 ) + 1 ( 1.21756207147491e+01 , 1.42470238788079e+01 , 1.04051155961944e+01 , 1.19946270847732e+01 ) ( -4.56551786872810e+00 , -6.40059697019808e+00 , -1.02528899048608e+01 , -4.06771193291355e-02 ) ( 1.19930000000000e+01 , 1.39910000000000e+01 , 9.99500000000000e+00 , 1.19930000000000e+01 ) + 2 ( 1.21730460027225e+01 , 1.42474017558768e+01 , 1.04061807237121e+01 , 1.19973140354256e+01 ) ( -4.67615006806166e+00 , -6.63504389691996e+00 , -1.04045180928018e+01 , -2.82850885640329e-01 ) ( 1.19860000000000e+01 , 1.39820000000000e+01 , 9.99000000000000e+00 , 1.19860000000000e+01 ) + 3 ( 1.21706185978867e+01 , 1.42476454576843e+01 , 1.04071659086200e+01 , 1.19998189022153e+01 ) ( -4.79046494716631e+00 , -6.86613644210809e+00 , -1.05541477154994e+01 , -5.20472555383211e-01 ) ( 1.19790000000000e+01 , 1.39730000000000e+01 , 9.98500000000000e+00 , 1.19790000000000e+01 ) + 4 ( 1.21683952007753e+01 , 1.42481001273688e+01 , 1.04075924776308e+01 , 1.20018588027655e+01 ) ( -4.90988001938302e+00 , -7.10250318422005e+00 , -1.06898119407688e+01 , -7.46470069137661e-01 ) ( 1.19720000000000e+01 , 1.39640000000000e+01 , 9.98000000000000e+00 , 1.19720000000000e+01 ) + 5 ( 1.21663636501510e+01 , 1.42484947491514e+01 , 1.04077166779264e+01 , 1.20033662039908e+01 ) ( -5.03409125377492e+00 , -7.33736872878623e+00 , -1.08179169481593e+01 , -9.59155099770514e-01 ) ( 1.19650000000000e+01 , 1.39550000000000e+01 , 9.97500000000000e+00 , 1.19650000000000e+01 ) + 6 ( 1.21637914428202e+01 , 1.42488413632141e+01 , 1.04074400269771e+01 , 1.20048328024046e+01 ) ( -5.14478607050619e+00 , -7.57103408035369e+00 , -1.09360006744287e+01 , -1.17082006011526e+00 ) ( 1.19580000000000e+01 , 1.39460000000000e+01 , 9.97000000000000e+00 , 1.19580000000000e+01 ) + 7 ( 1.21606504826560e+01 , 1.42491108211546e+01 , 1.04064186711875e+01 , 1.20059438853592e+01 ) ( -5.24126206639965e+00 , -7.80277052886533e+00 , -1.10354667796874e+01 , -1.37359713397900e+00 ) ( 1.19510000000000e+01 , 1.39370000000000e+01 , 9.96500000000000e+00 , 1.19510000000000e+01 ) + 8 ( 1.21578350901329e+01 , 1.42493400866675e+01 , 1.04052750916551e+01 , 1.20066641446701e+01 ) ( -5.34587725332165e+00 , -8.03350216668708e+00 , -1.11318772913779e+01 , -1.56660361675320e+00 ) ( 1.19440000000000e+01 , 1.39280000000000e+01 , 9.96000000000000e+00 , 1.19440000000000e+01 ) + 9 ( 1.21551529536114e+01 , 1.42495154307442e+01 , 1.04038460769366e+01 , 1.20069492651864e+01 ) ( -5.45382384028512e+00 , -8.26288576860619e+00 , -1.12211519234160e+01 , -1.74873162966009e+00 ) ( 1.19370000000000e+01 , 1.39190000000000e+01 , 9.95500000000000e+00 , 1.19370000000000e+01 ) + 10 ( 1.21523782650640e+01 , 1.42496785499675e+01 , 1.04020777830207e+01 , 1.20068009867444e+01 ) ( -5.55945662659898e+00 , -8.49196374918688e+00 , -1.13019445755174e+01 , -1.92002466861112e+00 ) ( 1.19300000000000e+01 , 1.39100000000000e+01 , 9.95000000000000e+00 , 1.19300000000000e+01 ) diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out index 49ea4044e..157b9cded 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -25,28 +27,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -107,14 +109,30 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped index d0176330c..56cddbb67 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 1.42698565162903e+01 + x 1.42698565162752e+01 } metadynamics { @@ -43,9 +43,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 8.33855405052094e-07 - 3.00574542266188e-04 8.54334028777445e-03 1.91497791869240e-02 - 3.38510199644364e-03 4.71875402495671e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 8.33855405317537e-07 + 3.00574542330873e-04 8.54334028864708e-03 1.91497791865179e-02 + 3.38510199591916e-03 4.71875402354643e-05 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients grid_parameters { @@ -77,9 +77,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 2.98417493685997e-05 - 6.93917949716513e-03 8.87295997352626e-02 -4.43203926688531e-02 - -5.08263278137392e-02 -1.30782612413995e-03 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 2.98417493776893e-05 + 6.93917949849616e-03 8.87295997392777e-02 -4.43203926802213e-02 + -5.08263278082148e-02 -1.30782612378422e-03 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj index ce3224f94..eabe053dd 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step d 0 1.42467449615693e+01 1 1.42470955327846e+01 - 2 1.42476939547291e+01 - 3 1.42483110732975e+01 - 4 1.42492943585138e+01 - 5 1.42503736285750e+01 - 6 1.42515602222333e+01 - 7 1.42528228624295e+01 - 8 1.42541950327222e+01 - 9 1.42556585606080e+01 - 10 1.42572498626192e+01 - 11 1.42590470996093e+01 - 12 1.42605989324750e+01 - 13 1.42621615963684e+01 - 14 1.42637368066359e+01 - 15 1.42651402747233e+01 - 16 1.42662547203391e+01 - 17 1.42670733056824e+01 - 18 1.42680933124264e+01 - 19 1.42689260105063e+01 - 20 1.42698565162903e+01 + 2 1.42476939547290e+01 + 3 1.42483110732973e+01 + 4 1.42492943585134e+01 + 5 1.42503736285743e+01 + 6 1.42515602222322e+01 + 7 1.42528228624278e+01 + 8 1.42541950327196e+01 + 9 1.42556585606043e+01 + 10 1.42572498626143e+01 + 11 1.42590470996029e+01 + 12 1.42605989324670e+01 + 13 1.42621615963588e+01 + 14 1.42637368066246e+01 + 15 1.42651402747104e+01 + 16 1.42662547203247e+01 + 17 1.42670733056670e+01 + 18 1.42680933124105e+01 + 19 1.42689260104905e+01 + 20 1.42698565162752e+01 diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf b/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf index f07621e5c..7af5ed5c9 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf @@ -1,79 +1,79 @@ # 1 # 0.00000000000000e+00 2.00000000000000e-01 76 0 - 1.00000000000000e-01 1.91497791869240e-02 - 3.00000000000000e-01 1.91497791869240e-02 - 5.00000000000000e-01 1.91497791869240e-02 - 7.00000000000000e-01 1.91497791869240e-02 - 9.00000000000000e-01 1.91497791869240e-02 - 1.10000000000000e+00 1.91497791869240e-02 - 1.30000000000000e+00 1.91497791869240e-02 - 1.50000000000000e+00 1.91497791869240e-02 - 1.70000000000000e+00 1.91497791869240e-02 - 1.90000000000000e+00 1.91497791869240e-02 - 2.10000000000000e+00 1.91497791869240e-02 - 2.30000000000000e+00 1.91497791869240e-02 - 2.50000000000000e+00 1.91497791869240e-02 - 2.70000000000000e+00 1.91497791869240e-02 - 2.90000000000000e+00 1.91497791869240e-02 - 3.10000000000000e+00 1.91497791869240e-02 - 3.30000000000000e+00 1.91497791869240e-02 - 3.50000000000000e+00 1.91497791869240e-02 - 3.70000000000000e+00 1.91497791869240e-02 - 3.90000000000000e+00 1.91497791869240e-02 - 4.10000000000000e+00 1.91497791869240e-02 - 4.30000000000000e+00 1.91497791869240e-02 - 4.50000000000000e+00 1.91497791869240e-02 - 4.70000000000000e+00 1.91497791869240e-02 - 4.90000000000000e+00 1.91497791869240e-02 - 5.10000000000000e+00 1.91497791869240e-02 - 5.30000000000000e+00 1.91497791869240e-02 - 5.50000000000000e+00 1.91497791869240e-02 - 5.70000000000000e+00 1.91497791869240e-02 - 5.90000000000000e+00 1.91497791869240e-02 - 6.10000000000000e+00 1.91497791869240e-02 - 6.30000000000000e+00 1.91497791869240e-02 - 6.50000000000000e+00 1.91497791869240e-02 - 6.70000000000000e+00 1.91497791869240e-02 - 6.90000000000000e+00 1.91497791869240e-02 - 7.10000000000000e+00 1.91497791869240e-02 - 7.30000000000000e+00 1.91497791869240e-02 - 7.50000000000000e+00 1.91497791869240e-02 - 7.70000000000000e+00 1.91497791869240e-02 - 7.90000000000000e+00 1.91497791869240e-02 - 8.10000000000000e+00 1.91497791869240e-02 - 8.30000000000000e+00 1.91497791869240e-02 - 8.50000000000000e+00 1.91497791869240e-02 - 8.70000000000000e+00 1.91497791869240e-02 - 8.90000000000000e+00 1.91497791869240e-02 - 9.10000000000000e+00 1.91497791869240e-02 - 9.30000000000000e+00 1.91497791869240e-02 - 9.50000000000000e+00 1.91497791869240e-02 - 9.70000000000000e+00 1.91497791869240e-02 - 9.90000000000000e+00 1.91497791869240e-02 - 1.01000000000000e+01 1.91497791869240e-02 - 1.03000000000000e+01 1.91497791869240e-02 - 1.05000000000000e+01 1.91497791869240e-02 - 1.07000000000000e+01 1.91497791869240e-02 - 1.09000000000000e+01 1.91497791869240e-02 - 1.11000000000000e+01 1.91497791869240e-02 - 1.13000000000000e+01 1.91497791869240e-02 - 1.15000000000000e+01 1.91497791869240e-02 - 1.17000000000000e+01 1.91497791869240e-02 - 1.19000000000000e+01 1.91497791869240e-02 - 1.21000000000000e+01 1.91497791869240e-02 - 1.23000000000000e+01 1.91497791869240e-02 - 1.25000000000000e+01 1.91497791869240e-02 - 1.27000000000000e+01 1.91497791869240e-02 - 1.29000000000000e+01 1.91497791869240e-02 - 1.31000000000000e+01 1.91497791869240e-02 - 1.33000000000000e+01 1.91497791869240e-02 - 1.35000000000000e+01 1.91497791869240e-02 - 1.37000000000000e+01 1.91489453315190e-02 - 1.39000000000000e+01 1.88492046446579e-02 - 1.41000000000000e+01 1.06064388991496e-02 + 1.00000000000000e-01 1.91497791865179e-02 + 3.00000000000000e-01 1.91497791865179e-02 + 5.00000000000000e-01 1.91497791865179e-02 + 7.00000000000000e-01 1.91497791865179e-02 + 9.00000000000000e-01 1.91497791865179e-02 + 1.10000000000000e+00 1.91497791865179e-02 + 1.30000000000000e+00 1.91497791865179e-02 + 1.50000000000000e+00 1.91497791865179e-02 + 1.70000000000000e+00 1.91497791865179e-02 + 1.90000000000000e+00 1.91497791865179e-02 + 2.10000000000000e+00 1.91497791865179e-02 + 2.30000000000000e+00 1.91497791865179e-02 + 2.50000000000000e+00 1.91497791865179e-02 + 2.70000000000000e+00 1.91497791865179e-02 + 2.90000000000000e+00 1.91497791865179e-02 + 3.10000000000000e+00 1.91497791865179e-02 + 3.30000000000000e+00 1.91497791865179e-02 + 3.50000000000000e+00 1.91497791865179e-02 + 3.70000000000000e+00 1.91497791865179e-02 + 3.90000000000000e+00 1.91497791865179e-02 + 4.10000000000000e+00 1.91497791865179e-02 + 4.30000000000000e+00 1.91497791865179e-02 + 4.50000000000000e+00 1.91497791865179e-02 + 4.70000000000000e+00 1.91497791865179e-02 + 4.90000000000000e+00 1.91497791865179e-02 + 5.10000000000000e+00 1.91497791865179e-02 + 5.30000000000000e+00 1.91497791865179e-02 + 5.50000000000000e+00 1.91497791865179e-02 + 5.70000000000000e+00 1.91497791865179e-02 + 5.90000000000000e+00 1.91497791865179e-02 + 6.10000000000000e+00 1.91497791865179e-02 + 6.30000000000000e+00 1.91497791865179e-02 + 6.50000000000000e+00 1.91497791865179e-02 + 6.70000000000000e+00 1.91497791865179e-02 + 6.90000000000000e+00 1.91497791865179e-02 + 7.10000000000000e+00 1.91497791865179e-02 + 7.30000000000000e+00 1.91497791865179e-02 + 7.50000000000000e+00 1.91497791865179e-02 + 7.70000000000000e+00 1.91497791865179e-02 + 7.90000000000000e+00 1.91497791865179e-02 + 8.10000000000000e+00 1.91497791865179e-02 + 8.30000000000000e+00 1.91497791865179e-02 + 8.50000000000000e+00 1.91497791865179e-02 + 8.70000000000000e+00 1.91497791865179e-02 + 8.90000000000000e+00 1.91497791865179e-02 + 9.10000000000000e+00 1.91497791865179e-02 + 9.30000000000000e+00 1.91497791865179e-02 + 9.50000000000000e+00 1.91497791865179e-02 + 9.70000000000000e+00 1.91497791865179e-02 + 9.90000000000000e+00 1.91497791865179e-02 + 1.01000000000000e+01 1.91497791865179e-02 + 1.03000000000000e+01 1.91497791865179e-02 + 1.05000000000000e+01 1.91497791865179e-02 + 1.07000000000000e+01 1.91497791865179e-02 + 1.09000000000000e+01 1.91497791865179e-02 + 1.11000000000000e+01 1.91497791865179e-02 + 1.13000000000000e+01 1.91497791865179e-02 + 1.15000000000000e+01 1.91497791865179e-02 + 1.17000000000000e+01 1.91497791865179e-02 + 1.19000000000000e+01 1.91497791865179e-02 + 1.21000000000000e+01 1.91497791865179e-02 + 1.23000000000000e+01 1.91497791865179e-02 + 1.25000000000000e+01 1.91497791865179e-02 + 1.27000000000000e+01 1.91497791865179e-02 + 1.29000000000000e+01 1.91497791865179e-02 + 1.31000000000000e+01 1.91497791865179e-02 + 1.33000000000000e+01 1.91497791865179e-02 + 1.35000000000000e+01 1.91497791865179e-02 + 1.37000000000000e+01 1.91489453311125e-02 + 1.39000000000000e+01 1.88492046441870e-02 + 1.41000000000000e+01 1.06064388978708e-02 1.43000000000000e+01 -0.00000000000000e+00 - 1.45000000000000e+01 1.57646771904804e-02 - 1.47000000000000e+01 1.91025916466745e-02 - 1.49000000000000e+01 1.91497791869240e-02 - 1.51000000000000e+01 1.91497791869240e-02 + 1.45000000000000e+01 1.57646771905987e-02 + 1.47000000000000e+01 1.91025916462824e-02 + 1.49000000000000e+01 1.91497791865179e-02 + 1.51000000000000e+01 1.91497791865179e-02 diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out index 791e3e5d1..51c6085f0 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "angle" @@ -55,42 +57,42 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] @@ -126,56 +128,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_6" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_7" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -218,11 +220,6 @@ colvars: # historyFreq = 5 colvars: # shared = off [default] colvars: # maxForce = [default] colvars: # integrate = on [default] -colvars: # pABFintegrateFreq = 0 [default] -colvars: # integrateInitMaxIterations = 10000 [default] -colvars: # integrateInitTol = 1e-06 [default] -colvars: # integrateMaxIterations = 100 [default] -colvars: # integrateTol = 0.0001 [default] colvars: Finished ABF setup. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -232,6 +229,29 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (7 scalable groups, 7 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - angle colvar component: +colvars: - dihedral colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - ABF colvar bias implementation: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - Poisson integration of 2D/3D free energy surfaces: +colvars: Henin2021 https://doi.org/10.1021/acs.jctc.1c00593 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "angle":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "angle":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "angle":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. @@ -240,11 +260,11 @@ colvars: Re-initialized atom group for variable "dihedral":0/1. 1 atoms: total m colvars: Re-initialized atom group for variable "dihedral":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "dihedral":0/3. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (7 scalable groups, 7 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "angle":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "angle":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "angle":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped index 8e53a7a8c..cf8ab20fa 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name angle - x 9.71572414998837e+01 + x 9.71572414999404e+01 } colvar { name dihedral - x 4.76248133821808e+01 + x 4.76248133822394e+01 } abf { @@ -256,8 +256,8 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 3.86055079861384e-01 -1.47156688632534e+00 - 1.21510007293019e-01 -3.46687391825760e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 3.86055080717640e-01 -1.47156688763172e+00 + 1.21510007787258e-01 -3.46687391789233e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj index dfd38fd88..7fe21a71e 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step angle ft_angle fa_angle dihedral ft_dihedral fa_dihedral 0 9.68498695196423e+01 0.00000000000000e+00 0.00000000000000e+00 4.86056572577460e+01 0.00000000000000e+00 0.00000000000000e+00 - 1 9.68581311788660e+01 -1.84451705170512e-02 1.84451705170512e-02 4.84876896364254e+01 -2.26204229896581e-02 2.26204229896581e-02 - 2 9.68825903830946e+01 -1.75928069356493e-02 2.72415739848758e-02 4.83727459141994e+01 1.09239386473433e-01 -3.19992702470586e-02 - 3 9.69105533161889e+01 -3.36465334276460e-02 3.84570851274245e-02 4.82565768693354e+01 1.87476845673922e-01 -9.44915521383659e-02 - 4 9.69406101257489e+01 -8.90986865550939e-02 6.07317567661980e-02 4.81501282214438e+01 2.91829502364863e-01 -1.67448927729582e-01 - 5 9.69674902853240e+01 -1.44712759211668e-01 8.96743086085316e-02 4.80499450162389e+01 4.19420612395337e-01 -2.51333050208649e-01 - 6 9.69953149267550e+01 -1.91014192106924e-01 0.00000000000000e+00 4.79483470270649e+01 5.72126049702663e-01 0.00000000000000e+00 - 7 9.70261917919283e+01 -3.39026774573669e-01 3.39026774573669e-01 4.78551169383663e+01 1.09938745929832e+00 -1.09938745929832e+00 - 8 9.70529963144229e+01 -4.61821781161425e-02 3.62117863631741e-01 4.77722438820399e+01 2.55842715985027e-01 -1.22730881729084e+00 - 9 9.70984141114285e+01 -2.94041075150722e-02 3.71919232803431e-01 4.76919701530380e+01 3.67640478440557e-01 -1.34985564343769e+00 - 10 9.71572414998837e+01 -5.65433882318097e-02 3.86055079861384e-01 4.76248133821808e+01 4.86844971550587e-01 -1.47156688632534e+00 + 1 9.68581311788645e+01 -1.84451708831746e-02 1.84451708831746e-02 4.84876896364246e+01 -2.26204233738360e-02 2.26204233738360e-02 + 2 9.68825903830917e+01 -1.75928069494324e-02 2.72415743578908e-02 4.83727459141996e+01 1.09239386526311e-01 -3.19992698893197e-02 + 3 9.69105533161851e+01 -3.36465334818358e-02 3.84570855185028e-02 4.82565768693385e+01 1.87476845825581e-01 -9.44915518311800e-02 + 4 9.69406101257451e+01 -8.90986866663562e-02 6.07317571850918e-02 4.81501282214520e+01 2.91829502654487e-01 -1.67448927494802e-01 + 5 9.69674902853217e+01 -1.44712759388158e-01 8.96743090627233e-02 4.80499450162547e+01 4.19420612850755e-01 -2.51333050064953e-01 + 6 9.69953149267565e+01 -1.91014192347208e-01 0.00000000000000e+00 4.79483470270909e+01 5.72126050345682e-01 0.00000000000000e+00 + 7 9.70261917919329e+01 -3.39026775359731e-01 3.39026775359731e-01 4.78551169384050e+01 1.09938746010351e+00 -1.09938746010351e+00 + 8 9.70529963144370e+01 -4.61821781835164e-02 3.62117864451490e-01 4.77722438820884e+01 2.55842716309053e-01 -1.22730881825804e+00 + 9 9.70984141114596e+01 -2.94041075882280e-02 3.71919233647566e-01 4.76919701530931e+01 3.67640478945815e-01 -1.34985564457331e+00 + 10 9.71572414999404e+01 -5.65433882802956e-02 3.86055080717640e-01 4.76248133822394e+01 4.86844972233643e-01 -1.47156688763172e+00 diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad b/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad index 02118c831..81d482591 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad @@ -506,7 +506,7 @@ 9.90000000000000e+01 3.30000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 3.90000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 4.50000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 - 9.90000000000000e+01 5.10000000000000e+01 8.96743086085316e-02 -2.51333050208651e-01 + 9.90000000000000e+01 5.10000000000000e+01 8.96743090627233e-02 -2.51333050064953e-01 9.90000000000000e+01 5.70000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 6.30000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 6.90000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 @@ -1439,8 +1439,8 @@ 9.90000000000000e+01 2.70000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 3.30000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 3.90000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 - 9.90000000000000e+01 4.50000000000000e+01 3.86055079861383e-01 -1.47156688632533e+00 - 9.90000000000000e+01 5.10000000000000e+01 1.21510007293019e-01 -3.46687391825762e-01 + 9.90000000000000e+01 4.50000000000000e+01 3.86055080717640e-01 -1.47156688763172e+00 + 9.90000000000000e+01 5.10000000000000e+01 1.21510007787258e-01 -3.46687391789233e-01 9.90000000000000e+01 5.70000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 6.30000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 6.90000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.pmf 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1.74000000000000e+02 1.32000000000000e+02 1.39807515900343e+00 + 1.74000000000000e+02 1.38000000000000e+02 1.39363995758019e+00 + 1.74000000000000e+02 1.44000000000000e+02 1.39002722809985e+00 + 1.74000000000000e+02 1.50000000000000e+02 1.38713424542676e+00 + 1.74000000000000e+02 1.56000000000000e+02 1.38487643056994e+00 + 1.74000000000000e+02 1.62000000000000e+02 1.38318705471226e+00 + 1.74000000000000e+02 1.68000000000000e+02 1.38201541680138e+00 + 1.74000000000000e+02 1.74000000000000e+02 1.38132631351919e+00 + 1.74000000000000e+02 1.80000000000000e+02 1.38109883649856e+00 - 1.80000000000000e+02 0.00000000000000e+00 1.71950717027158e+00 - 1.80000000000000e+02 6.00000000000000e+00 1.71763469034113e+00 - 1.80000000000000e+02 1.20000000000000e+01 1.71204109254773e+00 - 1.80000000000000e+02 1.80000000000000e+01 1.70280652254112e+00 - 1.80000000000000e+02 2.40000000000000e+01 1.69008997457239e+00 - 1.80000000000000e+02 3.00000000000000e+01 1.67415946813868e+00 - 1.80000000000000e+02 3.60000000000000e+01 1.65541840600784e+00 - 1.80000000000000e+02 4.20000000000000e+01 1.63441424578470e+00 - 1.80000000000000e+02 4.80000000000000e+01 1.61181912643233e+00 - 1.80000000000000e+02 5.40000000000000e+01 1.58838127862193e+00 - 1.80000000000000e+02 6.00000000000000e+01 1.56485578684440e+00 - 1.80000000000000e+02 6.60000000000000e+01 1.54193226170038e+00 - 1.80000000000000e+02 7.20000000000000e+01 1.52017775776025e+00 - 1.80000000000000e+02 7.80000000000000e+01 1.50000632286310e+00 - 1.80000000000000e+02 8.40000000000000e+01 1.48167451203620e+00 - 1.80000000000000e+02 9.00000000000000e+01 1.46529791209370e+00 - 1.80000000000000e+02 9.60000000000000e+01 1.45087910970048e+00 - 1.80000000000000e+02 1.02000000000000e+02 1.43833871846121e+00 - 1.80000000000000e+02 1.08000000000000e+02 1.42754465660285e+00 - 1.80000000000000e+02 1.14000000000000e+02 1.41833662258694e+00 - 1.80000000000000e+02 1.20000000000000e+02 1.41054452465612e+00 - 1.80000000000000e+02 1.26000000000000e+02 1.40400145185257e+00 - 1.80000000000000e+02 1.32000000000000e+02 1.39855177127351e+00 - 1.80000000000000e+02 1.38000000000000e+02 1.39405569373783e+00 - 1.80000000000000e+02 1.44000000000000e+02 1.39039153489000e+00 - 1.80000000000000e+02 1.50000000000000e+02 1.38745617270075e+00 - 1.80000000000000e+02 1.56000000000000e+02 1.38516474450159e+00 - 1.80000000000000e+02 1.62000000000000e+02 1.38344975278396e+00 - 1.80000000000000e+02 1.68000000000000e+02 1.38226031224452e+00 - 1.80000000000000e+02 1.74000000000000e+02 1.38156058387008e+00 - 1.80000000000000e+02 1.80000000000000e+02 1.38132948034468e+00 + 1.80000000000000e+02 0.00000000000000e+00 1.71950717310890e+00 + 1.80000000000000e+02 6.00000000000000e+00 1.71763469317717e+00 + 1.80000000000000e+02 1.20000000000000e+01 1.71204109537989e+00 + 1.80000000000000e+02 1.80000000000000e+01 1.70280652536677e+00 + 1.80000000000000e+02 2.40000000000000e+01 1.69008997738884e+00 + 1.80000000000000e+02 3.00000000000000e+01 1.67415947094321e+00 + 1.80000000000000e+02 3.60000000000000e+01 1.65541840879782e+00 + 1.80000000000000e+02 4.20000000000000e+01 1.63441424855771e+00 + 1.80000000000000e+02 4.80000000000000e+01 1.61181912918628e+00 + 1.80000000000000e+02 5.40000000000000e+01 1.58838128135519e+00 + 1.80000000000000e+02 6.00000000000000e+01 1.56485578955593e+00 + 1.80000000000000e+02 6.60000000000000e+01 1.54193226438972e+00 + 1.80000000000000e+02 7.20000000000000e+01 1.52017776042752e+00 + 1.80000000000000e+02 7.80000000000000e+01 1.50000632550894e+00 + 1.80000000000000e+02 8.40000000000000e+01 1.48167451466162e+00 + 1.80000000000000e+02 9.00000000000000e+01 1.46529791470002e+00 + 1.80000000000000e+02 9.60000000000000e+01 1.45087911228919e+00 + 1.80000000000000e+02 1.02000000000000e+02 1.43833872103392e+00 + 1.80000000000000e+02 1.08000000000000e+02 1.42754465916118e+00 + 1.80000000000000e+02 1.14000000000000e+02 1.41833662513247e+00 + 1.80000000000000e+02 1.20000000000000e+02 1.41054452719039e+00 + 1.80000000000000e+02 1.26000000000000e+02 1.40400145437701e+00 + 1.80000000000000e+02 1.32000000000000e+02 1.39855177378947e+00 + 1.80000000000000e+02 1.38000000000000e+02 1.39405569624656e+00 + 1.80000000000000e+02 1.44000000000000e+02 1.39039153739266e+00 + 1.80000000000000e+02 1.50000000000000e+02 1.38745617519842e+00 + 1.80000000000000e+02 1.56000000000000e+02 1.38516474699527e+00 + 1.80000000000000e+02 1.62000000000000e+02 1.38344975527461e+00 + 1.80000000000000e+02 1.68000000000000e+02 1.38226031473303e+00 + 1.80000000000000e+02 1.74000000000000e+02 1.38156058635732e+00 + 1.80000000000000e+02 1.80000000000000e+02 1.38132948283151e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state index 38b541ee8..ceba9352b 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state @@ -20,9 +20,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.53403289508330e-06 8.43235284919676e-04 - 3.21927752810740e-02 9.90603520983741e-02 2.46033418312340e-02 - 4.93589872784461e-04 4.23052788272303e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.53403286720768e-06 8.43235276972864e-04 + 3.21927751514002e-02 9.90603521389808e-02 2.46033419259411e-02 + 4.93589875891209e-04 4.23052788302019e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -45,9 +45,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 2.26292242192221e-05 8.26704506678145e-03 - 1.53420242800061e-01 -2.66708910635591e-02 -1.30444282281981e-01 - -5.10069712416846e-03 -6.37695701821339e-06 0.00000000000000e+00 + 0.00000000000000e+00 2.26292238292108e-05 8.26704499874479e-03 + 1.53420242499276e-01 -2.66708902934347e-02 -1.30444282639589e-01 + -5.10069715433551e-03 -6.37695701865853e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out index c68838faf..f11fa72fe 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep1.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -55,28 +57,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -143,6 +145,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -156,6 +159,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -170,15 +174,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Multiple-walker metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep1r.colvars.state". colvars: The final output state file will be "test.rep1.colvars.state". -colvars: Opening trajectory file "test.rep1.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep1r.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped index b96d93fd6..094d10a53 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 1.41656974949034e+01 + x 1.41656974969458e+01 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.53403289508330e-06 8.43235284919676e-04 - 3.21927752810740e-02 9.90603520983741e-02 2.46033418312340e-02 - 4.93589872784461e-04 4.23052788272303e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.53403286720768e-06 8.43235276972864e-04 + 3.21927751514002e-02 9.90603521389808e-02 2.46033419259411e-02 + 4.93589875891209e-04 4.23052788302019e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -55,9 +55,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 2.26292242192221e-05 8.26704506678145e-03 - 1.53420242800061e-01 -2.66708910635591e-02 -1.30444282281981e-01 - -5.10069712416846e-03 -6.37695701821339e-06 0.00000000000000e+00 + 0.00000000000000e+00 2.26292238292108e-05 8.26704499874479e-03 + 1.53420242499276e-01 -2.66708902934347e-02 -1.30444282639589e-01 + -5.10069715433551e-03 -6.37695701865853e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj index 441edf82b..5731bc76e 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj @@ -2,101 +2,101 @@ 0 1.42467449615693e+01 0.00000000000000e+00 1 1.42470955327846e+01 0.00000000000000e+00 2 1.42476657799120e+01 0.00000000000000e+00 - 3 1.42485380098361e+01 0.00000000000000e+00 - 4 1.42499968808366e+01 0.00000000000000e+00 - 5 1.42516048130998e+01 0.00000000000000e+00 - 6 1.42535349212370e+01 0.00000000000000e+00 - 7 1.42555542781187e+01 0.00000000000000e+00 - 8 1.42579210999843e+01 0.00000000000000e+00 - 9 1.42607955979387e+01 0.00000000000000e+00 - 10 1.42638739176632e+01 -1.41180095190593e-03 - 11 1.42668375588418e+01 -1.41180095190593e-03 - 12 1.42696059392705e+01 -1.41180095190593e-03 - 13 1.42727236830780e+01 -1.41180095190593e-03 - 14 1.42758764946774e+01 -1.41180095190593e-03 - 15 1.42787429047858e+01 -1.41180095190593e-03 - 16 1.42810489912851e+01 -1.41180095190593e-03 - 17 1.42825584062184e+01 -1.41180095190593e-03 - 18 1.42834947131793e+01 -1.41180095190593e-03 - 19 1.42840554431998e+01 -1.41180095190593e-03 - 20 1.42836137141615e+01 -4.81601991397794e-03 - 21 1.42824534007517e+01 -4.81601991397794e-03 - 22 1.42809048151132e+01 -4.81601991397794e-03 - 23 1.42792649820074e+01 -4.81601991397794e-03 - 24 1.42777803318261e+01 -4.81601991397794e-03 - 25 1.42752531196695e+01 -4.81601991397794e-03 - 26 1.42721001284912e+01 -4.81601991397794e-03 - 27 1.42684964153029e+01 -4.81601991397794e-03 - 28 1.42647910498358e+01 -4.81601991397794e-03 - 29 1.42606805882456e+01 -4.81601991397794e-03 - 30 1.42569926418246e+01 -5.52810720784699e-03 - 31 1.42531586691047e+01 -5.52810720784699e-03 - 32 1.42495999935438e+01 -5.52810720784699e-03 - 33 1.42462931130875e+01 -5.52810720784699e-03 - 34 1.42426029443764e+01 -5.52810720784699e-03 - 35 1.42381298875008e+01 -5.52810720784699e-03 - 36 1.42340878761072e+01 -5.52810720784699e-03 - 37 1.42306974074822e+01 -5.52810720784699e-03 - 38 1.42272038093346e+01 -5.52810720784699e-03 - 39 1.42243354344263e+01 -5.52810720784699e-03 - 40 1.42218646485599e+01 -2.67379444822040e-03 - 41 1.42190777077468e+01 -2.67379444822040e-03 - 42 1.42160211302678e+01 -2.67379444822040e-03 - 43 1.42124278513310e+01 -2.67379444822040e-03 - 44 1.42090572659494e+01 -2.67379444822040e-03 - 45 1.42058271938036e+01 -2.67379444822040e-03 - 46 1.42033823263127e+01 -2.67379444822040e-03 - 47 1.42003268228049e+01 -2.67379444822040e-03 - 48 1.41976446229193e+01 -2.67379444822040e-03 - 49 1.41956578972582e+01 -2.67379444822040e-03 - 50 1.41941111007313e+01 2.92915643758184e-03 - 51 1.41926279960324e+01 2.92915643758184e-03 - 52 1.41926027090037e+01 2.92915643758184e-03 - 53 1.41928452081821e+01 2.92915643758184e-03 - 54 1.41932447289925e+01 2.92915643758184e-03 - 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1.42213115692008e+01 1.07651864810836e-02 - 77 1.42222264800984e+01 1.07651864810836e-02 - 78 1.42228883722939e+01 1.07651864810836e-02 - 79 1.42232741594059e+01 1.07651864810836e-02 - 80 1.42237439344237e+01 1.34302339631847e-02 - 81 1.42241333527676e+01 1.34302339631847e-02 - 82 1.42242035696691e+01 1.34302339631847e-02 - 83 1.42237365420353e+01 1.34302339631847e-02 - 84 1.42227422602652e+01 1.34302339631847e-02 - 85 1.42207685317808e+01 1.34302339631847e-02 - 86 1.42180863416851e+01 1.34302339631847e-02 - 87 1.42142852895987e+01 1.34302339631847e-02 - 88 1.42099549129055e+01 1.34302339631847e-02 - 89 1.42054325297988e+01 1.34302339631847e-02 - 90 1.42007097380791e+01 1.83891584072187e-02 - 91 1.41956149687583e+01 1.83891584072187e-02 - 92 1.41905358606444e+01 1.83891584072187e-02 - 93 1.41851130561985e+01 1.83891584072187e-02 - 94 1.41798559764745e+01 1.83891584072187e-02 - 95 1.41754225260859e+01 1.83891584072187e-02 - 96 1.41724186121957e+01 1.83891584072187e-02 - 97 1.41698989963895e+01 1.83891584072187e-02 - 98 1.41682594906300e+01 1.83891584072187e-02 - 99 1.41669592353631e+01 1.83891584072187e-02 - 100 1.41656974949034e+01 2.66708910635591e-02 + 3 1.42485380098359e+01 0.00000000000000e+00 + 4 1.42499968808362e+01 0.00000000000000e+00 + 5 1.42516048130991e+01 0.00000000000000e+00 + 6 1.42535349212359e+01 0.00000000000000e+00 + 7 1.42555542781170e+01 0.00000000000000e+00 + 8 1.42579210999817e+01 0.00000000000000e+00 + 9 1.42607955979351e+01 0.00000000000000e+00 + 10 1.42638739176583e+01 -1.41180095141270e-03 + 11 1.42668375588355e+01 -1.41180095141270e-03 + 12 1.42696059392625e+01 -1.41180095141270e-03 + 13 1.42727236830683e+01 -1.41180095141270e-03 + 14 1.42758764946660e+01 -1.41180095141270e-03 + 15 1.42787429047727e+01 -1.41180095141270e-03 + 16 1.42810489912705e+01 -1.41180095141270e-03 + 17 1.42825584062025e+01 -1.41180095141270e-03 + 18 1.42834947131625e+01 -1.41180095141270e-03 + 19 1.42840554431827e+01 -1.41180095141270e-03 + 20 1.42836137141448e+01 -4.81601991180831e-03 + 21 1.42824534007361e+01 -4.81601991180831e-03 + 22 1.42809048150996e+01 -4.81601991180831e-03 + 23 1.42792649819969e+01 -4.81601991180831e-03 + 24 1.42777803318197e+01 -4.81601991180831e-03 + 25 1.42752531196685e+01 -4.81601991180831e-03 + 26 1.42721001284968e+01 -4.81601991180831e-03 + 27 1.42684964153165e+01 -4.81601991180831e-03 + 28 1.42647910498589e+01 -4.81601991180831e-03 + 29 1.42606805882796e+01 -4.81601991180831e-03 + 30 1.42569926418712e+01 -5.52810721041820e-03 + 31 1.42531586691654e+01 -5.52810721041820e-03 + 32 1.42495999936203e+01 -5.52810721041820e-03 + 33 1.42462931131815e+01 -5.52810721041820e-03 + 34 1.42426029444897e+01 -5.52810721041820e-03 + 35 1.42381298876351e+01 -5.52810721041820e-03 + 36 1.42340878762643e+01 -5.52810721041820e-03 + 37 1.42306974076639e+01 -5.52810721041820e-03 + 38 1.42272038095427e+01 -5.52810721041820e-03 + 39 1.42243354346624e+01 -5.52810721041820e-03 + 40 1.42218646488258e+01 -2.67379447755370e-03 + 41 1.42190777080442e+01 -2.67379447755370e-03 + 42 1.42160211305982e+01 -2.67379447755370e-03 + 43 1.42124278516958e+01 -2.67379447755370e-03 + 44 1.42090572663500e+01 -2.67379447755370e-03 + 45 1.42058271942412e+01 -2.67379447755370e-03 + 46 1.42033823267883e+01 -2.67379447755370e-03 + 47 1.42003268233193e+01 -2.67379447755370e-03 + 48 1.41976446234730e+01 -2.67379447755370e-03 + 49 1.41956578978518e+01 -2.67379447755370e-03 + 50 1.41941111013648e+01 2.92915634676080e-03 + 51 1.41926279967057e+01 2.92915634676080e-03 + 52 1.41926027097164e+01 2.92915634676080e-03 + 53 1.41928452089335e+01 2.92915634676080e-03 + 54 1.41932447297817e+01 2.92915634676080e-03 + 55 1.41940166346614e+01 2.92915634676080e-03 + 56 1.41951734104514e+01 2.92915634676080e-03 + 57 1.41967411071552e+01 2.92915634676080e-03 + 58 1.41989912333566e+01 2.92915634676080e-03 + 59 1.42012327627117e+01 2.92915634676080e-03 + 60 1.42036332173818e+01 7.60060814309682e-03 + 61 1.42058762807719e+01 7.60060814309682e-03 + 62 1.42077667923895e+01 7.60060814309682e-03 + 63 1.42098444758797e+01 7.60060814309682e-03 + 64 1.42116396739042e+01 7.60060814309682e-03 + 65 1.42136940032780e+01 7.60060814309682e-03 + 66 1.42154217558442e+01 7.60060814309682e-03 + 67 1.42168868960268e+01 7.60060814309682e-03 + 68 1.42178935094514e+01 7.60060814309682e-03 + 69 1.42184230283353e+01 7.60060814309682e-03 + 70 1.42187771926287e+01 1.07651861772312e-02 + 71 1.42193777496991e+01 1.07651861772312e-02 + 72 1.42195540781285e+01 1.07651861772312e-02 + 73 1.42196083093533e+01 1.07651861772312e-02 + 74 1.42197149208802e+01 1.07651861772312e-02 + 75 1.42202788377849e+01 1.07651861772312e-02 + 76 1.42213115704096e+01 1.07651861772312e-02 + 77 1.42222264813178e+01 1.07651861772312e-02 + 78 1.42228883735255e+01 1.07651861772312e-02 + 79 1.42232741606514e+01 1.07651861772312e-02 + 80 1.42237439356851e+01 1.34302335321981e-02 + 81 1.42241333540472e+01 1.34302335321981e-02 + 82 1.42242035709694e+01 1.34302335321981e-02 + 83 1.42237365433589e+01 1.34302335321981e-02 + 84 1.42227422616147e+01 1.34302335321981e-02 + 85 1.42207685331590e+01 1.34302335321981e-02 + 86 1.42180863430945e+01 1.34302335321981e-02 + 87 1.42142852910421e+01 1.34302335321981e-02 + 88 1.42099549143853e+01 1.34302335321981e-02 + 89 1.42054325313174e+01 1.34302335321981e-02 + 90 1.42007097396387e+01 1.83891578232104e-02 + 91 1.41956149703609e+01 1.83891578232104e-02 + 92 1.41905358622917e+01 1.83891578232104e-02 + 93 1.41851130578922e+01 1.83891578232104e-02 + 94 1.41798559782159e+01 1.83891578232104e-02 + 95 1.41754225278760e+01 1.83891578232104e-02 + 96 1.41724186140355e+01 1.83891578232104e-02 + 97 1.41698989982796e+01 1.83891578232104e-02 + 98 1.41682594925708e+01 1.83891578232104e-02 + 99 1.41669592373547e+01 1.83891578232104e-02 + 100 1.41656974969458e+01 2.66708902934347e-02 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf index 8e7f46287..b2d0a8859 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 9.90603520983742e-02 - 7.50000000000000e-01 9.90603520983742e-02 - 1.25000000000000e+00 9.90603520983742e-02 - 1.75000000000000e+00 9.90603520983742e-02 - 2.25000000000000e+00 9.90603520983742e-02 - 2.75000000000000e+00 9.90603520983742e-02 - 3.25000000000000e+00 9.90603520983742e-02 - 3.75000000000000e+00 9.90603520983742e-02 - 4.25000000000000e+00 9.90603520983742e-02 - 4.75000000000000e+00 9.90603520983742e-02 - 5.25000000000000e+00 9.90603520983742e-02 - 5.75000000000000e+00 9.90603520983742e-02 - 6.25000000000000e+00 9.90603520983742e-02 - 6.75000000000000e+00 9.90603520983742e-02 - 7.25000000000000e+00 9.90603520983742e-02 - 7.75000000000000e+00 9.90603520983742e-02 - 8.25000000000000e+00 9.90603520983742e-02 - 8.75000000000000e+00 9.90603520983742e-02 - 9.25000000000000e+00 9.90603520983742e-02 - 9.75000000000000e+00 9.90603520983742e-02 - 1.02500000000000e+01 9.90603520983742e-02 - 1.07500000000000e+01 9.90603520983742e-02 - 1.12500000000000e+01 9.90603520983742e-02 - 1.17500000000000e+01 9.90603520983742e-02 - 1.22500000000000e+01 9.90603520983742e-02 - 1.27500000000000e+01 9.90588180654791e-02 - 1.32500000000000e+01 9.82171168134545e-02 - 1.37500000000000e+01 6.68675768173003e-02 + 2.50000000000000e-01 9.90603521389808e-02 + 7.50000000000000e-01 9.90603521389808e-02 + 1.25000000000000e+00 9.90603521389808e-02 + 1.75000000000000e+00 9.90603521389808e-02 + 2.25000000000000e+00 9.90603521389808e-02 + 2.75000000000000e+00 9.90603521389808e-02 + 3.25000000000000e+00 9.90603521389808e-02 + 3.75000000000000e+00 9.90603521389808e-02 + 4.25000000000000e+00 9.90603521389808e-02 + 4.75000000000000e+00 9.90603521389808e-02 + 5.25000000000000e+00 9.90603521389808e-02 + 5.75000000000000e+00 9.90603521389808e-02 + 6.25000000000000e+00 9.90603521389808e-02 + 6.75000000000000e+00 9.90603521389808e-02 + 7.25000000000000e+00 9.90603521389808e-02 + 7.75000000000000e+00 9.90603521389808e-02 + 8.25000000000000e+00 9.90603521389808e-02 + 8.75000000000000e+00 9.90603521389808e-02 + 9.25000000000000e+00 9.90603521389808e-02 + 9.75000000000000e+00 9.90603521389808e-02 + 1.02500000000000e+01 9.90603521389808e-02 + 1.07500000000000e+01 9.90603521389808e-02 + 1.12500000000000e+01 9.90603521389808e-02 + 1.17500000000000e+01 9.90603521389808e-02 + 1.22500000000000e+01 9.90603521389808e-02 + 1.27500000000000e+01 9.90588181061136e-02 + 1.32500000000000e+01 9.82171168620079e-02 + 1.37500000000000e+01 6.68675769875805e-02 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 7.44570102671401e-02 - 1.52500000000000e+01 9.85667622255897e-02 - 1.57500000000000e+01 9.90599290455859e-02 - 1.62500000000000e+01 9.90603520983742e-02 - 1.67500000000000e+01 9.90603520983742e-02 - 1.72500000000000e+01 9.90603520983742e-02 - 1.77500000000000e+01 9.90603520983742e-02 - 1.82500000000000e+01 9.90603520983742e-02 - 1.87500000000000e+01 9.90603520983742e-02 - 1.92500000000000e+01 9.90603520983742e-02 - 1.97500000000000e+01 9.90603520983742e-02 - 2.02500000000000e+01 9.90603520983742e-02 - 2.07500000000000e+01 9.90603520983742e-02 - 2.12500000000000e+01 9.90603520983742e-02 - 2.17500000000000e+01 9.90603520983742e-02 - 2.22500000000000e+01 9.90603520983742e-02 - 2.27500000000000e+01 9.90603520983742e-02 - 2.32500000000000e+01 9.90603520983742e-02 - 2.37500000000000e+01 9.90603520983742e-02 - 2.42500000000000e+01 9.90603520983742e-02 - 2.47500000000000e+01 9.90603520983742e-02 + 1.47500000000000e+01 7.44570102130396e-02 + 1.52500000000000e+01 9.85667622630896e-02 + 1.57500000000000e+01 9.90599290861925e-02 + 1.62500000000000e+01 9.90603521389808e-02 + 1.67500000000000e+01 9.90603521389808e-02 + 1.72500000000000e+01 9.90603521389808e-02 + 1.77500000000000e+01 9.90603521389808e-02 + 1.82500000000000e+01 9.90603521389808e-02 + 1.87500000000000e+01 9.90603521389808e-02 + 1.92500000000000e+01 9.90603521389808e-02 + 1.97500000000000e+01 9.90603521389808e-02 + 2.02500000000000e+01 9.90603521389808e-02 + 2.07500000000000e+01 9.90603521389808e-02 + 2.12500000000000e+01 9.90603521389808e-02 + 2.17500000000000e+01 9.90603521389808e-02 + 2.22500000000000e+01 9.90603521389808e-02 + 2.27500000000000e+01 9.90603521389808e-02 + 2.32500000000000e+01 9.90603521389808e-02 + 2.37500000000000e+01 9.90603521389808e-02 + 2.42500000000000e+01 9.90603521389808e-02 + 2.47500000000000e+01 9.90603521389808e-02 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state index f25418e7c..f6e1b5a1e 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state @@ -17,9 +17,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 5.90367895903547e-05 - 7.72360347936990e-03 7.98103714989791e-02 6.51481916206231e-02 - 4.20150492815907e-03 2.14098479953629e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 5.90367888432614e-05 + 7.72360342049122e-03 7.98103713126329e-02 6.51481918280550e-02 + 4.20150496559186e-03 2.14098483126557e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -42,9 +42,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 7.25346810525990e-04 - 5.56809958916884e-02 1.70182688913198e-01 -1.91812601663509e-01 - -3.36985918329314e-02 -2.80399675255803e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 7.25346801924767e-04 + 5.56809955469972e-02 1.70182689379045e-01 -1.91812601541206e-01 + -3.36985920842485e-02 -2.80399679154532e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out index 239d8d6d2..c53fc7f3d 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep2.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -55,28 +57,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -143,6 +145,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -156,6 +159,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -170,22 +174,42 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Multiple-walker metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep2r.colvars.state". colvars: The final output state file will be "test.rep2.colvars.state". -colvars: Opening trajectory file "test.rep2.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep2r.colvars.state". colvars: The final output state file will be "test.rep2.colvars.state". colvars: Metadynamics bias "metadynamics1": accessing replica "rep1". -colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". -colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". colvars: Restarting metadynamics bias "metadynamics1" from step number 100. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: Synchronizing (emptying the buffer of) trajectory file "test.rep2.colvars.traj". colvars: Saving collective variables state to "test.rep2.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped index 22c1a118b..a6354098b 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 9.94700459588437e+00 + x 9.94700459880913e+00 } metadynamics { @@ -27,9 +27,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 5.90367895903547e-05 - 7.72360347936990e-03 7.98103714989791e-02 6.51481916206231e-02 - 4.20150492815907e-03 2.14098479953629e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 5.90367888432614e-05 + 7.72360342049122e-03 7.98103713126329e-02 6.51481918280550e-02 + 4.20150496559186e-03 2.14098483126557e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -52,9 +52,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 7.25346810525990e-04 - 5.56809958916884e-02 1.70182688913198e-01 -1.91812601663509e-01 - -3.36985918329314e-02 -2.80399675255803e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 7.25346801924767e-04 + 5.56809955469972e-02 1.70182689379045e-01 -1.91812601541206e-01 + -3.36985920842485e-02 -2.80399679154532e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj index 7ebb8134c..87c724e96 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj @@ -1,102 +1,102 @@ # step d fa_d 0 9.92876155419194e+00 0.00000000000000e+00 - 1 9.92863721108118e+00 0.00000000000000e+00 - 2 9.92825734340721e+00 0.00000000000000e+00 - 3 9.92755127525955e+00 0.00000000000000e+00 - 4 9.92667471909320e+00 0.00000000000000e+00 - 5 9.92575034311287e+00 0.00000000000000e+00 - 6 9.92495620963971e+00 0.00000000000000e+00 - 7 9.92461789359763e+00 0.00000000000000e+00 - 8 9.92536305405160e+00 0.00000000000000e+00 - 9 9.92598579851009e+00 0.00000000000000e+00 - 10 9.92698489552874e+00 -1.53692716384669e-02 - 11 9.92813713186662e+00 -1.53692716384669e-02 - 12 9.92958955154570e+00 -1.53692716384669e-02 - 13 9.93146245533227e+00 -1.53692716384669e-02 - 14 9.93387956304736e+00 -1.53692716384669e-02 - 15 9.93625622413464e+00 -1.53692716384669e-02 - 16 9.93875399312634e+00 -1.53692716384669e-02 - 17 9.94136244544969e+00 -1.53692716384669e-02 - 18 9.94440242006668e+00 -1.53692716384669e-02 - 19 9.94723046487128e+00 -1.53692716384669e-02 - 20 9.95024031480938e+00 -3.19982334674286e-02 - 21 9.95290175144380e+00 -3.19982334674286e-02 - 22 9.95500360288087e+00 -3.19982334674286e-02 - 23 9.95625077337936e+00 -3.19982334674286e-02 - 24 9.95679355585141e+00 -3.19982334674286e-02 - 25 9.95732344678751e+00 -3.19982334674286e-02 - 26 9.95731470341938e+00 -3.19982334674286e-02 - 27 9.95681072289397e+00 -3.19982334674286e-02 - 28 9.95602536353651e+00 -3.19982334674286e-02 - 29 9.95531430826202e+00 -3.19982334674286e-02 - 30 9.95424975090340e+00 -4.88206365646183e-02 - 31 9.95332421135175e+00 -4.88206365646183e-02 - 32 9.95229914704390e+00 -4.88206365646183e-02 - 33 9.95131483125902e+00 -4.88206365646183e-02 - 34 9.95060259346046e+00 -4.88206365646183e-02 - 35 9.94987218156172e+00 -4.88206365646183e-02 - 36 9.94977154482446e+00 -4.88206365646183e-02 - 37 9.95025457643273e+00 -4.88206365646183e-02 - 38 9.95141923881165e+00 -4.88206365646183e-02 - 39 9.95216006937876e+00 -4.88206365646183e-02 - 40 9.95360310805905e+00 -6.56123202254770e-02 - 41 9.95547794161392e+00 -6.56123202254770e-02 - 42 9.95752449888952e+00 -6.56123202254770e-02 - 43 9.95986469021403e+00 -6.56123202254770e-02 - 44 9.96229115210074e+00 -6.56123202254770e-02 - 45 9.96422304117613e+00 -6.56123202254770e-02 - 46 9.96619104663140e+00 -6.56123202254770e-02 - 47 9.96771829677501e+00 -6.56123202254770e-02 - 48 9.96865300781088e+00 -6.56123202254770e-02 - 49 9.96983841941765e+00 -6.56123202254770e-02 - 50 9.97072851554298e+00 -8.31549679728180e-02 - 51 9.97176839495805e+00 -8.31549679728180e-02 - 52 9.97294474857124e+00 -8.31549679728180e-02 - 53 9.97393162083410e+00 -8.31549679728180e-02 - 54 9.97422213877777e+00 -8.31549679728180e-02 - 55 9.97427923242988e+00 -8.31549679728180e-02 - 56 9.97509912744913e+00 -8.31549679728180e-02 - 57 9.97598939023862e+00 -8.31549679728180e-02 - 58 9.97736094367233e+00 -8.31549679728180e-02 - 59 9.97908316085552e+00 -8.31549679728180e-02 - 60 9.98144866203979e+00 -1.01101050961226e-01 - 61 9.98418248387209e+00 -1.01101050961226e-01 - 62 9.98724278941060e+00 -1.01101050961226e-01 - 63 9.98983902495251e+00 -1.01101050961226e-01 - 64 9.99205502421520e+00 -1.01101050961226e-01 - 65 9.99396375703816e+00 -1.01101050961226e-01 - 66 9.99521991101117e+00 -1.01101050961226e-01 - 67 9.99552925270898e+00 -1.01101050961226e-01 - 68 9.99539402263682e+00 -1.01101050961226e-01 - 69 9.99477561150299e+00 -1.01101050961226e-01 - 70 9.99375663796423e+00 -1.19446771910169e-01 - 71 9.99241934294185e+00 -1.19446771910169e-01 - 72 9.99028414209973e+00 -1.19446771910169e-01 - 73 9.98782436507227e+00 -1.19446771910169e-01 - 74 9.98501318696502e+00 -1.19446771910169e-01 - 75 9.98166896755343e+00 -1.19446771910169e-01 - 76 9.97818649745244e+00 -1.19446771910169e-01 - 77 9.97405361798055e+00 -1.19446771910169e-01 - 78 9.97043748875320e+00 -1.19446771910169e-01 - 79 9.96680015538000e+00 -1.19446771910169e-01 - 80 9.96387279550620e+00 -1.36704453245133e-01 - 81 9.96115537542108e+00 -1.36704453245133e-01 - 82 9.95917142341217e+00 -1.36704453245133e-01 - 83 9.95805513353189e+00 -1.36704453245133e-01 - 84 9.95728144754225e+00 -1.36704453245133e-01 - 85 9.95684688360727e+00 -1.36704453245133e-01 - 86 9.95695270400995e+00 -1.36704453245133e-01 - 87 9.95764400036554e+00 -1.36704453245133e-01 - 88 9.95799943199032e+00 -1.36704453245133e-01 - 89 9.95808582336709e+00 -1.36704453245133e-01 - 90 9.95829826791995e+00 -1.53714986181138e-01 - 91 9.95900434398949e+00 -1.53714986181138e-01 - 92 9.95935451963563e+00 -1.53714986181138e-01 - 93 9.95926444580604e+00 -1.53714986181138e-01 - 94 9.95895383108549e+00 -1.53714986181138e-01 - 95 9.95787595301329e+00 -1.53714986181138e-01 - 96 9.95651093200075e+00 -1.53714986181138e-01 - 97 9.95450881835695e+00 -1.53714986181138e-01 - 98 9.95215317071137e+00 -1.53714986181138e-01 - 99 9.94953653434610e+00 -1.53714986181138e-01 - 100 9.94700459588437e+00 -1.70182688913198e-01 + 1 9.92863721108117e+00 0.00000000000000e+00 + 2 9.92825734340718e+00 0.00000000000000e+00 + 3 9.92755127525950e+00 0.00000000000000e+00 + 4 9.92667471909311e+00 0.00000000000000e+00 + 5 9.92575034311276e+00 0.00000000000000e+00 + 6 9.92495620963959e+00 0.00000000000000e+00 + 7 9.92461789359752e+00 0.00000000000000e+00 + 8 9.92536305405157e+00 0.00000000000000e+00 + 9 9.92598579851022e+00 0.00000000000000e+00 + 10 9.92698489552914e+00 -1.53692716384904e-02 + 11 9.92813713186745e+00 -1.53692716384904e-02 + 12 9.92958955154718e+00 -1.53692716384904e-02 + 13 9.93146245533469e+00 -1.53692716384904e-02 + 14 9.93387956305109e+00 -1.53692716384904e-02 + 15 9.93625622414012e+00 -1.53692716384904e-02 + 16 9.93875399313412e+00 -1.53692716384904e-02 + 17 9.94136244546042e+00 -1.53692716384904e-02 + 18 9.94440242008114e+00 -1.53692716384904e-02 + 19 9.94723046489032e+00 -1.53692716384904e-02 + 20 9.95024031483397e+00 -3.19982334686605e-02 + 21 9.95290175147503e+00 -3.19982334686605e-02 + 22 9.95500360291990e+00 -3.19982334686605e-02 + 23 9.95625077342743e+00 -3.19982334686605e-02 + 24 9.95679355590983e+00 -3.19982334686605e-02 + 25 9.95732344685766e+00 -3.19982334686605e-02 + 26 9.95731470350271e+00 -3.19982334686605e-02 + 27 9.95681072299199e+00 -3.19982334686605e-02 + 28 9.95602536365077e+00 -3.19982334686605e-02 + 29 9.95531430839414e+00 -3.19982334686605e-02 + 30 9.95424975105506e+00 -4.88206365730334e-02 + 31 9.95332421152467e+00 -4.88206365730334e-02 + 32 9.95229914723985e+00 -4.88206365730334e-02 + 33 9.95131483147978e+00 -4.88206365730334e-02 + 34 9.95060259370787e+00 -4.88206365730334e-02 + 35 9.94987218183758e+00 -4.88206365730334e-02 + 36 9.94977154513057e+00 -4.88206365730334e-02 + 37 9.95025457677085e+00 -4.88206365730334e-02 + 38 9.95141923918344e+00 -4.88206365730334e-02 + 39 9.95216006978580e+00 -4.88206365730334e-02 + 40 9.95360310850276e+00 -6.56123202550344e-02 + 41 9.95547794209557e+00 -6.56123202550344e-02 + 42 9.95752449941017e+00 -6.56123202550344e-02 + 43 9.95986469077451e+00 -6.56123202550344e-02 + 44 9.96229115270165e+00 -6.56123202550344e-02 + 45 9.96422304181782e+00 -6.56123202550344e-02 + 46 9.96619104731396e+00 -6.56123202550344e-02 + 47 9.96771829749829e+00 -6.56123202550344e-02 + 48 9.96865300857455e+00 -6.56123202550344e-02 + 49 9.96983842022116e+00 -6.56123202550344e-02 + 50 9.97072851638560e+00 -8.31549680361093e-02 + 51 9.97176839583889e+00 -8.31549680361093e-02 + 52 9.97294474948930e+00 -8.31549680361093e-02 + 53 9.97393162178829e+00 -8.31549680361093e-02 + 54 9.97422213976697e+00 -8.31549680361093e-02 + 55 9.97427923345291e+00 -8.31549680361093e-02 + 56 9.97509912850479e+00 -8.31549680361093e-02 + 57 9.97598939132573e+00 -8.31549680361093e-02 + 58 9.97736094478977e+00 -8.31549680361093e-02 + 59 9.97908316200223e+00 -8.31549680361093e-02 + 60 9.98144866321475e+00 -1.01101051065911e-01 + 61 9.98418248507440e+00 -1.01101051065911e-01 + 62 9.98724279063945e+00 -1.01101051065911e-01 + 63 9.98983902620720e+00 -1.01101051065911e-01 + 64 9.99205502549511e+00 -1.01101051065911e-01 + 65 9.99396375834268e+00 -1.01101051065911e-01 + 66 9.99521991233981e+00 -1.01101051065911e-01 + 67 9.99552925406132e+00 -1.01101051065911e-01 + 68 9.99539402401249e+00 -1.01101051065911e-01 + 69 9.99477561290164e+00 -1.01101051065911e-01 + 70 9.99375663938557e+00 -1.19446772057086e-01 + 71 9.99241934438575e+00 -1.19446772057086e-01 + 72 9.99028414356615e+00 -1.19446772057086e-01 + 73 9.98782436656130e+00 -1.19446772057086e-01 + 74 9.98501318847694e+00 -1.19446772057086e-01 + 75 9.98166896908869e+00 -1.19446772057086e-01 + 76 9.97818649901180e+00 -1.19446772057086e-01 + 77 9.97405361956510e+00 -1.19446772057086e-01 + 78 9.97043749036436e+00 -1.19446772057086e-01 + 79 9.96680015701972e+00 -1.19446772057086e-01 + 80 9.96387279717675e+00 -1.36704453464043e-01 + 81 9.96115537712523e+00 -1.36704453464043e-01 + 82 9.95917142515307e+00 -1.36704453464043e-01 + 83 9.95805513531301e+00 -1.36704453464043e-01 + 84 9.95728144936743e+00 -1.36704453464043e-01 + 85 9.95684688548056e+00 -1.36704453464043e-01 + 86 9.95695270593551e+00 -1.36704453464043e-01 + 87 9.95764400234754e+00 -1.36704453464043e-01 + 88 9.95799943403282e+00 -1.36704453464043e-01 + 89 9.95808582547394e+00 -1.36704453464043e-01 + 90 9.95829827009459e+00 -1.53714986499153e-01 + 91 9.95900434623497e+00 -1.53714986499153e-01 + 92 9.95935452195446e+00 -1.53714986499153e-01 + 93 9.95926444820010e+00 -1.53714986499153e-01 + 94 9.95895383355610e+00 -1.53714986499153e-01 + 95 9.95787595556106e+00 -1.53714986499153e-01 + 96 9.95651093462575e+00 -1.53714986499153e-01 + 97 9.95450882105866e+00 -1.53714986499153e-01 + 98 9.95215317348883e+00 -1.53714986499153e-01 + 99 9.94953653719804e+00 -1.53714986499153e-01 + 100 9.94700459880913e+00 -1.70182689379045e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf index 5f62fc1ee..2f5afd073 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 9.90603520983742e-02 - 7.50000000000000e-01 9.90603520983742e-02 - 1.25000000000000e+00 9.90603520983742e-02 - 1.75000000000000e+00 9.90603520983742e-02 - 2.25000000000000e+00 9.90603520983742e-02 - 2.75000000000000e+00 9.90603520983742e-02 - 3.25000000000000e+00 9.90603520983742e-02 - 3.75000000000000e+00 9.90603520983742e-02 - 4.25000000000000e+00 9.90603520983742e-02 - 4.75000000000000e+00 9.90603520983742e-02 - 5.25000000000000e+00 9.90603520983742e-02 - 5.75000000000000e+00 9.90603520983742e-02 - 6.25000000000000e+00 9.90603520983742e-02 - 6.75000000000000e+00 9.90603520983742e-02 - 7.25000000000000e+00 9.90603520983742e-02 - 7.75000000000000e+00 9.90603520983742e-02 - 8.25000000000000e+00 9.90603520983742e-02 - 8.75000000000000e+00 9.90013153087839e-02 - 9.25000000000000e+00 9.13367486190043e-02 - 9.75000000000000e+00 1.92499805993951e-02 - 1.02500000000000e+01 3.39121604777511e-02 - 1.07500000000000e+01 9.48588471702151e-02 - 1.12500000000000e+01 9.90389422503788e-02 - 1.17500000000000e+01 9.90603520983742e-02 - 1.22500000000000e+01 9.90603520983742e-02 - 1.27500000000000e+01 9.90588180654791e-02 - 1.32500000000000e+01 9.82171168134545e-02 - 1.37500000000000e+01 6.68675768173003e-02 + 2.50000000000000e-01 9.90603521389808e-02 + 7.50000000000000e-01 9.90603521389808e-02 + 1.25000000000000e+00 9.90603521389808e-02 + 1.75000000000000e+00 9.90603521389808e-02 + 2.25000000000000e+00 9.90603521389808e-02 + 2.75000000000000e+00 9.90603521389808e-02 + 3.25000000000000e+00 9.90603521389808e-02 + 3.75000000000000e+00 9.90603521389808e-02 + 4.25000000000000e+00 9.90603521389808e-02 + 4.75000000000000e+00 9.90603521389808e-02 + 5.25000000000000e+00 9.90603521389808e-02 + 5.75000000000000e+00 9.90603521389808e-02 + 6.25000000000000e+00 9.90603521389808e-02 + 6.75000000000000e+00 9.90603521389808e-02 + 7.25000000000000e+00 9.90603521389808e-02 + 7.75000000000000e+00 9.90603521389808e-02 + 8.25000000000000e+00 9.90603521389808e-02 + 8.75000000000000e+00 9.90013153501375e-02 + 9.25000000000000e+00 9.13367487184896e-02 + 9.75000000000000e+00 1.92499808263479e-02 + 1.02500000000000e+01 3.39121603109258e-02 + 1.07500000000000e+01 9.48588471733889e-02 + 1.12500000000000e+01 9.90389422906681e-02 + 1.17500000000000e+01 9.90603521389808e-02 + 1.22500000000000e+01 9.90603521389808e-02 + 1.27500000000000e+01 9.90588181061136e-02 + 1.32500000000000e+01 9.82171168620079e-02 + 1.37500000000000e+01 6.68675769875806e-02 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 7.44570102671402e-02 - 1.52500000000000e+01 9.85667622255897e-02 - 1.57500000000000e+01 9.90599290455859e-02 - 1.62500000000000e+01 9.90603520983742e-02 - 1.67500000000000e+01 9.90603520983742e-02 - 1.72500000000000e+01 9.90603520983742e-02 - 1.77500000000000e+01 9.90603520983742e-02 - 1.82500000000000e+01 9.90603520983742e-02 - 1.87500000000000e+01 9.90603520983742e-02 - 1.92500000000000e+01 9.90603520983742e-02 - 1.97500000000000e+01 9.90603520983742e-02 - 2.02500000000000e+01 9.90603520983742e-02 - 2.07500000000000e+01 9.90603520983742e-02 - 2.12500000000000e+01 9.90603520983742e-02 - 2.17500000000000e+01 9.90603520983742e-02 - 2.22500000000000e+01 9.90603520983742e-02 - 2.27500000000000e+01 9.90603520983742e-02 - 2.32500000000000e+01 9.90603520983742e-02 - 2.37500000000000e+01 9.90603520983742e-02 - 2.42500000000000e+01 9.90603520983742e-02 - 2.47500000000000e+01 9.90603520983742e-02 + 1.47500000000000e+01 7.44570102130397e-02 + 1.52500000000000e+01 9.85667622630896e-02 + 1.57500000000000e+01 9.90599290861925e-02 + 1.62500000000000e+01 9.90603521389808e-02 + 1.67500000000000e+01 9.90603521389808e-02 + 1.72500000000000e+01 9.90603521389808e-02 + 1.77500000000000e+01 9.90603521389808e-02 + 1.82500000000000e+01 9.90603521389808e-02 + 1.87500000000000e+01 9.90603521389808e-02 + 1.92500000000000e+01 9.90603521389808e-02 + 1.97500000000000e+01 9.90603521389808e-02 + 2.02500000000000e+01 9.90603521389808e-02 + 2.07500000000000e+01 9.90603521389808e-02 + 2.12500000000000e+01 9.90603521389808e-02 + 2.17500000000000e+01 9.90603521389808e-02 + 2.22500000000000e+01 9.90603521389808e-02 + 2.27500000000000e+01 9.90603521389808e-02 + 2.32500000000000e+01 9.90603521389808e-02 + 2.37500000000000e+01 9.90603521389808e-02 + 2.42500000000000e+01 9.90603521389808e-02 + 2.47500000000000e+01 9.90603521389808e-02 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state index 30662bcfc..0f90b9de5 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state @@ -20,9 +20,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.25323473186721e-05 3.48877751270849e-03 - 8.48743679843641e-02 1.87767102998601e-01 3.74493268741002e-02 - 6.54251815918406e-04 4.23052788272303e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.25323465171985e-05 3.48877739229281e-03 + 8.48743669974108e-02 1.87767103667070e-01 3.74493273101570e-02 + 6.54251825834146e-04 4.23052788302019e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -45,9 +45,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.70780749827028e-04 3.06678375007270e-02 - 3.38095246589823e-01 -1.52211789178683e-01 -2.11534384625674e-01 - -6.90290098044747e-03 -6.37695701821339e-06 0.00000000000000e+00 + 0.00000000000000e+00 1.70780739637743e-04 3.06678366244801e-02 + 3.38095245919524e-01 -1.52211785481214e-01 -2.11534386688208e-01 + -6.90290108238559e-03 -6.37695701865853e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out index 2c9517acb..051450ff0 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep1.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -55,28 +57,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -143,6 +145,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -156,6 +159,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -170,27 +174,49 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Multiple-walker metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.rep1.colvars.state". +colvars: Loading state from file "test.rep1.colvars.state". colvars: Restarting collective variable "d" from value: 14.1657 colvars: Restarting metadynamics bias "metadynamics1" from step number 100. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: Restarting harmonicwalls bias "dw" from step number 100. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testres.rep1r.colvars.state". colvars: The final output state file will be "testres.rep1.colvars.state". -colvars: Opening trajectory file "testres.rep1.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "testres.rep1r.colvars.state". colvars: The final output state file will be "testres.rep1.colvars.state". colvars: Metadynamics bias "metadynamics1": accessing replica "rep2". -colvars: Metadynamics bias "metadynamics1": replica "rep2" has supplied a new state file, "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". -colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep2" from file "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". +colvars: Metadynamics bias "metadynamics1": replica "rep2" has supplied a new state file, "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". +colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep2" from file "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". colvars: Restarting metadynamics bias "metadynamics1" from step number 100. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: Saving collective variables state to "testres.rep1.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped index 19d64ce2c..3af8b69d2 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 1.40671697413825e+01 + x 1.40671697483701e+01 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.25323473186721e-05 3.48877751270849e-03 - 8.48743679843641e-02 1.87767102998601e-01 3.74493268741002e-02 - 6.54251815918406e-04 4.23052788272303e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.25323465171985e-05 3.48877739229281e-03 + 8.48743669974108e-02 1.87767103667070e-01 3.74493273101570e-02 + 6.54251825834146e-04 4.23052788302019e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -55,9 +55,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.70780749827028e-04 3.06678375007270e-02 - 3.38095246589823e-01 -1.52211789178683e-01 -2.11534384625674e-01 - -6.90290098044747e-03 -6.37695701821339e-06 0.00000000000000e+00 + 0.00000000000000e+00 1.70780739637743e-04 3.06678366244801e-02 + 3.38095245919524e-01 -1.52211785481214e-01 -2.11534386688208e-01 + -6.90290108238559e-03 -6.37695701865853e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj index 62aa833b8..ba8e3a579 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj @@ -1,102 +1,102 @@ # step d fa_d - 100 1.41656974949034e+01 2.66708910635591e-02 - 101 1.41645168157006e+01 2.66708910635591e-02 - 102 1.41639313701771e+01 2.66708910635591e-02 - 103 1.41639423472033e+01 2.66708910635591e-02 - 104 1.41647561685229e+01 2.66708910635591e-02 - 105 1.41658632119453e+01 2.66708910635591e-02 - 106 1.41673787364561e+01 2.66708910635591e-02 - 107 1.41690285518153e+01 2.66708910635591e-02 - 108 1.41710437175448e+01 2.66708910635591e-02 - 109 1.41735809930291e+01 2.66708910635591e-02 - 110 1.41763514554758e+01 3.39682716198089e-02 - 111 1.41790650953902e+01 3.39682716198089e-02 - 112 1.41816844506487e+01 3.39682716198089e-02 - 113 1.41848030075499e+01 3.39682716198089e-02 - 114 1.41881572660568e+01 3.39682716198089e-02 - 115 1.41914710967974e+01 3.39682716198089e-02 - 116 1.41945076494076e+01 3.39682716198089e-02 - 117 1.41970530460683e+01 3.39682716198089e-02 - 118 1.41993348356605e+01 3.39682716198089e-02 - 119 1.42015324335073e+01 3.39682716198089e-02 - 120 1.42029799127233e+01 3.87040720936605e-02 - 121 1.42039018544684e+01 3.87040720936605e-02 - 122 1.42045497495248e+01 3.87040720936605e-02 - 123 1.42051279114412e+01 3.87040720936605e-02 - 124 1.42057799795685e+01 3.87040720936605e-02 - 125 1.42052035513576e+01 3.87040720936605e-02 - 126 1.42037125375882e+01 3.87040720936605e-02 - 127 1.42013876723135e+01 3.87040720936605e-02 - 128 1.41985000473486e+01 3.87040720936605e-02 - 129 1.41946867923467e+01 3.87040720936605e-02 - 130 1.41907407007924e+01 4.46331801324967e-02 - 131 1.41860814679033e+01 4.46331801324967e-02 - 132 1.41811502743331e+01 4.46331801324967e-02 - 133 1.41759651315384e+01 4.46331801324967e-02 - 134 1.41699530822577e+01 4.46331801324967e-02 - 135 1.41627941449498e+01 4.46331801324967e-02 - 136 1.41557931697353e+01 4.46331801324967e-02 - 137 1.41492699032442e+01 4.46331801324967e-02 - 138 1.41425596910040e+01 4.46331801324967e-02 - 139 1.41364771167751e+01 4.46331801324967e-02 - 140 1.41308683038212e+01 5.59216777970916e-02 - 141 1.41250693674976e+01 5.59216777970916e-02 - 142 1.41191585670391e+01 5.59216777970916e-02 - 143 1.41128806923745e+01 5.59216777970916e-02 - 144 1.41069776728295e+01 5.59216777970916e-02 - 145 1.41013330391674e+01 5.59216777970916e-02 - 146 1.40965351204746e+01 5.59216777970916e-02 - 147 1.40911236002896e+01 5.59216777970916e-02 - 148 1.40860174184372e+01 5.59216777970916e-02 - 149 1.40814706978895e+01 5.59216777970916e-02 - 150 1.40771721097910e+01 7.10415219806404e-02 - 151 1.40727022525028e+01 7.10415219806404e-02 - 152 1.40694284472531e+01 7.10415219806404e-02 - 153 1.40661582191822e+01 7.10415219806404e-02 - 154 1.40627979744080e+01 7.10415219806404e-02 - 155 1.40596112294300e+01 7.10415219806404e-02 - 156 1.40566695259700e+01 7.10415219806404e-02 - 157 1.40540744514590e+01 7.10415219806404e-02 - 158 1.40521880891984e+01 7.10415219806404e-02 - 159 1.40504169052137e+01 7.10415219806404e-02 - 160 1.40490177822194e+01 8.77068112269737e-02 - 161 1.40477627135566e+01 8.77068112269737e-02 - 162 1.40465343708561e+01 8.77068112269737e-02 - 163 1.40459238392784e+01 8.77068112269737e-02 - 164 1.40454988972072e+01 8.77068112269737e-02 - 165 1.40458141226713e+01 8.77068112269737e-02 - 166 1.40462783821594e+01 8.77068112269737e-02 - 167 1.40469230222126e+01 8.77068112269737e-02 - 168 1.40475066640928e+01 8.77068112269737e-02 - 169 1.40479434618223e+01 8.77068112269737e-02 - 170 1.40484684727914e+01 1.04398841694391e-01 - 171 1.40494304078364e+01 1.04398841694391e-01 - 172 1.40500894404924e+01 1.04398841694391e-01 - 173 1.40506811219062e+01 1.04398841694391e-01 - 174 1.40513374542578e+01 1.04398841694391e-01 - 175 1.40524333136897e+01 1.04398841694391e-01 - 176 1.40539698754981e+01 1.04398841694391e-01 - 177 1.40553742388214e+01 1.04398841694391e-01 - 178 1.40565462699957e+01 1.04398841694391e-01 - 179 1.40575157738103e+01 1.04398841694391e-01 - 180 1.40587097767556e+01 1.20570598774338e-01 - 181 1.40600393128797e+01 1.20570598774338e-01 - 182 1.40613410306303e+01 1.20570598774338e-01 - 183 1.40624671206865e+01 1.20570598774338e-01 - 184 1.40634905260370e+01 1.20570598774338e-01 - 185 1.40640000664191e+01 1.20570598774338e-01 - 186 1.40642859267739e+01 1.20570598774338e-01 - 187 1.40639315838357e+01 1.20570598774338e-01 - 188 1.40634945833543e+01 1.20570598774338e-01 - 189 1.40632564759331e+01 1.20570598774338e-01 - 190 1.40631238563757e+01 1.36504071186495e-01 - 191 1.40628238849401e+01 1.36504071186495e-01 - 192 1.40626278569889e+01 1.36504071186495e-01 - 193 1.40620533035397e+01 1.36504071186495e-01 - 194 1.40614884933489e+01 1.36504071186495e-01 - 195 1.40614791703604e+01 1.36504071186495e-01 - 196 1.40625287898456e+01 1.36504071186495e-01 - 197 1.40636172326678e+01 1.36504071186495e-01 - 198 1.40650874921233e+01 1.36504071186495e-01 - 199 1.40663704922385e+01 1.36504071186495e-01 - 200 1.40671697413825e+01 1.52211789178683e-01 + 100 1.41656974969458e+01 2.66708902934347e-02 + 101 1.41645168177934e+01 2.66708902934347e-02 + 102 1.41639313723197e+01 2.66708902934347e-02 + 103 1.41639423493949e+01 2.66708902934347e-02 + 104 1.41647561707625e+01 2.66708902934347e-02 + 105 1.41658632142319e+01 2.66708902934347e-02 + 106 1.41673787387882e+01 2.66708902934347e-02 + 107 1.41690285541915e+01 2.66708902934347e-02 + 108 1.41710437199635e+01 2.66708902934347e-02 + 109 1.41735809954887e+01 2.66708902934347e-02 + 110 1.41763514579746e+01 3.39682706157757e-02 + 111 1.41790650979264e+01 3.39682706157757e-02 + 112 1.41816844532206e+01 3.39682706157757e-02 + 113 1.41848030101558e+01 3.39682706157757e-02 + 114 1.41881572686952e+01 3.39682706157757e-02 + 115 1.41914710994669e+01 3.39682706157757e-02 + 116 1.41945076521072e+01 3.39682706157757e-02 + 117 1.41970530487971e+01 3.39682706157757e-02 + 118 1.41993348384181e+01 3.39682706157757e-02 + 119 1.42015324362938e+01 3.39682706157757e-02 + 120 1.42029799155388e+01 3.87040708124342e-02 + 121 1.42039018573139e+01 3.87040708124342e-02 + 122 1.42045497524016e+01 3.87040708124342e-02 + 123 1.42051279143509e+01 3.87040708124342e-02 + 124 1.42057799825133e+01 3.87040708124342e-02 + 125 1.42052035543398e+01 3.87040708124342e-02 + 126 1.42037125406107e+01 3.87040708124342e-02 + 127 1.42013876753793e+01 3.87040708124342e-02 + 128 1.41985000504608e+01 3.87040708124342e-02 + 129 1.41946867955086e+01 3.87040708124342e-02 + 130 1.41907407040072e+01 4.46331785411240e-02 + 131 1.41860814711741e+01 4.46331785411240e-02 + 132 1.41811502776628e+01 4.46331785411240e-02 + 133 1.41759651349297e+01 4.46331785411240e-02 + 134 1.41699530857131e+01 4.46331785411240e-02 + 135 1.41627941484716e+01 4.46331785411240e-02 + 136 1.41557931733251e+01 4.46331785411240e-02 + 137 1.41492699069035e+01 4.46331785411240e-02 + 138 1.41425596947339e+01 4.46331785411240e-02 + 139 1.41364771205764e+01 4.46331785411240e-02 + 140 1.41308683076945e+01 5.59216758917605e-02 + 141 1.41250693714429e+01 5.59216758917605e-02 + 142 1.41191585710561e+01 5.59216758917605e-02 + 143 1.41128806964629e+01 5.59216758917605e-02 + 144 1.41069776769885e+01 5.59216758917605e-02 + 145 1.41013330433959e+01 5.59216758917605e-02 + 146 1.40965351247715e+01 5.59216758917605e-02 + 147 1.40911236046535e+01 5.59216758917605e-02 + 148 1.40860174228665e+01 5.59216758917605e-02 + 149 1.40814707023824e+01 5.59216758917605e-02 + 150 1.40771721143455e+01 7.10415197980919e-02 + 151 1.40727022571165e+01 7.10415197980919e-02 + 152 1.40694284519236e+01 7.10415197980919e-02 + 153 1.40661582239069e+01 7.10415197980919e-02 + 154 1.40627979791840e+01 7.10415197980919e-02 + 155 1.40596112342542e+01 7.10415197980919e-02 + 156 1.40566695308391e+01 7.10415197980919e-02 + 157 1.40540744563696e+01 7.10415197980919e-02 + 158 1.40521880941470e+01 7.10415197980919e-02 + 159 1.40504169101966e+01 7.10415197980919e-02 + 160 1.40490177872330e+01 8.77068087997524e-02 + 161 1.40477627185972e+01 8.77068087997524e-02 + 162 1.40465343759200e+01 8.77068087997524e-02 + 163 1.40459238443624e+01 8.77068087997524e-02 + 164 1.40454989023081e+01 8.77068087997524e-02 + 165 1.40458141277865e+01 8.77068087997524e-02 + 166 1.40462783872865e+01 8.77068087997524e-02 + 167 1.40469230273499e+01 8.77068087997524e-02 + 168 1.40475066692391e+01 8.77068087997524e-02 + 169 1.40479434669772e+01 8.77068087997524e-02 + 170 1.40484684779552e+01 1.04398839016414e-01 + 171 1.40494304130099e+01 1.04398839016414e-01 + 172 1.40500894456774e+01 1.04398839016414e-01 + 173 1.40506811271051e+01 1.04398839016414e-01 + 174 1.40513374594737e+01 1.04398839016414e-01 + 175 1.40524333189262e+01 1.04398839016414e-01 + 176 1.40539698807596e+01 1.04398839016414e-01 + 177 1.40553742441127e+01 1.04398839016414e-01 + 178 1.40565462753219e+01 1.04398839016414e-01 + 179 1.40575157791768e+01 1.04398839016414e-01 + 180 1.40587097821679e+01 1.20570595809343e-01 + 181 1.40600393183434e+01 1.20570595809343e-01 + 182 1.40613410361508e+01 1.20570595809343e-01 + 183 1.40624671262692e+01 1.20570595809343e-01 + 184 1.40634905316866e+01 1.20570595809343e-01 + 185 1.40640000721401e+01 1.20570595809343e-01 + 186 1.40642859325702e+01 1.20570595809343e-01 + 187 1.40639315897108e+01 1.20570595809343e-01 + 188 1.40634945893112e+01 1.20570595809343e-01 + 189 1.40632564819739e+01 1.20570595809343e-01 + 190 1.40631238625021e+01 1.36504067884959e-01 + 191 1.40628238911534e+01 1.36504067884959e-01 + 192 1.40626278632898e+01 1.36504067884959e-01 + 193 1.40620533099285e+01 1.36504067884959e-01 + 194 1.40614884998255e+01 1.36504067884959e-01 + 195 1.40614791769245e+01 1.36504067884959e-01 + 196 1.40625287964965e+01 1.36504067884959e-01 + 197 1.40636172394048e+01 1.36504067884959e-01 + 198 1.40650874989452e+01 1.36504067884959e-01 + 199 1.40663704991439e+01 1.36504067884959e-01 + 200 1.40671697483701e+01 1.52211785481214e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf index 6256d0183..5728a51c7 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 1.87767102998601e-01 - 7.50000000000000e-01 1.87767102998601e-01 - 1.25000000000000e+00 1.87767102998601e-01 - 1.75000000000000e+00 1.87767102998601e-01 - 2.25000000000000e+00 1.87767102998601e-01 - 2.75000000000000e+00 1.87767102998601e-01 - 3.25000000000000e+00 1.87767102998601e-01 - 3.75000000000000e+00 1.87767102998601e-01 - 4.25000000000000e+00 1.87767102998601e-01 - 4.75000000000000e+00 1.87767102998601e-01 - 5.25000000000000e+00 1.87767102998601e-01 - 5.75000000000000e+00 1.87767102998601e-01 - 6.25000000000000e+00 1.87767102998601e-01 - 6.75000000000000e+00 1.87767102998601e-01 - 7.25000000000000e+00 1.87767102998601e-01 - 7.75000000000000e+00 1.87767102998601e-01 - 8.25000000000000e+00 1.87767102998601e-01 - 8.75000000000000e+00 1.87708066209011e-01 - 9.25000000000000e+00 1.80043499519231e-01 - 9.75000000000000e+00 1.07956731499622e-01 - 1.02500000000000e+01 1.22618911377978e-01 - 1.07500000000000e+01 1.83565598070442e-01 - 1.12500000000000e+01 1.87745693150606e-01 - 1.17500000000000e+01 1.87767102998601e-01 - 1.22500000000000e+01 1.87767102998601e-01 - 1.27500000000000e+01 1.87754570651283e-01 - 1.32500000000000e+01 1.84278325485893e-01 - 1.37500000000000e+01 1.02892735014237e-01 + 2.50000000000000e-01 1.87767103667070e-01 + 7.50000000000000e-01 1.87767103667070e-01 + 1.25000000000000e+00 1.87767103667070e-01 + 1.75000000000000e+00 1.87767103667070e-01 + 2.25000000000000e+00 1.87767103667070e-01 + 2.75000000000000e+00 1.87767103667070e-01 + 3.25000000000000e+00 1.87767103667070e-01 + 3.75000000000000e+00 1.87767103667070e-01 + 4.25000000000000e+00 1.87767103667070e-01 + 4.75000000000000e+00 1.87767103667070e-01 + 5.25000000000000e+00 1.87767103667070e-01 + 5.75000000000000e+00 1.87767103667070e-01 + 6.25000000000000e+00 1.87767103667070e-01 + 6.75000000000000e+00 1.87767103667070e-01 + 7.25000000000000e+00 1.87767103667070e-01 + 7.75000000000000e+00 1.87767103667070e-01 + 8.25000000000000e+00 1.87767103667070e-01 + 8.75000000000000e+00 1.87708066878227e-01 + 9.25000000000000e+00 1.80043500246579e-01 + 9.75000000000000e+00 1.07956732354437e-01 + 1.02500000000000e+01 1.22618911839015e-01 + 1.07500000000000e+01 1.83565598701478e-01 + 1.12500000000000e+01 1.87745693818758e-01 + 1.17500000000000e+01 1.87767103667070e-01 + 1.22500000000000e+01 1.87767103667070e-01 + 1.27500000000000e+01 1.87754571320553e-01 + 1.32500000000000e+01 1.84278326274777e-01 + 1.37500000000000e+01 1.02892736669659e-01 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 1.50317776124501e-01 - 1.52500000000000e+01 1.87112851182683e-01 - 1.57500000000000e+01 1.87766679945813e-01 - 1.62500000000000e+01 1.87767102998601e-01 - 1.67500000000000e+01 1.87767102998601e-01 - 1.72500000000000e+01 1.87767102998601e-01 - 1.77500000000000e+01 1.87767102998601e-01 - 1.82500000000000e+01 1.87767102998601e-01 - 1.87500000000000e+01 1.87767102998601e-01 - 1.92500000000000e+01 1.87767102998601e-01 - 1.97500000000000e+01 1.87767102998601e-01 - 2.02500000000000e+01 1.87767102998601e-01 - 2.07500000000000e+01 1.87767102998601e-01 - 2.12500000000000e+01 1.87767102998601e-01 - 2.17500000000000e+01 1.87767102998601e-01 - 2.22500000000000e+01 1.87767102998601e-01 - 2.27500000000000e+01 1.87767102998601e-01 - 2.32500000000000e+01 1.87767102998601e-01 - 2.37500000000000e+01 1.87767102998601e-01 - 2.42500000000000e+01 1.87767102998601e-01 - 2.47500000000000e+01 1.87767102998601e-01 + 1.47500000000000e+01 1.50317776356913e-01 + 1.52500000000000e+01 1.87112851841236e-01 + 1.57500000000000e+01 1.87766680614282e-01 + 1.62500000000000e+01 1.87767103667070e-01 + 1.67500000000000e+01 1.87767103667070e-01 + 1.72500000000000e+01 1.87767103667070e-01 + 1.77500000000000e+01 1.87767103667070e-01 + 1.82500000000000e+01 1.87767103667070e-01 + 1.87500000000000e+01 1.87767103667070e-01 + 1.92500000000000e+01 1.87767103667070e-01 + 1.97500000000000e+01 1.87767103667070e-01 + 2.02500000000000e+01 1.87767103667070e-01 + 2.07500000000000e+01 1.87767103667070e-01 + 2.12500000000000e+01 1.87767103667070e-01 + 2.17500000000000e+01 1.87767103667070e-01 + 2.22500000000000e+01 1.87767103667070e-01 + 2.27500000000000e+01 1.87767103667070e-01 + 2.32500000000000e+01 1.87767103667070e-01 + 2.37500000000000e+01 1.87767103667070e-01 + 2.42500000000000e+01 1.87767103667070e-01 + 2.47500000000000e+01 1.87767103667070e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state index b13fd85e3..c2787a073 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state @@ -17,9 +17,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 4.94688080523780e-07 4.73585992341132e-04 - 2.87475270508744e-02 1.74745280616823e-01 1.04414171448857e-01 - 5.69106155906453e-03 2.62455918518392e-05 0.00000000000000e+00 + 0.00000000000000e+00 4.94688027692718e-07 4.73585964068546e-04 + 2.87475263076380e-02 1.74745280192386e-01 1.04414172539260e-01 + 5.69106166051415e-03 2.62455924536695e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -42,9 +42,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 7.40502520045617e-06 4.99357144931863e-03 - 1.69663406152221e-01 2.28926002246273e-01 -3.54750301243893e-01 - -4.70268695839609e-02 -3.46867170320607e-04 0.00000000000000e+00 + 0.00000000000000e+00 7.40502444565457e-06 4.99357118645503e-03 + 1.69663403453012e-01 2.28926007806402e-01 -3.54750303020055e-01 + -4.70268703518904e-02 -3.46867177951536e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out index 213231cf9..373c73703 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep2.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -55,28 +57,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -143,6 +145,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -156,6 +159,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -170,27 +174,49 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Metadynamics colvar bias implementation: +colvars: - Multiple-walker metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.rep2.colvars.state". +colvars: Loading state from file "test.rep2.colvars.state". colvars: Restarting collective variable "d" from value: 9.947 colvars: Restarting metadynamics bias "metadynamics1" from step number 100. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: Restarting harmonicwalls bias "dw" from step number 100. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testres.rep2r.colvars.state". colvars: The final output state file will be "testres.rep2.colvars.state". -colvars: Opening trajectory file "testres.rep2.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "testres.rep2r.colvars.state". colvars: The final output state file will be "testres.rep2.colvars.state". colvars: Metadynamics bias "metadynamics1": accessing replica "rep1". -colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". -colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". colvars: Restarting metadynamics bias "metadynamics1" from step number 200. +colvars: read biasing energy and forces from grids. +colvars: read 0 additional explicit hills. colvars: Saving collective variables state to "testres.rep2.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped index 5f3f08a24..ce8f94f06 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 9.71175738207289e+00 + x 9.71175738936231e+00 } metadynamics { @@ -27,9 +27,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 4.94688080523780e-07 4.73585992341132e-04 - 2.87475270508744e-02 1.74745280616823e-01 1.04414171448857e-01 - 5.69106155906453e-03 2.62455918518392e-05 0.00000000000000e+00 + 0.00000000000000e+00 4.94688027692718e-07 4.73585964068546e-04 + 2.87475263076380e-02 1.74745280192386e-01 1.04414172539260e-01 + 5.69106166051415e-03 2.62455924536695e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -52,9 +52,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 7.40502520045617e-06 4.99357144931863e-03 - 1.69663406152221e-01 2.28926002246273e-01 -3.54750301243893e-01 - -4.70268695839609e-02 -3.46867170320607e-04 0.00000000000000e+00 + 0.00000000000000e+00 7.40502444565457e-06 4.99357118645503e-03 + 1.69663403453012e-01 2.28926007806402e-01 -3.54750303020055e-01 + -4.70268703518904e-02 -3.46867177951536e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj index c28a19f9f..968ab38c3 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj @@ -1,102 +1,102 @@ # step d fa_d - 100 9.94700459588437e+00 -1.70182688913198e-01 - 101 9.94458507772995e+00 -1.70182688913198e-01 - 102 9.94237837514508e+00 -1.70182688913198e-01 - 103 9.94046457996010e+00 -1.70182688913198e-01 - 104 9.93917796988520e+00 -1.70182688913198e-01 - 105 9.93831816048514e+00 -1.70182688913198e-01 - 106 9.93730878764442e+00 -1.70182688913198e-01 - 107 9.93672533620511e+00 -1.70182688913198e-01 - 108 9.93648376088839e+00 -1.70182688913198e-01 - 109 9.93652761776498e+00 -1.70182688913198e-01 - 110 9.93706370695588e+00 -1.86126457148131e-01 - 111 9.93776112075882e+00 -1.86126457148131e-01 - 112 9.93854506029798e+00 -1.86126457148131e-01 - 113 9.93918085186220e+00 -1.86126457148131e-01 - 114 9.93937655398418e+00 -1.86126457148131e-01 - 115 9.93893038386686e+00 -1.86126457148131e-01 - 116 9.93789380210237e+00 -1.86126457148131e-01 - 117 9.93662176845159e+00 -1.86126457148131e-01 - 118 9.93489574805879e+00 -1.86126457148131e-01 - 119 9.93264204174611e+00 -1.86126457148131e-01 - 120 9.93021575754143e+00 -2.01684581228258e-01 - 121 9.92745576666947e+00 -2.01684581228258e-01 - 122 9.92406367114035e+00 -2.01684581228258e-01 - 123 9.91986260200830e+00 -2.01684581228258e-01 - 124 9.91533756814292e+00 -2.01684581228258e-01 - 125 9.91093484240737e+00 -2.01684581228258e-01 - 126 9.90665291579182e+00 -2.01684581228258e-01 - 127 9.90211123152112e+00 -2.01684581228258e-01 - 128 9.89781300213203e+00 -2.01684581228258e-01 - 129 9.89406396885698e+00 -2.01684581228258e-01 - 130 9.89014113666249e+00 -2.14600525240779e-01 - 131 9.88640594373758e+00 -2.14600525240779e-01 - 132 9.88226178497735e+00 -2.14600525240779e-01 - 133 9.87820929310142e+00 -2.14600525240779e-01 - 134 9.87355012458204e+00 -2.14600525240779e-01 - 135 9.86875344554473e+00 -2.14600525240779e-01 - 136 9.86400574168410e+00 -2.14600525240779e-01 - 137 9.85896120013053e+00 -2.14600525240779e-01 - 138 9.85422080643946e+00 -2.14600525240779e-01 - 139 9.84970383929048e+00 -2.14600525240779e-01 - 140 9.84571930339719e+00 -2.23905909555689e-01 - 141 9.84162990482619e+00 -2.23905909555689e-01 - 142 9.83714752694151e+00 -2.23905909555689e-01 - 143 9.83237840269532e+00 -2.23905909555689e-01 - 144 9.82753783768742e+00 -2.23905909555689e-01 - 145 9.82322257146133e+00 -2.23905909555689e-01 - 146 9.81960403148490e+00 -2.23905909555689e-01 - 147 9.81638214984508e+00 -2.23905909555689e-01 - 148 9.81411815280101e+00 -2.23905909555689e-01 - 149 9.81186120171889e+00 -2.23905909555689e-01 - 150 9.81023975732696e+00 -2.29929520564960e-01 - 151 9.80895196413704e+00 -2.29929520564960e-01 - 152 9.80803347273143e+00 -2.29929520564960e-01 - 153 9.80725709506516e+00 -2.29929520564960e-01 - 154 9.80685628234177e+00 -2.29929520564960e-01 - 155 9.80643124017792e+00 -2.29929520564960e-01 - 156 9.80651929062019e+00 -2.29929520564960e-01 - 157 9.80658365740485e+00 -2.29929520564960e-01 - 158 9.80608274371768e+00 -2.29929520564960e-01 - 159 9.80533153641205e+00 -2.29929520564960e-01 - 160 9.80408985591389e+00 -2.35357581465163e-01 - 161 9.80243195378187e+00 -2.35357581465163e-01 - 162 9.80032235258663e+00 -2.35357581465163e-01 - 163 9.79828002164672e+00 -2.35357581465163e-01 - 164 9.79526928693096e+00 -2.35357581465163e-01 - 165 9.79205899981332e+00 -2.35357581465163e-01 - 166 9.78836208455697e+00 -2.35357581465163e-01 - 167 9.78427949242546e+00 -2.35357581465163e-01 - 168 9.77985340193428e+00 -2.35357581465163e-01 - 169 9.77597576729126e+00 -2.35357581465163e-01 - 170 9.77231656680436e+00 -2.37624969895514e-01 - 171 9.76872764540608e+00 -2.37624969895514e-01 - 172 9.76445831928769e+00 -2.37624969895514e-01 - 173 9.76039937757358e+00 -2.37624969895514e-01 - 174 9.75645214354585e+00 -2.37624969895514e-01 - 175 9.75287081367028e+00 -2.37624969895514e-01 - 176 9.74968666022476e+00 -2.37624969895514e-01 - 177 9.74684973072586e+00 -2.37624969895514e-01 - 178 9.74348359335075e+00 -2.37624969895514e-01 - 179 9.74030679423950e+00 -2.37624969895514e-01 - 180 9.73711487809642e+00 -2.36313611463974e-01 - 181 9.73433464376223e+00 -2.36313611463974e-01 - 182 9.73173779878573e+00 -2.36313611463974e-01 - 183 9.72947842909980e+00 -2.36313611463974e-01 - 184 9.72710977092031e+00 -2.36313611463974e-01 - 185 9.72467705766697e+00 -2.36313611463974e-01 - 186 9.72244088949095e+00 -2.36313611463974e-01 - 187 9.72029111920384e+00 -2.36313611463974e-01 - 188 9.71845562125918e+00 -2.36313611463974e-01 - 189 9.71680423295022e+00 -2.36313611463974e-01 - 190 9.71521748810981e+00 -2.32792456745213e-01 - 191 9.71413764529071e+00 -2.32792456745213e-01 - 192 9.71307166091424e+00 -2.32792456745213e-01 - 193 9.71195900641790e+00 -2.32792456745213e-01 - 194 9.71186724184931e+00 -2.32792456745213e-01 - 195 9.71169949999982e+00 -2.32792456745213e-01 - 196 9.71157179938086e+00 -2.32792456745213e-01 - 197 9.71177699258930e+00 -2.32792456745213e-01 - 198 9.71199161585537e+00 -2.32792456745213e-01 - 199 9.71215448992823e+00 -2.32792456745213e-01 - 200 9.71175738207289e+00 -2.28926002246273e-01 + 100 9.94700459880913e+00 -1.70182689379045e-01 + 101 9.94458508072563e+00 -1.70182689379045e-01 + 102 9.94237837820968e+00 -1.70182689379045e-01 + 103 9.94046458309169e+00 -1.70182689379045e-01 + 104 9.93917797308190e+00 -1.70182689379045e-01 + 105 9.93831816374525e+00 -1.70182689379045e-01 + 106 9.93730879096641e+00 -1.70182689379045e-01 + 107 9.93672533958771e+00 -1.70182689379045e-01 + 108 9.93648376433042e+00 -1.70182689379045e-01 + 109 9.93652762126550e+00 -1.70182689379045e-01 + 110 9.93706371051391e+00 -1.86126457809144e-01 + 111 9.93776112437344e+00 -1.86126457809144e-01 + 112 9.93854506396815e+00 -1.86126457809144e-01 + 113 9.93918085558668e+00 -1.86126457809144e-01 + 114 9.93937655776149e+00 -1.86126457809144e-01 + 115 9.93893038769523e+00 -1.86126457809144e-01 + 116 9.93789380597970e+00 -1.86126457809144e-01 + 117 9.93662177237539e+00 -1.86126457809144e-01 + 118 9.93489575202623e+00 -1.86126457809144e-01 + 119 9.93264204575408e+00 -1.86126457809144e-01 + 120 9.93021576158670e+00 -2.01684582122971e-01 + 121 9.92745577074879e+00 -2.01684582122971e-01 + 122 9.92406367525066e+00 -2.01684582122971e-01 + 123 9.91986260614685e+00 -2.01684582122971e-01 + 124 9.91533757230742e+00 -2.01684582122971e-01 + 125 9.91093484659609e+00 -2.01684582122971e-01 + 126 9.90665292000386e+00 -2.01684582122971e-01 + 127 9.90211123575625e+00 -2.01684582122971e-01 + 128 9.89781300639078e+00 -2.01684582122971e-01 + 129 9.89406397314085e+00 -2.01684582122971e-01 + 130 9.89014114097385e+00 -2.14600526453355e-01 + 131 9.88640594807955e+00 -2.14600526453355e-01 + 132 9.88226178935358e+00 -2.14600526453355e-01 + 133 9.87820929751591e+00 -2.14600526453355e-01 + 134 9.87355012903898e+00 -2.14600526453355e-01 + 135 9.86875345004836e+00 -2.14600526453355e-01 + 136 9.86400574623842e+00 -2.14600526453355e-01 + 137 9.85896120473937e+00 -2.14600526453355e-01 + 138 9.85422081110592e+00 -2.14600526453355e-01 + 139 9.84970384401704e+00 -2.14600526453355e-01 + 140 9.84571930818557e+00 -2.23905911190324e-01 + 141 9.84162990967742e+00 -2.23905911190324e-01 + 142 9.83714753185596e+00 -2.23905911190324e-01 + 143 9.83237840767275e+00 -2.23905911190324e-01 + 144 9.82753784272710e+00 -2.23905911190324e-01 + 145 9.82322257656238e+00 -2.23905911190324e-01 + 146 9.81960403664628e+00 -2.23905911190324e-01 + 147 9.81638215506584e+00 -2.23905911190324e-01 + 148 9.81411815808055e+00 -2.23905911190324e-01 + 149 9.81186120705696e+00 -2.23905911190324e-01 + 150 9.81023976272379e+00 -2.29929522719298e-01 + 151 9.80895196959333e+00 -2.29929522719298e-01 + 152 9.80803347824830e+00 -2.29929522719298e-01 + 153 9.80725710064431e+00 -2.29929522719298e-01 + 154 9.80685628798525e+00 -2.29929522719298e-01 + 155 9.80643124588796e+00 -2.29929522719298e-01 + 156 9.80651929639905e+00 -2.29929522719298e-01 + 157 9.80658366325459e+00 -2.29929522719298e-01 + 158 9.80608274963996e+00 -2.29929522719298e-01 + 159 9.80533154240805e+00 -2.29929522719298e-01 + 160 9.80408986198415e+00 -2.35357584210514e-01 + 161 9.80243195992594e+00 -2.35357584210514e-01 + 162 9.80032235880316e+00 -2.35357584210514e-01 + 163 9.79828002793355e+00 -2.35357584210514e-01 + 164 9.79526929328518e+00 -2.35357584210514e-01 + 165 9.79205900623106e+00 -2.35357584210514e-01 + 166 9.78836209103374e+00 -2.35357584210514e-01 + 167 9.78427949895649e+00 -2.35357584210514e-01 + 168 9.77985340851435e+00 -2.35357584210514e-01 + 169 9.77597577391508e+00 -2.35357584210514e-01 + 170 9.77231657346676e+00 -2.37624973314339e-01 + 171 9.76872765210230e+00 -2.37624973314339e-01 + 172 9.76445832601357e+00 -2.37624973314339e-01 + 173 9.76039938432572e+00 -2.37624973314339e-01 + 174 9.75645215032161e+00 -2.37624973314339e-01 + 175 9.75287082046772e+00 -2.37624973314339e-01 + 176 9.74968666704269e+00 -2.37624973314339e-01 + 177 9.74684973756385e+00 -2.37624973314339e-01 + 178 9.74348360020917e+00 -2.37624973314339e-01 + 179 9.74030680111914e+00 -2.37624973314339e-01 + 180 9.73711488499836e+00 -2.36313615584043e-01 + 181 9.73433465068754e+00 -2.36313615584043e-01 + 182 9.73173780573565e+00 -2.36313615584043e-01 + 183 9.72947843607525e+00 -2.36313615584043e-01 + 184 9.72710977792195e+00 -2.36313615584043e-01 + 185 9.72467706469478e+00 -2.36313615584043e-01 + 186 9.72244089654436e+00 -2.36313615584043e-01 + 187 9.72029112628186e+00 -2.36313615584043e-01 + 188 9.71845562836040e+00 -2.36313615584043e-01 + 189 9.71680424007266e+00 -2.36313615584043e-01 + 190 9.71521749525137e+00 -2.32792461579337e-01 + 191 9.71413765244917e+00 -2.32792461579337e-01 + 192 9.71307166808760e+00 -2.32792461579337e-01 + 193 9.71195901360456e+00 -2.32792461579337e-01 + 194 9.71186724904802e+00 -2.32792461579337e-01 + 195 9.71169950721007e+00 -2.32792461579337e-01 + 196 9.71157180660297e+00 -2.32792461579337e-01 + 197 9.71177699982444e+00 -2.32792461579337e-01 + 198 9.71199162310558e+00 -2.32792461579337e-01 + 199 9.71215449719626e+00 -2.32792461579337e-01 + 200 9.71175738936231e+00 -2.28926007806402e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf index f66c76153..403599903 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 1.87767102998601e-01 - 7.50000000000000e-01 1.87767102998601e-01 - 1.25000000000000e+00 1.87767102998601e-01 - 1.75000000000000e+00 1.87767102998601e-01 - 2.25000000000000e+00 1.87767102998601e-01 - 2.75000000000000e+00 1.87767102998601e-01 - 3.25000000000000e+00 1.87767102998601e-01 - 3.75000000000000e+00 1.87767102998601e-01 - 4.25000000000000e+00 1.87767102998601e-01 - 4.75000000000000e+00 1.87767102998601e-01 - 5.25000000000000e+00 1.87767102998601e-01 - 5.75000000000000e+00 1.87767102998601e-01 - 6.25000000000000e+00 1.87767102998601e-01 - 6.75000000000000e+00 1.87767102998601e-01 - 7.25000000000000e+00 1.87767102998601e-01 - 7.75000000000000e+00 1.87767102998601e-01 - 8.25000000000000e+00 1.87766608310520e-01 - 8.75000000000000e+00 1.87293517006260e-01 - 9.25000000000000e+00 1.59019575947726e-01 - 9.75000000000000e+00 1.30218223817775e-02 - 1.02500000000000e+01 8.33529315497443e-02 - 1.07500000000000e+01 1.82076041439536e-01 - 1.12500000000000e+01 1.87740857406749e-01 - 1.17500000000000e+01 1.87767102998601e-01 - 1.22500000000000e+01 1.87767102998601e-01 - 1.27500000000000e+01 1.87754570651282e-01 - 1.32500000000000e+01 1.84278325485893e-01 - 1.37500000000000e+01 1.02892735014237e-01 + 2.50000000000000e-01 1.87767103667070e-01 + 7.50000000000000e-01 1.87767103667070e-01 + 1.25000000000000e+00 1.87767103667070e-01 + 1.75000000000000e+00 1.87767103667070e-01 + 2.25000000000000e+00 1.87767103667070e-01 + 2.75000000000000e+00 1.87767103667070e-01 + 3.25000000000000e+00 1.87767103667070e-01 + 3.75000000000000e+00 1.87767103667070e-01 + 4.25000000000000e+00 1.87767103667070e-01 + 4.75000000000000e+00 1.87767103667070e-01 + 5.25000000000000e+00 1.87767103667070e-01 + 5.75000000000000e+00 1.87767103667070e-01 + 6.25000000000000e+00 1.87767103667070e-01 + 6.75000000000000e+00 1.87767103667070e-01 + 7.25000000000000e+00 1.87767103667070e-01 + 7.75000000000000e+00 1.87767103667070e-01 + 8.25000000000000e+00 1.87766608979042e-01 + 8.75000000000000e+00 1.87293517703001e-01 + 9.25000000000000e+00 1.59019577359432e-01 + 9.75000000000000e+00 1.30218234746837e-02 + 1.02500000000000e+01 8.33529311278102e-02 + 1.07500000000000e+01 1.82076042006556e-01 + 1.12500000000000e+01 1.87740858074616e-01 + 1.17500000000000e+01 1.87767103667070e-01 + 1.22500000000000e+01 1.87767103667070e-01 + 1.27500000000000e+01 1.87754571320553e-01 + 1.32500000000000e+01 1.84278326274777e-01 + 1.37500000000000e+01 1.02892736669659e-01 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 1.50317776124501e-01 - 1.52500000000000e+01 1.87112851182683e-01 - 1.57500000000000e+01 1.87766679945813e-01 - 1.62500000000000e+01 1.87767102998601e-01 - 1.67500000000000e+01 1.87767102998601e-01 - 1.72500000000000e+01 1.87767102998601e-01 - 1.77500000000000e+01 1.87767102998601e-01 - 1.82500000000000e+01 1.87767102998601e-01 - 1.87500000000000e+01 1.87767102998601e-01 - 1.92500000000000e+01 1.87767102998601e-01 - 1.97500000000000e+01 1.87767102998601e-01 - 2.02500000000000e+01 1.87767102998601e-01 - 2.07500000000000e+01 1.87767102998601e-01 - 2.12500000000000e+01 1.87767102998601e-01 - 2.17500000000000e+01 1.87767102998601e-01 - 2.22500000000000e+01 1.87767102998601e-01 - 2.27500000000000e+01 1.87767102998601e-01 - 2.32500000000000e+01 1.87767102998601e-01 - 2.37500000000000e+01 1.87767102998601e-01 - 2.42500000000000e+01 1.87767102998601e-01 - 2.47500000000000e+01 1.87767102998601e-01 + 1.47500000000000e+01 1.50317776356913e-01 + 1.52500000000000e+01 1.87112851841236e-01 + 1.57500000000000e+01 1.87766680614282e-01 + 1.62500000000000e+01 1.87767103667070e-01 + 1.67500000000000e+01 1.87767103667070e-01 + 1.72500000000000e+01 1.87767103667070e-01 + 1.77500000000000e+01 1.87767103667070e-01 + 1.82500000000000e+01 1.87767103667070e-01 + 1.87500000000000e+01 1.87767103667070e-01 + 1.92500000000000e+01 1.87767103667070e-01 + 1.97500000000000e+01 1.87767103667070e-01 + 2.02500000000000e+01 1.87767103667070e-01 + 2.07500000000000e+01 1.87767103667070e-01 + 2.12500000000000e+01 1.87767103667070e-01 + 2.17500000000000e+01 1.87767103667070e-01 + 2.22500000000000e+01 1.87767103667070e-01 + 2.27500000000000e+01 1.87767103667070e-01 + 2.32500000000000e+01 1.87767103667070e-01 + 2.37500000000000e+01 1.87767103667070e-01 + 2.42500000000000e+01 1.87767103667070e-01 + 2.47500000000000e+01 1.87767103667070e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/namd-version.txt b/namd/tests/library/011_multiple_walker_mtd/namd-version.txt index e2b19c981..157cac038 100644 --- a/namd/tests/library/011_multiple_walker_mtd/namd-version.txt +++ b/namd/tests/library/011_multiple_walker_mtd/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out index 6f057103a..3ff945377 100644 --- a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out +++ b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: Warning: no collective variables defined. colvars: Collective variables initialized, 0 in total. colvars: No collective variables biases were defined. @@ -19,8 +21,6 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration: colvars: # units = "" [default] @@ -29,6 +29,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d0" @@ -42,28 +43,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -74,7 +75,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -99,28 +100,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -137,28 +138,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 2 atoms requested: total mass = 15.015, total charge = -0.31. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -175,28 +176,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 3 atoms requested: total mass = 16.023, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -207,7 +208,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -232,28 +233,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -270,28 +271,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 2 atoms requested: total mass = 15.015, total charge = -0.31. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -308,28 +309,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 3 atoms requested: total mass = 16.023, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -346,28 +347,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 28.034, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -384,28 +385,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 5 atoms requested: total mass = 29.042, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -422,28 +423,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 6 atoms requested: total mass = 41.053, total charge = -0.27. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -460,28 +461,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 7 atoms requested: total mass = 42.061, total charge = -0.18. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -492,7 +493,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -513,9 +514,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (14 scalable groups, 56 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (14 scalable groups, 56 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d0":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. colvars: Re-initialized atom group for variable "d0":0/1. 1 atoms: total mass = 1.008, total charge = 0.09. colvars: Re-initialized atom group for variable "d1":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. diff --git a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj index 764d968c2..e61993948 100644 --- a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj +++ b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step d0 d1 d2 0 9.68028971673885e+00 2.83439401925857e+01 6.55272039460079e+01 - 1 9.68459329037381e+00 2.83503517848797e+01 6.55348311139484e+01 - 2 9.68863510078556e+00 2.83568986120180e+01 6.55435199472981e+01 - 3 9.69270450129925e+00 2.83637753156007e+01 6.55522671059886e+01 - 4 9.69567146228222e+00 2.83683142733634e+01 6.55581718661156e+01 - 5 9.69861372979398e+00 2.83728360758814e+01 6.55643117777734e+01 - 6 9.69989691779190e+00 2.83755769999609e+01 6.55687963598000e+01 - 7 9.69881248553272e+00 2.83761329501348e+01 6.55711659393180e+01 - 8 9.69696590312749e+00 2.83755659868676e+01 6.55723453524207e+01 - 9 9.69437508780854e+00 2.83738021776574e+01 6.55721051238709e+01 - 10 9.69142876312061e+00 2.83713870794876e+01 6.55715234770360e+01 - 11 9.68736616558516e+00 2.83668242787558e+01 6.55679613898842e+01 - 12 9.68269170482564e+00 2.83619773540213e+01 6.55640905411503e+01 - 13 9.67603219505517e+00 2.83539684891505e+01 6.55557350086236e+01 - 14 9.67131225684547e+00 2.83481344964496e+01 6.55501180059041e+01 - 15 9.66613278115654e+00 2.83417789199746e+01 6.55442094172513e+01 - 16 9.66208835205202e+00 2.83361112761420e+01 6.55383049476216e+01 - 17 9.65853060632552e+00 2.83296225777924e+01 6.55305098869110e+01 - 18 9.65562060425861e+00 2.83230675649562e+01 6.55226790315953e+01 - 19 9.65479770180415e+00 2.83184820768533e+01 6.55167907309839e+01 - 20 9.65474241874427e+00 2.83146389466025e+01 6.55122068151804e+01 + 1 9.68459329037158e+00 2.83503517848776e+01 6.55348311139462e+01 + 2 9.68863510077707e+00 2.83568986120102e+01 6.55435199472898e+01 + 3 9.69270450128096e+00 2.83637753155840e+01 6.55522671059708e+01 + 4 9.69567146225122e+00 2.83683142733353e+01 6.55581718660859e+01 + 5 9.69861372974800e+00 2.83728360758402e+01 6.55643117777301e+01 + 6 9.69989691772941e+00 2.83755769999054e+01 6.55687963597424e+01 + 7 9.69881248545288e+00 2.83761329500648e+01 6.55711659392461e+01 + 8 9.69696590303006e+00 2.83755659867833e+01 6.55723453523354e+01 + 9 9.69437508769387e+00 2.83738021775598e+01 6.55721051237738e+01 + 10 9.69142876298948e+00 2.83713870793780e+01 6.55715234769294e+01 + 11 9.68736616543871e+00 2.83668242786358e+01 6.55679613897708e+01 + 12 9.68269170466530e+00 2.83619773538931e+01 6.55640905410330e+01 + 13 9.67603219488243e+00 2.83539684890163e+01 6.55557350085058e+01 + 14 9.67131225666176e+00 2.83481344963114e+01 6.55501180057890e+01 + 15 9.66613278096313e+00 2.83417789198344e+01 6.55442094171420e+01 + 16 9.66208835184987e+00 2.83361112760016e+01 6.55383049475210e+01 + 17 9.65853060611532e+00 2.83296225776533e+01 6.55305098868216e+01 + 18 9.65562060404079e+00 2.83230675648197e+01 6.55226790315196e+01 + 19 9.65479770157889e+00 2.83184820767205e+01 6.55167907309241e+01 + 20 9.65474241851144e+00 2.83146389464743e+01 6.55122068151385e+01 diff --git a/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out b/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out index bc4c60690..2c7067791 100644 --- a/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out +++ b/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out @@ -1,40 +1,100 @@ -TCL: TOTAL FORCE: ( 1.384807019055856e-9 3.878058707496024e-10 9.441096737727861e-9 ) -TCL: TOTAL TORQUE: ( 9.617198148959005e-9 -6.671102603661438e-8 1.3296069245605224e-9 ) -TCL: TOTAL FORCE: ( 1.3845898871878148e-9 3.876407805858406e-10 9.440526915760472e-9 ) -TCL: TOTAL TORQUE: ( 9.58525481209449e-9 -6.669777796730614e-8 1.3328811387935957e-9 ) -TCL: TOTAL FORCE: ( 1.384747011501375e-9 3.876299281557749e-10 9.440897230650336e-9 ) -TCL: TOTAL TORQUE: ( 9.551191837431361e-9 -6.668942509335807e-8 1.3372550289325602e-9 ) -TCL: TOTAL FORCE: ( 1.3847027136026924e-9 3.8810379909826054e-10 9.441948223276597e-9 ) -TCL: TOTAL TORQUE: ( 9.519129040569396e-9 -6.668528440556543e-8 1.3450211500121156e-9 ) -TCL: TOTAL FORCE: ( 1.3846692126229243e-9 3.8859587769835e-10 9.44301592475938e-9 ) -TCL: TOTAL TORQUE: ( 9.487008512110151e-9 -6.668641860940738e-8 1.3531361586771595e-9 ) -TCL: TOTAL FORCE: ( 1.3843895196874456e-9 3.892627331580911e-10 9.443209769699479e-9 ) -TCL: TOTAL TORQUE: ( 9.455814797831863e-9 -6.668312035884583e-8 1.3625308659115376e-9 ) -TCL: TOTAL FORCE: ( 1.3839312196228803e-9 3.896173383921564e-10 9.442643722490374e-9 ) -TCL: TOTAL TORQUE: ( 9.423963831522997e-9 -6.66716588604288e-8 1.3697779022159295e-9 ) -TCL: TOTAL FORCE: ( 1.3834813572533022e-9 3.8981154415473895e-10 9.441210035987524e-9 ) -TCL: TOTAL TORQUE: ( 9.39311961545286e-9 -6.665373897263294e-8 1.375589642194086e-9 ) -TCL: TOTAL FORCE: ( 1.383253483977498e-9 3.8989927952925996e-10 9.43917471962763e-9 ) -TCL: TOTAL TORQUE: ( 9.36619892755175e-9 -6.663279394913957e-8 1.3798079900873006e-9 ) -TCL: TOTAL FORCE: ( 1.383288567025076e-9 3.903983525344046e-10 9.43607558756554e-9 ) -TCL: TOTAL TORQUE: ( 9.336882378363498e-9 -6.660509610512122e-8 1.3869025372592603e-9 ) -TCL: TOTAL FORCE: ( 1.3836645162967898e-9 3.910716472876885e-10 9.431551373229041e-9 ) -TCL: TOTAL TORQUE: ( 9.307735915342619e-9 -6.656929452120153e-8 1.3947462074170858e-9 ) -TCL: TOTAL FORCE: ( 1.383956810263598e-9 3.916388602309695e-10 9.426974978410385e-9 ) -TCL: TOTAL TORQUE: ( 9.281833523999694e-9 -6.653200479433963e-8 1.4013895599518378e-9 ) -TCL: TOTAL FORCE: ( 1.3839795143244515e-9 3.9211683899864624e-10 9.422767954792022e-9 ) -TCL: TOTAL TORQUE: ( 9.256830413306716e-9 -6.64963777374794e-8 1.4075592358331335e-9 ) -TCL: TOTAL FORCE: ( 1.3838287182821318e-9 3.9261055517769705e-10 9.417791990706803e-9 ) -TCL: TOTAL TORQUE: ( 9.234642384114977e-9 -6.64554629103975e-8 1.4134880488292367e-9 ) -TCL: TOTAL FORCE: ( 1.3835778911452934e-9 3.927678460247108e-10 9.412744972348008e-9 ) -TCL: TOTAL TORQUE: ( 9.216622132157681e-9 -6.640994820727997e-8 1.4163497041863593e-9 ) -TCL: TOTAL FORCE: ( 1.3833555689846122e-9 3.9301065180019634e-10 9.407115364457042e-9 ) -TCL: TOTAL TORQUE: ( 9.198239947494358e-9 -6.635960181355927e-8 1.4197321096531823e-9 ) -TCL: TOTAL FORCE: ( 1.3832198719754274e-9 3.9355749215097546e-10 9.401293632471663e-9 ) -TCL: TOTAL TORQUE: ( 9.17791531662715e-9 -6.630868121249023e-8 1.425466855664581e-9 ) -TCL: TOTAL FORCE: ( 1.3833443557320635e-9 3.940626436271799e-10 9.394919009420022e-9 ) -TCL: TOTAL TORQUE: ( 9.155735281041189e-9 -6.625382553693271e-8 1.4308377815908102e-9 ) -TCL: TOTAL FORCE: ( 1.383406056376657e-9 3.941313664324042e-10 9.38953176321533e-9 ) -TCL: TOTAL TORQUE: ( 9.135093126388938e-9 -6.620808390422894e-8 1.4332044995235549e-9 ) -TCL: TOTAL FORCE: ( 1.3834732248696469e-9 3.936540260429666e-10 9.384015065005968e-9 ) -TCL: TOTAL TORQUE: ( 9.11666298009095e-9 -6.615982339752691e-8 1.4313049634395725e-9 ) +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013848072 0.0000000003878053 0.0000000094410965 } +TCL: TOTAL TORQUE: { 0.0000000096171986 -0.0000000667110256 0.0000000013296057 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013845900 0.0000000003876409 0.0000000094405268 } +TCL: TOTAL TORQUE: { 0.0000000095852526 -0.0000000666977762 0.0000000013328793 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013847470 0.0000000003876303 0.0000000094408976 } +TCL: TOTAL TORQUE: { 0.0000000095511905 -0.0000000666894295 0.0000000013372524 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013847025 0.0000000003881038 0.0000000094419481 } +TCL: TOTAL TORQUE: { 0.0000000095191286 -0.0000000666852835 0.0000000013450220 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013846686 0.0000000003885957 0.0000000094430159 } +TCL: TOTAL TORQUE: { 0.0000000094870103 -0.0000000666864186 0.0000000013531377 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013843890 0.0000000003892623 0.0000000094432095 } +TCL: TOTAL TORQUE: { 0.0000000094558161 -0.0000000666831221 0.0000000013625325 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013839316 0.0000000003896171 0.0000000094426439 } +TCL: TOTAL TORQUE: { 0.0000000094239665 -0.0000000666716580 0.0000000013697786 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013834814 0.0000000003898117 0.0000000094412102 } +TCL: TOTAL TORQUE: { 0.0000000093931183 -0.0000000666537403 0.0000000013755888 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013832539 0.0000000003898992 0.0000000094391743 } +TCL: TOTAL TORQUE: { 0.0000000093661994 -0.0000000666327935 0.0000000013798055 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013832885 0.0000000003903983 0.0000000094360750 } +TCL: TOTAL TORQUE: { 0.0000000093368824 -0.0000000666050974 0.0000000013869035 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013836644 0.0000000003910720 0.0000000094315508 } +TCL: TOTAL TORQUE: { 0.0000000093077337 -0.0000000665692967 0.0000000013947463 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013839568 0.0000000003916391 0.0000000094269754 } +TCL: TOTAL TORQUE: { 0.0000000092818309 -0.0000000665320030 0.0000000014013880 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013839793 0.0000000003921171 0.0000000094227682 } +TCL: TOTAL TORQUE: { 0.0000000092568291 -0.0000000664963768 0.0000000014075589 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013838283 0.0000000003926106 0.0000000094177920 } +TCL: TOTAL TORQUE: { 0.0000000092346419 -0.0000000664554638 0.0000000014134884 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013835781 0.0000000003927679 0.0000000094127447 } +TCL: TOTAL TORQUE: { 0.0000000092166221 -0.0000000664099504 0.0000000014163500 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013833556 0.0000000003930108 0.0000000094071154 } +TCL: TOTAL TORQUE: { 0.0000000091982395 -0.0000000663596005 0.0000000014197321 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013832197 0.0000000003935579 0.0000000094012935 } +TCL: TOTAL TORQUE: { 0.0000000091779127 -0.0000000663086817 0.0000000014254637 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013833440 0.0000000003940628 0.0000000093949191 } +TCL: TOTAL TORQUE: { 0.0000000091557357 -0.0000000662538246 0.0000000014308384 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013834062 0.0000000003941312 0.0000000093895322 } +TCL: TOTAL TORQUE: { 0.0000000091350936 -0.0000000662080812 0.0000000014332043 } +TCL: NUM. ATOMS REQUESTED: 6 +TCL: NUM. ATOMS USED: 6 +TCL: NUM. ATOM GROUPS USED: 0 +TCL: TOTAL FORCE: { 0.0000000013834729 0.0000000003936539 0.0000000093840155 } +TCL: TOTAL TORQUE: { 0.0000000091166648 -0.0000000661598230 0.0000000014313052 } diff --git a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out index c84bb7e88..90737e554 100644 --- a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out +++ b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "r" @@ -25,25 +27,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 5 atoms requested: total mass = 60.055, total charge = 0.35. @@ -64,7 +66,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -92,6 +94,7 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "r" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -102,13 +105,29 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (6 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "r":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (6 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "r":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: The final output state file will be "test.colvars.state". colvars: Debugging gradients for cvc rmsd0001 @@ -132,11 +151,11 @@ colvars: dx(interp) = -1.35149604087641e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.75153e-07 colvars: refPosGroup atom 0, component 0: colvars: dx(actual) = -1.32256818830001e-08 -colvars: dx(interp) = -1.32256806784027e-08 +colvars: dx(interp) = -1.32256806784028e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.10802e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.65148816633609e-09 -colvars: dx(interp) = 5.65148916474418e-09 +colvars: dx(interp) = 5.65148916474421e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.76663e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70015094119935e-08 @@ -164,7 +183,7 @@ colvars: dx(interp) = 1.64047652855846e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.00693e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44798905777589e-09 -colvars: dx(interp) = 9.44799082028361e-09 +colvars: dx(interp) = 9.44799082028362e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.86548e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.49833905283003e-08 @@ -190,7 +209,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02938776286510e-08 colvars: dx(interp) = 3.02938806702505e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.00403e-07. -colvars: Gradient sum: ( 0.973323 , -0.185412 , -0.13515 ) Fit gradient sum: ( -0.973323 , 0.185412 , 0.13515 ) Total ( -1.11022e-16 , -5.55112e-17 , -2.22045e-16 ) +colvars: Gradient sum: ( 0.973323 , -0.185412 , -0.13515 ) Fit gradient sum: ( -0.973323 , 0.185412 , 0.13515 ) Total ( -3.33067e-16 , 3.05311e-16 , 5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234785 , 0.269301 , -0.173026 ) @@ -232,7 +251,7 @@ colvars: dx(interp) = 8.53838213116278e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.71227e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.15095546613520e-10 -colvars: dx(interp) = 8.15096690566021e-10 +colvars: dx(interp) = 8.15096690566031e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.40346e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26069001693941e-08 @@ -252,11 +271,11 @@ colvars: dx(interp) = -1.49873663013446e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.94117e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.07673869820246e-09 -colvars: dx(interp) = 1.07674116921777e-09 +colvars: dx(interp) = 1.07674116921778e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.29491e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.95859750219097e-09 -colvars: dx(interp) = 9.95860073923379e-09 +colvars: dx(interp) = 9.95860073923380e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.25050e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43292595566891e-08 @@ -270,7 +289,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02918081729331e-08 colvars: dx(interp) = 3.02918110782712e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.59117e-08. -colvars: Gradient sum: ( 0.973303 , -0.185528 , -0.135131 ) Fit gradient sum: ( -0.973303 , 0.185528 , 0.135131 ) Total ( 1.11022e-16 , -1.11022e-16 , 2.77556e-17 ) +colvars: Gradient sum: ( 0.973303 , -0.185528 , -0.135131 ) Fit gradient sum: ( -0.973303 , 0.185528 , 0.135131 ) Total ( 0 , -2.22045e-16 , 1.94289e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234756 , 0.269374 , -0.172978 ) @@ -312,7 +331,7 @@ colvars: dx(interp) = 8.53613239284918e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.92870e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.18408452119002e-10 -colvars: dx(interp) = 8.18402186831449e-10 +colvars: dx(interp) = 8.18402186831441e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.65545e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26106322951136e-08 @@ -324,7 +343,7 @@ colvars: dx(interp) = 1.64127071165021e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.64922e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44612565945135e-09 -colvars: dx(interp) = 9.44611973805956e-09 +colvars: dx(interp) = 9.44611973805957e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.26859e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.49949652694659e-08 @@ -332,7 +351,7 @@ colvars: dx(interp) = -1.49949667603800e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.94276e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.08642161933403e-09 -colvars: dx(interp) = 1.08642112294384e-09 +colvars: dx(interp) = 1.08642112294382e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.56904e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.95594184871607e-09 @@ -340,7 +359,7 @@ colvars: dx(interp) = 9.95594165715356e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.92410e-08. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43341960523458e-08 -colvars: dx(interp) = 1.43341893744115e-08 +colvars: dx(interp) = 1.43341893744116e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.65874e-07. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.30965638334146e-08 @@ -350,7 +369,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02961637999033e-08 colvars: dx(interp) = 3.02961588118116e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.64644e-07. -colvars: Gradient sum: ( 0.973277 , -0.185665 , -0.135133 ) Fit gradient sum: ( -0.973277 , 0.185665 , 0.135133 ) Total ( 0 , 2.77556e-16 , -5.55112e-17 ) +colvars: Gradient sum: ( 0.973277 , -0.185665 , -0.135133 ) Fit gradient sum: ( -0.973277 , 0.185665 , 0.135133 ) Total ( 0 , -2.77556e-17 , -1.66533e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234717 , 0.269457 , -0.172922 ) @@ -372,11 +391,11 @@ colvars: dx(interp) = -1.35095571144321e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.93919e-08 colvars: refPosGroup atom 0, component 0: colvars: dx(actual) = -1.32276785080876e-08 -colvars: dx(interp) = -1.32276807821042e-08 +colvars: dx(interp) = -1.32276807821041e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.71914e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.61136204169088e-09 -colvars: dx(interp) = 5.61135643011219e-09 +colvars: dx(interp) = 5.61135643011218e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.00004e-06. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70074335620529e-08 @@ -384,19 +403,19 @@ colvars: dx(interp) = -3.70074373671765e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.02821e-07. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.08169099128008e-08 -colvars: dx(interp) = -3.08169108969144e-08 +colvars: dx(interp) = -3.08169108969143e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.19342e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53347614793165e-09 -colvars: dx(interp) = 8.53347204237836e-09 +colvars: dx(interp) = 8.53347204237835e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.81111e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.19884604652543e-10 -colvars: dx(interp) = 8.19880913108477e-10 +colvars: dx(interp) = 8.19880913108474e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.50252e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26149719348723e-08 -colvars: dx(interp) = -5.26149677696461e-08 +colvars: dx(interp) = -5.26149677696460e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.91643e-08. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64202287322723e-08 @@ -404,7 +423,7 @@ colvars: dx(interp) = 1.64202293878008e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.99220e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44173628170120e-09 -colvars: dx(interp) = 9.44173782371807e-09 +colvars: dx(interp) = 9.44173782371806e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.63319e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50037209323273e-08 @@ -430,7 +449,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03022300585098e-08 colvars: dx(interp) = 3.03022309014118e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.78165e-08. -colvars: Gradient sum: ( 0.973258 , -0.185792 , -0.135096 ) Fit gradient sum: ( -0.973258 , 0.185792 , 0.135096 ) Total ( -2.22045e-16 , -2.77556e-17 , 0 ) +colvars: Gradient sum: ( 0.973258 , -0.185792 , -0.135096 ) Fit gradient sum: ( -0.973258 , 0.185792 , 0.135096 ) Total ( 0 , -1.38778e-16 , -5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234673 , 0.269532 , -0.172868 ) @@ -460,11 +479,11 @@ colvars: dx(interp) = 5.59468663743374e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.84774e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70104338287547e-08 -colvars: dx(interp) = -3.70104348510151e-08 +colvars: dx(interp) = -3.70104348510150e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.76209e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.08071026466905e-08 -colvars: dx(interp) = -3.08070979989616e-08 +colvars: dx(interp) = -3.08070979989617e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.50865e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53082937624094e-09 @@ -472,11 +491,11 @@ colvars: dx(interp) = 8.53082896971171e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.76541e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.21989587507232e-10 -colvars: dx(interp) = 8.21992304895594e-10 +colvars: dx(interp) = 8.21992304895591e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.30587e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26181160864780e-08 -colvars: dx(interp) = -5.26181139628722e-08 +colvars: dx(interp) = -5.26181139628721e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.03588e-08. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64276485747905e-08 @@ -484,7 +503,7 @@ colvars: dx(interp) = 1.64276457374503e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.72717e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43767197725265e-09 -colvars: dx(interp) = 9.43767316290167e-09 +colvars: dx(interp) = 9.43767316290166e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.25629e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50121302056050e-08 @@ -492,11 +511,11 @@ colvars: dx(interp) = -1.50121288821272e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.81606e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.10627063065749e-09 -colvars: dx(interp) = 1.10626880712028e-09 +colvars: dx(interp) = 1.10626880712029e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.64836e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94974769241708e-09 -colvars: dx(interp) = 9.94974605686308e-09 +colvars: dx(interp) = 9.94974605686307e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.64381e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43403262597985e-08 @@ -510,7 +529,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03069658258437e-08 colvars: dx(interp) = 3.03069655364643e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.54828e-09. -colvars: Gradient sum: ( 0.973239 , -0.185915 , -0.135059 ) Fit gradient sum: ( -0.973239 , 0.185915 , 0.135059 ) Total ( -2.22045e-16 , 2.77556e-17 , -1.11022e-16 ) +colvars: Gradient sum: ( 0.973239 , -0.185915 , -0.135059 ) Fit gradient sum: ( -0.973239 , 0.185915 , 0.135059 ) Total ( 0 , 2.22045e-16 , -1.38778e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234607 , 0.269564 , -0.172831 ) @@ -536,7 +555,7 @@ colvars: dx(interp) = -1.32278620619718e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.45370e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.58072343892491e-09 -colvars: dx(interp) = 5.58072846304627e-09 +colvars: dx(interp) = 5.58072846304628e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.00263e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70086290502059e-08 @@ -548,11 +567,11 @@ colvars: dx(interp) = -3.07984711538700e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.33569e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.52902282133527e-09 -colvars: dx(interp) = 8.52902381842601e-09 +colvars: dx(interp) = 8.52902381842602e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.16906e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.21517076587952e-10 -colvars: dx(interp) = 8.21520935813319e-10 +colvars: dx(interp) = 8.21520935813326e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.69768e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26158636660057e-08 @@ -564,7 +583,7 @@ colvars: dx(interp) = 1.64322611396739e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.85733e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43348865689586e-09 -colvars: dx(interp) = 9.43349355322966e-09 +colvars: dx(interp) = 9.43349355322967e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.19037e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50185890390730e-08 @@ -572,7 +591,7 @@ colvars: dx(interp) = -1.50185908462051e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.20326e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.11479359077293e-09 -colvars: dx(interp) = 1.11479734212100e-09 +colvars: dx(interp) = 1.11479734212101e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.36506e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94741355953010e-09 @@ -590,7 +609,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03068983242838e-08 colvars: dx(interp) = 3.03068956667397e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.76878e-08. -colvars: Gradient sum: ( 0.973222 , -0.186041 , -0.135007 ) Fit gradient sum: ( -0.973222 , 0.186041 , 0.135007 ) Total ( -1.11022e-16 , -2.498e-16 , 0 ) +colvars: Gradient sum: ( 0.973222 , -0.186041 , -0.135007 ) Fit gradient sum: ( -0.973222 , 0.186041 , 0.135007 ) Total ( -1.11022e-16 , 1.66533e-16 , 1.11022e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234537 , 0.269561 , -0.17281 ) @@ -628,11 +647,11 @@ colvars: dx(interp) = -3.07916615664810e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.56497e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.52869419531999e-09 -colvars: dx(interp) = 8.52868892238299e-09 +colvars: dx(interp) = 8.52868892238300e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.18258e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.19877499225186e-10 -colvars: dx(interp) = 8.19875243528287e-10 +colvars: dx(interp) = 8.19875243528284e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.75126e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26105150555622e-08 @@ -664,13 +683,13 @@ colvars: dx(interp) = 1.43339758956300e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.78098e-09. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.30378747797977e-08 -colvars: dx(interp) = -1.30378745728902e-08 +colvars: dx(interp) = -1.30378745728901e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.58697e-08. colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03053191430536e-08 colvars: dx(interp) = 3.03053173599431e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.88382e-08. -colvars: Gradient sum: ( 0.973204 , -0.186178 , -0.134953 ) Fit gradient sum: ( -0.973204 , 0.186178 , 0.134953 ) Total ( 3.33067e-16 , -1.66533e-16 , -1.94289e-16 ) +colvars: Gradient sum: ( 0.973204 , -0.186178 , -0.134953 ) Fit gradient sum: ( -0.973204 , 0.186178 , 0.134953 ) Total ( 0 , 0 , -4.16334e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234465 , 0.26953 , -0.172803 ) @@ -708,11 +727,11 @@ colvars: dx(interp) = -3.07862418575286e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.39617e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.52950954310927e-09 -colvars: dx(interp) = 8.52950262791877e-09 +colvars: dx(interp) = 8.52950262791878e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.10737e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.18326739704389e-10 -colvars: dx(interp) = 8.18323711303201e-10 +colvars: dx(interp) = 8.18323711303208e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.70072e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26022727598274e-08 @@ -724,7 +743,7 @@ colvars: dx(interp) = 1.64395237187071e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.28199e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.42581479534965e-09 -colvars: dx(interp) = 9.42581605591192e-09 +colvars: dx(interp) = 9.42581605591191e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.33735e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50253089969965e-08 @@ -732,7 +751,7 @@ colvars: dx(interp) = -1.50253124431236e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.29355e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.12816245234626e-09 -colvars: dx(interp) = 1.12815789618418e-09 +colvars: dx(interp) = 1.12815789618417e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.03857e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94434401491162e-09 @@ -750,7 +769,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03002405388497e-08 colvars: dx(interp) = 3.03002411548953e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.03314e-08. -colvars: Gradient sum: ( 0.973182 , -0.186322 , -0.134914 ) Fit gradient sum: ( -0.973182 , 0.186322 , 0.134914 ) Total ( -3.33067e-16 , 1.38778e-16 , -8.32667e-17 ) +colvars: Gradient sum: ( 0.973182 , -0.186322 , -0.134914 ) Fit gradient sum: ( -0.973182 , 0.186322 , 0.134914 ) Total ( -2.22045e-16 , 8.32667e-17 , 0 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.2344 , 0.269471 , -0.172812 ) @@ -776,7 +795,7 @@ colvars: dx(interp) = -1.32356119387801e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.51720e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.55776402677566e-09 -colvars: dx(interp) = 5.55776415678251e-09 +colvars: dx(interp) = 5.55776415678252e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.33919e-08. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.69885455597796e-08 @@ -784,15 +803,15 @@ colvars: dx(interp) = -3.69885421692242e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.16650e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.07832497270510e-08 -colvars: dx(interp) = -3.07832430368367e-08 +colvars: dx(interp) = -3.07832430368368e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.17333e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53208881324008e-09 -colvars: dx(interp) = 8.53209051317431e-09 +colvars: dx(interp) = 8.53209051317432e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.99240e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.16180900642394e-10 -colvars: dx(interp) = 8.16182049051574e-10 +colvars: dx(interp) = 8.16182049051563e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.40705e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25918135707570e-08 @@ -808,7 +827,7 @@ colvars: dx(interp) = 9.42484522140630e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.10575e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50250638597527e-08 -colvars: dx(interp) = -1.50250574958698e-08 +colvars: dx(interp) = -1.50250574958697e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.23551e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.13177911487128e-09 @@ -816,11 +835,11 @@ colvars: dx(interp) = 1.13178194955547e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.50463e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94482007854458e-09 -colvars: dx(interp) = 9.94482275879586e-09 +colvars: dx(interp) = 9.94482275879587e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.69512e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43201948077376e-08 -colvars: dx(interp) = 1.43202002666371e-08 +colvars: dx(interp) = 1.43202002666372e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.81203e-07. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.30169226508769e-08 @@ -830,7 +849,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02934708429348e-08 colvars: dx(interp) = 3.02934722035031e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.49129e-08. -colvars: Gradient sum: ( 0.973155 , -0.186464 , -0.134908 ) Fit gradient sum: ( -0.973155 , 0.186464 , 0.134908 ) Total ( 3.33067e-16 , 0 , -5.55112e-17 ) +colvars: Gradient sum: ( 0.973155 , -0.186464 , -0.134908 ) Fit gradient sum: ( -0.973155 , 0.186464 , 0.134908 ) Total ( -1.11022e-16 , 1.11022e-16 , 2.77556e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234296 , 0.269417 , -0.172808 ) @@ -856,7 +875,7 @@ colvars: dx(interp) = -1.32422526736177e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.36098e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.55336931995498e-09 -colvars: dx(interp) = 5.55337024450271e-09 +colvars: dx(interp) = 5.55337024450270e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.66484e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.69760897456217e-08 @@ -868,11 +887,11 @@ colvars: dx(interp) = -3.07767415223223e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.03519e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53379233944906e-09 -colvars: dx(interp) = 8.53379552462335e-09 +colvars: dx(interp) = 8.53379552462336e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.73243e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.17991008261743e-10 -colvars: dx(interp) = 8.17993039794562e-10 +colvars: dx(interp) = 8.17993039794563e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.48356e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25781533866621e-08 @@ -884,7 +903,7 @@ colvars: dx(interp) = 1.64451465632283e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.31202e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.42628552991209e-09 -colvars: dx(interp) = 9.42628948602319e-09 +colvars: dx(interp) = 9.42628948602318e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.19689e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50267567278206e-08 @@ -892,11 +911,11 @@ colvars: dx(interp) = -1.50267515866314e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.42136e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.13714904159679e-09 -colvars: dx(interp) = 1.13714937112552e-09 +colvars: dx(interp) = 1.13714937112551e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.89785e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94296200929057e-09 -colvars: dx(interp) = 9.94296464169270e-09 +colvars: dx(interp) = 9.94296464169271e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.64750e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43117819817462e-08 @@ -910,7 +929,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02822567022076e-08 colvars: dx(interp) = 3.02822597447637e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.00473e-07. -colvars: Gradient sum: ( 0.973121 , -0.186623 , -0.134934 ) Fit gradient sum: ( -0.973121 , 0.186623 , 0.134934 ) Total ( -1.11022e-16 , 1.11022e-16 , -3.88578e-16 ) +colvars: Gradient sum: ( 0.973121 , -0.186623 , -0.134934 ) Fit gradient sum: ( -0.973121 , 0.186623 , 0.134934 ) Total ( -2.22045e-16 , 1.11022e-16 , -8.32667e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234174 , 0.269337 , -0.172813 ) @@ -944,15 +963,15 @@ colvars: dx(interp) = -3.69593977936285e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.28040e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.07704990376578e-08 -colvars: dx(interp) = -3.07704988193406e-08 +colvars: dx(interp) = -3.07704988193405e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.09502e-09. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53549586565805e-09 -colvars: dx(interp) = 8.53549862619539e-09 +colvars: dx(interp) = 8.53549862619538e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.23419e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.20783441213280e-10 -colvars: dx(interp) = 8.20780197348790e-10 +colvars: dx(interp) = 8.20780197348801e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.95216e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25603880419112e-08 @@ -964,7 +983,7 @@ colvars: dx(interp) = 1.64463866462574e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.80441e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43124334185086e-09 -colvars: dx(interp) = 9.43124625857664e-09 +colvars: dx(interp) = 9.43124625857663e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.09262e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50269396925751e-08 @@ -976,7 +995,7 @@ colvars: dx(interp) = 1.14190518785238e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.20873e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94215909599916e-09 -colvars: dx(interp) = 9.94215964550207e-09 +colvars: dx(interp) = 9.94215964550208e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.52700e-08. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43026106513844e-08 @@ -990,7 +1009,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02664240336981e-08 colvars: dx(interp) = 3.02664253559446e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.36869e-08. -colvars: Gradient sum: ( 0.973081 , -0.186777 , -0.135012 ) Fit gradient sum: ( -0.973081 , 0.186777 , 0.135012 ) Total ( 0 , 2.77556e-16 , -2.22045e-16 ) +colvars: Gradient sum: ( 0.973081 , -0.186777 , -0.135012 ) Fit gradient sum: ( -0.973081 , 0.186777 , 0.135012 ) Total ( 1.11022e-16 , 8.32667e-17 , 2.498e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234049 , 0.269251 , -0.172818 ) @@ -1016,7 +1035,7 @@ colvars: dx(interp) = -1.32624504625399e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.50484e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.54771517613517e-09 -colvars: dx(interp) = 5.54771226834333e-09 +colvars: dx(interp) = 5.54771226834331e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.24142e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.69424064672330e-08 @@ -1028,11 +1047,11 @@ colvars: dx(interp) = -3.07644895154988e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.47710e-09. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53744630546771e-09 -colvars: dx(interp) = 8.53744794265350e-09 +colvars: dx(interp) = 8.53744794265352e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.91765e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.23895618395909e-10 -colvars: dx(interp) = 8.23894751207838e-10 +colvars: dx(interp) = 8.23894751207842e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.05255e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25424947994679e-08 @@ -1044,7 +1063,7 @@ colvars: dx(interp) = 1.64481466417069e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.82325e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43529698815837e-09 -colvars: dx(interp) = 9.43529750666334e-09 +colvars: dx(interp) = 9.43529750666335e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.49538e-08. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50270977883338e-08 @@ -1056,7 +1075,7 @@ colvars: dx(interp) = 1.14616428729916e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.44466e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94072202331608e-09 -colvars: dx(interp) = 9.94071820020491e-09 +colvars: dx(interp) = 9.94071820020490e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.84591e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42922811363633e-08 @@ -1070,7 +1089,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02509981509047e-08 colvars: dx(interp) = 3.02509964189633e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.72524e-08. -colvars: Gradient sum: ( 0.973043 , -0.186923 , -0.135085 ) Fit gradient sum: ( -0.973043 , 0.186923 , 0.135085 ) Total ( 1.11022e-16 , 2.22045e-16 , 2.77556e-16 ) +colvars: Gradient sum: ( 0.973043 , -0.186923 , -0.135085 ) Fit gradient sum: ( -0.973043 , 0.186923 , 0.135085 ) Total ( -1.11022e-16 , 5.55112e-17 , 5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233924 , 0.269169 , -0.17282 ) @@ -1108,11 +1127,11 @@ colvars: dx(interp) = -3.07585788706113e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.46834e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53809289935725e-09 -colvars: dx(interp) = 8.53808936876944e-09 +colvars: dx(interp) = 8.53808936876943e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.13510e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.26105406304123e-10 -colvars: dx(interp) = 8.26104904082126e-10 +colvars: dx(interp) = 8.26104904082130e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.07939e-07. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25262713324537e-08 @@ -1124,7 +1143,7 @@ colvars: dx(interp) = 1.64489014094928e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.75055e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43667011199523e-09 -colvars: dx(interp) = 9.43666776859372e-09 +colvars: dx(interp) = 9.43666776859373e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.48329e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50279149124799e-08 @@ -1132,7 +1151,7 @@ colvars: dx(interp) = -1.50279164684174e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.03536e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.15079323848022e-09 -colvars: dx(interp) = 1.15079570362508e-09 +colvars: dx(interp) = 1.15079570362507e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.14213e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.93875737265171e-09 @@ -1150,7 +1169,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02379525862762e-08 colvars: dx(interp) = 3.02379521612961e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.40545e-08. -colvars: Gradient sum: ( 0.973014 , -0.187041 , -0.135129 ) Fit gradient sum: ( -0.973014 , 0.187041 , 0.135129 ) Total ( 0 , 8.32667e-17 , 1.11022e-16 ) +colvars: Gradient sum: ( 0.973014 , -0.187041 , -0.135129 ) Fit gradient sum: ( -0.973014 , 0.187041 , 0.135129 ) Total ( 1.11022e-16 , -1.11022e-16 , 0 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233783 , 0.269072 , -0.172824 ) @@ -1192,7 +1211,7 @@ colvars: dx(interp) = 8.53851757305771e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.45711e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.28652702011823e-10 -colvars: dx(interp) = 8.28651094684908e-10 +colvars: dx(interp) = 8.28651094684910e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.93969e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25080263713562e-08 @@ -1200,7 +1219,7 @@ colvars: dx(interp) = -5.25080262626950e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.06942e-09. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64482276687750e-08 -colvars: dx(interp) = 1.64482285289396e-08 +colvars: dx(interp) = 1.64482285289397e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.22953e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43820843701815e-09 @@ -1224,13 +1243,13 @@ colvars: dx(interp) = 1.42696604177533e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.65875e-07. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.29644650570526e-08 -colvars: dx(interp) = -1.29644631624476e-08 +colvars: dx(interp) = -1.29644631624477e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.46138e-07. colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02220222181404e-08 colvars: dx(interp) = 3.02220270034202e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.58338e-07. -colvars: Gradient sum: ( 0.972987 , -0.187152 , -0.135166 ) Fit gradient sum: ( -0.972987 , 0.187152 , 0.135166 ) Total ( -2.22045e-16 , 5.55112e-17 , -2.498e-16 ) +colvars: Gradient sum: ( 0.972987 , -0.187152 , -0.135166 ) Fit gradient sum: ( -0.972987 , 0.187152 , 0.135166 ) Total ( -1.11022e-16 , 5.55112e-17 , -8.32667e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233652 , 0.268975 , -0.172829 ) @@ -1256,7 +1275,7 @@ colvars: dx(interp) = -1.32848260553267e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.79536e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.53572121475554e-09 -colvars: dx(interp) = 5.53571877378613e-09 +colvars: dx(interp) = 5.53571877378612e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.40949e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68913646298097e-08 @@ -1268,11 +1287,11 @@ colvars: dx(interp) = -3.07470135653119e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.93636e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53970405501059e-09 -colvars: dx(interp) = 8.53970370599939e-09 +colvars: dx(interp) = 8.53970370599940e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.08692e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.31423818681287e-10 -colvars: dx(interp) = 8.31424273287319e-10 +colvars: dx(interp) = 8.31424273287314e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.46780e-07. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24915630961686e-08 @@ -1284,7 +1303,7 @@ colvars: dx(interp) = 1.64490443312681e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.36057e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43796862884483e-09 -colvars: dx(interp) = 9.43796707135716e-09 +colvars: dx(interp) = 9.43796707135715e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.65024e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50295562661995e-08 @@ -1296,7 +1315,7 @@ colvars: dx(interp) = 1.15783892166374e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.03950e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.93288296058381e-09 -colvars: dx(interp) = 9.93288148106965e-09 +colvars: dx(interp) = 9.93288148106967e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.48951e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42566420890944e-08 @@ -1310,7 +1329,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02093123849545e-08 colvars: dx(interp) = 3.02093113112382e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.55426e-08. -colvars: Gradient sum: ( 0.972963 , -0.187251 , -0.135202 ) Fit gradient sum: ( -0.972963 , 0.187251 , 0.135202 ) Total ( 0 , -2.77556e-17 , -5.55112e-17 ) +colvars: Gradient sum: ( 0.972963 , -0.187251 , -0.135202 ) Fit gradient sum: ( -0.972963 , 0.187251 , 0.135202 ) Total ( 0 , 0 , 5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233501 , 0.268891 , -0.17282 ) @@ -1364,7 +1383,7 @@ colvars: dx(interp) = 1.64524625852538e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.02999e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43822975330022e-09 -colvars: dx(interp) = 9.43822725654555e-09 +colvars: dx(interp) = 9.43822725654554e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.64536e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50321763925376e-08 @@ -1381,7 +1400,7 @@ colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.12540e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42431844096791e-08 colvars: dx(interp) = 1.42431843748016e-08 -colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.44871e-09. +colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.44872e-09. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.29516273261743e-08 colvars: dx(interp) = -1.29516244952331e-08 @@ -1390,7 +1409,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01953040349190e-08 colvars: dx(interp) = 3.01953067756868e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.07680e-08. -colvars: Gradient sum: ( 0.972936 , -0.18736 , -0.135247 ) Fit gradient sum: ( -0.972936 , 0.18736 , 0.135247 ) Total ( -3.33067e-16 , 1.94289e-16 , 2.77556e-17 ) +colvars: Gradient sum: ( 0.972936 , -0.18736 , -0.135247 ) Fit gradient sum: ( -0.972936 , 0.18736 , 0.135247 ) Total ( -1.11022e-16 , 1.11022e-16 , -5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233334 , 0.268839 , -0.172792 ) @@ -1416,7 +1435,7 @@ colvars: dx(interp) = -1.32982975870102e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.68116e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.52796031172420e-09 -colvars: dx(interp) = 5.52796395730563e-09 +colvars: dx(interp) = 5.52796395730564e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.59480e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68559884833530e-08 @@ -1432,7 +1451,7 @@ colvars: dx(interp) = 8.54029141083031e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.23973e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.48276116016677e-10 -colvars: dx(interp) = 8.48275187664044e-10 +colvars: dx(interp) = 8.48275187664032e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.09440e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24580787697460e-08 @@ -1444,7 +1463,7 @@ colvars: dx(interp) = 1.64581994897726e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.86623e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44032407801387e-09 -colvars: dx(interp) = 9.44032745458434e-09 +colvars: dx(interp) = 9.44032745458435e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.57675e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50375996099683e-08 @@ -1452,7 +1471,7 @@ colvars: dx(interp) = -1.50376008458710e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.21875e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.16808074324126e-09 -colvars: dx(interp) = 1.16807984581744e-09 +colvars: dx(interp) = 1.16807984581743e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.68289e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.91784787629513e-09 @@ -1470,7 +1489,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01791249768257e-08 colvars: dx(interp) = 3.01791291797173e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.39265e-07. -colvars: Gradient sum: ( 0.972906 , -0.187482 , -0.135296 ) Fit gradient sum: ( -0.972906 , 0.187482 , 0.135296 ) Total ( -3.33067e-16 , 1.66533e-16 , -5.55112e-17 ) +colvars: Gradient sum: ( 0.972906 , -0.187482 , -0.135296 ) Fit gradient sum: ( -0.972906 , 0.187482 , 0.135296 ) Total ( -1.11022e-16 , -1.66533e-16 , 5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233163 , 0.26881 , -0.172755 ) @@ -1496,7 +1515,7 @@ colvars: dx(interp) = -1.33079579182108e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.61708e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.52538281795023e-09 -colvars: dx(interp) = 5.52538365273265e-09 +colvars: dx(interp) = 5.52538365273264e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.51081e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68380721482708e-08 @@ -1508,11 +1527,11 @@ colvars: dx(interp) = -3.07143629147814e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.96154e-09. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.54108606063164e-09 -colvars: dx(interp) = 8.54108462786949e-09 +colvars: dx(interp) = 8.54108462786948e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.67749e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.63986215904333e-10 -colvars: dx(interp) = 8.63984483685953e-10 +colvars: dx(interp) = 8.63984483685957e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.00491e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24407806068439e-08 @@ -1532,7 +1551,7 @@ colvars: dx(interp) = -1.50443213074023e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.15626e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.17551302025731e-09 -colvars: dx(interp) = 1.17551172995609e-09 +colvars: dx(interp) = 1.17551172995610e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.09765e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.90585391491550e-09 @@ -1550,7 +1569,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01599225593918e-08 colvars: dx(interp) = 3.01599231791652e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.05496e-08. -colvars: Gradient sum: ( 0.972861 , -0.187655 , -0.135377 ) Fit gradient sum: ( -0.972861 , 0.187655 , 0.135377 ) Total ( -4.44089e-16 , -2.77556e-17 , -8.32667e-17 ) +colvars: Gradient sum: ( 0.972861 , -0.187655 , -0.135377 ) Fit gradient sum: ( -0.972861 , 0.187655 , 0.135377 ) Total ( 0 , -1.66533e-16 , -2.22045e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233016 , 0.268793 , -0.172714 ) @@ -1584,7 +1603,7 @@ colvars: dx(interp) = -3.68237786462595e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.36274e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.07013916511778e-08 -colvars: dx(interp) = -3.07013933891593e-08 +colvars: dx(interp) = -3.07013933891594e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.66092e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.54437764985505e-09 @@ -1592,11 +1611,11 @@ colvars: dx(interp) = 8.54437233935429e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.21520e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.80977069073197e-10 -colvars: dx(interp) = 8.80974516357787e-10 +colvars: dx(interp) = 8.80974516357789e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.89760e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24269960777701e-08 -colvars: dx(interp) = -5.24269988263055e-08 +colvars: dx(interp) = -5.24269988263056e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.24260e-08. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64836180260863e-08 @@ -1604,7 +1623,7 @@ colvars: dx(interp) = 1.64836152925342e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.65834e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44961797699762e-09 -colvars: dx(interp) = 9.44961894491784e-09 +colvars: dx(interp) = 9.44961894491783e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.02430e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50513521646189e-08 @@ -1612,11 +1631,11 @@ colvars: dx(interp) = -1.50513524198364e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.69564e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.18215304212299e-09 -colvars: dx(interp) = 1.18215354891989e-09 +colvars: dx(interp) = 1.18215354891988e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.28707e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.89235360293605e-09 -colvars: dx(interp) = 9.89235145488878e-09 +colvars: dx(interp) = 9.89235145488877e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.17142e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42107428047211e-08 @@ -1630,7 +1649,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01451859030522e-08 colvars: dx(interp) = 3.01451822120947e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.22439e-07. -colvars: Gradient sum: ( 0.972812 , -0.187862 , -0.135443 ) Fit gradient sum: ( -0.972812 , 0.187862 , 0.135443 ) Total ( 0 , 8.32667e-17 , -2.77556e-17 ) +colvars: Gradient sum: ( 0.972812 , -0.187862 , -0.135443 ) Fit gradient sum: ( -0.972812 , 0.187862 , 0.135443 ) Total ( -3.33067e-16 , 2.22045e-16 , -3.88578e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.232895 , 0.268756 , -0.172689 ) @@ -1656,7 +1675,7 @@ colvars: dx(interp) = -1.33145349553423e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.89118e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.53619017296114e-09 -colvars: dx(interp) = 5.53619602088123e-09 +colvars: dx(interp) = 5.53619602088125e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.05631e-06. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68101620296102e-08 @@ -1684,7 +1703,7 @@ colvars: dx(interp) = 1.64991576726264e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.27652e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.45344957870020e-09 -colvars: dx(interp) = 9.45345422358397e-09 +colvars: dx(interp) = 9.45345422358396e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.91343e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50559547051898e-08 @@ -1692,7 +1711,7 @@ colvars: dx(interp) = -1.50559499577201e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.15322e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.18710907770492e-09 -colvars: dx(interp) = 1.18711101841254e-09 +colvars: dx(interp) = 1.18711101841253e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.63482e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.88098136645021e-09 @@ -1710,7 +1729,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01317442108484e-08 colvars: dx(interp) = 3.01317461182275e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.33013e-08. -colvars: Gradient sum: ( 0.972755 , -0.188099 , -0.135521 ) Fit gradient sum: ( -0.972755 , 0.188099 , 0.135521 ) Total ( -1.11022e-16 , -8.32667e-17 , 2.77556e-16 ) +colvars: Gradient sum: ( 0.972755 , -0.188099 , -0.135521 ) Fit gradient sum: ( -0.972755 , 0.188099 , 0.135521 ) Total ( 0 , 2.77556e-17 , 8.32667e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.232767 , 0.268736 , -0.172656 ) @@ -1736,7 +1755,7 @@ colvars: dx(interp) = -1.33169569565328e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.26978e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.54423351672995e-09 -colvars: dx(interp) = 5.54423349146829e-09 +colvars: dx(interp) = 5.54423349146830e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.55638e-09. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.67969441583682e-08 @@ -1744,15 +1763,15 @@ colvars: dx(interp) = -3.67969415711082e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.03118e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.06796579252477e-08 -colvars: dx(interp) = -3.06796542496761e-08 +colvars: dx(interp) = -3.06796542496762e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.19805e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.55582804604182e-09 -colvars: dx(interp) = 8.55583619604507e-09 +colvars: dx(interp) = 8.55583619604505e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.52567e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 9.12068642833219e-10 -colvars: dx(interp) = 9.12071277135838e-10 +colvars: dx(interp) = 9.12071277135839e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.88827e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.23999084123261e-08 @@ -1772,11 +1791,11 @@ colvars: dx(interp) = -1.50616518663852e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.10329e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.19267085096908e-09 -colvars: dx(interp) = 1.19267017999368e-09 +colvars: dx(interp) = 1.19267017999369e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.62582e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.86899095778426e-09 -colvars: dx(interp) = 9.86899596501446e-09 +colvars: dx(interp) = 9.86899596501447e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.07370e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.41884619608845e-08 @@ -1790,5 +1809,5 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01179419182063e-08 colvars: dx(interp) = 3.01179465384051e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.53404e-07. -colvars: Gradient sum: ( 0.972697 , -0.188344 , -0.135599 ) Fit gradient sum: ( -0.972697 , 0.188344 , 0.135599 ) Total ( 0 , -8.32667e-17 , -3.05311e-16 ) +colvars: Gradient sum: ( 0.972697 , -0.188344 , -0.135599 ) Fit gradient sum: ( -0.972697 , 0.188344 , 0.135599 ) Total ( -2.22045e-16 , 1.11022e-16 , -1.11022e-16 ) colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj index 92e7f7f59..0aee73595 100644 --- a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj +++ b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step r fa_r 0 1.42934254297405e+01 -1.42934254297405e+00 - 1 1.42933316010585e+01 -1.42933316010585e+00 - 2 1.42929135723286e+01 -1.42929135723286e+00 - 3 1.42923486101217e+01 -1.42923486101217e+00 - 4 1.42923026875859e+01 -1.42923026875859e+00 - 5 1.42924344310521e+01 -1.42924344310521e+00 - 6 1.42922522296184e+01 -1.42922522296184e+00 - 7 1.42921269629840e+01 -1.42921269629840e+00 - 8 1.42921521124096e+01 -1.42921521124096e+00 - 9 1.42925995746822e+01 -1.42925995746822e+00 - 10 1.42932888390452e+01 -1.42932888390452e+00 - 11 1.42938611783395e+01 -1.42938611783396e+00 - 12 1.42940308415572e+01 -1.42940308415572e+00 - 13 1.42939753495160e+01 -1.42939753495160e+00 - 14 1.42930019085598e+01 -1.42930019085598e+00 - 15 1.42917673901553e+01 -1.42917673901553e+00 - 16 1.42906595564010e+01 -1.42906595564010e+00 - 17 1.42898165380707e+01 -1.42898165380707e+00 - 18 1.42887881292130e+01 -1.42887881292130e+00 - 19 1.42873640416160e+01 -1.42873640416160e+00 - 20 1.42859393553985e+01 -1.42859393553985e+00 + 1 1.42933316010584e+01 -1.42933316010584e+00 + 2 1.42929135723284e+01 -1.42929135723284e+00 + 3 1.42923486101213e+01 -1.42923486101213e+00 + 4 1.42923026875853e+01 -1.42923026875853e+00 + 5 1.42924344310511e+01 -1.42924344310511e+00 + 6 1.42922522296169e+01 -1.42922522296169e+00 + 7 1.42921269629819e+01 -1.42921269629819e+00 + 8 1.42921521124067e+01 -1.42921521124067e+00 + 9 1.42925995746785e+01 -1.42925995746785e+00 + 10 1.42932888390403e+01 -1.42932888390403e+00 + 11 1.42938611783336e+01 -1.42938611783336e+00 + 12 1.42940308415500e+01 -1.42940308415500e+00 + 13 1.42939753495075e+01 -1.42939753495075e+00 + 14 1.42930019085500e+01 -1.42930019085500e+00 + 15 1.42917673901443e+01 -1.42917673901443e+00 + 16 1.42906595563889e+01 -1.42906595563889e+00 + 17 1.42898165380577e+01 -1.42898165380577e+00 + 18 1.42887881291995e+01 -1.42887881291995e+00 + 19 1.42873640416024e+01 -1.42873640416024e+00 + 20 1.42859393553853e+01 -1.42859393553853e+00 diff --git a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped index b42918a80..8c6776e10 100644 --- a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name angle - x 9.03916964164922e+01 + x 9.03916964165211e+01 } restraint { diff --git a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj index 5e9454d4b..b71ea85f2 100644 --- a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj +++ b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step angle fa_angle 0 8.94641033519923e+01 2.92663795777991e+00 - 1 8.94912729262462e+01 2.91909085382051e+00 - 2 8.95442152151567e+01 2.90438466245647e+00 - 3 8.96073749975041e+01 2.88684027847108e+00 - 4 8.96877844443377e+01 2.86450432101732e+00 - 5 8.97771650948268e+01 2.83967636254810e+00 - 6 8.98769301106680e+01 2.81196385814778e+00 - 7 8.99890383094529e+01 2.78082269181864e+00 - 8 9.01041412594477e+01 2.74884965015340e+00 - 9 9.02399071760696e+01 2.71113689553622e+00 - 10 9.03916964164922e+01 2.66897321764106e+00 + 1 8.94912729262455e+01 2.91909085382069e+00 + 2 8.95442152151541e+01 2.90438466245720e+00 + 3 8.96073749974988e+01 2.88684027847255e+00 + 4 8.96877844443296e+01 2.86450432101956e+00 + 5 8.97771650948167e+01 2.83967636255091e+00 + 6 8.98769301106577e+01 2.81196385815065e+00 + 7 8.99890383094453e+01 2.78082269182076e+00 + 8 9.01041412594469e+01 2.74884965015365e+00 + 9 9.02399071760806e+01 2.71113689553318e+00 + 10 9.03916964165211e+01 2.66897321763303e+00 diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out index 6bf9ea6a6..8b2c94159 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 0 colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,6 +119,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -125,15 +130,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped index f7587bf73..f96f926f7 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685416874363e+00 + x 3.21685416853788e+00 } restraint { diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj index 8aaf17fd1..450a1752e 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hp_one - 0 3.20554673468334e+00 -4.96887477549335e-02 1.92888410426048e-02 - 1 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 - 2 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 - 3 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 - 4 3.20472669830023e+00 -4.96756271728037e-02 1.92786557422765e-02 - 5 3.20472669830023e+00 0.00000000000000e+00 1.92786557422765e-02 - 6 3.20472669830023e+00 0.00000000000000e+00 1.92786557422765e-02 - 7 3.20472669830023e+00 0.00000000000000e+00 1.92786557422765e-02 - 8 3.21245897759072e+00 -4.97993436414515e-02 1.93748017743701e-02 - 9 3.21245897759072e+00 0.00000000000000e+00 1.93748017743701e-02 - 10 3.21245897759072e+00 0.00000000000000e+00 1.93748017743701e-02 - 11 3.21245897759072e+00 0.00000000000000e+00 1.93748017743701e-02 - 12 3.22129314152384e+00 -4.99406902643814e-02 1.94849417506475e-02 - 13 3.22129314152384e+00 0.00000000000000e+00 1.94849417506475e-02 - 14 3.22129314152384e+00 0.00000000000000e+00 1.94849417506475e-02 - 15 3.22129314152384e+00 0.00000000000000e+00 1.94849417506475e-02 - 16 3.22320461245070e+00 -4.99712737992112e-02 1.95088141024666e-02 - 17 3.22320461245070e+00 0.00000000000000e+00 1.95088141024666e-02 - 18 3.22320461245070e+00 0.00000000000000e+00 1.95088141024666e-02 - 19 3.22320461245070e+00 0.00000000000000e+00 1.95088141024666e-02 - 20 3.21685416874363e+00 -4.98696666998981e-02 1.94295598184291e-02 + 0 3.20554673468334e+00 -4.96887477549335e-02 1.92888410426048e-02 + 1 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 + 2 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 + 3 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 + 4 3.20472669829003e+00 -4.96756271726405e-02 1.92786557421498e-02 + 5 3.20472669829003e+00 0.00000000000000e+00 1.92786557421498e-02 + 6 3.20472669829003e+00 0.00000000000000e+00 1.92786557421498e-02 + 7 3.20472669829003e+00 0.00000000000000e+00 1.92786557421498e-02 + 8 3.21245897755043e+00 -4.97993436408069e-02 1.93748017738685e-02 + 9 3.21245897755043e+00 0.00000000000000e+00 1.93748017738685e-02 + 10 3.21245897755043e+00 0.00000000000000e+00 1.93748017738685e-02 + 11 3.21245897755043e+00 0.00000000000000e+00 1.93748017738685e-02 + 12 3.22129314143762e+00 -4.99406902630019e-02 1.94849417495711e-02 + 13 3.22129314143762e+00 0.00000000000000e+00 1.94849417495711e-02 + 14 3.22129314143762e+00 0.00000000000000e+00 1.94849417495711e-02 + 15 3.22129314143762e+00 0.00000000000000e+00 1.94849417495711e-02 + 16 3.22320461230820e+00 -4.99712737969313e-02 1.95088141006865e-02 + 17 3.22320461230820e+00 0.00000000000000e+00 1.95088141006865e-02 + 18 3.22320461230820e+00 0.00000000000000e+00 1.95088141006865e-02 + 19 3.22320461230820e+00 0.00000000000000e+00 1.95088141006865e-02 + 20 3.21685416853788e+00 -4.98696666966061e-02 1.94295598158639e-02 diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out index 6f4f440d6..ca317540a 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +91,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 0 colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,6 +119,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -125,20 +130,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "hp_one" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped index 566d795a4..c5c46002b 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397142195016e+00 + x 3.21397142146894e+00 } restraint { diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj index e5c68ffe3..25e47276b 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hp_one - 20 3.21685416874363e+00 -4.98696666998981e-02 1.94295598184291e-02 - 21 3.21685416874363e+00 0.00000000000000e+00 1.94295598184291e-02 - 22 3.21685416874363e+00 0.00000000000000e+00 1.94295598184291e-02 - 23 3.21685416874363e+00 0.00000000000000e+00 1.94295598184291e-02 - 24 3.20781524526346e+00 -4.97250439242154e-02 1.93170311973840e-02 - 25 3.20781524526346e+00 0.00000000000000e+00 1.93170311973840e-02 - 26 3.20781524526346e+00 0.00000000000000e+00 1.93170311973840e-02 - 27 3.20781524526346e+00 0.00000000000000e+00 1.93170311973840e-02 - 28 3.20267947278925e+00 -4.96428715646280e-02 1.92532398217355e-02 - 29 3.20267947278925e+00 0.00000000000000e+00 1.92532398217355e-02 - 30 3.20267947278925e+00 0.00000000000000e+00 1.92532398217355e-02 - 31 3.20267947278925e+00 0.00000000000000e+00 1.92532398217355e-02 - 32 3.20367252495752e+00 -4.96587603993203e-02 1.92655662843524e-02 - 33 3.20367252495752e+00 0.00000000000000e+00 1.92655662843524e-02 - 34 3.20367252495752e+00 0.00000000000000e+00 1.92655662843524e-02 - 35 3.20367252495752e+00 0.00000000000000e+00 1.92655662843524e-02 - 36 3.20851202070242e+00 -4.97361923312387e-02 1.93256939657028e-02 - 37 3.20851202070242e+00 0.00000000000000e+00 1.93256939657028e-02 - 38 3.20851202070242e+00 0.00000000000000e+00 1.93256939657028e-02 - 39 3.20851202070242e+00 0.00000000000000e+00 1.93256939657028e-02 - 40 3.21397142195016e+00 -4.98235427512026e-02 1.93936360334447e-02 + 20 3.21685416853788e+00 -4.98696666966061e-02 1.94295598158639e-02 + 21 3.21685416853788e+00 0.00000000000000e+00 1.94295598158639e-02 + 22 3.21685416853788e+00 0.00000000000000e+00 1.94295598158639e-02 + 23 3.21685416853788e+00 0.00000000000000e+00 1.94295598158639e-02 + 24 3.20781524498993e+00 -4.97250439198388e-02 1.93170311939836e-02 + 25 3.20781524498993e+00 0.00000000000000e+00 1.93170311939836e-02 + 26 3.20781524498993e+00 0.00000000000000e+00 1.93170311939836e-02 + 27 3.20781524498993e+00 0.00000000000000e+00 1.93170311939836e-02 + 28 3.20267947244878e+00 -4.96428715591806e-02 1.92532398175101e-02 + 29 3.20267947244878e+00 0.00000000000000e+00 1.92532398175101e-02 + 30 3.20267947244878e+00 0.00000000000000e+00 1.92532398175101e-02 + 31 3.20267947244878e+00 0.00000000000000e+00 1.92532398175101e-02 + 32 3.20367252455682e+00 -4.96587603929091e-02 1.92655662793778e-02 + 33 3.20367252455682e+00 0.00000000000000e+00 1.92655662793778e-02 + 34 3.20367252455682e+00 0.00000000000000e+00 1.92655662793778e-02 + 35 3.20367252455682e+00 0.00000000000000e+00 1.92655662793778e-02 + 36 3.20851202025206e+00 -4.97361923240330e-02 1.93256939601031e-02 + 37 3.20851202025206e+00 0.00000000000000e+00 1.93256939601031e-02 + 38 3.20851202025206e+00 0.00000000000000e+00 1.93256939601031e-02 + 39 3.20851202025206e+00 0.00000000000000e+00 1.93256939601031e-02 + 40 3.21397142146894e+00 -4.98235427435031e-02 1.93936360274506e-02 diff --git a/namd/tests/library/016_mts_bias/namd-version.txt b/namd/tests/library/016_mts_bias/namd-version.txt index 08ab1004b..157cac038 100644 --- a/namd/tests/library/016_mts_bias/namd-version.txt +++ b/namd/tests/library/016_mts_bias/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out index 90ba327a0..e9eb1b9a5 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out +++ b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -12,6 +15,7 @@ colvars: # colvarsTrajFrequency = 10 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "c" @@ -25,28 +29,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -63,28 +67,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = 0.51. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -97,37 +101,6 @@ colvars: Warning: Variable r1 is absent from expression "x". colvars: Warning: Variable r2 is absent from expression "x". colvars: Warning: Variable r3 is absent from expression "x". colvars: Warning: Variable r2 is absent from expression "cos(x) + r1 + r3". -colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt x. -colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt x. -colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt x. -colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt x. -colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt x. -colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt x. -colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt x. -colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r1. -colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r1. -colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r1. -colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r1. -colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r1. -colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r1. -colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r1. -colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r1. -colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r2. -colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r2. -colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r2. -colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r2. -colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r2. -colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r2. -colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r2. -colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r2. -colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r3. -colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r3. -colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r3. -colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r3. -colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r3. -colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r3. -colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r3. -colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r3. colvars: Expecting colvar value of type n-dimensional vector of size 2. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] @@ -158,6 +131,7 @@ colvars: # centers = { ( 20 , -5 ) } colvars: # targetCenters = { ( 20 , -5 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 100 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "c" will be rescaled to 100 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -168,17 +142,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). -colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. -colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. -colvars: Re-initialized atom group for variable "c":1/0. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: Re-initialized atom group for variable "c":1/1. 1 atoms: total mass = 12.011, total charge = 0.51. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceVec colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - Custom functions (Lepton): +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "c":1/0. 1 atoms: total mass = 12.011, total charge = 0.51. diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped index cb77abf4e..aff97d707 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name c - x ( 1.65450803775141e+01 , -2.58120974253005e+00 ) + x ( 1.65450803779147e+01 , -2.58120974399207e+00 ) } restraint { diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj index d7ab641d2..bfd90c361 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj +++ b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj @@ -1,4 +1,4 @@ # step c 0 ( 1.47736880982107e+01 , 5.47598531906441e-01 ) - 10 ( 1.64732268956053e+01 , -1.86635726975950e+00 ) - 20 ( 1.65450803775141e+01 , -2.58120974253006e+00 ) + 10 ( 1.64732268956376e+01 , -1.86635727005636e+00 ) + 20 ( 1.65450803779147e+01 , -2.58120974399207e+00 ) diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped index 5b04314b5..e7fddb9d1 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name c - x ( 1.75996935759052e+01 , -3.48707550156878e+00 ) + x ( 1.75996935761212e+01 , -3.48707549970946e+00 ) } restraint { diff --git a/namd/tests/library/017_custom_function/namd-version.txt b/namd/tests/library/017_custom_function/namd-version.txt index 04e884681..157cac038 100644 --- a/namd/tests/library/017_custom_function/namd-version.txt +++ b/namd/tests/library/017_custom_function/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.12 for Linux-x86_64-multicore +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/018_pathCV/AutoDiff/test.colvars.out b/namd/tests/library/018_pathCV/AutoDiff/test.colvars.out index 44602f5d0..6a672dfff 100644 --- a/namd/tests/library/018_pathCV/AutoDiff/test.colvars.out +++ b/namd/tests/library/018_pathCV/AutoDiff/test.colvars.out @@ -1,12 +1,11 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration: colvars: # units = "" [default] @@ -15,6 +14,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "s" @@ -28,14 +28,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 104 atoms requested: total mass = 727.821, total charge = 6.70552e-08. @@ -43,7 +43,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: Initializing a new "rmsd" component. colvars: # name = "" [default] @@ -55,21 +55,21 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 104 atoms requested: total mass = 727.821, total charge = 6.70552e-08. colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/310turn-ideal.xyz" colvars: # refPositionsCol = "" [default] -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: This colvar uses scripted function "pathCVs". @@ -122,21 +122,21 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 104 atoms requested: total mass = 727.821, total charge = 6.70552e-08. colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: Initializing a new "rmsd" component. colvars: # name = "" [default] @@ -148,21 +148,21 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 104 atoms requested: total mass = 727.821, total charge = 6.70552e-08. colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/310turn-ideal.xyz" colvars: # refPositionsCol = "" [default] -colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: This colvar uses scripted function "pathCVz". @@ -218,11 +218,6 @@ colvars: # shared = off [default] colvars: # maxForce = [default] colvars: # CZARestimator = on [default] colvars: # integrate = on [default] -colvars: # pABFintegrateFreq = 0 [default] -colvars: # integrateInitMaxIterations = 10000 [default] -colvars: # integrateInitTol = 1e-06 [default] -colvars: # integrateMaxIterations = 100 [default] -colvars: # integrateTol = 0.0001 [default] colvars: # UIestimator = off [default] colvars: Finished ABF setup. colvars: ---------------------------------------------------------------------- @@ -233,6 +228,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- @@ -246,6 +242,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { -0.2 } colvars: # upperWalls = { 1.2 } @@ -261,9 +258,42 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (104 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - BAOA integrator: +colvars: BouRabee2010 https://doi.org/10.1137/090758842 +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - harmonicWalls colvar bias implementation: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - ABF colvar bias implementation: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - Poisson integration of 2D/3D free energy surfaces: +colvars: Henin2021 https://doi.org/10.1021/acs.jctc.1c00593 +colvars: +colvars: - CZAR eABF estimator: +colvars: - eABF implementation: +colvars: Lesage2017 https://doi.org/10.1021/acs.jpcb.6b10055 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - Scripted functions (Tcl): +colvars: n/a +colvars: +colvars: updating target temperature (T = 300 K). colvars: Updating NAMD interface: colvars: updating atomic data (104 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "s":0/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08. colvars: Re-initialized atom group for variable "s":1/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08. colvars: Re-initialized atom group for variable "z":0/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08. @@ -277,5 +307,5 @@ colvars: PathCV STEP 6 next pathCV flags 1 1 colvars: PathCV WARNING: less than 2 RMSDs are above threshold, selecting 2 closest images colvars: PathCV STEP 11 next pathCV flags 1 1 colvars: Saving collective variables state to "test.colvars.state". -colvars: Integrated in 143 steps, error: 9.52755e-07 -colvars: Integrated in 143 steps, error: 8.74992e-07 +colvars: Integrated in 143 steps, error: 9.02625e-07 +colvars: Integrated in 142 steps, error: 9.86746e-07 diff --git a/namd/tests/library/018_pathCV/AutoDiff/test.colvars.state.stripped b/namd/tests/library/018_pathCV/AutoDiff/test.colvars.state.stripped index addd2a2f0..b92ecc6e5 100644 --- a/namd/tests/library/018_pathCV/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/018_pathCV/AutoDiff/test.colvars.state.stripped @@ -5,16 +5,16 @@ configuration { colvar { name s - x 1.88162886110026e-215 - extended_x 1.51318200440576e-04 - extended_v 4.15297363896536e-05 + x 1.88169145390613e-215 + extended_x 1.40893578825849e-04 + extended_v 4.15362186545699e-05 } colvar { name z - x 4.99981821584820e-01 - extended_x 5.04130336462937e-01 - extended_v -3.06412816932531e-05 + x 4.99983213750952e-01 + extended_x 5.04137015603104e-01 + extended_v -3.06370867449497e-05 } abf { @@ -201,7 +201,7 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -5.05394403557552e-03 9.61026562737795e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + -2.52634040637666e-03 9.86346225256722e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -211,7 +211,7 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.16448816297608e-01 7.02396019515835e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 2.72854053576603e-01 7.04290046777368e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -634,8 +634,8 @@ z_gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 7.78303220576288e-01 2.01155592501129e+01 - 2.29409131340735e-01 4.89567878545001e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 6.99268139691302e-01 2.01229199330169e+01 + 1.94876889121305e-01 4.91661450024477e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/018_pathCV/AutoDiff/test.colvars.traj b/namd/tests/library/018_pathCV/AutoDiff/test.colvars.traj index bf44f480b..9cf5172d1 100644 --- a/namd/tests/library/018_pathCV/AutoDiff/test.colvars.traj +++ b/namd/tests/library/018_pathCV/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step s r_s z r_z 0 3.00814883534435e-215 3.00814883534435e-215 5.04223676928709e-01 5.04223676928709e-01 - 1 2.79773744065899e-215 -8.47753442854012e-07 5.04053981240470e-01 5.04215184762215e-01 - 2 2.60900632724628e-215 5.84013717452316e-06 5.04017885810743e-01 5.04206024707080e-01 - 3 2.48746158657393e-215 1.83444183792222e-05 5.03925949021255e-01 5.04194621361562e-01 - 4 2.33749398457775e-215 3.30663322771117e-05 5.03744457918909e-01 5.04179636036195e-01 - 5 2.19481225930835e-215 4.50102286359236e-05 5.03426140315685e-01 5.04168625648446e-01 - 6 2.06818775768437e-215 6.23252616516950e-05 5.02953441020839e-01 5.04160718764085e-01 - 7 1.99241404617557e-215 7.84867300879842e-05 5.02333036275841e-01 5.04157231816793e-01 - 8 1.94602382038457e-215 1.04106424125391e-04 5.01588199274176e-01 5.04151900677087e-01 - 9 1.90193758423791e-215 1.30553332245749e-04 5.00771453810440e-01 5.04145657103784e-01 - 10 1.88162886110026e-215 1.51318200440576e-04 4.99981821584820e-01 5.04130336462937e-01 + 1 2.79773744080269e-215 -4.23770774320244e-07 5.04053981240426e-01 5.04219431906761e-01 + 2 2.60900847780748e-215 2.49556789490259e-06 5.04017921282668e-01 5.04210587066118e-01 + 3 2.48746781445528e-215 1.20892555960855e-05 5.03926056790795e-01 5.04200282559501e-01 + 4 2.33750613647379e-215 2.56988998248665e-05 5.03744681560205e-01 5.04187067003941e-01 + 5 2.19483238621295e-215 3.90282685346562e-05 5.03426534412398e-01 5.04174033567399e-01 + 6 2.06821654791110e-215 5.36535999110737e-05 5.02954037863991e-01 5.04164509109472e-01 + 7 1.99245194229624e-215 7.03868185877368e-05 5.02333848769048e-01 5.04158701221282e-01 + 8 1.94607036513624e-215 9.12708950263107e-05 5.01589215390416e-01 5.04154123763789e-01 + 9 1.90199211917260e-215 1.17295911614485e-04 5.00772663551120e-01 5.04148101532508e-01 + 10 1.88169145390613e-215 1.40893578825849e-04 4.99983213750952e-01 5.04137015603104e-01 diff --git a/namd/tests/library/018_pathCV/AutoDiff/test.pmf b/namd/tests/library/018_pathCV/AutoDiff/test.pmf index c6d9993a3..68438f4fa 100644 --- a/namd/tests/library/018_pathCV/AutoDiff/test.pmf +++ b/namd/tests/library/018_pathCV/AutoDiff/test.pmf @@ -2,1220 +2,1220 @@ # -2.25000000000000e-01 5.00000000000000e-02 29 0 # -5.25000000000000e-01 5.00000000000000e-02 41 0 - -2.00000000000000e-01 -5.00000000000000e-01 5.70517047513764e-02 - -2.00000000000000e-01 -4.50000000000000e-01 5.70314133512830e-02 - -2.00000000000000e-01 -4.00000000000000e-01 5.69701421808571e-02 - -2.00000000000000e-01 -3.50000000000000e-01 5.68666911787773e-02 - -2.00000000000000e-01 -3.00000000000000e-01 5.67190424847436e-02 - -2.00000000000000e-01 -2.50000000000000e-01 5.65243452970642e-02 - -2.00000000000000e-01 -2.00000000000000e-01 5.62788845639861e-02 - -2.00000000000000e-01 -1.50000000000000e-01 5.59781651275093e-02 - -2.00000000000000e-01 -1.00000000000000e-01 5.56170820377633e-02 - -2.00000000000000e-01 -5.00000000000000e-02 5.51902886232320e-02 - -2.00000000000000e-01 0.00000000000000e+00 5.46930729733900e-02 - -2.00000000000000e-01 5.00000000000000e-02 5.41231306987124e-02 - -2.00000000000000e-01 1.00000000000000e-01 5.34841272779175e-02 - -2.00000000000000e-01 1.50000000000000e-01 5.27925332820017e-02 - -2.00000000000000e-01 2.00000000000000e-01 5.20905600971221e-02 - -2.00000000000000e-01 2.50000000000000e-01 5.14698076526550e-02 - -2.00000000000000e-01 3.00000000000000e-01 5.11120137701121e-02 - -2.00000000000000e-01 3.50000000000000e-01 5.13514952600134e-02 - -2.00000000000000e-01 4.00000000000000e-01 5.27452718369350e-02 - -2.00000000000000e-01 4.50000000000000e-01 5.60670091683773e-02 - -2.00000000000000e-01 5.00000000000000e-01 6.19606129807167e-02 - -2.00000000000000e-01 5.50000000000000e-01 6.97624576413127e-02 - -2.00000000000000e-01 6.00000000000000e-01 7.58579533281349e-02 - -2.00000000000000e-01 6.50000000000000e-01 7.94768301846018e-02 - -2.00000000000000e-01 7.00000000000000e-01 8.11734593823368e-02 - -2.00000000000000e-01 7.50000000000000e-01 8.16784413870776e-02 - -2.00000000000000e-01 8.00000000000000e-01 8.15376633810764e-02 - -2.00000000000000e-01 8.50000000000000e-01 8.10890739849921e-02 - -2.00000000000000e-01 9.00000000000000e-01 8.05226640484542e-02 - -2.00000000000000e-01 9.50000000000000e-01 7.99384339102008e-02 - -2.00000000000000e-01 1.00000000000000e+00 7.93856823442703e-02 - -2.00000000000000e-01 1.05000000000000e+00 7.88863999817826e-02 - -2.00000000000000e-01 1.10000000000000e+00 7.84484408252454e-02 - -2.00000000000000e-01 1.15000000000000e+00 7.80726720895413e-02 - -2.00000000000000e-01 1.20000000000000e+00 7.77568047877663e-02 - -2.00000000000000e-01 1.25000000000000e+00 7.74973669193293e-02 - -2.00000000000000e-01 1.30000000000000e+00 7.72907230904643e-02 - -2.00000000000000e-01 1.35000000000000e+00 7.71335889959089e-02 - -2.00000000000000e-01 1.40000000000000e+00 7.70232920587822e-02 - -2.00000000000000e-01 1.45000000000000e+00 7.69578965205320e-02 - -2.00000000000000e-01 1.50000000000000e+00 7.69362317921545e-02 + -2.00000000000000e-01 -5.00000000000000e-01 5.69586149951569e-02 + -2.00000000000000e-01 -4.50000000000000e-01 5.69382966644937e-02 + -2.00000000000000e-01 -4.00000000000000e-01 5.68769461750447e-02 + -2.00000000000000e-01 -3.50000000000000e-01 5.67733665267178e-02 + -2.00000000000000e-01 -3.00000000000000e-01 5.66255457146456e-02 + -2.00000000000000e-01 -2.50000000000000e-01 5.64306427548948e-02 + -2.00000000000000e-01 -2.00000000000000e-01 5.61849600753329e-02 + -2.00000000000000e-01 -1.50000000000000e-01 5.58840288715106e-02 + -2.00000000000000e-01 -1.00000000000000e-01 5.55227848234053e-02 + -2.00000000000000e-01 -5.00000000000000e-02 5.50959454137594e-02 + -2.00000000000000e-01 0.00000000000000e+00 5.45988989681669e-02 + -2.00000000000000e-01 5.00000000000000e-02 5.40294992011255e-02 + -2.00000000000000e-01 1.00000000000000e-01 5.33916589593868e-02 + -2.00000000000000e-01 1.50000000000000e-01 5.27022394910228e-02 + -2.00000000000000e-01 2.00000000000000e-01 5.20040670648128e-02 + -2.00000000000000e-01 2.50000000000000e-01 5.13897033729455e-02 + -2.00000000000000e-01 3.00000000000000e-01 5.10423626115960e-02 + -2.00000000000000e-01 3.50000000000000e-01 5.12985377781979e-02 + -2.00000000000000e-01 4.00000000000000e-01 5.27181985397260e-02 + -2.00000000000000e-01 4.50000000000000e-01 5.60782581523479e-02 + -2.00000000000000e-01 5.00000000000000e-01 6.20237943536309e-02 + -2.00000000000000e-01 5.50000000000000e-01 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1.25000000000000e+00 7.11302234016283e-02 + 1.20000000000000e+00 1.30000000000000e+00 7.12459520822547e-02 + 1.20000000000000e+00 1.35000000000000e+00 7.13358501394341e-02 + 1.20000000000000e+00 1.40000000000000e+00 7.13999868099928e-02 + 1.20000000000000e+00 1.45000000000000e+00 7.14384354298744e-02 + 1.20000000000000e+00 1.50000000000000e+00 7.14512501512653e-02 diff --git a/namd/tests/library/018_pathCV/namd-version.txt b/namd/tests/library/018_pathCV/namd-version.txt index 8b2783508..157cac038 100644 --- a/namd/tests/library/018_pathCV/namd-version.txt +++ b/namd/tests/library/018_pathCV/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2019-08-17". -colvars: Using NAMD interface, version "2019-08-17". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out index 4d96ba271..8f6da7076 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_dihed" @@ -32,56 +34,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -97,56 +99,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -162,56 +164,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -453,7 +455,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -485,53 +487,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -546,53 +548,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -607,53 +609,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -896,7 +898,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -917,6 +919,25 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - dihedral colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - gspathCV colvar component: +colvars: - gzpathCV colvar component: +colvars: n/a +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -943,11 +964,11 @@ colvars: Re-initialized atom group for variable "gpath_z_dihed":0/10. 1 atoms: t colvars: Re-initialized atom group for variable "gpath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped index 0a6f34748..d940cb619 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped @@ -10,6 +10,6 @@ colvar { colvar { name gpath_z_dihed - x 9.55645131452184e+01 + x 9.55645131452191e+01 } diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj index 5fac76756..ddaf3721c 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step gpath_s_dihed gpath_z_dihed 0 7.83123228264734e-01 3.83533978043175e+01 - 1 7.82945678970628e-01 4.29689076394209e+01 - 2 7.82818444070286e-01 4.79082192050889e+01 - 3 7.82680619902823e-01 5.32968526519463e+01 - 4 7.82481029251750e-01 5.95665170545922e+01 - 5 7.82394193117627e-01 6.58557656139234e+01 - 6 7.82260880668904e-01 7.22764122107678e+01 - 7 7.82016364258954e-01 7.87726707676512e+01 - 8 7.81934087543136e-01 8.51257353163675e+01 - 9 7.81821580461319e-01 8.98923615763004e+01 - 10 7.81811987245692e-01 9.36566870572305e+01 + 1 7.82945678970628e-01 4.29689076394212e+01 + 2 7.82818444070286e-01 4.79082192050887e+01 + 3 7.82680619902823e-01 5.32968526519466e+01 + 4 7.82481029251750e-01 5.95665170545919e+01 + 5 7.82394193117627e-01 6.58557656139231e+01 + 6 7.82260880668904e-01 7.22764122107677e+01 + 7 7.82016364258954e-01 7.87726707676510e+01 + 8 7.81934087543136e-01 8.51257353163676e+01 + 9 7.81821580461319e-01 8.98923615763005e+01 + 10 7.81811987245692e-01 9.36566870572311e+01 11 7.81676091324908e-01 9.70906581768438e+01 12 7.81497401408420e-01 1.00284195800025e+02 13 7.81382447528542e-01 1.01730136329478e+02 - 14 7.81310203934944e-01 1.02632785559218e+02 + 14 7.81310203934944e-01 1.02632785559219e+02 15 7.81107670050000e-01 1.02580995635213e+02 16 7.81000240562519e-01 1.01690738350632e+02 17 7.81032069099019e-01 1.00431749174877e+02 - 18 7.81089334289029e-01 9.86347657918941e+01 + 18 7.81089334289029e-01 9.86347657918943e+01 19 7.81314767005367e-01 9.68745522484514e+01 - 20 7.81476379939767e-01 9.55645131452184e+01 + 20 7.81476379939767e-01 9.55645131452191e+01 diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out index ac4527f9d..591e79589 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_dihed" @@ -32,56 +34,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -97,56 +99,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -162,56 +164,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -453,7 +455,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -485,53 +487,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -546,53 +548,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -607,53 +609,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -896,7 +898,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -917,6 +919,25 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - dihedral colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - gspathCV colvar component: +colvars: - gzpathCV colvar component: +colvars: n/a +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -942,17 +963,17 @@ colvars: Re-initialized atom group for variable "gpath_z_dihed":0/9. 1 atoms: to colvars: Re-initialized atom group for variable "gpath_z_dihed":0/10. 1 atoms: total mass = 12.01, total charge = 0.0337. colvars: Re-initialized atom group for variable "gpath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "gpath_s_dihed" from value: 0.781476 colvars: Restarting collective variable "gpath_z_dihed" from value: 95.5645 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj index 5b9068d9b..d5ec83feb 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step gpath_s_dihed gpath_z_dihed - 20 7.81476379939767e-01 9.55645131452184e+01 - 21 7.81240698201971e-01 1.06229693509576e+02 + 20 7.81476379939767e-01 9.55645131452191e+01 + 21 7.81240698201971e-01 1.06229693509577e+02 22 7.81005545091406e-01 1.17334167235362e+02 - 23 7.80723779014191e-01 1.28845704977403e+02 + 23 7.80723779014191e-01 1.28845704977404e+02 24 7.80348823600053e-01 1.41207832230497e+02 - 25 7.80052868542975e-01 1.53573472293346e+02 + 25 7.80052868542975e-01 1.53573472293347e+02 26 7.79695411661275e-01 1.65225530758384e+02 27 7.79227129868925e-01 1.75833882118768e+02 28 7.78924791555966e-01 1.85072740224480e+02 - 29 7.78616822792614e-01 1.91408513274006e+02 - 30 7.78445744037639e-01 1.96072266414114e+02 + 29 7.78616822792614e-01 1.91408513274007e+02 + 30 7.78445744037639e-01 1.96072266414115e+02 31 7.78198587511674e-01 1.99830728112820e+02 - 32 7.77969198638703e-01 2.02348834208335e+02 - 33 7.77870454975722e-01 2.01925240313578e+02 + 32 7.77969198638703e-01 2.02348834208334e+02 + 33 7.77870454975722e-01 2.01925240313579e+02 34 7.77892445039517e-01 2.00152956848502e+02 - 35 7.77861620836214e-01 1.96872674617572e+02 - 36 7.78012144635351e-01 1.92375777763846e+02 + 35 7.77861620836214e-01 1.96872674617573e+02 + 36 7.78012144635351e-01 1.92375777763847e+02 37 7.78402492011077e-01 1.87024840666577e+02 38 7.78909881410184e-01 1.81082923676999e+02 - 39 7.79681670070840e-01 1.75290823442270e+02 + 39 7.79681670070840e-01 1.75290823442271e+02 40 7.80475723743606e-01 1.69997870041256e+02 diff --git a/namd/tests/library/019_gpathCV/namd-version.txt b/namd/tests/library/019_gpathCV/namd-version.txt index 90b3a010a..157cac038 100644 --- a/namd/tests/library/019_gpathCV/namd-version.txt +++ b/namd/tests/library/019_gpathCV/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA -colvars: Initializing the collective variables module, version "2019-10-21". -colvars: Using NAMD interface, version "2019-10-21". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj b/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj index a2d265a65..f4d864ba8 100644 --- a/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj +++ b/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step gpath_s_cartesian gpath_z_cartesian 0 5.30720368611864e-01 8.61059914994141e-02 - 1 5.30717690590865e-01 8.54273375358691e-02 - 2 5.30714251957229e-01 8.51458403558881e-02 - 3 5.30710055975446e-01 8.51321853522884e-02 - 4 5.30704973571852e-01 8.52949333585581e-02 - 5 5.30697460621445e-01 8.55508921045210e-02 - 6 5.30685286827787e-01 8.56177474112286e-02 - 7 5.30670902617345e-01 8.57812083900463e-02 - 8 5.30652367951073e-01 8.59993861857883e-02 - 9 5.30632081382459e-01 8.62909912963239e-02 - 10 5.30606987319570e-01 8.66946366005642e-02 + 1 5.30717690590865e-01 8.54273375358692e-02 + 2 5.30714251957229e-01 8.51458403558880e-02 + 3 5.30710055975446e-01 8.51321853522883e-02 + 4 5.30704973571852e-01 8.52949333585580e-02 + 5 5.30697460621445e-01 8.55508921045213e-02 + 6 5.30685286827787e-01 8.56177474112287e-02 + 7 5.30670902617345e-01 8.57812083900462e-02 + 8 5.30652367951073e-01 8.59993861857884e-02 + 9 5.30632081382459e-01 8.62909912963241e-02 + 10 5.30606987319570e-01 8.66946366005643e-02 11 5.30579540524640e-01 8.73047828339237e-02 - 12 5.30552631793952e-01 8.81730152476007e-02 - 13 5.30524058862923e-01 8.91926063197970e-02 + 12 5.30552631793952e-01 8.81730152476006e-02 + 13 5.30524058862923e-01 8.91926063197971e-02 14 5.30493980557183e-01 9.03283581585283e-02 15 5.30463117047670e-01 9.15212996991972e-02 16 5.30431734419221e-01 9.30006426174987e-02 - 17 5.30399413235259e-01 9.44575442040145e-02 - 18 5.30368252449657e-01 9.62800980538579e-02 + 17 5.30399413235259e-01 9.44575442040143e-02 + 18 5.30368252449657e-01 9.62800980538578e-02 19 5.30333234090156e-01 9.82010258065717e-02 20 5.30301765703773e-01 1.00592004206710e-01 diff --git a/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj b/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj index 0b4049f9a..44c3cc8ee 100644 --- a/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj @@ -1,6 +1,6 @@ # step gpath_s_cartesian gpath_z_cartesian 20 5.30301765703773e-01 1.00592004206710e-01 - 21 5.30299068311154e-01 1.01776105919981e-01 + 21 5.30299068311154e-01 1.01776105919982e-01 22 5.30296225733479e-01 1.02913020025282e-01 23 5.30293151382629e-01 1.03888660431483e-01 24 5.30289871026115e-01 1.04670153673202e-01 @@ -10,9 +10,9 @@ 28 5.30250537018860e-01 1.05411857890215e-01 29 5.30235512500134e-01 1.05013013758426e-01 30 5.30216395990587e-01 1.04566807352862e-01 - 31 5.30195586650359e-01 1.04225738170004e-01 + 31 5.30195586650359e-01 1.04225738170003e-01 32 5.30176202069296e-01 1.03881270572137e-01 - 33 5.30155909450721e-01 1.03435901761180e-01 + 33 5.30155909450721e-01 1.03435901761179e-01 34 5.30134759237002e-01 1.02902765055984e-01 35 5.30113387291624e-01 1.02318158639028e-01 36 5.30092042017102e-01 1.01828820799264e-01 diff --git a/namd/tests/library/020_gpath/namd-version.txt b/namd/tests/library/020_gpath/namd-version.txt index 355758d76..157cac038 100644 --- a/namd/tests/library/020_gpath/namd-version.txt +++ b/namd/tests/library/020_gpath/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 3.0b3 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-18. +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out index 2825984f5..8b007336e 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_distanceVec" @@ -32,8 +34,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -44,14 +47,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -67,8 +70,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -79,14 +83,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -102,8 +106,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -114,14 +119,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -137,8 +142,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -149,14 +155,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -172,8 +178,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -184,14 +191,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -207,8 +214,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -219,14 +227,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -242,8 +250,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -254,14 +263,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -277,8 +286,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -289,14 +299,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -312,8 +322,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -324,14 +335,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -347,8 +358,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -359,14 +371,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -382,8 +394,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -394,14 +407,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -417,8 +430,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -429,14 +443,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -452,8 +466,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -464,14 +479,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -487,8 +502,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -499,14 +515,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -522,8 +538,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -534,14 +551,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -557,8 +574,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -569,14 +587,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -592,8 +610,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -604,14 +623,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -627,8 +646,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -639,14 +659,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -662,8 +682,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -674,14 +695,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -697,8 +718,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -709,14 +731,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3160,12 +3182,11 @@ colvars: # useSecondClosestFrame = on [default] colvars: Geometric path s(σ) will use the second closest frame to compute s_(m-1) colvars: # useThirdClosestFrame = off [default] colvars: Geometric path s(σ) will use the neighbouring frame to compute s_(m+1) -colvars: Geometric path s(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3197,8 +3218,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3209,14 +3231,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3232,8 +3254,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3244,14 +3267,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3267,8 +3290,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3279,14 +3303,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3302,8 +3326,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3314,14 +3339,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3337,8 +3362,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3349,14 +3375,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3372,8 +3398,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3384,14 +3411,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3407,8 +3434,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3419,14 +3447,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3442,8 +3470,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3454,14 +3483,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3477,8 +3506,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3489,14 +3519,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3512,8 +3542,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3524,14 +3555,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3547,8 +3578,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3559,14 +3591,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3582,8 +3614,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3594,14 +3627,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3617,8 +3650,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3629,14 +3663,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3652,8 +3686,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3664,14 +3699,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3687,8 +3722,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3699,14 +3735,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3722,8 +3758,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3734,14 +3771,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3757,8 +3794,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3769,14 +3807,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3792,8 +3830,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3804,14 +3843,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3827,8 +3866,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3839,14 +3879,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3862,8 +3902,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3874,14 +3915,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6327,12 +6368,11 @@ colvars: # useThirdClosestFrame = off [default] colvars: Geometric path z(σ) will use the neighbouring frame to compute s_(m+1) colvars: # useZsquare = on colvars: Geometric path z(σ) will use the square of distance from current frame to path compute z -colvars: Geometric path z(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6353,6 +6393,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceVec colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - gspathCV colvar component: +colvars: - gzpathCV colvar component: +colvars: n/a +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6435,11 +6495,11 @@ colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/38. 0 at colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj index 8e7ee67dd..e5d0bb3cf 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj @@ -2,15 +2,15 @@ 0 3.77171678533515e-02 6.76736838399185e+02 1 3.77408160662234e-02 6.76814886658536e+02 2 3.77652902052649e-02 6.76904118559529e+02 - 3 3.77885901836011e-02 6.77002173338061e+02 + 3 3.77885901836011e-02 6.77002173338060e+02 4 3.78148176804083e-02 6.77104722272709e+02 5 3.78372534576845e-02 6.77211769234532e+02 - 6 3.78552413890631e-02 6.77324430169633e+02 + 6 3.78552413890631e-02 6.77324430169634e+02 7 3.78833685463047e-02 6.77427790438348e+02 - 8 3.79119516235519e-02 6.77529691393681e+02 + 8 3.79119516235524e-02 6.77529691393681e+02 9 3.79430521380542e-02 6.77636436765019e+02 - 10 3.79763962901923e-02 6.77753499558135e+02 - 11 3.80148985287519e-02 6.77879781194716e+02 + 10 3.79763962901917e-02 6.77753499558135e+02 + 11 3.80148985287524e-02 6.77879781194716e+02 12 3.80574676219839e-02 6.77995499164433e+02 13 3.80958506694046e-02 6.78083025670623e+02 14 3.81395612603290e-02 6.78153378635457e+02 diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out index e11c82e21..1d14cbe04 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_distanceVec" @@ -32,8 +34,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -44,14 +47,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -67,8 +70,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -79,14 +83,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -102,8 +106,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -114,14 +119,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -137,8 +142,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -149,14 +155,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -172,8 +178,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -184,14 +191,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -207,8 +214,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -219,14 +227,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -242,8 +250,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -254,14 +263,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -277,8 +286,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -289,14 +299,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -312,8 +322,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -324,14 +335,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -347,8 +358,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -359,14 +371,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -382,8 +394,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -394,14 +407,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -417,8 +430,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -429,14 +443,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -452,8 +466,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -464,14 +479,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -487,8 +502,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -499,14 +515,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -522,8 +538,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -534,14 +551,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -557,8 +574,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -569,14 +587,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -592,8 +610,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -604,14 +623,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -627,8 +646,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -639,14 +659,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -662,8 +682,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -674,14 +695,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -697,8 +718,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -709,14 +731,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3160,12 +3182,11 @@ colvars: # useSecondClosestFrame = on [default] colvars: Geometric path s(σ) will use the second closest frame to compute s_(m-1) colvars: # useThirdClosestFrame = off [default] colvars: Geometric path s(σ) will use the neighbouring frame to compute s_(m+1) -colvars: Geometric path s(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3197,8 +3218,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3209,14 +3231,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3232,8 +3254,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3244,14 +3267,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3267,8 +3290,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3279,14 +3303,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3302,8 +3326,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3314,14 +3339,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3337,8 +3362,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3349,14 +3375,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3372,8 +3398,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3384,14 +3411,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3407,8 +3434,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3419,14 +3447,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3442,8 +3470,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3454,14 +3483,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3477,8 +3506,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3489,14 +3519,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3512,8 +3542,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3524,14 +3555,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3547,8 +3578,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3559,14 +3591,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3582,8 +3614,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3594,14 +3627,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3617,8 +3650,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3629,14 +3663,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3652,8 +3686,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3664,14 +3699,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3687,8 +3722,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3699,14 +3735,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3722,8 +3758,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3734,14 +3771,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3757,8 +3794,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3769,14 +3807,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3792,8 +3830,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3804,14 +3843,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3827,8 +3866,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3839,14 +3879,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3862,8 +3902,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3874,14 +3915,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6327,12 +6368,11 @@ colvars: # useThirdClosestFrame = off [default] colvars: Geometric path z(σ) will use the neighbouring frame to compute s_(m+1) colvars: # useZsquare = on colvars: Geometric path z(σ) will use the square of distance from current frame to path compute z -colvars: Geometric path z(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6353,6 +6393,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceVec colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - gspathCV colvar component: +colvars: - gzpathCV colvar component: +colvars: n/a +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6434,17 +6494,17 @@ colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/37. 1 at colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/38. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "gpath_s_distanceVec" from value: 0.0384565 colvars: Restarting collective variable "gpath_z_distanceVec" from value: 678.131 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj index defbf6a45..81de6b0bc 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj @@ -10,10 +10,10 @@ 28 3.86084059020791e-02 6.78925279191111e+02 29 3.86298828548808e-02 6.79025716470530e+02 30 3.86527796201097e-02 6.79134948406694e+02 - 31 3.86798568836977e-02 6.79251839399435e+02 + 31 3.86798568836978e-02 6.79251839399435e+02 32 3.87098949985802e-02 6.79356485630484e+02 33 3.87343129795344e-02 6.79430860596411e+02 - 34 3.87624579979557e-02 6.79485989524982e+02 + 34 3.87624579979551e-02 6.79485989524982e+02 35 3.87892874098554e-02 6.79502594982682e+02 36 3.88193203791849e-02 6.79495678267542e+02 37 3.88506047395243e-02 6.79480901306783e+02 diff --git a/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt b/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt index 90b3a010a..157cac038 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt +++ b/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA -colvars: Initializing the collective variables module, version "2019-10-21". -colvars: Using NAMD interface, version "2019-10-21". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out index 27624c699..4dbd24972 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_distanceVec" @@ -32,8 +34,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -44,14 +47,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -67,8 +70,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -79,14 +83,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -102,8 +106,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -114,14 +119,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -137,8 +142,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -149,14 +155,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -172,8 +178,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -184,14 +191,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -207,8 +214,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -219,14 +227,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -242,8 +250,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -254,14 +263,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -277,8 +286,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -289,14 +299,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -312,8 +322,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -324,14 +335,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -347,8 +358,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -359,14 +371,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -382,8 +394,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -394,14 +407,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -417,8 +430,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -429,14 +443,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -452,8 +466,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -464,14 +479,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -487,8 +502,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -499,14 +515,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -522,8 +538,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -534,14 +551,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -557,8 +574,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -569,14 +587,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -592,8 +610,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -604,14 +623,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -627,8 +646,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -639,14 +659,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -662,8 +682,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -674,14 +695,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -697,8 +718,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -709,14 +731,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3157,35 +3179,6 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] -colvars: Distance between frame 1 and 2 is 1.24993 -colvars: Distance between frame 2 and 3 is 1.22263 -colvars: Distance between frame 3 and 4 is 1.15797 -colvars: Distance between frame 4 and 5 is 1.20671 -colvars: Distance between frame 5 and 6 is 1.22068 -colvars: Distance between frame 6 and 7 is 1.27376 -colvars: Distance between frame 7 and 8 is 1.16679 -colvars: Distance between frame 8 and 9 is 1.23641 -colvars: Distance between frame 9 and 10 is 1.23647 -colvars: Distance between frame 10 and 11 is 1.24224 -colvars: Distance between frame 11 and 12 is 1.21755 -colvars: Distance between frame 12 and 13 is 1.2113 -colvars: Distance between frame 13 and 14 is 1.25829 -colvars: Distance between frame 14 and 15 is 1.14361 -colvars: Distance between frame 15 and 16 is 1.25482 -colvars: Distance between frame 16 and 17 is 1.19127 -colvars: Distance between frame 17 and 18 is 1.21515 -colvars: Distance between frame 18 and 19 is 1.28854 -colvars: Distance between frame 19 and 20 is 1.21558 -colvars: Distance between frame 20 and 21 is 1.18825 -colvars: Distance between frame 21 and 22 is 1.29888 -colvars: Distance between frame 22 and 23 is 1.23365 -colvars: Distance between frame 23 and 24 is 1.17305 -colvars: Distance between frame 24 and 25 is 1.32493 -colvars: Distance between frame 25 and 26 is 1.21926 -colvars: Distance between frame 26 and 27 is 1.1941 -colvars: Distance between frame 27 and 28 is 1.28306 -colvars: Distance between frame 28 and 29 is 1.24978 -colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -3212,7 +3205,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3244,8 +3237,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3256,14 +3250,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3279,8 +3273,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3291,14 +3286,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3314,8 +3309,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3326,14 +3322,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3349,8 +3345,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3361,14 +3358,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3384,8 +3381,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3396,14 +3394,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3419,8 +3417,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3431,14 +3430,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3454,8 +3453,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3466,14 +3466,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3489,8 +3489,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3501,14 +3502,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3524,8 +3525,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3536,14 +3538,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3559,8 +3561,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3571,14 +3574,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3594,8 +3597,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3606,14 +3610,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3629,8 +3633,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3641,14 +3646,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3664,8 +3669,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3676,14 +3682,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3699,8 +3705,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3711,14 +3718,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3734,8 +3741,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3746,14 +3754,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3769,8 +3777,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3781,14 +3790,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3804,8 +3813,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3816,14 +3826,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3839,8 +3849,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3851,14 +3862,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3874,8 +3885,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3886,14 +3898,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3909,8 +3921,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3921,14 +3934,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6369,35 +6382,6 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] -colvars: Distance between frame 1 and 2 is 1.24993 -colvars: Distance between frame 2 and 3 is 1.22263 -colvars: Distance between frame 3 and 4 is 1.15797 -colvars: Distance between frame 4 and 5 is 1.20671 -colvars: Distance between frame 5 and 6 is 1.22068 -colvars: Distance between frame 6 and 7 is 1.27376 -colvars: Distance between frame 7 and 8 is 1.16679 -colvars: Distance between frame 8 and 9 is 1.23641 -colvars: Distance between frame 9 and 10 is 1.23647 -colvars: Distance between frame 10 and 11 is 1.24224 -colvars: Distance between frame 11 and 12 is 1.21755 -colvars: Distance between frame 12 and 13 is 1.2113 -colvars: Distance between frame 13 and 14 is 1.25829 -colvars: Distance between frame 14 and 15 is 1.14361 -colvars: Distance between frame 15 and 16 is 1.25482 -colvars: Distance between frame 16 and 17 is 1.19127 -colvars: Distance between frame 17 and 18 is 1.21515 -colvars: Distance between frame 18 and 19 is 1.28854 -colvars: Distance between frame 19 and 20 is 1.21558 -colvars: Distance between frame 20 and 21 is 1.18825 -colvars: Distance between frame 21 and 22 is 1.29888 -colvars: Distance between frame 22 and 23 is 1.23365 -colvars: Distance between frame 23 and 24 is 1.17305 -colvars: Distance between frame 24 and 25 is 1.32493 -colvars: Distance between frame 25 and 26 is 1.21926 -colvars: Distance between frame 26 and 27 is 1.1941 -colvars: Distance between frame 27 and 28 is 1.28306 -colvars: Distance between frame 28 and 29 is 1.24978 -colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -6424,7 +6408,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6445,6 +6429,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceVec colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - aspathCV colvar component: +colvars: - azpathCV colvar component: +colvars: n/a +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6527,11 +6531,11 @@ colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/38. 0 at colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj index 8c3fd2f17..358b06848 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj @@ -7,10 +7,10 @@ 5 3.71951763458571e-02 6.76437235131064e+02 6 3.72110087084931e-02 6.76548721440867e+02 7 3.72351763642007e-02 6.76650733895917e+02 - 8 3.72595960457659e-02 6.76751383624712e+02 + 8 3.72595960457660e-02 6.76751383624712e+02 9 3.72860044867264e-02 6.76856908644382e+02 - 10 3.73141938916315e-02 6.76972778630392e+02 - 11 3.73465707477625e-02 6.77097844460360e+02 + 10 3.73141938916311e-02 6.76972778630392e+02 + 11 3.73465707477626e-02 6.77097844460360e+02 12 3.73823307193035e-02 6.77212255632268e+02 13 3.74145603254307e-02 6.77298631416326e+02 14 3.74510510199529e-02 6.77367872060677e+02 diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out index a31a3d332..81cb87adf 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_distanceVec" @@ -32,8 +34,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -44,14 +47,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -67,8 +70,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -79,14 +83,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -102,8 +106,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -114,14 +119,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -137,8 +142,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -149,14 +155,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -172,8 +178,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -184,14 +191,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -207,8 +214,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -219,14 +227,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -242,8 +250,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -254,14 +263,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -277,8 +286,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -289,14 +299,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -312,8 +322,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -324,14 +335,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -347,8 +358,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -359,14 +371,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -382,8 +394,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -394,14 +407,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -417,8 +430,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -429,14 +443,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -452,8 +466,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -464,14 +479,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -487,8 +502,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -499,14 +515,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -522,8 +538,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -534,14 +551,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -557,8 +574,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -569,14 +587,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -592,8 +610,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -604,14 +623,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -627,8 +646,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -639,14 +659,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -662,8 +682,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -674,14 +695,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -697,8 +718,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -709,14 +731,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3157,35 +3179,6 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] -colvars: Distance between frame 1 and 2 is 1.24993 -colvars: Distance between frame 2 and 3 is 1.22263 -colvars: Distance between frame 3 and 4 is 1.15797 -colvars: Distance between frame 4 and 5 is 1.20671 -colvars: Distance between frame 5 and 6 is 1.22068 -colvars: Distance between frame 6 and 7 is 1.27376 -colvars: Distance between frame 7 and 8 is 1.16679 -colvars: Distance between frame 8 and 9 is 1.23641 -colvars: Distance between frame 9 and 10 is 1.23647 -colvars: Distance between frame 10 and 11 is 1.24224 -colvars: Distance between frame 11 and 12 is 1.21755 -colvars: Distance between frame 12 and 13 is 1.2113 -colvars: Distance between frame 13 and 14 is 1.25829 -colvars: Distance between frame 14 and 15 is 1.14361 -colvars: Distance between frame 15 and 16 is 1.25482 -colvars: Distance between frame 16 and 17 is 1.19127 -colvars: Distance between frame 17 and 18 is 1.21515 -colvars: Distance between frame 18 and 19 is 1.28854 -colvars: Distance between frame 19 and 20 is 1.21558 -colvars: Distance between frame 20 and 21 is 1.18825 -colvars: Distance between frame 21 and 22 is 1.29888 -colvars: Distance between frame 22 and 23 is 1.23365 -colvars: Distance between frame 23 and 24 is 1.17305 -colvars: Distance between frame 24 and 25 is 1.32493 -colvars: Distance between frame 25 and 26 is 1.21926 -colvars: Distance between frame 26 and 27 is 1.1941 -colvars: Distance between frame 27 and 28 is 1.28306 -colvars: Distance between frame 28 and 29 is 1.24978 -colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -3212,7 +3205,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3244,8 +3237,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3256,14 +3250,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3279,8 +3273,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3291,14 +3286,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3314,8 +3309,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3326,14 +3322,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3349,8 +3345,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3361,14 +3358,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3384,8 +3381,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3396,14 +3394,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3419,8 +3417,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3431,14 +3430,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3454,8 +3453,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3466,14 +3466,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3489,8 +3489,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3501,14 +3502,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3524,8 +3525,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3536,14 +3538,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3559,8 +3561,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3571,14 +3574,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3594,8 +3597,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3606,14 +3610,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3629,8 +3633,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3641,14 +3646,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3664,8 +3669,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3676,14 +3682,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3699,8 +3705,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3711,14 +3718,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3734,8 +3741,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3746,14 +3754,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3769,8 +3777,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3781,14 +3790,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3804,8 +3813,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3816,14 +3826,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3839,8 +3849,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3851,14 +3862,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3874,8 +3885,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3886,14 +3898,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3909,8 +3921,9 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3921,14 +3934,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6369,35 +6382,6 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] -colvars: Distance between frame 1 and 2 is 1.24993 -colvars: Distance between frame 2 and 3 is 1.22263 -colvars: Distance between frame 3 and 4 is 1.15797 -colvars: Distance between frame 4 and 5 is 1.20671 -colvars: Distance between frame 5 and 6 is 1.22068 -colvars: Distance between frame 6 and 7 is 1.27376 -colvars: Distance between frame 7 and 8 is 1.16679 -colvars: Distance between frame 8 and 9 is 1.23641 -colvars: Distance between frame 9 and 10 is 1.23647 -colvars: Distance between frame 10 and 11 is 1.24224 -colvars: Distance between frame 11 and 12 is 1.21755 -colvars: Distance between frame 12 and 13 is 1.2113 -colvars: Distance between frame 13 and 14 is 1.25829 -colvars: Distance between frame 14 and 15 is 1.14361 -colvars: Distance between frame 15 and 16 is 1.25482 -colvars: Distance between frame 16 and 17 is 1.19127 -colvars: Distance between frame 17 and 18 is 1.21515 -colvars: Distance between frame 18 and 19 is 1.28854 -colvars: Distance between frame 19 and 20 is 1.21558 -colvars: Distance between frame 20 and 21 is 1.18825 -colvars: Distance between frame 21 and 22 is 1.29888 -colvars: Distance between frame 22 and 23 is 1.23365 -colvars: Distance between frame 23 and 24 is 1.17305 -colvars: Distance between frame 24 and 25 is 1.32493 -colvars: Distance between frame 25 and 26 is 1.21926 -colvars: Distance between frame 26 and 27 is 1.1941 -colvars: Distance between frame 27 and 28 is 1.28306 -colvars: Distance between frame 28 and 29 is 1.24978 -colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -6424,7 +6408,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6445,6 +6429,26 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceVec colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - aspathCV colvar component: +colvars: - azpathCV colvar component: +colvars: n/a +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6526,17 +6530,17 @@ colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/37. 1 at colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/38. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "apath_s_distanceVec" from value: 0.0377147 colvars: Restarting collective variable "apath_z_distanceVec" from value: 677.339 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj index 9306d59e6..2a0e6503c 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj @@ -13,10 +13,10 @@ 31 3.79086164652580e-02 6.78450434800659e+02 32 3.79338795931516e-02 6.78554453096444e+02 33 3.79543432866692e-02 6.78628383973525e+02 - 34 3.79777414197512e-02 6.78683148858527e+02 + 34 3.79777414197508e-02 6.78683148858527e+02 35 3.79999682058412e-02 6.78699467676242e+02 36 3.80248319961822e-02 6.78692254801370e+02 - 37 3.80506503259599e-02 6.78677248372969e+02 + 37 3.80506503259602e-02 6.78677248372969e+02 38 3.80831517398857e-02 6.78640840179385e+02 39 3.81094518561156e-02 6.78584570499380e+02 40 3.81323012651889e-02 6.78535020169896e+02 diff --git a/namd/tests/library/022_apathCV_distanceVec/namd-version.txt b/namd/tests/library/022_apathCV_distanceVec/namd-version.txt index 90b3a010a..157cac038 100644 --- a/namd/tests/library/022_apathCV_distanceVec/namd-version.txt +++ b/namd/tests/library/022_apathCV_distanceVec/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA -colvars: Initializing the collective variables module, version "2019-10-21". -colvars: Using NAMD interface, version "2019-10-21". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out index 833f3b0c7..e7178f688 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out +++ b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_dihed" @@ -32,56 +34,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -97,56 +99,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -162,56 +164,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -446,37 +448,6 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] -colvars: Distance between frame 1 and 2 is 13.3844 -colvars: Distance between frame 2 and 3 is 13.3844 -colvars: Distance between frame 3 and 4 is 13.4029 -colvars: Distance between frame 4 and 5 is 13.4142 -colvars: Distance between frame 5 and 6 is 13.4056 -colvars: Distance between frame 6 and 7 is 13.42 -colvars: Distance between frame 7 and 8 is 13.3375 -colvars: Distance between frame 8 and 9 is 13.4007 -colvars: Distance between frame 9 and 10 is 13.0106 -colvars: Distance between frame 10 and 11 is 13.3842 -colvars: Distance between frame 11 and 12 is 11.9956 -colvars: Distance between frame 12 and 13 is 13.2179 -colvars: Distance between frame 13 and 14 is 13.2532 -colvars: Distance between frame 14 and 15 is 13.4171 -colvars: Distance between frame 15 and 16 is 13.4199 -colvars: Distance between frame 16 and 17 is 13.4188 -colvars: Distance between frame 17 and 18 is 13.3433 -colvars: Distance between frame 18 and 19 is 13.2697 -colvars: Distance between frame 19 and 20 is 13.0715 -colvars: Distance between frame 20 and 21 is 13.3511 -colvars: Distance between frame 21 and 22 is 12.7202 -colvars: Distance between frame 22 and 23 is 13.2064 -colvars: Distance between frame 23 and 24 is 13.3364 -colvars: Distance between frame 24 and 25 is 13.3914 -colvars: Distance between frame 25 and 26 is 13.4199 -colvars: Distance between frame 26 and 27 is 13.4148 -colvars: Distance between frame 27 and 28 is 13.3844 -colvars: Distance between frame 28 and 29 is 13.3858 -colvars: Distance between frame 29 and 30 is 13.204 -colvars: Distance between frame 30 and 31 is 13.2614 -colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -486,7 +457,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -518,56 +489,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -583,56 +554,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -648,56 +619,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -932,37 +903,6 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] -colvars: Distance between frame 1 and 2 is 13.3844 -colvars: Distance between frame 2 and 3 is 13.3844 -colvars: Distance between frame 3 and 4 is 13.4029 -colvars: Distance between frame 4 and 5 is 13.4142 -colvars: Distance between frame 5 and 6 is 13.4056 -colvars: Distance between frame 6 and 7 is 13.42 -colvars: Distance between frame 7 and 8 is 13.3375 -colvars: Distance between frame 8 and 9 is 13.4007 -colvars: Distance between frame 9 and 10 is 13.0106 -colvars: Distance between frame 10 and 11 is 13.3842 -colvars: Distance between frame 11 and 12 is 11.9956 -colvars: Distance between frame 12 and 13 is 13.2179 -colvars: Distance between frame 13 and 14 is 13.2532 -colvars: Distance between frame 14 and 15 is 13.4171 -colvars: Distance between frame 15 and 16 is 13.4199 -colvars: Distance between frame 16 and 17 is 13.4188 -colvars: Distance between frame 17 and 18 is 13.3433 -colvars: Distance between frame 18 and 19 is 13.2697 -colvars: Distance between frame 19 and 20 is 13.0715 -colvars: Distance between frame 20 and 21 is 13.3511 -colvars: Distance between frame 21 and 22 is 12.7202 -colvars: Distance between frame 22 and 23 is 13.2064 -colvars: Distance between frame 23 and 24 is 13.3364 -colvars: Distance between frame 24 and 25 is 13.3914 -colvars: Distance between frame 25 and 26 is 13.4199 -colvars: Distance between frame 26 and 27 is 13.4148 -colvars: Distance between frame 27 and 28 is 13.3844 -colvars: Distance between frame 28 and 29 is 13.3858 -colvars: Distance between frame 29 and 30 is 13.204 -colvars: Distance between frame 30 and 31 is 13.2614 -colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -972,7 +912,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -993,6 +933,25 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - dihedral colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - aspathCV colvar component: +colvars: - azpathCV colvar component: +colvars: n/a +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -1019,11 +978,11 @@ colvars: Re-initialized atom group for variable "apath_z_dihed":0/10. 1 atoms: t colvars: Re-initialized atom group for variable "apath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped index 2279fe2bc..36fd4bb55 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped @@ -10,6 +10,6 @@ colvar { colvar { name apath_z_dihed - x 4.37232316380883e+00 + x 4.37232316380885e+00 } diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj index f2cfedfcc..815ea7a8e 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj +++ b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj @@ -9,14 +9,14 @@ 7 7.81951384906762e-01 -1.12708542497330e+01 8 7.81862402327513e-01 -5.04973060370784e+00 9 7.81744790117315e-01 -4.11017372635214e-01 - 10 7.81727932105477e-01 3.23713799393062e+00 - 11 7.81587394970700e-01 6.52501229704612e+00 + 10 7.81727932105477e-01 3.23713799393060e+00 + 11 7.81587394970700e-01 6.52501229704586e+00 12 7.81406177092293e-01 9.56998059334305e+00 - 13 7.81288506120401e-01 1.08957744035001e+01 + 13 7.81288506120401e-01 1.08957744034999e+01 14 7.81213577479822e-01 1.17023277179725e+01 15 7.81012363824849e-01 1.15317460999164e+01 - 16 7.80904107517137e-01 1.05479253244909e+01 - 17 7.80932778795886e-01 9.25509175496145e+00 - 18 7.80986172825268e-01 7.43274003628034e+00 + 16 7.80904107517137e-01 1.05479253244908e+01 + 17 7.80932778795886e-01 9.25509175496143e+00 + 18 7.80986172825268e-01 7.43274003628036e+00 19 7.81202292537037e-01 5.68220000516656e+00 - 20 7.81356397470272e-01 4.37232316380883e+00 + 20 7.81356397470272e-01 4.37232316380885e+00 diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out index 813a12275..9828f21a4 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_dihed" @@ -32,56 +34,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -97,56 +99,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -162,56 +164,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -446,37 +448,6 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] -colvars: Distance between frame 1 and 2 is 13.3844 -colvars: Distance between frame 2 and 3 is 13.3844 -colvars: Distance between frame 3 and 4 is 13.4029 -colvars: Distance between frame 4 and 5 is 13.4142 -colvars: Distance between frame 5 and 6 is 13.4056 -colvars: Distance between frame 6 and 7 is 13.42 -colvars: Distance between frame 7 and 8 is 13.3375 -colvars: Distance between frame 8 and 9 is 13.4007 -colvars: Distance between frame 9 and 10 is 13.0106 -colvars: Distance between frame 10 and 11 is 13.3842 -colvars: Distance between frame 11 and 12 is 11.9956 -colvars: Distance between frame 12 and 13 is 13.2179 -colvars: Distance between frame 13 and 14 is 13.2532 -colvars: Distance between frame 14 and 15 is 13.4171 -colvars: Distance between frame 15 and 16 is 13.4199 -colvars: Distance between frame 16 and 17 is 13.4188 -colvars: Distance between frame 17 and 18 is 13.3433 -colvars: Distance between frame 18 and 19 is 13.2697 -colvars: Distance between frame 19 and 20 is 13.0715 -colvars: Distance between frame 20 and 21 is 13.3511 -colvars: Distance between frame 21 and 22 is 12.7202 -colvars: Distance between frame 22 and 23 is 13.2064 -colvars: Distance between frame 23 and 24 is 13.3364 -colvars: Distance between frame 24 and 25 is 13.3914 -colvars: Distance between frame 25 and 26 is 13.4199 -colvars: Distance between frame 26 and 27 is 13.4148 -colvars: Distance between frame 27 and 28 is 13.3844 -colvars: Distance between frame 28 and 29 is 13.3858 -colvars: Distance between frame 29 and 30 is 13.204 -colvars: Distance between frame 30 and 31 is 13.2614 -colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -486,7 +457,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -518,56 +489,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -583,56 +554,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -648,56 +619,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -932,37 +903,6 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] -colvars: Distance between frame 1 and 2 is 13.3844 -colvars: Distance between frame 2 and 3 is 13.3844 -colvars: Distance between frame 3 and 4 is 13.4029 -colvars: Distance between frame 4 and 5 is 13.4142 -colvars: Distance between frame 5 and 6 is 13.4056 -colvars: Distance between frame 6 and 7 is 13.42 -colvars: Distance between frame 7 and 8 is 13.3375 -colvars: Distance between frame 8 and 9 is 13.4007 -colvars: Distance between frame 9 and 10 is 13.0106 -colvars: Distance between frame 10 and 11 is 13.3842 -colvars: Distance between frame 11 and 12 is 11.9956 -colvars: Distance between frame 12 and 13 is 13.2179 -colvars: Distance between frame 13 and 14 is 13.2532 -colvars: Distance between frame 14 and 15 is 13.4171 -colvars: Distance between frame 15 and 16 is 13.4199 -colvars: Distance between frame 16 and 17 is 13.4188 -colvars: Distance between frame 17 and 18 is 13.3433 -colvars: Distance between frame 18 and 19 is 13.2697 -colvars: Distance between frame 19 and 20 is 13.0715 -colvars: Distance between frame 20 and 21 is 13.3511 -colvars: Distance between frame 21 and 22 is 12.7202 -colvars: Distance between frame 22 and 23 is 13.2064 -colvars: Distance between frame 23 and 24 is 13.3364 -colvars: Distance between frame 24 and 25 is 13.3914 -colvars: Distance between frame 25 and 26 is 13.4199 -colvars: Distance between frame 26 and 27 is 13.4148 -colvars: Distance between frame 27 and 28 is 13.3844 -colvars: Distance between frame 28 and 29 is 13.3858 -colvars: Distance between frame 29 and 30 is 13.204 -colvars: Distance between frame 30 and 31 is 13.2614 -colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -972,7 +912,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -993,6 +933,25 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - dihedral colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - aspathCV colvar component: +colvars: - azpathCV colvar component: +colvars: n/a +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -1018,17 +977,17 @@ colvars: Re-initialized atom group for variable "apath_z_dihed":0/9. 1 atoms: to colvars: Re-initialized atom group for variable "apath_z_dihed":0/10. 1 atoms: total mass = 12.01, total charge = 0.0337. colvars: Re-initialized atom group for variable "apath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "apath_s_dihed" from value: 0.781356 colvars: Restarting collective variable "apath_z_dihed" from value: 4.37232 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj index 5c831af6c..c7068744f 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step apath_s_dihed apath_z_dihed - 20 7.81356397470272e-01 4.37232316380883e+00 + 20 7.81356397470272e-01 4.37232316380885e+00 21 7.81121297977296e-01 1.48408014536711e+01 22 7.80887161764356e-01 2.57385064204216e+01 - 23 7.80608432401527e-01 3.70202491380727e+01 - 24 7.80239933131218e-01 4.91093814693698e+01 - 25 7.79948040898093e-01 6.12096791457024e+01 + 23 7.80608432401527e-01 3.70202491380729e+01 + 24 7.80239933131218e-01 4.91093814693695e+01 + 25 7.79948040898093e-01 6.12096791457022e+01 26 7.79597382762391e-01 7.25781789569762e+01 - 27 7.79139962688763e-01 8.28720619927337e+01 - 28 7.78844243269635e-01 9.18816600988182e+01 - 29 7.78543385360186e-01 9.80096734023498e+01 + 27 7.79139962688763e-01 8.28720619927340e+01 + 28 7.78844243269635e-01 9.18816600988179e+01 + 29 7.78543385360186e-01 9.80096734023500e+01 30 7.78375612820579e-01 1.02527289564776e+02 31 7.78133685857404e-01 1.06109051968502e+02 32 7.77909386932695e-01 1.08483291935737e+02 - 33 7.77812868144174e-01 1.08011291253484e+02 - 34 7.77834700404172e-01 1.06277606048477e+02 - 35 7.77805205280961e-01 1.03033626610267e+02 - 36 7.77952856594698e-01 9.86638072614035e+01 + 33 7.77812868144173e-01 1.08011291253484e+02 + 34 7.77834700404172e-01 1.06277606048478e+02 + 35 7.77805205280960e-01 1.03033626610267e+02 + 36 7.77952856594698e-01 9.86638072614039e+01 37 7.78335111156798e-01 9.35772864178580e+01 38 7.78830800008326e-01 8.79413506004191e+01 - 39 7.79581636252493e-01 8.25355761517518e+01 + 39 7.79581636252493e-01 8.25355761517521e+01 40 7.80351655557853e-01 7.76247569132204e+01 diff --git a/namd/tests/library/023_apathCV/namd-version.txt b/namd/tests/library/023_apathCV/namd-version.txt index 90b3a010a..157cac038 100644 --- a/namd/tests/library/023_apathCV/namd-version.txt +++ b/namd/tests/library/023_apathCV/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA -colvars: Initializing the collective variables module, version "2019-10-21". -colvars: Using NAMD interface, version "2019-10-21". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out index 584abb889..054d4b4fb 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +57,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +89,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,28 +114,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -144,7 +146,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -172,6 +174,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.001 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -182,17 +185,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped index 1500d4fef..dc898032e 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name one - x 3.21687540056419e+00 + x 3.21687540035845e+00 } colvar { name two - x 3.24433796455973e+00 + x 3.24433796460560e+00 } restraint { diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj index b7cc76f65..6a7d2b487 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one two 0 3.20554673468334e+00 -3.10554673468334e-03 3.24960869251665e+00 - 1 3.20437145934575e+00 -3.10437145934575e-03 3.24790015328139e+00 - 2 3.20384019096733e+00 -3.10384019096733e-03 3.24647131781566e+00 - 3 3.20396699952362e+00 -3.10396699952362e-03 3.24540254818933e+00 - 4 3.20472779828314e+00 -3.10472779828314e-03 3.24474238729480e+00 - 5 3.20606250100725e+00 -3.10606250100725e-03 3.24450566312581e+00 - 6 3.20787906480694e+00 -3.10787906480694e-03 3.24467445124404e+00 - 7 3.21005887076690e+00 -3.11005887076690e-03 3.24520146026706e+00 - 8 3.21246317931445e+00 -3.11246317931445e-03 3.24601517487488e+00 - 9 3.21494069579163e+00 -3.11494069579163e-03 3.24702593003580e+00 - 10 3.21733635389196e+00 -3.11733635389196e-03 3.24813222862814e+00 - 11 3.21950110810599e+00 -3.11950110810599e-03 3.24922682019398e+00 - 12 3.22130200113352e+00 -3.12130200113352e-03 3.25020238851898e+00 - 13 3.22263134347621e+00 -3.12263134347621e-03 3.25095680348327e+00 - 14 3.22341377064230e+00 -3.12341377064230e-03 3.25139789467301e+00 - 15 3.22361031727151e+00 -3.12361031727151e-03 3.25144752036343e+00 - 16 3.22321924445923e+00 -3.12321924445923e-03 3.25104461580106e+00 - 17 3.22227396709780e+00 -3.12227396709780e-03 3.25014689317864e+00 - 18 3.22083879579240e+00 -3.12083879579240e-03 3.24873103004102e+00 - 19 3.21900323747919e+00 -3.11900323747919e-03 3.24679144030174e+00 - 20 3.21687540056419e+00 -3.11687540056419e-03 3.24433796455973e+00 + 1 3.20437145934513e+00 -3.10437145934513e-03 3.24790015328133e+00 + 2 3.20384019096481e+00 -3.10384019096481e-03 3.24647131781550e+00 + 3 3.20396699951790e+00 -3.10396699951790e-03 3.24540254818910e+00 + 4 3.20472779827294e+00 -3.10472779827294e-03 3.24474238729463e+00 + 5 3.20606250099130e+00 -3.10606250099130e-03 3.24450566312591e+00 + 6 3.20787906478401e+00 -3.10787906478401e-03 3.24467445124469e+00 + 7 3.21005887073584e+00 -3.11005887073584e-03 3.24520146026858e+00 + 8 3.21246317927417e+00 -3.11246317927417e-03 3.24601517487763e+00 + 9 3.21494069574114e+00 -3.11494069574114e-03 3.24702593004012e+00 + 10 3.21733635383034e+00 -3.11733635383034e-03 3.24813222863437e+00 + 11 3.21950110803244e+00 -3.11950110803244e-03 3.24922682020241e+00 + 12 3.22130200104731e+00 -3.12130200104731e-03 3.25020238852994e+00 + 13 3.22263134337672e+00 -3.12263134337672e-03 3.25095680349705e+00 + 14 3.22341377052897e+00 -3.12341377052897e-03 3.25139789468993e+00 + 15 3.22361031714383e+00 -3.12361031714383e-03 3.25144752038385e+00 + 16 3.22321924431675e+00 -3.12321924431675e-03 3.25104461582539e+00 + 17 3.22227396694008e+00 -3.12227396694008e-03 3.25014689320737e+00 + 18 3.22083879561905e+00 -3.12083879561905e-03 3.24873103007473e+00 + 19 3.21900323728982e+00 -3.11900323728982e-03 3.24679144034112e+00 + 20 3.21687540035845e+00 -3.11687540035845e-03 3.24433796460560e+00 diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out index 4ef6865a5..924e11490 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.new.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "two" @@ -55,28 +57,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,7 +89,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,6 +117,7 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "two" will be rescaled to 0.001 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -125,19 +128,35 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "two" from value: 3.24434 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped index e7f40a07f..fdc8f77c4 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name two - x 3.14862665152884e+00 + x 3.14862665177989e+00 } restraint { diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj index 7ce7af5cf..105050dcc 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step two - 20 3.24433796455973e+00 - 21 3.24139291201932e+00 - 22 3.23798801576814e+00 - 23 3.23416154803027e+00 - 24 3.22995568088397e+00 - 25 3.22541422324222e+00 - 26 3.22058076815832e+00 - 27 3.21549743755863e+00 - 28 3.21020446900326e+00 - 29 3.20474085858739e+00 - 30 3.19914608353898e+00 - 31 3.19346261286550e+00 - 32 3.18773858967743e+00 - 33 3.18202996211599e+00 - 34 3.17640140665043e+00 - 35 3.17092573590606e+00 - 36 3.16568187371138e+00 - 37 3.16075175397829e+00 - 38 3.15621655954144e+00 - 39 3.15215255842149e+00 - 40 3.14862665152884e+00 + 20 3.24433796460560e+00 + 21 3.24139291207264e+00 + 22 3.23798801582996e+00 + 23 3.23416154810177e+00 + 24 3.22995568096637e+00 + 25 3.22541422333673e+00 + 26 3.22058076826608e+00 + 27 3.21549743768062e+00 + 28 3.21020446914023e+00 + 29 3.20474085873977e+00 + 30 3.19914608370685e+00 + 31 3.19346261304852e+00 + 32 3.18773858987485e+00 + 33 3.18202996232668e+00 + 34 3.17640140687287e+00 + 35 3.17092573613846e+00 + 36 3.16568187395172e+00 + 37 3.16075175422443e+00 + 38 3.15621655979123e+00 + 39 3.15215255867285e+00 + 40 3.14862665177989e+00 diff --git a/namd/tests/library/024_flexible_restart/namd-version.txt b/namd/tests/library/024_flexible_restart/namd-version.txt index 47e185902..157cac038 100644 --- a/namd/tests/library/024_flexible_restart/namd-version.txt +++ b/namd/tests/library/024_flexible_restart/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-01-27". -colvars: Using NAMD interface, version "2019-12-04". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out index c7ba00d0a..622c1934d 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -12,6 +15,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -25,25 +29,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -63,7 +67,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -88,25 +92,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -128,7 +132,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -153,25 +157,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -197,25 +201,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -241,25 +245,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -282,7 +286,7 @@ colvars: # period = 0 [default] colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -300,6 +304,7 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { rmsd_sym } +colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] @@ -309,6 +314,7 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 100 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd_sym" will be rescaled to 100 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -319,18 +325,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. -colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. -colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. -colvars: Re-initialized atom group for variable "rmsd_min":1/0. 4 atoms: total mass = 15.035, total charge = 0. -colvars: Re-initialized atom group for variable "rmsd_min":2/0. 4 atoms: total mass = 15.035, total charge = 0. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Symmetry-adapted RMSD: +colvars: Ebrahimi2022 https://doi.org/10.1021/acs.jctc.1c01235 +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - Custom functions (Lepton): +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped index 993abc8ee..0067e4445 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped @@ -5,17 +5,17 @@ configuration { colvar { name rmsd - x 1.67010101996501e+00 + x 1.67010101996502e+00 } colvar { name rmsd_sym - x 1.06269628600354e+00 + x 1.06269628600355e+00 } colvar { name rmsd_min - x 1.06269628600354e+00 + x 1.06269628600355e+00 } restraint { diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj index 6974d2232..652bfe40b 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj @@ -3,20 +3,20 @@ 1 2.65583548116796e+00 2.49357076354985e+00 2.49357076354985e+00 2 1.74533483223524e+00 1.47077556782424e+00 1.47077556782424e+00 3 1.40555434624453e+00 1.03079831602729e+00 1.03079831602729e+00 - 4 2.06648653553550e+00 1.82627061136782e+00 1.82627061136782e+00 - 5 2.54017219029394e+00 2.33735720111240e+00 2.33735720111240e+00 - 6 2.44511763951316e+00 2.20810814129124e+00 2.20810814129124e+00 + 4 2.06648653553549e+00 1.82627061136782e+00 1.82627061136782e+00 + 5 2.54017219029395e+00 2.33735720111240e+00 2.33735720111240e+00 + 6 2.44511763951317e+00 2.20810814129125e+00 2.20810814129125e+00 7 1.90917369343023e+00 1.54370117101215e+00 1.54370117101215e+00 - 8 1.46846059624425e+00 8.57092838197605e-01 8.57092838197605e-01 + 8 1.46846059624425e+00 8.57092838197608e-01 8.57092838197608e-01 9 1.73306101411381e+00 1.20805207461003e+00 1.20805207461003e+00 10 2.23122614737732e+00 1.83168666851452e+00 1.83168666851452e+00 11 2.40879160755837e+00 2.03136190092487e+00 2.03136190092487e+00 - 12 2.16660397964880e+00 1.72654978561155e+00 1.72654978561155e+00 - 13 1.72124086387256e+00 1.10943093382589e+00 1.10943093382589e+00 - 14 1.54507113594670e+00 8.13315046570531e-01 8.13315046570531e-01 - 15 1.84201976466439e+00 1.30057662388302e+00 1.30057662388302e+00 - 16 2.18866124657311e+00 1.76429607011380e+00 1.76429607011380e+00 + 12 2.16660397964881e+00 1.72654978561156e+00 1.72654978561156e+00 + 13 1.72124086387257e+00 1.10943093382589e+00 1.10943093382589e+00 + 14 1.54507113594669e+00 8.13315046570523e-01 8.13315046570523e-01 + 15 1.84201976466438e+00 1.30057662388300e+00 1.30057662388300e+00 + 16 2.18866124657310e+00 1.76429607011378e+00 1.76429607011378e+00 17 2.26240711868798e+00 1.85743190829637e+00 1.85743190829637e+00 18 1.99090416866217e+00 1.51280845285182e+00 1.51280845285182e+00 - 19 1.59604958772556e+00 9.31109046188012e-01 9.31109046188012e-01 - 20 1.67010101996501e+00 1.06269628600354e+00 1.06269628600354e+00 + 19 1.59604958772557e+00 9.31109046188018e-01 9.31109046188018e-01 + 20 1.67010101996502e+00 1.06269628600355e+00 1.06269628600355e+00 diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out index 8b384c5c1..0b153b893 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -12,6 +15,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -25,25 +29,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -63,7 +67,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -88,25 +92,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -128,7 +132,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -153,25 +157,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -197,25 +201,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -241,25 +245,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -282,7 +286,7 @@ colvars: # period = 0 [default] colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -300,6 +304,7 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { rmsd_sym } +colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] @@ -309,6 +314,7 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 100 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd_sym" will be rescaled to 100 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -319,25 +325,40 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. -colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. -colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. -colvars: Re-initialized atom group for variable "rmsd_min":1/0. 4 atoms: total mass = 15.035, total charge = 0. -colvars: Re-initialized atom group for variable "rmsd_min":2/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Symmetry-adapted RMSD: +colvars: Ebrahimi2022 https://doi.org/10.1021/acs.jctc.1c01235 +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - rmsd colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - Custom functions (Lepton): +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "rmsd" from value: 1.6701 colvars: Restarting collective variable "rmsd_sym" from value: 1.0627 colvars: Restarting collective variable "rmsd_min" from value: 1.0627 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped index fdae84add..512353c31 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped @@ -10,12 +10,12 @@ colvar { colvar { name rmsd_sym - x 7.26619298562136e-01 + x 7.26619298562140e-01 } colvar { name rmsd_min - x 7.26619298562136e-01 + x 7.26619298562140e-01 } restraint { diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj index b66d34d1e..c1832014e 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step rmsd rmsd_sym rmsd_min - 20 1.67010101996501e+00 1.06269628600354e+00 1.06269628600354e+00 - 21 2.04433892429578e+00 1.60292722878381e+00 1.60292722878381e+00 - 22 2.06240612835228e+00 1.64334625236222e+00 1.64334625236222e+00 - 23 1.72479860434134e+00 1.21752251761603e+00 1.21752251761603e+00 - 24 1.45281664722968e+00 8.31805423263468e-01 8.31805423263468e-01 - 25 1.62193082908377e+00 1.13819710156539e+00 1.13819710156539e+00 - 26 1.91428771037449e+00 1.54849490838439e+00 1.54849490838439e+00 - 27 1.93241576009644e+00 1.57970290898642e+00 1.57970290898642e+00 - 28 1.64032456570087e+00 1.19887684608299e+00 1.19887684608299e+00 - 29 1.42831104802460e+00 8.67878207872020e-01 8.67878207872020e-01 - 30 1.71179394524434e+00 1.27004409838273e+00 1.27004409838273e+00 - 31 2.10204997402056e+00 1.75291645597024e+00 1.75291645597024e+00 - 32 2.16523333046785e+00 1.81717671975520e+00 1.81717671975520e+00 - 33 1.85227206897975e+00 1.41097165384593e+00 1.41097165384593e+00 - 34 1.51283191580260e+00 8.90242598276096e-01 8.90242598276096e-01 - 35 1.65809367768181e+00 1.09671669300779e+00 1.09671669300779e+00 - 36 2.03497663158023e+00 1.59379893021680e+00 1.59379893021680e+00 - 37 2.17858401892649e+00 1.75248645511788e+00 1.75248645511788e+00 - 38 1.99046986313608e+00 1.48057223445693e+00 1.48057223445693e+00 - 39 1.64708037387980e+00 9.18991758873705e-01 9.18991758873705e-01 - 40 1.57261614568718e+00 7.26619298562136e-01 7.26619298562136e-01 + 20 1.67010101996502e+00 1.06269628600355e+00 1.06269628600355e+00 + 21 2.04433892429580e+00 1.60292722878384e+00 1.60292722878384e+00 + 22 2.06240612835231e+00 1.64334625236225e+00 1.64334625236225e+00 + 23 1.72479860434135e+00 1.21752251761604e+00 1.21752251761604e+00 + 24 1.45281664722968e+00 8.31805423263470e-01 8.31805423263470e-01 + 25 1.62193082908379e+00 1.13819710156541e+00 1.13819710156541e+00 + 26 1.91428771037452e+00 1.54849490838443e+00 1.54849490838443e+00 + 27 1.93241576009646e+00 1.57970290898645e+00 1.57970290898645e+00 + 28 1.64032456570088e+00 1.19887684608300e+00 1.19887684608300e+00 + 29 1.42831104802460e+00 8.67878207872016e-01 8.67878207872016e-01 + 30 1.71179394524437e+00 1.27004409838276e+00 1.27004409838276e+00 + 31 2.10204997402061e+00 1.75291645597029e+00 1.75291645597029e+00 + 32 2.16523333046788e+00 1.81717671975523e+00 1.81717671975523e+00 + 33 1.85227206897976e+00 1.41097165384594e+00 1.41097165384594e+00 + 34 1.51283191580260e+00 8.90242598276090e-01 8.90242598276090e-01 + 35 1.65809367768181e+00 1.09671669300780e+00 1.09671669300780e+00 + 36 2.03497663158024e+00 1.59379893021682e+00 1.59379893021682e+00 + 37 2.17858401892652e+00 1.75248645511792e+00 1.75248645511792e+00 + 38 1.99046986313611e+00 1.48057223445696e+00 1.48057223445696e+00 + 39 1.64708037387981e+00 9.18991758873730e-01 9.18991758873730e-01 + 40 1.57261614568718e+00 7.26619298562140e-01 7.26619298562140e-01 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out b/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out index d6f4b9ad4..75a651d7a 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -130,16 +134,29 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - ABF colvar bias implementation: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.grad b/namd/tests/library/026_ABF_energy/AutoDiff/test.grad index 16cf7fcda..46dea61eb 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.grad +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.17682470708695e+01 + 3.25000000000000e+00 -1.17682469793588e+01 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf b/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf index d27977925..665e2643f 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 5.88412353543475e+00 - 5.00000000000000e-01 5.88412353543475e+00 - 1.00000000000000e+00 5.88412353543475e+00 - 1.50000000000000e+00 5.88412353543475e+00 - 2.00000000000000e+00 5.88412353543475e+00 - 2.50000000000000e+00 5.88412353543475e+00 - 3.00000000000000e+00 5.88412353543475e+00 + 0.00000000000000e+00 5.88412348967941e+00 + 5.00000000000000e-01 5.88412348967941e+00 + 1.00000000000000e+00 5.88412348967941e+00 + 1.50000000000000e+00 5.88412348967941e+00 + 2.00000000000000e+00 5.88412348967941e+00 + 2.50000000000000e+00 5.88412348967941e+00 + 3.00000000000000e+00 5.88412348967941e+00 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out index 8def9ee51..865f10f4c 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out @@ -1,9 +1,12 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +45,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -130,21 +134,34 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - ABF colvar bias implementation: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.14228 colvars: Restarting abf bias "abf1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad index 8b57bb739..d348c12f2 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -2.34801645799521e+01 + 3.25000000000000e+00 -2.34801644956595e+01 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf index d2eb54957..08a4d3d5b 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 1.17400822899760e+01 - 5.00000000000000e-01 1.17400822899760e+01 - 1.00000000000000e+00 1.17400822899760e+01 - 1.50000000000000e+00 1.17400822899760e+01 - 2.00000000000000e+00 1.17400822899760e+01 - 2.50000000000000e+00 1.17400822899760e+01 - 3.00000000000000e+00 1.17400822899760e+01 + 0.00000000000000e+00 1.17400822478297e+01 + 5.00000000000000e-01 1.17400822478297e+01 + 1.00000000000000e+00 1.17400822478297e+01 + 1.50000000000000e+00 1.17400822478297e+01 + 2.00000000000000e+00 1.17400822478297e+01 + 2.50000000000000e+00 1.17400822478297e+01 + 3.00000000000000e+00 1.17400822478297e+01 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/namd-version.txt b/namd/tests/library/026_ABF_energy/namd-version.txt index 402dbcc14..157cac038 100644 --- a/namd/tests/library/026_ABF_energy/namd-version.txt +++ b/namd/tests/library/026_ABF_energy/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-06-02". -colvars: Using NAMD interface, version "2020-05-04". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state index ad2a42cd1..ac87bdbc5 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state +++ b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state @@ -11,10 +11,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 8.70939573129658e-05 - 2.70056900100952e-03 3.08054911071083e-02 1.29272634593393e-01 - 1.99567890853138e-01 1.13339251339767e-01 2.36796683891457e-02 - 1.82002141201432e-03 5.14615642408155e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 8.70939574046587e-05 + 2.70056900312946e-03 3.08054911230446e-02 1.29272634625682e-01 + 1.99567890849616e-01 1.13339251307472e-01 2.36796683760721e-02 + 1.82002141052347e-03 5.14615641849260e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -26,10 +26,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 6.85295348342052e-04 - 1.58481831330982e-02 1.19169844898782e-01 2.41540944190337e-01 - -2.62507762651161e-02 -2.41586884557496e-01 -9.78334327140598e-02 - -1.11595284128016e-02 -4.18461587121564e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 6.85295349016874e-04 + 1.58481831440929e-02 1.19169844943943e-01 2.41540944181510e-01 + -2.62507763713641e-02 -2.41586884549233e-01 -9.78334326726952e-02 + -1.11595284046322e-02 -4.18461586694560e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state index ad2a42cd1..ac87bdbc5 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state +++ b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state @@ -11,10 +11,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 8.70939573129658e-05 - 2.70056900100952e-03 3.08054911071083e-02 1.29272634593393e-01 - 1.99567890853138e-01 1.13339251339767e-01 2.36796683891457e-02 - 1.82002141201432e-03 5.14615642408155e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 8.70939574046587e-05 + 2.70056900312946e-03 3.08054911230446e-02 1.29272634625682e-01 + 1.99567890849616e-01 1.13339251307472e-01 2.36796683760721e-02 + 1.82002141052347e-03 5.14615641849260e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -26,10 +26,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 6.85295348342052e-04 - 1.58481831330982e-02 1.19169844898782e-01 2.41540944190337e-01 - -2.62507762651161e-02 -2.41586884557496e-01 -9.78334327140598e-02 - -1.11595284128016e-02 -4.18461587121564e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 6.85295349016874e-04 + 1.58481831440929e-02 1.19169844943943e-01 2.41540944181510e-01 + -2.62507763713641e-02 -2.41586884549233e-01 -9.78334326726952e-02 + -1.11595284046322e-02 -4.18461586694560e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state index 8dcab87f9..30f1b680a 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state +++ b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state @@ -11,10 +11,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.80472754695334e-04 - 5.54447035307032e-03 6.26727287728974e-02 2.60655275982959e-01 - 3.98862365627901e-01 2.24567790825392e-01 4.65199212813745e-02 - 3.54565765888724e-03 9.94306270273247e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.80472755097040e-04 + 5.54447036223268e-03 6.26727288407827e-02 2.60655276117922e-01 + 3.98862365610485e-01 2.24567790690383e-01 4.65199212276517e-02 + 3.54565765284328e-03 9.94306268035517e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -26,10 +26,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.41667561192491e-03 - 3.24357194776196e-02 2.41314963834041e-01 4.82392264961036e-01 - -5.94386857287638e-02 -4.82536713017911e-01 -1.92985724190331e-01 - -2.17993242369277e-02 -8.10150854396533e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.41667561487056e-03 + 3.24357195248848e-02 2.41314964024310e-01 4.82392264917098e-01 + -5.94386861724842e-02 -4.82536712977343e-01 -1.92985724018794e-01 + -2.17993242036534e-02 -8.10150852681438e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out index 93db4f3a8..5a868114a 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +43,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +57,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -113,7 +115,34 @@ colvars: # outputFile = "" [default] colvars: # outputFileDX = "none" [default] colvars: # gatherVectorColvars = off [default] colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. +colvars: Initializing a new "metadynamics" instance. +colvars: # name = "metadynamics1" [default] +colvars: # colvars = { one } +colvars: # stepZeroData = off [default] +colvars: # outputEnergy = off [default] +colvars: # outputFreq = 10 [default] +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] +colvars: # hillWeight = 0.1 +colvars: # newHillFrequency = 10 +colvars: # gaussianSigmas = [default] +colvars: # hillWidth = 2 +colvars: Half-widths of the Gaussian hills (sigma's): +colvars: one: 0.5 +colvars: # multipleReplicas = off [default] +colvars: # useGrids = on [default] +colvars: # gridsUpdateFrequency = 10 [default] +colvars: # rebinGrids = off [default] +colvars: # writeFreeEnergyFile = on [default] +colvars: # keepHills = off [default] +colvars: # keepFreeEnergyFiles = off [default] +colvars: # writeHillsTrajectory = off [default] +colvars: # wellTempered = off [default] +colvars: # biasTemperature = -1 [default] +colvars: # ebMeta = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 2 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- @@ -121,16 +150,31 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". @@ -147,12 +191,6 @@ colvars: Saving collective variables state to "test.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". colvars: Writing the histogram file "test.histogram1.dat". -colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.tmp.colvars.state". -colvars: Writing the histogram file "test.histogram1.dat". -colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.tmp.colvars.state". -colvars: Writing the histogram file "test.histogram1.dat". colvars: Saving collective variables state to "test.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped index b62b4fcd0..eb8fb4fb7 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21415030906913e+00 + x 3.21415030858830e+00 } histogram { @@ -32,10 +32,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.80472754695334e-04 - 5.54447035307032e-03 6.26727287728974e-02 2.60655275982959e-01 - 3.98862365627901e-01 2.24567790825392e-01 4.65199212813745e-02 - 3.54565765888724e-03 9.94306270273247e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.80472755097040e-04 + 5.54447036223268e-03 6.26727288407827e-02 2.60655276117922e-01 + 3.98862365610485e-01 2.24567790690383e-01 4.65199212276517e-02 + 3.54565765284328e-03 9.94306268035517e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -47,10 +47,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.41667561192491e-03 - 3.24357194776196e-02 2.41314963834041e-01 4.82392264961036e-01 - -5.94386857287638e-02 -4.82536713017911e-01 -1.92985724190331e-01 - -2.17993242369277e-02 -8.10150854396533e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.41667561487056e-03 + 3.24357195248848e-02 2.41314964024310e-01 4.82392264917098e-01 + -5.94386861724842e-02 -4.82536712977343e-01 -1.92985724018794e-01 + -2.17993242036534e-02 -8.10150852681438e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj index e04394664..31091a629 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj @@ -1,44 +1,44 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 1.30367508599117e-02 - 11 3.21950387402611e+00 1.30367508599117e-02 - 12 3.22130559667303e+00 1.30367508599117e-02 - 13 3.22263598363115e+00 1.30367508599117e-02 - 14 3.22341966120443e+00 1.30367508599117e-02 - 15 3.22361765312655e+00 1.30367508599117e-02 - 16 3.22322820827659e+00 1.30367508599117e-02 - 17 3.22228472844791e+00 1.30367508599117e-02 - 18 3.22085151070423e+00 1.30367508599117e-02 - 19 3.21901804842838e+00 1.30367508599117e-02 - 20 3.21689243687284e+00 2.62507762651161e-02 - 20 3.21689243687284e+00 2.62507762651161e-02 - 20 3.21689243687284e+00 2.62507762651161e-02 - 21 3.21459439262285e+00 2.62507762651161e-02 - 22 3.21224726559843e+00 2.62507762651161e-02 - 23 3.20997056390844e+00 2.62507762651161e-02 - 24 3.20787270665228e+00 2.62507762651161e-02 - 25 3.20604492549381e+00 2.62507762651161e-02 - 26 3.20455694872830e+00 2.62507762651161e-02 - 27 3.20345479595789e+00 2.62507762651161e-02 - 28 3.20276061095329e+00 2.62507762651161e-02 - 29 3.20247408294778e+00 2.62507762651161e-02 - 30 3.20257503707633e+00 4.51356212534586e-02 - 31 3.20302710767604e+00 4.51356212534586e-02 - 32 3.20378117631245e+00 4.51356212534586e-02 - 33 3.20478014934277e+00 4.51356212534586e-02 - 34 3.20596369604249e+00 4.51356212534586e-02 - 35 3.20727281823071e+00 4.51356212534586e-02 - 36 3.20865380579304e+00 4.51356212534586e-02 - 37 3.21006125769230e+00 4.51356212534586e-02 - 38 3.21146012440951e+00 4.51356212534586e-02 - 39 3.21282692152683e+00 4.51356212534586e-02 - 40 3.21415030906913e+00 5.94386857287638e-02 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000757e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 1.30367508844061e-02 + 11 3.21950387395255e+00 1.30367508844061e-02 + 12 3.22130559658681e+00 1.30367508844061e-02 + 13 3.22263598353165e+00 1.30367508844061e-02 + 14 3.22341966109109e+00 1.30367508844061e-02 + 15 3.22361765299886e+00 1.30367508844061e-02 + 16 3.22322820813411e+00 1.30367508844061e-02 + 17 3.22228472829020e+00 1.30367508844061e-02 + 18 3.22085151053088e+00 1.30367508844061e-02 + 19 3.21901804823901e+00 1.30367508844061e-02 + 20 3.21689243666711e+00 2.62507763713641e-02 + 20 3.21689243666711e+00 2.62507763713641e-02 + 20 3.21689243666711e+00 2.62507763713641e-02 + 21 3.21459439240045e+00 2.62507763713641e-02 + 22 3.21224726535912e+00 2.62507763713641e-02 + 23 3.20997056365207e+00 2.62507763713641e-02 + 24 3.20787270637879e+00 2.62507763713641e-02 + 25 3.20604492520325e+00 2.62507763713641e-02 + 26 3.20455694842083e+00 2.62507763713641e-02 + 27 3.20345479563379e+00 2.62507763713641e-02 + 28 3.20276061061291e+00 2.62507763713641e-02 + 29 3.20247408259157e+00 2.62507763713641e-02 + 30 3.20257503670478e+00 4.51356215063288e-02 + 31 3.20302710728970e+00 4.51356215063288e-02 + 32 3.20378117591190e+00 4.51356215063288e-02 + 33 3.20478014892865e+00 4.51356215063288e-02 + 34 3.20596369561551e+00 4.51356215063288e-02 + 35 3.20727281779169e+00 4.51356215063288e-02 + 36 3.20865380534294e+00 4.51356215063288e-02 + 37 3.21006125723226e+00 4.51356215063288e-02 + 38 3.21146012394088e+00 4.51356215063288e-02 + 39 3.21282692105120e+00 4.51356215063288e-02 + 40 3.21415030858830e+00 5.94386861724842e-02 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf b/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf index d85393c4f..af5f3fa27 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.98862365627901e-01 - 7.50000000000000e-01 3.98862365627901e-01 - 1.25000000000000e+00 3.98681892873206e-01 - 1.75000000000000e+00 3.93317895274831e-01 - 2.25000000000000e+00 3.36189636855004e-01 - 2.75000000000000e+00 1.38207089644942e-01 + 2.50000000000000e-01 3.98862365610485e-01 + 7.50000000000000e-01 3.98862365610485e-01 + 1.25000000000000e+00 3.98681892855388e-01 + 1.75000000000000e+00 3.93317895248252e-01 + 2.25000000000000e+00 3.36189636769702e-01 + 2.75000000000000e+00 1.38207089492563e-01 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.74294574802509e-01 - 4.25000000000000e+00 3.52342444346527e-01 - 4.75000000000000e+00 3.95316707969014e-01 - 5.25000000000000e+00 3.98762935000874e-01 - 5.75000000000000e+00 3.98862365627901e-01 - 6.25000000000000e+00 3.98862365627901e-01 - 6.75000000000000e+00 3.98862365627901e-01 - 7.25000000000000e+00 3.98862365627901e-01 - 7.75000000000000e+00 3.98862365627901e-01 - 8.25000000000000e+00 3.98862365627901e-01 - 8.75000000000000e+00 3.98862365627901e-01 - 9.25000000000000e+00 3.98862365627901e-01 - 9.75000000000000e+00 3.98862365627901e-01 + 3.75000000000000e+00 1.74294574920103e-01 + 4.25000000000000e+00 3.52342444382833e-01 + 4.75000000000000e+00 3.95316707957642e-01 + 5.25000000000000e+00 3.98762934983682e-01 + 5.75000000000000e+00 3.98862365610485e-01 + 6.25000000000000e+00 3.98862365610485e-01 + 6.75000000000000e+00 3.98862365610485e-01 + 7.25000000000000e+00 3.98862365610485e-01 + 7.75000000000000e+00 3.98862365610485e-01 + 8.25000000000000e+00 3.98862365610485e-01 + 8.75000000000000e+00 3.98862365610485e-01 + 9.25000000000000e+00 3.98862365610485e-01 + 9.75000000000000e+00 3.98862365610485e-01 diff --git a/namd/tests/library/027_multiple_runs/namd-version.txt b/namd/tests/library/027_multiple_runs/namd-version.txt index 402dbcc14..157cac038 100644 --- a/namd/tests/library/027_multiple_runs/namd-version.txt +++ b/namd/tests/library/027_multiple_runs/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-06-02". -colvars: Using NAMD interface, version "2020-05-04". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out index f8931d8a7..9a80820be 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out @@ -1,17 +1,21 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "test.legacy.in": +colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 10 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "c" @@ -56,18 +60,13 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. colvars: Warning: Variable r2 is absent from expression "atan2(r3, r1) * 180 / 3.1415926". -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r1. -colvars: Warning: Variable r1 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r3 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r3. colvars: Expecting colvar value of type scalar number. colvars: # period = 360 colvars: # wrapAround = 0 colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -95,6 +94,7 @@ colvars: # centers = { -179 } colvars: # targetCenters = { -179 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.01 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "c" will be rescaled to 0.01 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -105,15 +105,31 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. -colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - Custom functions (Lepton): +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out index fc34e52ef..b5c095d75 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out @@ -1,17 +1,21 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "test.legacy.in": +colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 10 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "c" @@ -56,18 +60,13 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. colvars: Warning: Variable r2 is absent from expression "atan2(r3, r1) * 180 / 3.1415926". -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r1. -colvars: Warning: Variable r1 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r3 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r3. colvars: Expecting colvar value of type scalar number. colvars: # period = 360 colvars: # wrapAround = 0 colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -95,6 +94,7 @@ colvars: # centers = { -179 } colvars: # targetCenters = { -179 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.01 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "c" will be rescaled to 0.01 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -105,20 +105,36 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. -colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: - Custom functions (Lepton): +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "c" from value: 157.339 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/028_periodic_custom_function/namd-version.txt b/namd/tests/library/028_periodic_custom_function/namd-version.txt index fb5cc08df..157cac038 100644 --- a/namd/tests/library/028_periodic_custom_function/namd-version.txt +++ b/namd/tests/library/028_periodic_custom_function/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 3.0alpha8 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2021-03-09". -colvars: Using NAMD interface, version "2021-03-02". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.out b/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.out index 9367eb566..953bbf98c 100644 --- a/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.out +++ b/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.out @@ -1,9 +1,10 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,6 +14,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "end_to_end_distance" @@ -151,7 +153,7 @@ colvars: # outputFileDX = "none" [default] colvars: # gatherVectorColvars = off [default] colvars: # CollectAfterSteps = 0 [default] colvars: # CumulantExpansion = on [default] -colvars: # WriteGradients = on [default] +colvars: # WritePMFGradients = on [default] colvars: # historyFreq = 10 colvars: WARNING: there are 2 time-dependent biases with non-zero force parameters: colvars: { production_abf, production_mtd } @@ -164,6 +166,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -177,6 +180,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 3 } colvars: # upperWalls = { 14 } @@ -197,45 +201,54 @@ colvars: Warning: enabling wrapAll can lead to inconsistent results for Colvars colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - BAOA integrator: +colvars: BouRabee2010 https://doi.org/10.1137/090758842 +colvars: +colvars: - reweightaMD colvar bias implementation (NAMD): +colvars: Chen2021 https://doi.org/10.1021/acs.jctc.1c00103 +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Metadynamics colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - harmonicWalls colvar bias implementation: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - ABF colvar bias implementation: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - CZAR eABF estimator: +colvars: - eABF implementation: +colvars: Lesage2017 https://doi.org/10.1021/acs.jpcb.6b10055 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "end_to_end_distance":0/0. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "end_to_end_distance":0/1. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Initializing step number as firstTimestep. colvars: Updating NAMD interface: colvars: Warning: enabling wrapAll can lead to inconsistent results for Colvars calculations: please disable wrapAll, as is the default option in NAMD. colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "end_to_end_distance":0/0. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "end_to_end_distance":0/1. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". colvars: Prepared sample and gradient buffers at step 500000000. colvars: Metadynamics bias "production_mtd": new upper boundary for colvar "end_to_end_distance", at 16.2. -colvars: Writing the accelerated MD PMF file "test.production_amd.reweight.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.reweight.grad". -colvars: Writing the accelerated MD count file "test.production_amd.count". -colvars: Writing the accelerated MD PMF file "test.production_amd.reweight.hist.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.reweight.hist.grad". -colvars: Writing the accelerated MD count file "test.production_amd.hist.count". -colvars: Writing the accelerated MD PMF file using cumulant expansion: "test.production_amd.cumulant.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.cumulant.grad". -colvars: Writing the accelerated MD PMF file using cumulant expansion: "test.production_amd.cumulant.hist.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.cumulant.hist.grad". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Writing the accelerated MD PMF file "test.production_amd.reweight.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.reweight.grad". -colvars: Writing the accelerated MD count file "test.production_amd.count". -colvars: Writing the accelerated MD PMF file "test.production_amd.reweight.hist.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.reweight.hist.grad". -colvars: Writing the accelerated MD count file "test.production_amd.hist.count". -colvars: Writing the accelerated MD PMF file using cumulant expansion: "test.production_amd.cumulant.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.cumulant.grad". -colvars: Writing the accelerated MD PMF file using cumulant expansion: "test.production_amd.cumulant.hist.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.cumulant.hist.grad". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.colvars.state". colvars: Writing the accelerated MD PMF file "test.production_amd.reweight.pmf". @@ -248,16 +261,6 @@ colvars: Writing the accelerated MD PMF file using cumulant expansion: "test.p colvars: Writing the accelerated MD gradients file "test.production_amd.cumulant.grad". colvars: Writing the accelerated MD PMF file using cumulant expansion: "test.production_amd.cumulant.hist.pmf". colvars: Writing the accelerated MD gradients file "test.production_amd.cumulant.hist.grad". -colvars: Writing the accelerated MD PMF file "test.production_amd.reweight.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.reweight.grad". -colvars: Writing the accelerated MD count file "test.production_amd.count". -colvars: Writing the accelerated MD PMF file "test.production_amd.reweight.hist.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.reweight.hist.grad". -colvars: Writing the accelerated MD count file "test.production_amd.hist.count". -colvars: Writing the accelerated MD PMF file using cumulant expansion: "test.production_amd.cumulant.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.cumulant.grad". -colvars: Writing the accelerated MD PMF file using cumulant expansion: "test.production_amd.cumulant.hist.pmf". -colvars: Writing the accelerated MD gradients file "test.production_amd.cumulant.hist.grad". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.colvars.state". colvars: Writing the accelerated MD PMF file "test.production_amd.reweight.pmf". diff --git a/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.state.stripped b/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.state.stripped index 068879497..7eddd64b0 100644 --- a/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.state.stripped @@ -5,9 +5,9 @@ configuration { colvar { name end_to_end_distance - x 1.45658595679527e+01 - extended_x 1.45679030161301e+01 - extended_v -3.36435197039109e-04 + x 1.45658974873707e+01 + extended_x 1.45679724556133e+01 + extended_v -3.38170305625943e-04 } abf { diff --git a/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.traj b/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.traj index 04ba1fe63..1d73f6422 100644 --- a/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.traj +++ b/namd/tests/library/029_reweightamd/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step end_to_end_distance r_end_to_end_distance 500000000 1.45755558523024e+01 1.45755558523024e+01 - 500000001 1.45693359473303e+01 1.45755446081083e+01 - 500000002 1.45628402190201e+01 1.45754140089661e+01 - 500000003 1.45566980726478e+01 1.45751765694009e+01 - 500000004 1.45518722505900e+01 1.45751147140370e+01 - 500000005 1.45481722064913e+01 1.45748892991244e+01 - 500000006 1.45465111153725e+01 1.45749016780397e+01 - 500000007 1.45465013918011e+01 1.45750705918230e+01 - 500000008 1.45480404597657e+01 1.45748366095764e+01 - 500000009 1.45519258972887e+01 1.45743007914383e+01 - 500000010 1.45581216093189e+01 1.45738263846955e+01 - 500000011 1.45621006734552e+01 1.45732654404771e+01 - 500000012 1.45669373702181e+01 1.45727559925024e+01 - 500000013 1.45711318686060e+01 1.45719919701784e+01 - 500000014 1.45751961651583e+01 1.45713341151667e+01 - 500000015 1.45777741345957e+01 1.45706842018549e+01 - 500000016 1.45789047468076e+01 1.45700236082559e+01 - 500000017 1.45784967568080e+01 1.45693339831311e+01 - 500000018 1.45763907761870e+01 1.45687607451921e+01 - 500000019 1.45718203234566e+01 1.45682394513271e+01 - 500000020 1.45658595679527e+01 1.45679030161301e+01 + 500000001 1.45693359473303e+01 1.45755502358228e+01 + 500000002 1.45628402410838e+01 1.45754763156054e+01 + 500000003 1.45566983601392e+01 1.45752862080976e+01 + 500000004 1.45518732211679e+01 1.45751274162263e+01 + 500000005 1.45481738712624e+01 1.45749722682313e+01 + 500000006 1.45465137388615e+01 1.45748524055470e+01 + 500000007 1.45465046874642e+01 1.45749287358700e+01 + 500000008 1.45480437633554e+01 1.45748820642582e+01 + 500000009 1.45519292949635e+01 1.45744842122370e+01 + 500000010 1.45581257379899e+01 1.45739682718371e+01 + 500000011 1.45621059888141e+01 1.45734429362649e+01 + 500000012 1.45669444392867e+01 1.45729021680397e+01 + 500000013 1.45711410887856e+01 1.45722624634006e+01 + 500000014 1.45752083670870e+01 1.45715508189035e+01 + 500000015 1.45777898545186e+01 1.45708983011225e+01 + 500000016 1.45789244204116e+01 1.45702458137939e+01 + 500000017 1.45785207566311e+01 1.45695741760963e+01 + 500000018 1.45764194478224e+01 1.45689461002292e+01 + 500000019 1.45718536943028e+01 1.45684011973632e+01 + 500000020 1.45658974873707e+01 1.45679724556133e+01 diff --git a/namd/tests/library/029_reweightamd/namd-version.txt b/namd/tests/library/029_reweightamd/namd-version.txt index fffa4ec38..157cac038 100644 --- a/namd/tests/library/029_reweightamd/namd-version.txt +++ b/namd/tests/library/029_reweightamd/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2021-03-09". -colvars: Using NAMD interface, version "2021-03-02". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out index 1152d4a8f..e3bbc2221 100644 --- a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out +++ b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out @@ -4,6 +4,7 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "end_to_end_distance" @@ -86,7 +88,6 @@ colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # scaledBiasingForce = on colvars: # scaledBiasingForceFactorsGrid = "factors.grid" -colvars: Reading scaling factors for the forces of bias production_abf from factors.grid colvars: # applyBias = on [default] colvars: # updateBias = on [default] colvars: # hideJacobian = off [default] @@ -108,7 +109,6 @@ colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # scaledBiasingForce = on colvars: # scaledBiasingForceFactorsGrid = "factors.grid" -colvars: Reading scaling factors for the forces of bias production_mtd from factors.grid colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # hillWeight = 2 @@ -142,6 +142,7 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -155,6 +156,7 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 13 } colvars: # upperWalls = { 15 } @@ -194,17 +196,17 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "end_to_end_distance":0/0. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "end_to_end_distance":0/1. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: Warning: enabling wrapAll can lead to inconsistent results for Colvars calculations: please disable wrapAll, as is the default option in NAMD. colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "end_to_end_distance":0/0. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "end_to_end_distance":0/1. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.colvars.state". diff --git a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped index 2983b7392..aaafe01d2 100644 --- a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped @@ -61,9 +61,9 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 -2.46034201565942e+01 -1.71228758550407e+01 -4.35028348233554e+00 8.77100343862862e+00 0.00000000000000e+00 2.41578842131827e+01 - 0.00000000000000e+00 3.67760957979561e+01 0.00000000000000e+00 0.00000000000000e+00 4.03080315983995e+01 0.00000000000000e+00 4.91740802690014e+01 0.00000000000000e+00 - 4.58607749339655e+01 0.00000000000000e+00 5.28741550375132e+01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 -2.46034201565941e+01 -1.71228758550381e+01 -4.35028348233383e+00 8.77100343862926e+00 0.00000000000000e+00 2.41578842132070e+01 + 0.00000000000000e+00 3.67760957979660e+01 0.00000000000000e+00 0.00000000000000e+00 4.03080315984188e+01 0.00000000000000e+00 4.91740802690052e+01 0.00000000000000e+00 + 4.58607749339768e+01 0.00000000000000e+00 5.28741550375003e+01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -129,20 +129,20 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 2.61587935066948e-05 1.94683970632219e-04 - 1.08251565029956e-03 5.09475130902452e-03 2.04659308796341e-02 - 7.06125286653960e-02 2.09435976415474e-01 5.34918613697393e-01 - 1.17861358817316e+00 2.24504431300069e+00 3.70656454838293e+00 - 5.32145917169682e+00 6.67261938563242e+00 7.35195926071138e+00 - 7.18021399808696e+00 6.29685877472059e+00 5.06102998507698e+00 - 3.86183081585080e+00 2.97265484622012e+00 2.49720984195906e+00 - 2.38143486949602e+00 2.47333896395524e+00 2.62156486038390e+00 - 2.76069831296907e+00 2.91199826509736e+00 3.10017196004723e+00 - 3.27504048000479e+00 3.31818588496156e+00 3.12189683918944e+00 - 2.66602374122993e+00 2.03536975844466e+00 1.37396310594875e+00 - 8.12936839979314e-01 4.18576183808133e-01 1.86468431860379e-01 - 7.15657207977159e-02 2.35824489723058e-02 6.65642098673127e-03 - 1.60673261084573e-03 3.28034119055107e-04 5.79178127982759e-05 + 0.00000000000000e+00 2.61587935067117e-05 1.94683970632333e-04 + 1.08251565030012e-03 5.09475130902687e-03 2.04659308796424e-02 + 7.06125286654209e-02 2.09435976415536e-01 5.34918613697524e-01 + 1.17861358817339e+00 2.24504431300101e+00 3.70656454838329e+00 + 5.32145917169711e+00 6.67261938563254e+00 7.35195926071128e+00 + 7.18021399808668e+00 6.29685877472027e+00 5.06102998507674e+00 + 3.86183081585070e+00 2.97265484622017e+00 2.49720984195920e+00 + 2.38143486949621e+00 2.47333896395547e+00 2.62156486038421e+00 + 2.76069831296951e+00 2.91199826509797e+00 3.10017196004795e+00 + 3.27504048000548e+00 3.31818588496202e+00 3.12189683918950e+00 + 2.66602374122956e+00 2.03536975844399e+00 1.37396310594800e+00 + 8.12936839978680e-01 4.18576183807702e-01 1.86468431860140e-01 + 7.15657207976055e-02 2.35824489722632e-02 6.65642098671754e-03 + 1.60673261084200e-03 3.28034119054257e-04 5.79178127981109e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -204,20 +204,20 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 4.98572553752153e-03 3.44543416760067e-02 - 1.75326645541099e-01 7.47482721294938e-01 2.68947029660812e+00 - 8.20870614494365e+00 2.11986301746983e+01 4.61909880344138e+01 - 8.44826248580294e+01 1.28506873925868e+02 1.59712391231045e+02 - 1.55977235774219e+02 1.07039391871382e+02 2.56744580181185e+01 - -5.75055838168864e+01 -1.12829758918545e+02 -1.27599236648721e+02 - -1.07606408348132e+02 -6.85243194218847e+01 -2.75641170223432e+01 - 1.69829679655862e+00 1.39955997855602e+01 1.45571151643426e+01 - 1.37895289828585e+01 1.70425441756459e+01 1.97475224737359e+01 - 1.31056573124861e+01 -6.41279019646412e+00 -3.32095989551069e+01 - -5.64631191592285e+01 -6.71337049513984e+01 -6.28686158484858e+01 - -4.82254030908433e+01 -3.07787466327079e+01 -1.64540466073052e+01 - -7.39576145058497e+00 -2.79968734691153e+00 -8.93905835952760e-01 - -2.41013764581735e-01 -5.42598821860181e-02 -1.05068277897928e-02 + 0.00000000000000e+00 4.98572553752462e-03 3.44543416760259e-02 + 1.75326645541183e-01 7.47482721295256e-01 2.68947029660910e+00 + 8.20870614494615e+00 2.11986301747035e+01 4.61909880344223e+01 + 8.44826248580398e+01 1.28506873925876e+02 1.59712391231044e+02 + 1.55977235774206e+02 1.07039391871361e+02 2.56744580180974e+01 + -5.75055838168977e+01 -1.12829758918543e+02 -1.27599236648709e+02 + -1.07606408348117e+02 -6.85243194218725e+01 -2.75641170223360e+01 + 1.69829679656285e+00 1.39955997855656e+01 1.45571151643531e+01 + 1.37895289828742e+01 1.70425441756613e+01 1.97475224737415e+01 + 1.31056573124731e+01 -6.41279019649712e+00 -3.32095989551511e+01 + -5.64631191592674e+01 -6.71337049514181e+01 -6.28686158484828e+01 + -4.82254030908254e+01 -3.07787466326868e+01 -1.64540466072889e+01 + -7.39576145057542e+00 -2.79968734690709e+00 -8.93905835951089e-01 + -2.41013764581217e-01 -5.42598821858858e-02 -1.05068277897643e-02 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj index 90721e014..d76c74714 100644 --- a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj +++ b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj @@ -3,20 +3,20 @@ 1 1.45695261014138e+01 0.00000000000000e+00 2 1.45635632664853e+01 0.00000000000000e+00 3 1.45582489261713e+01 -2.58411685289576e+01 - 4 1.45527923170544e+01 -2.07125939557735e+01 + 4 1.45527923170544e+01 -2.07125939557695e+01 5 1.45473541901844e+01 0.00000000000000e+00 6 1.45442591718140e+01 0.00000000000000e+00 7 1.45431535519741e+01 0.00000000000000e+00 8 1.45439619694008e+01 0.00000000000000e+00 9 1.45475029536962e+01 0.00000000000000e+00 - 10 1.45537536789397e+01 1.61692398555902e+01 - 11 1.45592642275934e+01 1.61692398555902e+01 + 10 1.45537536789397e+01 1.61692398556099e+01 + 11 1.45592642275934e+01 1.61692398556099e+01 12 1.45670515013898e+01 0.00000000000000e+00 - 13 1.45744569915016e+01 1.47925560209933e+02 - 14 1.45916606161846e+01 1.32015920190301e+02 - 15 1.46158023047859e+01 7.80198886000819e+01 + 13 1.45744569915016e+01 1.47925560209934e+02 + 14 1.45916606161846e+01 1.32015920190288e+02 + 15 1.46158023047859e+01 7.80198886000781e+01 16 1.46427017872138e+01 0.00000000000000e+00 - 17 1.46664306062950e+01 0.00000000000000e+00 + 17 1.46664306062949e+01 0.00000000000000e+00 18 1.46862961461938e+01 0.00000000000000e+00 19 1.47010927350238e+01 0.00000000000000e+00 - 20 1.47116192100262e+01 5.64631191592285e+01 + 20 1.47116192100262e+01 5.64631191592674e+01 diff --git a/namd/tests/library/030_scaledBiasingForce/namd-version.txt b/namd/tests/library/030_scaledBiasingForce/namd-version.txt index a8b4c8892..157cac038 100644 --- a/namd/tests/library/030_scaledBiasingForce/namd-version.txt +++ b/namd/tests/library/030_scaledBiasingForce/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2022-01-19. -colvars: Using NAMD interface, version "2021-10-13". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.out b/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.out index d6c3e3625..cbe302858 100644 --- a/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.out +++ b/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.out @@ -4,6 +4,7 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -12,6 +13,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "nn_output_1" @@ -450,106 +452,7 @@ colvars: # layer1_activation = "tanh" colvars: The activation function for layer[1] is tanh colvars: # layer2_activation = "tanh" colvars: The activation function for layer[2] is tanh -colvars: Layer 0 : has 6 input nodes and 12 output nodes. -colvars: weights[0][0] = -2.9535 -colvars: weights[0][1] = -0.598211 -colvars: weights[0][2] = 0.241177 -colvars: weights[0][3] = 0.12947 -colvars: weights[0][4] = 0.440179 -colvars: weights[0][5] = -0.876459 -colvars: biases[0] = 0.161657 -colvars: weights[1][0] = 0.107366 -colvars: weights[1][1] = -0.0457882 -colvars: weights[1][2] = 0.0748285 -colvars: weights[1][3] = 0.156815 -colvars: weights[1][4] = 0.703526 -colvars: weights[1][5] = 0.241432 -colvars: biases[1] = -0.632794 -colvars: weights[2][0] = 0.513796 -colvars: weights[2][1] = -1.5317 -colvars: weights[2][2] = -0.0686078 -colvars: weights[2][3] = 0.0673673 -colvars: weights[2][4] = 0.196759 -colvars: weights[2][5] = 0.24494 -colvars: biases[2] = -0.211808 -colvars: weights[3][0] = -0.294562 -colvars: weights[3][1] = -0.847604 -colvars: weights[3][2] = 0.0499617 -colvars: weights[3][3] = 0.278501 -colvars: weights[3][4] = 0.147737 -colvars: weights[3][5] = 0.0557929 -colvars: biases[3] = -0.883388 -colvars: weights[4][0] = 1.07255 -colvars: weights[4][1] = 0.406689 -colvars: weights[4][2] = -0.0419776 -colvars: weights[4][3] = 0.45796 -colvars: weights[4][4] = 0.577049 -colvars: weights[4][5] = 0.0100782 -colvars: biases[4] = 0.742559 -colvars: weights[5][0] = 0.449182 -colvars: weights[5][1] = -1.05176 -colvars: weights[5][2] = 0.0394351 -colvars: weights[5][3] = 0.292022 -colvars: weights[5][4] = -0.118907 -colvars: weights[5][5] = -0.47341 -colvars: biases[5] = -0.737871 -colvars: weights[6][0] = -0.944659 -colvars: weights[6][1] = -0.511769 -colvars: weights[6][2] = 0.178793 -colvars: weights[6][3] = -0.633922 -colvars: weights[6][4] = -0.00172785 -colvars: weights[6][5] = -0.429998 -colvars: biases[6] = 0.00994667 -colvars: weights[7][0] = -0.638807 -colvars: weights[7][1] = -0.221756 -colvars: weights[7][2] = 0.214317 -colvars: weights[7][3] = -0.920973 -colvars: weights[7][4] = -0.241485 -colvars: weights[7][5] = -0.408489 -colvars: biases[7] = -0.522987 -colvars: weights[8][0] = -0.234213 -colvars: weights[8][1] = -0.307255 -colvars: weights[8][2] = 0.053139 -colvars: weights[8][3] = 0.121992 -colvars: weights[8][4] = 0.505387 -colvars: weights[8][5] = 0.192305 -colvars: biases[8] = -0.196265 -colvars: weights[9][0] = 2.77237 -colvars: weights[9][1] = -3.33375 -colvars: weights[9][2] = -0.23642 -colvars: weights[9][3] = 0.18987 -colvars: weights[9][4] = -0.244024 -colvars: weights[9][5] = 0.108861 -colvars: biases[9] = 2.3784 -colvars: weights[10][0] = 0.541434 -colvars: weights[10][1] = 0.0763588 -colvars: weights[10][2] = -0.180858 -colvars: weights[10][3] = 0.905805 -colvars: weights[10][4] = 0.435476 -colvars: weights[10][5] = 0.280653 -colvars: biases[10] = 0.87492 -colvars: weights[11][0] = 1.74269 -colvars: weights[11][1] = -1.64159 -colvars: weights[11][2] = -0.144023 -colvars: weights[11][3] = 0.1227 -colvars: weights[11][4] = -0.263546 -colvars: weights[11][5] = -0.111931 -colvars: biases[11] = 0.984634 -colvars: Layer 1 : has 12 input nodes and 1 output nodes. -colvars: weights[0][0] = 0.341442 -colvars: weights[0][1] = 0.477212 -colvars: weights[0][2] = 0.465421 -colvars: weights[0][3] = 0.796558 -colvars: weights[0][4] = 0.571714 -colvars: weights[0][5] = -0.303513 -colvars: weights[0][6] = 0.718882 -colvars: weights[0][7] = -0.999872 -colvars: weights[0][8] = -1.06988 -colvars: weights[0][9] = 1.18542 -colvars: weights[0][10] = -0.797083 -colvars: weights[0][11] = -0.713431 -colvars: biases[0] = -0.15288 -colvars: Warning: cannot cite unknown feature "NeuralNetwork colvar component" +colvars: Warning: cannot cite unknown feature "NeuralNetwork colvar component (derived from neuralNetwork)" colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.01 @@ -611,6 +514,12 @@ colvars: updating grid object data (0 grid objects in total). colvars: colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: colvars: +colvars: - BAOA integrator: +colvars: BouRabee2010 https://doi.org/10.1137/090758842 +colvars: +colvars: - neuralNetwork colvar component: +colvars: Chen2022 https://doi.org/10.1021/acs.jcim.1c01010 +colvars: colvars: - Colvars module: colvars: - Colvars-NAMD interface: colvars: - Optimal rotation via flexible fitting: @@ -627,6 +536,7 @@ colvars: colvars: - NAMD engine: colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "nn_output_1":0/0. 1 atoms: total mass = 12.011, total charge = 0.51. colvars: Re-initialized atom group for variable "nn_output_1":0/1. 1 atoms: total mass = 14.007, total charge = -0.47. colvars: Re-initialized atom group for variable "nn_output_1":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. @@ -653,12 +563,11 @@ colvars: Re-initialized atom group for variable "nn_output_1":0/22. 1 atoms: tot colvars: Re-initialized atom group for variable "nn_output_1":0/23. 1 atoms: total mass = 14.007, total charge = -0.47. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (11 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "nn_output_1":0/0. 1 atoms: total mass = 12.011, total charge = 0.51. colvars: Re-initialized atom group for variable "nn_output_1":0/1. 1 atoms: total mass = 14.007, total charge = -0.47. colvars: Re-initialized atom group for variable "nn_output_1":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. diff --git a/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.state.stripped b/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.state.stripped index 2b90f8763..10afb7dc5 100644 --- a/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.state.stripped @@ -5,9 +5,9 @@ configuration { colvar { name nn_output_1 - x 4.26943252814275e-01 - extended_x 4.27181632632770e-01 - extended_v -1.80742442300696e-05 + x 4.26944443559188e-01 + extended_x 4.27183631213753e-01 + extended_v -1.80960155650553e-05 } abf { @@ -61,7 +61,7 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 5.97075471798650e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 5.98666421389892e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -115,7 +115,7 @@ z_gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 5.97075471798650e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 5.98666421389892e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.traj b/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.traj index ee31d239a..4fb0ea1d1 100644 --- a/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.traj +++ b/namd/tests/library/031_neuralnetwork/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step nn_output_1 r_nn_output_1 0 4.27348452931304e-01 4.27348452931304e-01 - 1 4.27087400544899e-01 4.27348171826451e-01 - 2 4.26872449841523e-01 4.27344995138961e-01 - 3 4.26690641734216e-01 4.27339335868139e-01 - 4 4.26521984974831e-01 4.27338352623853e-01 - 5 4.26348782957326e-01 4.27333649320732e-01 - 6 4.26237986306272e-01 4.27335297557551e-01 - 7 4.26159119823266e-01 4.27341288086432e-01 - 8 4.26065140004549e-01 4.27337624261422e-01 - 9 4.25982327211413e-01 4.27326751284842e-01 - 10 4.25889821691884e-01 4.27317612124617e-01 - 11 4.25796380107146e-01 4.27306325283953e-01 - 12 4.25853273875579e-01 4.27296206178797e-01 - 13 4.25946758708552e-01 4.27279489786973e-01 - 14 4.26004982039489e-01 4.27265090179969e-01 - 15 4.25996648098236e-01 4.27250457384053e-01 - 16 4.26004686486549e-01 4.27235048351846e-01 - 17 4.26150792725303e-01 4.27218365788428e-01 - 18 4.26358491527167e-01 4.27204077561140e-01 - 19 4.26610336700383e-01 4.27190669754885e-01 - 20 4.26943252814275e-01 4.27181632632770e-01 + 1 4.27087400544899e-01 4.27348312414008e-01 + 2 4.26872450296396e-01 4.27346551743906e-01 + 3 4.26690647683911e-01 4.27342076152309e-01 + 4 4.26522005235959e-01 4.27338674601854e-01 + 5 4.26348818295766e-01 4.27335730155590e-01 + 6 4.26238043055371e-01 4.27334079828963e-01 + 7 4.26159193274459e-01 4.27337761524583e-01 + 8 4.26065217585930e-01 4.27338778273542e-01 + 9 4.25982411875574e-01 4.27331353969824e-01 + 10 4.25889928078528e-01 4.27321182692511e-01 + 11 4.25796519562365e-01 4.27310793395096e-01 + 12 4.25853460937317e-01 4.27299903044534e-01 + 13 4.25947005263650e-01 4.27286305999077e-01 + 14 4.26005311535346e-01 4.27270581213223e-01 + 15 4.25997078773281e-01 4.27255905652364e-01 + 16 4.26005236400443e-01 4.27240725046359e-01 + 17 4.26151479874847e-01 4.27224521443315e-01 + 18 4.26359335262689e-01 4.27208896839964e-01 + 19 4.26611349581861e-01 4.27194935615553e-01 + 20 4.26944443559188e-01 4.27183631213753e-01 diff --git a/namd/tests/library/031_neuralnetwork/AutoDiff/test.grad b/namd/tests/library/031_neuralnetwork/AutoDiff/test.grad index 90605d565..1f400ab92 100644 --- a/namd/tests/library/031_neuralnetwork/AutoDiff/test.grad +++ b/namd/tests/library/031_neuralnetwork/AutoDiff/test.grad @@ -143,7 +143,7 @@ 3.95000000000000e-01 0.00000000000000e+00 4.05000000000000e-01 0.00000000000000e+00 4.15000000000000e-01 0.00000000000000e+00 - 4.25000000000000e-01 5.97075473808997e+00 + 4.25000000000000e-01 5.98666421389892e+00 4.35000000000000e-01 0.00000000000000e+00 4.45000000000000e-01 0.00000000000000e+00 4.55000000000000e-01 0.00000000000000e+00 diff --git a/namd/tests/library/031_neuralnetwork/AutoDiff/test.pmf b/namd/tests/library/031_neuralnetwork/AutoDiff/test.pmf index 5e30b5ca2..a542ac129 100644 --- a/namd/tests/library/031_neuralnetwork/AutoDiff/test.pmf +++ b/namd/tests/library/031_neuralnetwork/AutoDiff/test.pmf @@ -144,61 +144,61 @@ 4.00000000000000e-01 0.00000000000000e+00 4.10000000000000e-01 0.00000000000000e+00 4.20000000000000e-01 0.00000000000000e+00 - 4.30000000000000e-01 5.97075473808997e-02 - 4.40000000000000e-01 5.97075473808997e-02 - 4.50000000000000e-01 5.97075473808997e-02 - 4.60000000000000e-01 5.97075473808997e-02 - 4.70000000000000e-01 5.97075473808997e-02 - 4.80000000000000e-01 5.97075473808997e-02 - 4.90000000000000e-01 5.97075473808997e-02 - 5.00000000000000e-01 5.97075473808997e-02 - 5.10000000000000e-01 5.97075473808997e-02 - 5.20000000000000e-01 5.97075473808997e-02 - 5.30000000000000e-01 5.97075473808997e-02 - 5.40000000000000e-01 5.97075473808997e-02 - 5.50000000000000e-01 5.97075473808997e-02 - 5.60000000000000e-01 5.97075473808997e-02 - 5.70000000000000e-01 5.97075473808997e-02 - 5.80000000000000e-01 5.97075473808997e-02 - 5.90000000000000e-01 5.97075473808997e-02 - 6.00000000000000e-01 5.97075473808997e-02 - 6.10000000000000e-01 5.97075473808997e-02 - 6.20000000000000e-01 5.97075473808997e-02 - 6.30000000000000e-01 5.97075473808997e-02 - 6.40000000000000e-01 5.97075473808997e-02 - 6.50000000000000e-01 5.97075473808997e-02 - 6.60000000000000e-01 5.97075473808997e-02 - 6.70000000000000e-01 5.97075473808997e-02 - 6.80000000000000e-01 5.97075473808997e-02 - 6.90000000000000e-01 5.97075473808997e-02 - 7.00000000000000e-01 5.97075473808997e-02 - 7.10000000000000e-01 5.97075473808997e-02 - 7.20000000000000e-01 5.97075473808997e-02 - 7.30000000000000e-01 5.97075473808997e-02 - 7.40000000000000e-01 5.97075473808997e-02 - 7.50000000000000e-01 5.97075473808997e-02 - 7.60000000000000e-01 5.97075473808997e-02 - 7.70000000000000e-01 5.97075473808997e-02 - 7.80000000000000e-01 5.97075473808997e-02 - 7.90000000000000e-01 5.97075473808997e-02 - 8.00000000000000e-01 5.97075473808997e-02 - 8.10000000000000e-01 5.97075473808997e-02 - 8.20000000000000e-01 5.97075473808997e-02 - 8.30000000000000e-01 5.97075473808997e-02 - 8.40000000000000e-01 5.97075473808997e-02 - 8.50000000000000e-01 5.97075473808997e-02 - 8.60000000000000e-01 5.97075473808997e-02 - 8.70000000000000e-01 5.97075473808997e-02 - 8.80000000000000e-01 5.97075473808997e-02 - 8.90000000000000e-01 5.97075473808997e-02 - 9.00000000000000e-01 5.97075473808997e-02 - 9.10000000000000e-01 5.97075473808997e-02 - 9.20000000000000e-01 5.97075473808997e-02 - 9.30000000000000e-01 5.97075473808997e-02 - 9.40000000000000e-01 5.97075473808997e-02 - 9.50000000000000e-01 5.97075473808997e-02 - 9.60000000000000e-01 5.97075473808997e-02 - 9.70000000000000e-01 5.97075473808997e-02 - 9.80000000000000e-01 5.97075473808997e-02 - 9.90000000000000e-01 5.97075473808997e-02 - 1.00000000000000e+00 5.97075473808997e-02 + 4.30000000000000e-01 5.98666421389892e-02 + 4.40000000000000e-01 5.98666421389892e-02 + 4.50000000000000e-01 5.98666421389892e-02 + 4.60000000000000e-01 5.98666421389892e-02 + 4.70000000000000e-01 5.98666421389892e-02 + 4.80000000000000e-01 5.98666421389892e-02 + 4.90000000000000e-01 5.98666421389892e-02 + 5.00000000000000e-01 5.98666421389892e-02 + 5.10000000000000e-01 5.98666421389892e-02 + 5.20000000000000e-01 5.98666421389892e-02 + 5.30000000000000e-01 5.98666421389892e-02 + 5.40000000000000e-01 5.98666421389892e-02 + 5.50000000000000e-01 5.98666421389892e-02 + 5.60000000000000e-01 5.98666421389892e-02 + 5.70000000000000e-01 5.98666421389892e-02 + 5.80000000000000e-01 5.98666421389892e-02 + 5.90000000000000e-01 5.98666421389892e-02 + 6.00000000000000e-01 5.98666421389892e-02 + 6.10000000000000e-01 5.98666421389892e-02 + 6.20000000000000e-01 5.98666421389892e-02 + 6.30000000000000e-01 5.98666421389892e-02 + 6.40000000000000e-01 5.98666421389892e-02 + 6.50000000000000e-01 5.98666421389892e-02 + 6.60000000000000e-01 5.98666421389892e-02 + 6.70000000000000e-01 5.98666421389892e-02 + 6.80000000000000e-01 5.98666421389892e-02 + 6.90000000000000e-01 5.98666421389892e-02 + 7.00000000000000e-01 5.98666421389892e-02 + 7.10000000000000e-01 5.98666421389892e-02 + 7.20000000000000e-01 5.98666421389892e-02 + 7.30000000000000e-01 5.98666421389892e-02 + 7.40000000000000e-01 5.98666421389892e-02 + 7.50000000000000e-01 5.98666421389892e-02 + 7.60000000000000e-01 5.98666421389892e-02 + 7.70000000000000e-01 5.98666421389892e-02 + 7.80000000000000e-01 5.98666421389892e-02 + 7.90000000000000e-01 5.98666421389892e-02 + 8.00000000000000e-01 5.98666421389892e-02 + 8.10000000000000e-01 5.98666421389892e-02 + 8.20000000000000e-01 5.98666421389892e-02 + 8.30000000000000e-01 5.98666421389892e-02 + 8.40000000000000e-01 5.98666421389892e-02 + 8.50000000000000e-01 5.98666421389892e-02 + 8.60000000000000e-01 5.98666421389892e-02 + 8.70000000000000e-01 5.98666421389892e-02 + 8.80000000000000e-01 5.98666421389892e-02 + 8.90000000000000e-01 5.98666421389892e-02 + 9.00000000000000e-01 5.98666421389892e-02 + 9.10000000000000e-01 5.98666421389892e-02 + 9.20000000000000e-01 5.98666421389892e-02 + 9.30000000000000e-01 5.98666421389892e-02 + 9.40000000000000e-01 5.98666421389892e-02 + 9.50000000000000e-01 5.98666421389892e-02 + 9.60000000000000e-01 5.98666421389892e-02 + 9.70000000000000e-01 5.98666421389892e-02 + 9.80000000000000e-01 5.98666421389892e-02 + 9.90000000000000e-01 5.98666421389892e-02 + 1.00000000000000e+00 5.98666421389892e-02 diff --git a/namd/tests/library/031_neuralnetwork/namd-version.txt b/namd/tests/library/031_neuralnetwork/namd-version.txt index a8832c1ef..157cac038 100644 --- a/namd/tests/library/031_neuralnetwork/namd-version.txt +++ b/namd/tests/library/031_neuralnetwork/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2021-12-20. -colvars: Using NAMD interface, version "2021-10-13". +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Using NAMD interface, version "2023-07-06". From 6994ef6c58b145bb608276200803fbe171321ac3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Wed, 26 Jul 2023 11:44:57 +0200 Subject: [PATCH 006/162] Save failed CI test diffs as artifacts --- .github/workflows/backend-template.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/.github/workflows/backend-template.yml b/.github/workflows/backend-template.yml index 8654eff09..72259b407 100644 --- a/.github/workflows/backend-template.yml +++ b/.github/workflows/backend-template.yml @@ -162,6 +162,13 @@ jobs: apptainer exec ${{github.workspace}}/devel-tools/${{ inputs.container_name }}.sif \ ./run_tests.sh ${{github.workspace}}/${{ inputs.backend_name }}-source/${{ inputs.rpath_exe }} 0??_* + - name: Save failed library test artifact + if: ${{ failure() }} + uses: actions/upload-artifact@v3 + with: + name: failed-library-test-diffs-${{ inputs.backend_name }} + path: ${{ inputs.test_lib_directory }}/*/*.diff + - name: Run regression tests for ${{ inputs.backend_name }} interface code if: ${{ inputs.test_interface_directory }} shell: bash @@ -169,3 +176,11 @@ jobs: run: | apptainer exec ${{github.workspace}}/devel-tools/${{ inputs.container_name }}.sif \ ./run_tests.sh ${{github.workspace}}/${{ inputs.backend_name }}-source/${{ inputs.rpath_exe }} + + - name: Save failed interface test artifact + if: ${{ failure() }} + uses: actions/upload-artifact@v3 + with: + name: failed-interface-test-diffs-${{ inputs.backend_name }} + path: ${{ inputs.test_interface_directory }}/*/*.diff + From 3a2ccdc5af18c7e898a311f69ed2886da7461b2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Wed, 26 Jul 2023 14:53:51 +0200 Subject: [PATCH 007/162] Detailed comments on integrator --- src/colvar.cpp | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/colvar.cpp b/src/colvar.cpp index af101ca51..efa7242e2 100644 --- a/src/colvar.cpp +++ b/src/colvar.cpp @@ -1871,16 +1871,23 @@ void colvar::update_extended_Lagrangian() // BAOA (GSD) integrator as formulated in https://doi.org/10.1021/acs.jctc.2c00585 // starting from x_t, f_t, v_(t-1/2) + // Variation: the velocity step is split in two to estimate the kinetic energy at time t + // so this is more of a "BBAOA" scheme: a rearranged BAOAB where the second B is deferred + // to the next time step for implementation reasons (waiting for the force calculation) // [B] Eq. (10a) split into two half-steps - // This reduces to leapfrog when gamma = 0 + // would reduce to leapfrog when gamma = 0 if this was the reported velocity v_ext += 0.5 * dt * f_ext / ext_mass; + // Kinetic energy at t kinetic_energy = 0.5 * ext_mass * v_ext * v_ext; // Potential energy at t potential_energy = 0.5 * ext_force_k * this->dist2(x_ext, x); + // Total energy will lag behind position by one timestep + // (current kinetic energy is not accessible before the next force calculation) + v_ext += 0.5 * dt * f_ext / ext_mass; // Final v_ext lags behind x_ext by half a timestep From f0549d364422ca46c6d57cdb0df2bc0bcdb21768 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Wed, 26 Jul 2023 14:58:37 +0200 Subject: [PATCH 008/162] Change upper wall parameter in regtest --- .../AutoDiff/test.colvars.out | 2 +- .../AutoDiff/test.colvars.state.stripped | 8 ++-- .../AutoDiff/test.colvars.traj | 42 +++++++++---------- .../AutoDiff/test.restart.colvars.out | 2 +- .../test.restart.colvars.state.stripped | 8 ++-- .../AutoDiff/test.restart.colvars.traj | 42 +++++++++---------- .../test.in | 2 +- 7 files changed, 53 insertions(+), 53 deletions(-) diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out index 5b1c03881..ec75406ef 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out @@ -130,7 +130,7 @@ colvars: # forceConstant = 0.001 colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } -colvars: # upperWalls = { 0.2 } +colvars: # upperWalls = { 0.3 } colvars: # lowerWallConstant = 0.001 [default] colvars: # upperWallConstant = 0.001 [default] colvars: The lower wall force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped index 83b0d62b7..868eb59c6 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21549617587205e+00 - v 1.63765399419808e-04 - extended_x 3.20653014354441e+00 - extended_v 1.63765399419808e-04 + x 3.21549621301549e+00 + v 1.63839888121770e-04 + extended_x 3.20653095017852e+00 + extended_v 1.63839888121770e-04 } restraint { diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj index ea3cb4584..64538e290 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 -1.20221869387334e-02 - 1 3.20437148316484e+00 3.20554661526430e+00 -1.17525151850328e-03 -1.19419048416827e-07 -1.20221864610572e-02 - 2 3.20384207658198e+00 3.20554521661731e+00 -5.29406582859160e-04 -1.39864698615333e-06 -1.20221808664692e-02 - 3 3.20397336372329e+00 3.20554201761950e+00 1.31287141313052e-04 -3.19899781308815e-06 -1.20221680704780e-02 - 4 3.20474099372294e+00 3.20553715100348e+00 7.67629999647745e-04 -4.86661601385684e-06 -1.20221486040139e-02 - 5 3.20608361725515e+00 3.20553137919306e+00 1.34262353221182e-03 -5.77181042148448e-06 -1.20221255167722e-02 - 6 3.20790704366680e+00 3.20552603300132e+00 1.82342641164146e-03 -5.34619173897510e-06 -1.20221041320053e-02 - 7 3.21008979708265e+00 3.20552291735469e+00 2.18275341585361e-03 -3.11564663055446e-06 -1.20220916694188e-02 - 8 3.21248979691190e+00 3.20552418961958e+00 2.39999982925276e-03 1.27226489358961e-06 -1.20220967584783e-02 - 9 3.21495218466242e+00 3.20553221724516e+00 2.46238775052099e-03 8.02762557980444e-06 -1.20221288689807e-02 - 10 3.21731838884401e+00 3.20554942258746e+00 2.36620418158973e-03 1.72053422961567e-05 -1.20221976903498e-02 - 11 3.21943620052261e+00 3.20557812401472e+00 2.11781167860092e-03 2.87014272571360e-05 -1.20223124960589e-02 - 12 3.22117010488210e+00 3.20562038339497e+00 1.73390435948928e-03 4.22593802508272e-05 -1.20224815335799e-02 - 13 3.22241068502092e+00 3.20567787031321e+00 1.24058013882022e-03 5.74869182386481e-05 -1.20227114812528e-02 - 14 3.22308184564051e+00 3.20575175243336e+00 6.71160619590605e-04 7.38821201480224e-05 -1.20230070097334e-02 - 15 3.22314498293928e+00 3.20584261924273e+00 6.31372987673906e-05 9.08668093725243e-05 -1.20233704769709e-02 - 16 3.22259983048180e+00 3.20595044336978e+00 -5.45152457477549e-04 1.07824127056634e-04 -1.20238017734791e-02 - 17 3.22148232853223e+00 3.20607458034818e+00 -1.11750194957105e-03 1.24136978399328e-04 -1.20242983213927e-02 - 18 3.21986023795765e+00 3.20621380472449e+00 -1.62209057458140e-03 1.39224376306895e-04 -1.20248552188980e-02 - 19 3.21782725344634e+00 3.20636637814499e+00 -2.03298451131184e-03 1.52573420503577e-04 -1.20254655125800e-02 - 20 3.21549617587205e+00 3.20653014354441e+00 -2.33107757428819e-03 1.63765399419808e-04 -1.20261205741777e-02 + 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 -1.16221869387334e-02 + 1 3.20437148316484e+00 3.20554661923758e+00 -1.17525151850328e-03 -1.15445759728991e-07 -1.16221864769503e-02 + 2 3.20384207658804e+00 3.20554522853325e+00 -5.29406576805336e-04 -1.39070433041396e-06 -1.16221809141330e-02 + 3 3.20397336375347e+00 3.20554204143963e+00 1.31287165431537e-04 -3.18709362372464e-06 -1.16221681657585e-02 + 4 3.20474099381307e+00 3.20553719067761e+00 7.67630059602453e-04 -4.85076201650243e-06 -1.16221487627105e-02 + 5 3.20608361746435e+00 3.20553143865541e+00 1.34262365128279e-03 -5.75202220486511e-06 -1.16221257546216e-02 + 6 3.20790704408264e+00 3.20552611616669e+00 1.82342661828994e-03 -5.32248871654545e-06 -1.16221044646668e-02 + 7 3.21008979782599e+00 3.20552302811470e+00 2.18275374334675e-03 -3.08805199324812e-06 -1.16220921124588e-02 + 8 3.21248979814124e+00 3.20552433183893e+00 2.40000031525378e-03 1.30372423308412e-06 -1.16220973273557e-02 + 9 3.21495218657788e+00 3.20553239475798e+00 2.46238843663571e-03 8.06291905077686e-06 -1.16221295790319e-02 + 10 3.21731839169077e+00 3.20554963919372e+00 2.36620511289365e-03 1.72444357411129e-05 -1.16221985567749e-02 + 11 3.21943620459394e+00 3.20557838347673e+00 2.11781290316582e-03 2.87442830099992e-05 -1.16223135339069e-02 + 12 3.22117011052185e+00 3.20562068943396e+00 1.73390592791511e-03 4.23059572215591e-05 -1.16224827577358e-02 + 13 3.22241069262564e+00 3.20567822660596e+00 1.24058210378664e-03 5.75371720037448e-05 -1.16227129064238e-02 + 14 3.22308185566108e+00 3.20575216260901e+00 6.71163035445232e-04 7.39360030463537e-05 -1.16230086504360e-02 + 15 3.22314499588221e+00 3.20584308687961e+00 6.31402211261900e-05 9.09242706060132e-05 -1.16233723475184e-02 + 16 3.22259984691011e+00 3.20595097199241e+00 -5.45148972103338e-04 1.07885112795286e-04 -1.16238038879696e-02 + 17 3.22148234906601e+00 3.20607517342430e+00 -1.11749784410220e-03 1.24201431890135e-04 -1.16243006936972e-02 + 18 3.21986026327429e+00 3.20621446566228e+00 -1.62208579171264e-03 1.39292237986185e-04 -1.16248578626491e-02 + 19 3.21782728428053e+00 3.20636711029040e+00 -2.03297899376365e-03 1.52644628112363e-04 -1.16254684411616e-02 + 20 3.21549621301549e+00 3.20653095017852e+00 -2.33107126504306e-03 1.63839888121770e-04 -1.16261238007141e-02 diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out index 71e67a3d0..af642ac95 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out @@ -130,7 +130,7 @@ colvars: # forceConstant = 0.001 colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } -colvars: # upperWalls = { 0.2 } +colvars: # upperWalls = { 0.3 } colvars: # lowerWallConstant = 0.001 [default] colvars: # upperWallConstant = 0.001 [default] colvars: The lower wall force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped index 740730ef2..67e9debbf 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21130917292044e+00 - v 1.00951348854985e-04 - extended_x 3.20938126631322e+00 - extended_v 1.00951348854985e-04 + x 3.21130958093225e+00 + v 1.01074979342738e-04 + extended_x 3.20938413437057e+00 + extended_v 1.01074979342738e-04 } restraint { diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj index e35e1b0ba..457fcb155 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 20 3.21549617587205e+00 3.20653014354441e+00 0.00000000000000e+00 1.63765399419808e-04 -1.20261205741776e-02 - 21 3.21299146691002e+00 3.20670263860492e+00 -2.50470896202648e-03 1.72495060509838e-04 -1.20268105544197e-02 - 22 3.21044140002284e+00 3.20688122102521e+00 -2.55006688718051e-03 1.78582420285797e-04 -1.20275248841008e-02 - 23 3.20797012436086e+00 3.20706319772925e+00 -2.47127566198468e-03 1.81976704044760e-04 -1.20282527909170e-02 - 24 3.20569018980129e+00 3.20724595005470e+00 -2.27993455957121e-03 1.82752325450367e-04 -1.20289838002188e-02 - 25 3.20369626842688e+00 3.20742704741977e+00 -1.99392137440801e-03 1.81097365062805e-04 -1.20297081896791e-02 - 26 3.20206071195224e+00 3.20760434315979e+00 -1.63555647464264e-03 1.77295740027368e-04 -1.20304173726392e-02 - 27 3.20083128306446e+00 3.20777604805432e+00 -1.22942888777944e-03 1.71704894527817e-04 -1.20311041922173e-02 - 28 3.20003097897692e+00 3.20794077923291e+00 -8.00304087535064e-04 1.64731178591497e-04 -1.20317631169316e-02 - 29 3.19965949808046e+00 3.20809758423739e+00 -3.71480896461218e-04 1.56805004478955e-04 -1.20323903369496e-02 - 30 3.19969592066247e+00 3.20824594166424e+00 3.64225820090880e-05 1.48357426850803e-04 -1.20329837666570e-02 - 31 3.20010221754926e+00 3.20838574103230e+00 4.06296886787061e-04 1.39799368064253e-04 -1.20335429641292e-02 - 32 3.20082741979556e+00 3.20851724535854e+00 7.25202246302015e-04 1.31504326231438e-04 -1.20340689814341e-02 - 33 3.20181227110765e+00 3.20864104059407e+00 9.84851312094914e-04 1.23795235534061e-04 -1.20345641623763e-02 - 34 3.20299412053733e+00 3.20875797656227e+00 1.18184942967092e-03 1.16935968202223e-04 -1.20350319062491e-02 - 35 3.20431162261699e+00 3.20886910428595e+00 1.31750207966386e-03 1.11127723682791e-04 -1.20354764171438e-02 - 36 3.20570880302891e+00 3.20897561440447e+00 1.39718041191950e-03 1.06510118513249e-04 -1.20359024576179e-02 - 37 3.20713815036053e+00 3.20907878075410e+00 1.42934733162248e-03 1.03166349632568e-04 -1.20363151230164e-02 - 38 3.20856270818102e+00 3.20917991221892e+00 1.42455782049122e-03 1.01131464818439e-04 -1.20367196488757e-02 - 39 3.20995731353255e+00 3.20928031496436e+00 1.39460535153013e-03 1.00402745444511e-04 -1.20371212598575e-02 - 40 3.21130917292044e+00 3.20938126631322e+00 1.35185938788940e-03 1.00951348854985e-04 -1.20375250652529e-02 + 20 3.21549621301549e+00 3.20653095017852e+00 0.00000000000000e+00 1.63839888121770e-04 -1.16261238007141e-02 + 21 3.21299151121102e+00 3.20670352294153e+00 -2.50470180446749e-03 1.72572763011582e-04 -1.16268140917661e-02 + 22 3.21044145238583e+00 3.20688218620849e+00 -2.55005882518766e-03 1.78663266959169e-04 -1.16275287448340e-02 + 23 3.20797018574579e+00 3.20706424683154e+00 -2.47126664004549e-03 1.82060623050948e-04 -1.16282569873262e-02 + 24 3.20569026122289e+00 3.20724708607441e+00 -2.27992452289572e-03 1.82839242865593e-04 -1.16289883442976e-02 + 25 3.20369635095381e+00 3.20742827327941e+00 -1.99391026908335e-03 1.81187205005368e-04 -1.16297130931177e-02 + 26 3.20206080670596e+00 3.20760566170420e+00 -1.63554424784840e-03 1.77388424785744e-04 -1.16304226468168e-02 + 27 3.20083139121777e+00 3.20777746204889e+00 -1.22941548818822e-03 1.71800344689496e-04 -1.16311098481956e-02 + 28 3.20003110175216e+00 3.20794229136206e+00 -8.00289465613613e-04 1.64829313172020e-04 -1.16317691654482e-02 + 29 3.19965963674732e+00 3.20809919710311e+00 -3.71465004831428e-04 1.56905741050733e-04 -1.16323967884124e-02 + 30 3.19969607653556e+00 3.20824765778478e+00 3.64397882326450e-05 1.48460681671230e-04 -1.16329906311391e-02 + 31 3.20010239198518e+00 3.20838756284098e+00 4.06315449623662e-04 1.39905056202667e-04 -1.16335502513639e-02 + 32 3.20082761419017e+00 3.20851917520268e+00 7.25222204989162e-04 1.31612361694413e-04 -1.16340767008107e-02 + 33 3.20181248689262e+00 3.20864308073407e+00 9.84872702445738e-04 1.23905531389011e-04 -1.16345723229363e-02 + 34 3.20299435917704e+00 3.20876012917077e+00 1.18187228442679e-03 1.17048436698551e-04 -1.16350405166831e-02 + 35 3.20431188560568e+00 3.20887137144714e+00 1.31752642863958e-03 1.11242276370810e-04 -1.16354854857885e-02 + 36 3.20570909188769e+00 3.20897799811350e+00 1.39720628201090e-03 1.06626666360912e-04 -1.16359119924540e-02 + 37 3.20713846663531e+00 3.20908128291664e+00 1.42937474761640e-03 1.03284803139886e-04 -1.16363251316666e-02 + 38 3.20856305344034e+00 3.20918253465077e+00 1.42458680502822e-03 1.01251734130282e-04 -1.16367301386031e-02 + 39 3.20995768936497e+00 3.20928305939123e+00 1.39463592463418e-03 1.00524740461639e-04 -1.16371322375649e-02 + 40 3.21130958093225e+00 3.20938413437057e+00 1.35189156727877e-03 1.01074979342738e-04 -1.16375365374823e-02 diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/test.in b/namd/tests/library/000_distance-wall-bypassExtended-off/test.in index 5a5def555..770d32a5b 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/test.in +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/test.in @@ -30,7 +30,7 @@ colvar { harmonicWalls { colvars one lowerWalls 0.1 - upperWalls 0.2 + upperWalls 0.3 forceConstant 0.001 bypassExtendedLagrangian off } From a61218e2392ad37d68f0d97412050599a5dc8f33 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Thu, 7 Sep 2023 10:56:10 +0200 Subject: [PATCH 009/162] Do not warn of differences in output log --- gromacs/tests/interface/run_tests.sh | 6 ++---- gromacs/tests/library/run_tests.sh | 6 ++---- lammps/tests/library/run_tests.sh | 7 +++---- namd/tests/library/run_tests.sh | 6 ++---- vmd/tests/interface/run_tests.sh | 6 ++---- 5 files changed, 11 insertions(+), 20 deletions(-) diff --git a/gromacs/tests/interface/run_tests.sh b/gromacs/tests/interface/run_tests.sh index b579038dc..1cdfc2e2e 100755 --- a/gromacs/tests/interface/run_tests.sh +++ b/gromacs/tests/interface/run_tests.sh @@ -291,10 +291,8 @@ for dir in ${DIRLIST} ; do fi if [ $RETVAL -ne 0 ] then - if [ ${base} != ${base%.out} ] + if [ ${base} == ${base%.out} ] # Ignore differences in stdout log then - echo -n "(warning: differences in log file $base) " - else echo -e "\n*** Failure for file $(${TPUT_RED})$base$(${TPUT_CLEAR}): see `pwd`/$base.diff " SUCCESS=0 ALL_SUCCESS=0 @@ -321,7 +319,7 @@ for dir in ${DIRLIST} ; do if [ "x${gen_ref_output}" == 'xyes' ]; then echo "Reference files copied successfully." else - echo "$(${TPUT_GREEN})Success!$(${TPUT_CLEAR})" + echo " $(${TPUT_GREEN})Success!$(${TPUT_CLEAR})" fi cleanup_files fi diff --git a/gromacs/tests/library/run_tests.sh b/gromacs/tests/library/run_tests.sh index 078bef5b3..103a09c8c 100755 --- a/gromacs/tests/library/run_tests.sh +++ b/gromacs/tests/library/run_tests.sh @@ -245,10 +245,8 @@ for dir in ${DIRLIST} ; do fi if [ $RETVAL -ne 0 ] then - if [ ${base} != ${base%.out} ] + if [ ${base} == ${base%.out} ] # Ignore differences in stdout log then - echo -n "(warning: differences in log file $base) " - else echo -e "\n*** Failure for file $(${TPUT_RED})$base$(${TPUT_CLEAR}): see `pwd`/$base.diff " SUCCESS=0 ALL_SUCCESS=0 @@ -275,7 +273,7 @@ for dir in ${DIRLIST} ; do if [ "x${gen_ref_output}" == 'xyes' ]; then echo "Reference files copied successfully." else - echo "$(${TPUT_GREEN})Success!$(${TPUT_CLEAR})" + echo " $(${TPUT_GREEN})Success!$(${TPUT_CLEAR})" fi cleanup_files fi diff --git a/lammps/tests/library/run_tests.sh b/lammps/tests/library/run_tests.sh index 514bf18c7..25b9e0895 100755 --- a/lammps/tests/library/run_tests.sh +++ b/lammps/tests/library/run_tests.sh @@ -172,6 +172,7 @@ for dir in ${DIRLIST} ; do "${extra_args[@]}" \ -echo log > /dev/null + # Output of Colvars module, minus the version numbers for log_file in *.out ; do if [ x${log_file%.colvars.out} != x${log_file} ] ; then @@ -236,10 +237,8 @@ for dir in ${DIRLIST} ; do RETVAL=$? if [ $RETVAL -ne 0 ] then - if [ ${base##*\.} = 'out' ] + if [ ${base} == ${base%.out} ] # Ignore differences in stdout log then - echo -n "(warning: differences in log file $base) " - else echo -e "\n*** Failure for file $(${TPUT_RED})$base$(${TPUT_CLEAR}): see `pwd`/$base.diff " SUCCESS=0 ALL_SUCCESS=0 @@ -268,7 +267,7 @@ for dir in ${DIRLIST} ; do if [ "x${gen_ref_output}" == 'xyes' ]; then echo "Reference files copied successfully." else - echo "$(${TPUT_GREEN})Success!$(${TPUT_CLEAR})" + echo " $(${TPUT_GREEN})Success!$(${TPUT_CLEAR})" fi cleanup_files fi diff --git a/namd/tests/library/run_tests.sh b/namd/tests/library/run_tests.sh index b67af39e2..fe4362409 100755 --- a/namd/tests/library/run_tests.sh +++ b/namd/tests/library/run_tests.sh @@ -244,10 +244,8 @@ for dir in ${DIRLIST} ; do fi if [ $RETVAL -ne 0 ] then - if [ ${base} != ${base%.out} ] + if [ ${base} == ${base%.out} ] # Ignore differences in stdout log then - echo -n "(warning: differences in log file $base) " - else echo -e "\n*** Failure for file $(${TPUT_RED})$base$(${TPUT_CLEAR}): see `pwd`/$base.diff " SUCCESS=0 ALL_SUCCESS=0 @@ -276,7 +274,7 @@ for dir in ${DIRLIST} ; do if [ "x${gen_ref_output}" == 'xyes' ]; then echo "Reference files copied successfully." else - echo "$(${TPUT_GREEN})Success!$(${TPUT_CLEAR})" + echo " $(${TPUT_GREEN})Success!$(${TPUT_CLEAR})" fi cleanup_files fi diff --git a/vmd/tests/interface/run_tests.sh b/vmd/tests/interface/run_tests.sh index 7681db075..ef8566ef5 100755 --- a/vmd/tests/interface/run_tests.sh +++ b/vmd/tests/interface/run_tests.sh @@ -78,10 +78,8 @@ do RETVAL=$? if [ $RETVAL -ne 0 ] then - if [ ${base##*\.} = 'out' ] + if [ ${base} == ${base%.out} ] # Ignore differences in stdout log then - echo -n "(warning: differences in log file $base) " - else echo -e "\n*** Failure for file $base: see $dir/$base.diff ***" SUCCESS=0 ALL_SUCCESS=0 @@ -91,7 +89,7 @@ do if [ $SUCCESS -eq 1 ] then - echo "Success!" + echo " Success!" cleanup_files fi From a5fc108c73aea157159168c04f237497dbb3dbc7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Thu, 7 Sep 2023 15:14:40 +0200 Subject: [PATCH 010/162] Restore most test outputs to master branch except those with extended Lagrangian --- .../AutoDiff/test.colvars.out | 64 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 66 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../000_alpha_harmonic-fixed/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 52 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 54 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../000_angle_harmonic-fixed/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 146 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 149 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../000_dihedralPC_abf2d/namd-version.txt | 2 +- .../AutoDiff/test.restart.colvars.out | 2 +- .../namd-version.txt | 2 +- .../AutoDiff/test.colvars.out | 67 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 69 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 6 +- .../AutoDiff/test.colvars.traj | 2 +- .../AutoDiff/test.histogram1.dat | 146 +- .../AutoDiff/test.restart.colvars.out | 6 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 18 +- .../AutoDiff/test.restart.histogram1.dat | 146 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 67 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 44 +- .../AutoDiff/test.restart.colvars.out | 69 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 44 +- .../000_dihedralwalls/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 53 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 55 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 41 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 43 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.one.corrfunc.dat | 10 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.one.corrfunc.dat | 10 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 62 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 64 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 61 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 63 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.two.corrfunc.dat | 10 +- .../AutoDiff/test.two.corrfunc.dat | 10 +- .../000_distance-corrfunc/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 3 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 6004 +++---- .../AutoDiff/test.restart.colvars.out | 3 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 6004 +++---- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 3 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 14404 ++++++++-------- .../AutoDiff/test.restart.colvars.out | 3 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 14404 ++++++++-------- .../namd-version.txt | 4 +- .../AutoDiff/test.restart.colvars.out | 2 +- .../namd-version.txt | 2 +- .../AutoDiff/test.restart.colvars.out | 2 +- .../namd-version.txt | 2 +- .../000_distance-extended/namd-version.txt | 2 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 14 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 72 +- .../AutoDiff/test.restart.colvars.out | 50 +- .../test.restart.colvars.state.stripped | 14 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 72 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../000_distance-grid_abf/AutoDiff/test.grad | 2 +- .../000_distance-grid_abf/AutoDiff/test.pmf | 14 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.grad | 2 +- .../AutoDiff/test.restart.pmf | 14 +- .../000_distance-grid_abf/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 48 +- .../AutoDiff/test.colvars.state.stripped | 6 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.harmonic1.ti.force | 2 +- .../AutoDiff/test.harmonic1.ti.pmf | 28 +- .../AutoDiff/test.restart.colvars.out | 50 +- .../test.restart.colvars.state.stripped | 6 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.harmonic1.ti.force | 2 +- .../AutoDiff/test.restart.harmonic1.ti.pmf | 14 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 48 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.harmonic1.ti.force | 2 +- .../AutoDiff/test.harmonic1.ti.pmf | 28 +- .../AutoDiff/test.restart.colvars.out | 50 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.harmonic1.ti.force | 2 +- .../AutoDiff/test.restart.harmonic1.ti.pmf | 14 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 50 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 50 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 42 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 42 +- .../namd-version.txt | 6 +- .../test.colvars.metadynamics1.hills.traj | 4 +- .../AutoDiff/test.colvars.out | 24 +- .../AutoDiff/test.colvars.state.stripped | 26 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 38 +- ...t.restart.colvars.metadynamics1.hills.traj | 4 +- .../AutoDiff/test.restart.colvars.out | 27 +- .../test.restart.colvars.state.stripped | 86 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 108 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 24 +- .../AutoDiff/test.colvars.state.stripped | 30 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 38 +- .../AutoDiff/test.restart.colvars.out | 27 +- .../test.restart.colvars.state.stripped | 78 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 106 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 10 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 38 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 10 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 38 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 12 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 38 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 12 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 38 +- .../namd-version.txt | 6 +- .../test.colvars.metadynamics1.hills.traj | 2 +- .../AutoDiff/test.colvars.out | 42 +- .../AutoDiff/test.colvars.state.stripped | 16 +- .../AutoDiff/test.colvars.traj | 32 +- .../AutoDiff/test.pmf | 38 +- .../AutoDiff/test.restart.colvars.out | 44 +- .../test.restart.colvars.state.stripped | 16 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 38 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 10 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.pmf | 38 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 10 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.pmf | 38 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.one.runave.traj | 14 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../000_distance-runave/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 2 +- .../AutoDiff/test.colvars.state.stripped | 8 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 4 +- .../test.restart.colvars.state.stripped | 8 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 2 +- .../test.in | 2 +- .../000_distance/AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../000_distance/AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../library/000_distance/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 186 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 192 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 49 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 49 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 49 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 3 +- .../AutoDiff/test.restart.colvars.out | 3 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 49 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 6 +- .../AutoDiff/test.histogram1.dat | 50 +- .../AutoDiff/test.restart.colvars.out | 6 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 49 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 51 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 58 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 60 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 38 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 32 +- .../AutoDiff/test.restart.colvars.out | 38 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 38 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 45 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.hr.hist.dat | 12 +- .../AutoDiff/test.restart.colvars.out | 47 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.hr.hist.dat | 12 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 58 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 60 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 48 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 44 +- .../AutoDiff/test.restart.colvars.out | 50 +- .../test.restart.colvars.state.stripped | 2 +- 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.../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 72 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 74 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 142 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 146 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 4 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 4 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 44 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 81 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 32 +- .../AutoDiff/test.restart.colvars.out | 81 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 39 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 41 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 31 +- .../AutoDiff/test.restart.colvars.out | 33 +- .../000_hbond_harmonic-fixed/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 40 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 42 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 41 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 43 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 39 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 41 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 39 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 41 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 40 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 42 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 40 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 42 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 48 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 41 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 43 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../000_rmsd_harmonic-fixed/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 37 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 39 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 37 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 39 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 55 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 57 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 48 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 50 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 40 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 42 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../000_tilt_harmonic-fixed/namd-version.txt | 4 +- .../001_10ala_RMSD/AutoDiff/test.colvars.out | 66 +- .../001_10ala_RMSD/AutoDiff/test.colvars.traj | 4 +- .../AutoDiff/test.colvars.out | 41 +- .../AutoDiff/test.colvars.traj | 2 +- .../AutoDiff/test.colvars.out | 37 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 20 +- .../AutoDiff/testres.colvars.out | 39 +- .../AutoDiff/testres.colvars.state.stripped | 4 +- .../AutoDiff/testres.colvars.traj | 22 +- .../003_10ala_SMD_restart/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 62 +- .../AutoDiff/test.colvars.traj | 20 +- .../005_Tcl_script/AutoDiff/test.Tcl.out | 6 +- .../005_Tcl_script/AutoDiff/test.colvars.out | 586 +- .../005_Tcl_script/AutoDiff/test.colvars.traj | 68 +- .../library/005_Tcl_script/AutoDiff/test.grad | 24 +- .../library/005_Tcl_script/AutoDiff/test.pmf | 24 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.colvars.traj | 44 +- .../AutoDiff/test.Tcl.out | 2 +- .../AutoDiff/test.colvars.out | 110 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 48 +- .../007_scripted_cv_biases/namd-version.txt | 8 +- .../AutoDiff/test.colvars.out | 40 +- .../AutoDiff/test.colvars.traj | 20 +- .../009_mtd_expand/AutoDiff/test.colvars.out | 38 +- .../AutoDiff/test.colvars.state.stripped | 14 +- .../009_mtd_expand/AutoDiff/test.colvars.traj | 38 +- .../library/009_mtd_expand/AutoDiff/test.pmf | 150 +- .../AutoDiff/test.colvars.out | 80 +- .../AutoDiff/test.colvars.state.stripped | 8 +- .../AutoDiff/test.colvars.traj | 20 +- .../AutoDiff/test.hist.grad | 6 +- .../010_angle_dihedral/AutoDiff/test.pmf | 1920 +- ...test.rep1.colvars.metadynamics1.rep1.state | 12 +- .../AutoDiff/test.rep1.colvars.out | 42 +- .../AutoDiff/test.rep1.colvars.state.stripped | 14 +- .../AutoDiff/test.rep1.colvars.traj | 196 +- .../AutoDiff/test.rep1.pmf | 98 +- ...test.rep2.colvars.metadynamics1.rep2.state | 12 +- .../AutoDiff/test.rep2.colvars.out | 48 +- .../AutoDiff/test.rep2.colvars.state.stripped | 14 +- .../AutoDiff/test.rep2.colvars.traj | 200 +- .../AutoDiff/test.rep2.pmf | 98 +- ...tres.rep1.colvars.metadynamics1.rep1.state | 12 +- .../AutoDiff/testres.rep1.colvars.out | 52 +- .../testres.rep1.colvars.state.stripped | 14 +- .../AutoDiff/testres.rep1.colvars.traj | 202 +- .../AutoDiff/testres.rep1.pmf | 98 +- ...tres.rep2.colvars.metadynamics1.rep2.state | 12 +- .../AutoDiff/testres.rep2.colvars.out | 52 +- .../testres.rep2.colvars.state.stripped | 14 +- .../AutoDiff/testres.rep2.colvars.traj | 202 +- .../AutoDiff/testres.rep2.pmf | 98 +- .../011_multiple_walker_mtd/namd-version.txt | 6 +- .../012_cvc_loop/AutoDiff/test.colvars.out | 164 +- .../012_cvc_loop/AutoDiff/test.colvars.traj | 40 +- .../014_refposgroup/AutoDiff/test.Tcl.out | 140 +- .../014_refposgroup/AutoDiff/test.colvars.out | 275 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../015_dummy_atom/AutoDiff/test.colvars.traj | 20 +- .../016_mts_bias/AutoDiff/test.colvars.out | 47 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../016_mts_bias/AutoDiff/test.colvars.traj | 42 +- .../AutoDiff/test.restart.colvars.out | 49 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../library/016_mts_bias/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 94 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../AutoDiff/test.colvars.traj | 4 +- .../test.restart.colvars.state.stripped | 2 +- .../017_custom_function/namd-version.txt | 4 +- .../tests/library/018_pathCV/namd-version.txt | 2 +- .../019_gpathCV/AutoDiff/test.colvars.out | 177 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../019_gpathCV/AutoDiff/test.colvars.traj | 26 +- .../AutoDiff/test.restart.colvars.out | 179 +- .../AutoDiff/test.restart.colvars.traj | 22 +- .../library/019_gpathCV/namd-version.txt | 6 +- .../020_gpath/AutoDiff/test.colvars.traj | 28 +- .../AutoDiff/test.restart.colvars.traj | 6 +- namd/tests/library/020_gpath/namd-version.txt | 4 +- .../AutoDiff/test.colvars.out | 476 +- .../AutoDiff/test.colvars.traj | 10 +- .../AutoDiff/test.restart.colvars.out | 478 +- .../AutoDiff/test.restart.colvars.traj | 4 +- .../021_gpathCV_distanceVec/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 532 +- .../AutoDiff/test.colvars.traj | 6 +- .../AutoDiff/test.restart.colvars.out | 534 +- .../AutoDiff/test.restart.colvars.traj | 4 +- .../022_apathCV_distanceVec/namd-version.txt | 6 +- .../023_apathCV/AutoDiff/test.colvars.out | 239 +- .../AutoDiff/test.colvars.state.stripped | 2 +- .../023_apathCV/AutoDiff/test.colvars.traj | 14 +- .../AutoDiff/test.restart.colvars.out | 241 +- .../AutoDiff/test.restart.colvars.traj | 24 +- .../library/023_apathCV/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 55 +- .../AutoDiff/test.colvars.state.stripped | 4 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.restart.colvars.out | 43 +- .../test.restart.colvars.state.stripped | 2 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../024_flexible_restart/namd-version.txt | 6 +- .../025_sym_rmsd/AutoDiff/test.colvars.out | 109 +- .../AutoDiff/test.colvars.state.stripped | 6 +- .../025_sym_rmsd/AutoDiff/test.colvars.traj | 22 +- .../AutoDiff/test.restart.colvars.out | 111 +- .../test.restart.colvars.state.stripped | 4 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../026_ABF_energy/AutoDiff/test.colvars.out | 45 +- .../library/026_ABF_energy/AutoDiff/test.grad | 2 +- .../library/026_ABF_energy/AutoDiff/test.pmf | 14 +- .../AutoDiff/test.restart.colvars.out | 45 +- .../026_ABF_energy/AutoDiff/test.restart.grad | 2 +- .../026_ABF_energy/AutoDiff/test.restart.pmf | 14 +- .../library/026_ABF_energy/namd-version.txt | 6 +- .../AutoDiff/mtd-0.colvars.state | 16 +- .../AutoDiff/mtd-1.colvars.state | 16 +- .../AutoDiff/mtd-2.colvars.state | 16 +- .../AutoDiff/test.colvars.out | 72 +- .../AutoDiff/test.colvars.state.stripped | 18 +- .../AutoDiff/test.colvars.traj | 84 +- .../027_multiple_runs/AutoDiff/test.pmf | 38 +- .../027_multiple_runs/namd-version.txt | 6 +- .../AutoDiff/test.colvars.out | 46 +- .../AutoDiff/test.restart.colvars.out | 46 +- .../namd-version.txt | 6 +- .../library/029_reweightamd/namd-version.txt | 2 +- .../AutoDiff/test.colvars.out | 10 +- .../AutoDiff/test.colvars.state.stripped | 62 +- .../AutoDiff/test.colvars.traj | 16 +- .../030_scaledBiasingForce/namd-version.txt | 6 +- .../031_neuralnetwork/namd-version.txt | 2 +- 814 files changed, 32850 insertions(+), 36751 deletions(-) diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out index 208b0e2dd..8b9e9c148 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -68,7 +64,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -96,7 +92,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.1 according to the specified width (0.1). colvars: ---------------------------------------------------------------------- @@ -107,28 +102,43 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - alpha colvar component: -colvars: - angle colvar component: -colvars: - hBond colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. +colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/3. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/4. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/5. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/6. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/7. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/8. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/9. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/10. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/11. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/12. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/13. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/14. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/15. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/16. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/17. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/18. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/19. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/20. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/21. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/22. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/23. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/24. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/25. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/26. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/27. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/28. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/29. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 2c3923d92..759c485d6 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 8.42013109670389e-01 + x 8.42013109784351e-01 } restraint { diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj index 1d9d7dbb8..59a13c0cf 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 8.44342403972232e-01 -7.44342403972232e-02 - 1 8.44098854642285e-01 -7.44098854642285e-02 - 2 8.43793147696887e-01 -7.43793147696886e-02 - 3 8.43428641474561e-01 -7.43428641474561e-02 - 4 8.43016163379186e-01 -7.43016163379186e-02 - 5 8.42574360353300e-01 -7.42574360353300e-02 - 6 8.42128240610470e-01 -7.42128240610470e-02 - 7 8.41706134434711e-01 -7.41706134434711e-02 - 8 8.41335763240474e-01 -7.41335763240474e-02 - 9 8.41040339208587e-01 -7.41040339208587e-02 - 10 8.40835525411341e-01 -7.40835525411341e-02 - 11 8.40727764204272e-01 -7.40727764204272e-02 - 12 8.40714100924275e-01 -7.40714100924275e-02 - 13 8.40783338958624e-01 -7.40783338958624e-02 - 14 8.40918192455347e-01 -7.40918192455347e-02 - 15 8.41098021792410e-01 -7.41098021792409e-02 - 16 8.41301655271500e-01 -7.41301655271500e-02 - 17 8.41509729929472e-01 -7.41509729929472e-02 - 18 8.41706023128253e-01 -7.41706023128253e-02 - 19 8.41877486404754e-01 -7.41877486404754e-02 - 20 8.42013109670389e-01 -7.42013109670389e-02 + 0 8.44342403972268e-01 -7.44342403972268e-02 + 1 8.44098854642590e-01 -7.44098854642590e-02 + 2 8.43793147698295e-01 -7.43793147698295e-02 + 3 8.43428641477914e-01 -7.43428641477913e-02 + 4 8.43016163376308e-01 -7.43016163376308e-02 + 5 8.42574360346050e-01 -7.42574360346050e-02 + 6 8.42128240619594e-01 -7.42128240619594e-02 + 7 8.41706134441275e-01 -7.41706134441275e-02 + 8 8.41335763262530e-01 -7.41335763262530e-02 + 9 8.41040339242422e-01 -7.41040339242422e-02 + 10 8.40835525453342e-01 -7.40835525453342e-02 + 11 8.40727764254687e-01 -7.40727764254687e-02 + 12 8.40714100983289e-01 -7.40714100983289e-02 + 13 8.40783339024046e-01 -7.40783339024046e-02 + 14 8.40918192530856e-01 -7.40918192530856e-02 + 15 8.41098021877668e-01 -7.41098021877668e-02 + 16 8.41301655357182e-01 -7.41301655357182e-02 + 17 8.41509730022086e-01 -7.41509730022086e-02 + 18 8.41706023231625e-01 -7.41706023231625e-02 + 19 8.41877486515835e-01 -7.41877486515835e-02 + 20 8.42013109784351e-01 -7.42013109784350e-02 diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out index e2f8eb508..09ba41c2e 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -68,7 +64,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -96,7 +92,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.1 according to the specified width (0.1). colvars: ---------------------------------------------------------------------- @@ -107,33 +102,48 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - alpha colvar component: -colvars: - angle colvar component: -colvars: - hBond colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. +colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/3. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/4. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/5. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/6. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/7. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/8. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/9. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/10. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/11. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/12. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/13. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/14. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/15. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/16. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/17. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/18. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/19. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/20. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/21. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/22. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/23. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "one":0/24. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/25. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/26. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/27. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/28. 2 atoms: total mass = 30.006, total charge = -0.98. +colvars: Re-initialized atom group for variable "one":0/29. 2 atoms: total mass = 30.006, total charge = -0.98. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.842013 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (22 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "one":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 7359bbe19..e09e94eee 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 8.32317621377386e-01 + x 8.32317621580914e-01 } restraint { diff --git a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 5d21a33d1..f161a80a9 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_alpha_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 8.42013109670389e-01 -7.42013109670389e-02 - 21 8.42102179859247e-01 -7.42102179859247e-02 - 22 8.42132753897807e-01 -7.42132753897807e-02 - 23 8.42091111194279e-01 -7.42091111194279e-02 - 24 8.41962602226785e-01 -7.41962602226785e-02 - 25 8.41733788173401e-01 -7.41733788173401e-02 - 26 8.41395277535143e-01 -7.41395277535143e-02 - 27 8.40944388629140e-01 -7.40944388629140e-02 - 28 8.40386797315513e-01 -7.40386797315513e-02 - 29 8.39736648516850e-01 -7.39736648516849e-02 - 30 8.39015059742126e-01 -7.39015059742125e-02 - 31 8.38247391201732e-01 -7.38247391201732e-02 - 32 8.37459941069716e-01 -7.37459941069716e-02 - 33 8.36676804346260e-01 -7.36676804346260e-02 - 34 8.35917530408746e-01 -7.35917530408746e-02 - 35 8.35195977166090e-01 -7.35195977166090e-02 - 36 8.34520437212929e-01 -7.34520437212929e-02 - 37 8.33894755921237e-01 -7.33894755921237e-02 - 38 8.33319850305569e-01 -7.33319850305569e-02 - 39 8.32794899843751e-01 -7.32794899843751e-02 - 40 8.32317621377386e-01 -7.32317621377385e-02 + 20 8.42013109784351e-01 -7.42013109784350e-02 + 21 8.42102179978755e-01 -7.42102179978755e-02 + 22 8.42132754021507e-01 -7.42132754021507e-02 + 23 8.42091111321136e-01 -7.42091111321136e-02 + 24 8.41962602356096e-01 -7.41962602356095e-02 + 25 8.41733788301857e-01 -7.41733788301857e-02 + 26 8.41395277661295e-01 -7.41395277661295e-02 + 27 8.40944388762035e-01 -7.40944388762035e-02 + 28 8.40386797451279e-01 -7.40386797451279e-02 + 29 8.39736648652815e-01 -7.39736648652815e-02 + 30 8.39015059877273e-01 -7.39015059877273e-02 + 31 8.38247391341335e-01 -7.38247391341335e-02 + 32 8.37459941212710e-01 -7.37459941212710e-02 + 33 8.36676804493709e-01 -7.36676804493709e-02 + 34 8.35917530561721e-01 -7.35917530561721e-02 + 35 8.35195977325575e-01 -7.35195977325575e-02 + 36 8.34520437356997e-01 -7.34520437356996e-02 + 37 8.33894756096833e-01 -7.33894756096832e-02 + 38 8.33319850486250e-01 -7.33319850486250e-02 + 39 8.32794900028858e-01 -7.32794900028857e-02 + 40 8.32317621580914e-01 -7.32317621580914e-02 diff --git a/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt b/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_alpha_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out index efee19466..4a19c8550 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,42 +55,42 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] @@ -133,7 +129,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -144,27 +139,16 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - angle colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index d398132a2..43525b56b 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.00164524891460e+02 + x 1.00164524892654e+02 } restraint { diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj index 259181bc9..2c8f412a0 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.03254732139588e+02 -4.12618928558351e-01 - 1 1.03132366162310e+02 -4.12129464649240e-01 - 2 1.03006339773933e+02 -4.11625359095731e-01 - 3 1.02876690769855e+02 -4.11106763079420e-01 - 4 1.02743412368037e+02 -4.10573649472149e-01 - 5 1.02606460567606e+02 -4.10025842270424e-01 - 6 1.02465768469001e+02 -4.09463073876003e-01 - 7 1.02321276095485e+02 -4.08885104381940e-01 - 8 1.02172974776860e+02 -4.08291899107440e-01 - 9 1.02020953811828e+02 -4.07683815247310e-01 - 10 1.01865429972566e+02 -4.07061719890263e-01 - 11 1.01706742242777e+02 -4.06426968971107e-01 - 12 1.01545305106535e+02 -4.05781220426139e-01 - 13 1.01381527031664e+02 -4.05126108126656e-01 - 14 1.01215712239860e+02 -4.04462848959438e-01 - 15 1.01047968158544e+02 -4.03791872634177e-01 - 16 1.00878136637506e+02 -4.03112546550023e-01 - 17 1.00705758988893e+02 -4.02423035955572e-01 - 18 1.00530077455794e+02 -4.01720309823177e-01 - 19 1.00350071436460e+02 -4.01000285745841e-01 - 20 1.00164524891460e+02 -4.00258099565841e-01 + 1 1.03132366162315e+02 -4.12129464649258e-01 + 2 1.03006339773950e+02 -4.11625359095801e-01 + 3 1.02876690770137e+02 -4.11106763080547e-01 + 4 1.02743412368775e+02 -4.10573649475101e-01 + 5 1.02606460567804e+02 -4.10025842271217e-01 + 6 1.02465768469158e+02 -4.09463073876632e-01 + 7 1.02321276095597e+02 -4.08885104382386e-01 + 8 1.02172974776925e+02 -4.08291899107700e-01 + 9 1.02020953811854e+02 -4.07683815247416e-01 + 10 1.01865429972567e+02 -4.07061719890269e-01 + 11 1.01706742242773e+02 -4.06426968971090e-01 + 12 1.01545305106549e+02 -4.05781220426196e-01 + 13 1.01381527031724e+02 -4.05126108126898e-01 + 14 1.01215712239996e+02 -4.04462848959984e-01 + 15 1.01047968160132e+02 -4.03791872640529e-01 + 16 1.00878136638138e+02 -4.03112546552552e-01 + 17 1.00705758990434e+02 -4.02423035961734e-01 + 18 1.00530077456623e+02 -4.01720309826491e-01 + 19 1.00350071437758e+02 -4.01000285751032e-01 + 20 1.00164524892654e+02 -4.00258099570617e-01 diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 3752c7683..7b64bde0e 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,42 +55,42 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] @@ -133,7 +129,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -144,32 +139,21 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - angle colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 100.165 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (3 scalable groups, 12 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 19ffa9256..186ad215e 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.50832224152502e+01 + x 9.50832224199785e+01 } restraint { diff --git a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index f3070f2f5..1173041f5 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.00164524891460e+02 -4.00258099565841e-01 - 21 9.99721208590562e+01 -3.99488483436225e-01 - 22 9.97715541522898e+01 -3.98686216609159e-01 - 23 9.95616505536277e+01 -3.97846602214511e-01 - 24 9.93414788135756e+01 -3.96965915254302e-01 - 25 9.91104429898799e+01 -3.96041771959520e-01 - 26 9.88683487906183e+01 -3.95073395162473e-01 - 27 9.86154431829325e+01 -3.94061772731730e-01 - 28 9.83524306231076e+01 -3.93009722492431e-01 - 29 9.80804706453528e+01 -3.91921882581411e-01 - 30 9.78011567145892e+01 -3.90804626858357e-01 - 31 9.75164710990926e+01 -3.89665884396371e-01 - 32 9.72287071984055e+01 -3.88514828793622e-01 - 33 9.69403528472622e+01 -3.87361411389049e-01 - 34 9.66539367587656e+01 -3.86215747035062e-01 - 35 9.63718539644472e+01 -3.85087415857789e-01 - 36 9.60961965658487e+01 -3.83984786263395e-01 - 37 9.58286196853218e+01 -3.82914478741287e-01 - 38 9.55702653322208e+01 -3.81881061328883e-01 - 39 9.53217520988444e+01 -3.80887008395378e-01 - 40 9.50832224152502e+01 -3.79932889661001e-01 + 20 1.00164524892654e+02 -4.00258099570617e-01 + 21 9.99721208604643e+01 -3.99488483441857e-01 + 22 9.97715541539098e+01 -3.98686216615639e-01 + 23 9.95616505554525e+01 -3.97846602221810e-01 + 24 9.93414788155942e+01 -3.96965915262377e-01 + 25 9.91104429920789e+01 -3.96041771968316e-01 + 26 9.88683487929842e+01 -3.95073395171937e-01 + 27 9.86154431854530e+01 -3.94061772741812e-01 + 28 9.83524306257732e+01 -3.93009722503093e-01 + 29 9.80804706481534e+01 -3.91921882592614e-01 + 30 9.78011567175226e+01 -3.90804626870090e-01 + 31 9.75164711021598e+01 -3.89665884408639e-01 + 32 9.72287072016144e+01 -3.88514828806458e-01 + 33 9.69403528506243e+01 -3.87361411402497e-01 + 34 9.66539367622950e+01 -3.86215747049180e-01 + 35 9.63718539681591e+01 -3.85087415872637e-01 + 36 9.60961965697586e+01 -3.83984786279034e-01 + 37 9.58286196894440e+01 -3.82914478757776e-01 + 38 9.55702653365613e+01 -3.81881061346245e-01 + 39 9.53217521034107e+01 -3.80887008413643e-01 + 40 9.50832224199785e+01 -3.79932889679914e-01 diff --git a/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_angle_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out index d1e4a4135..23b8999d1 100644 --- a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,29 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - coordNum pairlist: -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out index 43e5df3df..49e0fbd49 100644 --- a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,34 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - coordNum pairlist: -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt index 157cac038..b7bf5455c 100644 --- a/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-aniso-pairlist_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-10-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out index 6b75c3857..6e7b06fa6 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,26 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 952b2b371..309db4bf6 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.50382512265436e-04 + x 4.50382512360039e-04 } restraint { diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj index 9c31c9ffe..112ced7b7 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 4.88336530020493e-04 3.98046653879918e-04 - 1 5.03969504628764e-04 3.97984121981485e-04 - 2 5.19354539513055e-04 3.97922581841948e-04 - 3 5.32983502677849e-04 3.97868065989289e-04 - 4 5.43368523998496e-04 3.97826525904006e-04 - 5 5.49278854725414e-04 3.97802884581098e-04 - 6 5.49958947547140e-04 3.97800164209811e-04 - 7 5.45267296533856e-04 3.97818930813865e-04 - 8 5.35697517312449e-04 3.97857209930750e-04 - 9 5.22279865846730e-04 3.97910880536613e-04 - 10 5.06396380407222e-04 3.97974414478371e-04 - 11 4.89562687024283e-04 3.98041749251903e-04 - 12 4.73229283972216e-04 3.98107082864111e-04 - 13 4.58638307492123e-04 3.98165446770032e-04 - 14 4.46747589785476e-04 3.98213009640858e-04 - 15 4.38212375483778e-04 3.98247150498065e-04 - 16 4.33402944446411e-04 3.98266388222214e-04 - 17 4.32434896997806e-04 3.98270260412009e-04 - 18 4.35195093328268e-04 3.98259219626687e-04 - 19 4.41356151324242e-04 3.98234575394703e-04 - 20 4.50382512265436e-04 3.98198469950938e-04 + 1 5.03969504626528e-04 3.97984121981494e-04 + 2 5.19354539504346e-04 3.97922581841983e-04 + 3 5.32983502659005e-04 3.97868065989364e-04 + 4 5.43368523967091e-04 3.97826525904132e-04 + 5 5.49278854680875e-04 3.97802884581276e-04 + 6 5.49958947491071e-04 3.97800164210036e-04 + 7 5.45267296469905e-04 3.97818930814120e-04 + 8 5.35697517245723e-04 3.97857209931017e-04 + 9 5.22279865782907e-04 3.97910880536868e-04 + 10 5.06396380351657e-04 3.97974414478593e-04 + 11 4.89562686981327e-04 3.98041749252075e-04 + 12 4.73229283944885e-04 3.98107082864221e-04 + 13 4.58638307482096e-04 3.98165446770072e-04 + 14 4.46747589793320e-04 3.98213009640827e-04 + 15 4.38212375509248e-04 3.98247150497963e-04 + 16 4.33402944488714e-04 3.98266388222045e-04 + 17 4.32434897055776e-04 3.98270260411777e-04 + 18 4.35195093400421e-04 3.98259219626398e-04 + 19 4.41356151408746e-04 3.98234575394365e-04 + 20 4.50382512360039e-04 3.98198469950560e-04 diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out index cd3aa273f..27e93bffc 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,31 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.000450383 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 673940f1b..f07d92582 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.07333860034785e-04 + x 5.07333860152640e-04 } restraint { diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 69dbc17d4..7cece45e3 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 4.50382512265436e-04 3.98198469950938e-04 - 21 4.61538871220812e-04 3.98153844515117e-04 - 22 4.73915291286790e-04 3.98104338834853e-04 - 23 4.86481082339776e-04 3.98054075670641e-04 - 24 4.98171600123441e-04 3.98007313599506e-04 - 25 5.08000918764789e-04 3.97967996324941e-04 - 26 5.15183038861356e-04 3.97939267844555e-04 - 27 5.19238454925296e-04 3.97923046180299e-04 - 28 5.20063102812949e-04 3.97919747588748e-04 - 29 5.17943198908027e-04 3.97928227204368e-04 - 30 5.13510005699675e-04 3.97945959977201e-04 - 31 5.07642202407253e-04 3.97969431190371e-04 - 32 5.01335749082877e-04 3.97994657003669e-04 - 33 4.95567637174033e-04 3.98017729451304e-04 - 34 4.91176737636651e-04 3.98035293049453e-04 - 35 4.88775079019952e-04 3.98044899683920e-04 - 36 4.88691484967476e-04 3.98045234060130e-04 - 37 4.90943355320849e-04 3.98036226578717e-04 - 38 4.95233101502291e-04 3.98019067593991e-04 - 39 5.00971349382943e-04 3.97996114602468e-04 - 40 5.07333860034785e-04 3.97970664559861e-04 + 20 4.50382512360039e-04 3.98198469950560e-04 + 21 4.61538871322809e-04 3.98153844514709e-04 + 22 4.73915291393088e-04 3.98104338834428e-04 + 23 4.86481082447120e-04 3.98054075670212e-04 + 24 4.98171600228783e-04 3.98007313599085e-04 + 25 5.08000918865736e-04 3.97967996324537e-04 + 26 5.15183038956578e-04 3.97939267844174e-04 + 27 5.19238455014736e-04 3.97923046179941e-04 + 28 5.20063102897763e-04 3.97919747588409e-04 + 29 5.17943198990256e-04 3.97928227204039e-04 + 30 5.13510005781771e-04 3.97945959976873e-04 + 31 5.07642202491579e-04 3.97969431190034e-04 + 32 5.01335749171320e-04 3.97994657003315e-04 + 33 4.95567637267788e-04 3.98017729450929e-04 + 34 4.91176737736178e-04 3.98035293049055e-04 + 35 4.88775079125039e-04 3.98044899683500e-04 + 36 4.88691485077369e-04 3.98045234059691e-04 + 37 4.90943355434415e-04 3.98036226578262e-04 + 38 4.95233101618235e-04 3.98019067593527e-04 + 39 5.00971349500124e-04 3.97996114602000e-04 + 40 5.07333860152640e-04 3.97970664559389e-04 diff --git a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-aniso_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out index 9c06635fa..58f41ca99 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,26 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 91bd082de..3f8e0f234 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.66463134760762e+00 + x 2.66463134738076e+00 } restraint { diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj index d266cabe9..7cf1cd53e 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 2.67119635178005e+00 -1.02847854071202e-02 - 1 2.67227384619314e+00 -1.02890953847726e-02 - 2 2.67273226510484e+00 -1.02909290604194e-02 - 3 2.67255372187147e+00 -1.02902148874859e-02 - 4 2.67175941876139e+00 -1.02870376750455e-02 - 5 2.67040901315621e+00 -1.02816360526248e-02 - 6 2.66859725099990e+00 -1.02743890039996e-02 - 7 2.66644846891371e+00 -1.02657938756549e-02 - 8 2.66410945078046e+00 -1.02564378031219e-02 - 9 2.66174084177962e+00 -1.02469633671185e-02 - 10 2.65950718929972e+00 -1.02380287571989e-02 - 11 2.65756592974274e+00 -1.02302637189710e-02 - 12 2.65605614350359e+00 -1.02242245740144e-02 - 13 2.65508832518654e+00 -1.02203533007461e-02 - 14 2.65473648510148e+00 -1.02189459404059e-02 - 15 2.65503349631646e+00 -1.02201339852658e-02 - 16 2.65596999020253e+00 -1.02238799608101e-02 - 17 2.65749649096805e+00 -1.02299859638722e-02 - 18 2.65952812759685e+00 -1.02381125103874e-02 - 19 2.66195123574845e+00 -1.02478049429938e-02 - 20 2.66463134760762e+00 -1.02585253904305e-02 + 1 2.67227384619251e+00 -1.02890953847700e-02 + 2 2.67273226510223e+00 -1.02909290604089e-02 + 3 2.67255372186561e+00 -1.02902148874625e-02 + 4 2.67175941875083e+00 -1.02870376750033e-02 + 5 2.67040901313963e+00 -1.02816360525585e-02 + 6 2.66859725097598e+00 -1.02743890039039e-02 + 7 2.66644846888120e+00 -1.02657938755248e-02 + 8 2.66410945073814e+00 -1.02564378029526e-02 + 9 2.66174084172640e+00 -1.02469633669056e-02 + 10 2.65950718923457e+00 -1.02380287569383e-02 + 11 2.65756592966473e+00 -1.02302637186589e-02 + 12 2.65605614341187e+00 -1.02242245736475e-02 + 13 2.65508832508033e+00 -1.02203533003213e-02 + 14 2.65473648498004e+00 -1.02189459399202e-02 + 15 2.65503349617912e+00 -1.02201339847165e-02 + 16 2.65596999004862e+00 -1.02238799601945e-02 + 17 2.65749649079691e+00 -1.02299859631876e-02 + 18 2.65952812740781e+00 -1.02381125096312e-02 + 19 2.66195123554084e+00 -1.02478049421634e-02 + 20 2.66463134738076e+00 -1.02585253895231e-02 diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out index c20b26d4f..deed28969 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,31 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 2.66463 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 4c8e4e3f2..59a098582 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.67525299255671e+00 + x 2.67525299195737e+00 } restraint { diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 63f1a55dd..bf12f4d2d 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.66463134760762e+00 -1.02585253904305e-02 - 21 2.66742226053972e+00 -1.02696890421589e-02 - 22 2.67017590948386e+00 -1.02807036379355e-02 - 23 2.67275254986108e+00 -1.02910101994443e-02 - 24 2.67503043669944e+00 -1.03001217467977e-02 - 25 2.67691398874566e+00 -1.03076559549827e-02 - 26 2.67833957672623e+00 -1.03133583069049e-02 - 27 2.67927850954533e+00 -1.03171140381813e-02 - 28 2.67973729619981e+00 -1.03189491847993e-02 - 29 2.67975557122547e+00 -1.03190222849019e-02 - 30 2.67940194174935e+00 -1.03176077669974e-02 - 31 2.67876786491929e+00 -1.03150714596772e-02 - 32 2.67795953937304e+00 -1.03118381574922e-02 - 33 2.67708810619769e+00 -1.03083524247908e-02 - 34 2.67625892947302e+00 -1.03050357178921e-02 - 35 2.67556129291865e+00 -1.03022451716746e-02 - 36 2.67505997743329e+00 -1.03002399097332e-02 - 37 2.67478990214567e+00 -1.02991596085827e-02 - 38 2.67475432209952e+00 -1.02990172883981e-02 - 39 2.67492634553313e+00 -1.02997053821325e-02 - 40 2.67525299255671e+00 -1.03010119702268e-02 + 20 2.66463134738076e+00 -1.02585253895231e-02 + 21 2.66742226029295e+00 -1.02696890411718e-02 + 22 2.67017590921653e+00 -1.02807036368661e-02 + 23 2.67275254957261e+00 -1.02910101982905e-02 + 24 2.67503043638932e+00 -1.03001217455573e-02 + 25 2.67691398841351e+00 -1.03076559536541e-02 + 26 2.67833957637177e+00 -1.03133583054871e-02 + 27 2.67927850916844e+00 -1.03171140366738e-02 + 28 2.67973729580054e+00 -1.03189491832022e-02 + 29 2.67975557080403e+00 -1.03190222832161e-02 + 30 2.67940194130612e+00 -1.03176077652245e-02 + 31 2.67876786445484e+00 -1.03150714578194e-02 + 32 2.67795953888813e+00 -1.03118381555525e-02 + 33 2.67708810569326e+00 -1.03083524227731e-02 + 34 2.67625892895020e+00 -1.03050357158008e-02 + 35 2.67556129237875e+00 -1.03022451695150e-02 + 36 2.67505997687781e+00 -1.03002399075112e-02 + 37 2.67478990157628e+00 -1.02991596063051e-02 + 38 2.67475432151807e+00 -1.02990172860723e-02 + 39 2.67492634494164e+00 -1.02997053797666e-02 + 40 2.67525299195737e+00 -1.03010119678295e-02 diff --git a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt index 157cac038..4d05e12c8 100644 --- a/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-group2centeronly_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2019-08-05". +colvars: Using NAMD interface, version "2019-08-01". diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out index d0660361f..ec53ee630 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,29 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - coordNum pairlist: -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 3ff2bc585..b646c70df 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01411698412338e+01 + x 1.01411698403566e+01 } restraint { diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj index c8adc634d..8c250f8de 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.01481368521529e+01 -4.01925474086114e-02 - 1 1.01543539600401e+01 -4.02174158401602e-02 - 2 1.01579705670330e+01 -4.02318822681319e-02 - 3 1.01589102870876e+01 -4.02356411483502e-02 - 4 1.01572731010582e+01 -4.02290924042330e-02 - 5 1.01533217576642e+01 -4.02132870306567e-02 - 6 1.01474576215661e+01 -4.01898304862643e-02 - 7 1.01401899753189e+01 -4.01607599012755e-02 - 8 1.01321020978184e+01 -4.01284083912734e-02 - 9 1.01238160001145e+01 -4.00952640004581e-02 - 10 1.01159565520821e+01 -4.00638262083286e-02 - 11 1.01091157350611e+01 -4.00364629402443e-02 - 12 1.01038185758135e+01 -4.00152743032539e-02 - 13 1.01004931566581e+01 -4.00019726266324e-02 - 14 1.00994472487512e+01 -3.99977889950050e-02 - 15 1.01008533190591e+01 -4.00034132762363e-02 - 16 1.01047425600561e+01 -4.00189702402245e-02 - 17 1.01110075583774e+01 -4.00440302335097e-02 - 18 1.01194127100383e+01 -4.00776508401532e-02 - 19 1.01296114941134e+01 -4.01184459764537e-02 - 20 1.01411698412338e+01 -4.01646793649352e-02 + 1 1.01543539600385e+01 -4.02174158401538e-02 + 2 1.01579705670262e+01 -4.02318822681049e-02 + 3 1.01589102870716e+01 -4.02356411482866e-02 + 4 1.01572731010286e+01 -4.02290924041145e-02 + 5 1.01533217576159e+01 -4.02132870304636e-02 + 6 1.01474576214938e+01 -4.01898304859752e-02 + 7 1.01401899752170e+01 -4.01607599008680e-02 + 8 1.01321020976811e+01 -4.01284083907245e-02 + 9 1.01238159999362e+01 -4.00952639997449e-02 + 10 1.01159565518573e+01 -4.00638262074292e-02 + 11 1.01091157347845e+01 -4.00364629391381e-02 + 12 1.01038185754805e+01 -4.00152743019222e-02 + 13 1.01004931562647e+01 -4.00019726250588e-02 + 14 1.00994472482940e+01 -3.99977889931759e-02 + 15 1.01008533185352e+01 -4.00034132741409e-02 + 16 1.01047425594636e+01 -4.00189702378545e-02 + 17 1.01110075577148e+01 -4.00440302308591e-02 + 18 1.01194127093045e+01 -4.00776508372182e-02 + 19 1.01296114933081e+01 -4.01184459732322e-02 + 20 1.01411698403566e+01 -4.01646793614266e-02 diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out index cec376268..25d4265e0 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,34 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - coordNum pairlist: -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 10.1412 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 8264680de..a5a2b6938 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01841922804199e+01 + x 1.01841922784258e+01 } restraint { diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 3d6793224..c07a48c82 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.01411698412338e+01 -4.01646793649352e-02 - 21 1.01535946552464e+01 -4.02143786209857e-02 - 22 1.01663658704350e+01 -4.02654634817400e-02 - 23 1.01789693407977e+01 -4.03158773631909e-02 - 24 1.01909269862300e+01 -4.03637079449202e-02 - 25 1.02018206336654e+01 -4.04072825346614e-02 - 26 1.02113074887461e+01 -4.04452299549842e-02 - 27 1.02191274705721e+01 -4.04765098822886e-02 - 28 1.02251046852595e+01 -4.05004187410379e-02 - 29 1.02291462135776e+01 -4.05165848543106e-02 - 30 1.02312399822203e+01 -4.05249599288811e-02 - 31 1.02314518101113e+01 -4.05258072404452e-02 - 32 1.02299198133700e+01 -4.05196792534798e-02 - 33 1.02268443918197e+01 -4.05073775672787e-02 - 34 1.02224730723386e+01 -4.04898922893544e-02 - 35 1.02170817762737e+01 -4.04683271050948e-02 - 36 1.02109552451751e+01 -4.04438209807005e-02 - 37 1.02043693152234e+01 -4.04174772608938e-02 - 38 1.01975763299143e+01 -4.03903053196573e-02 - 39 1.01907933864549e+01 -4.03631735458195e-02 - 40 1.01841922804199e+01 -4.03367691216797e-02 + 20 1.01411698403566e+01 -4.01646793614266e-02 + 21 1.01535946542976e+01 -4.02143786171906e-02 + 22 1.01663658694150e+01 -4.02654634776601e-02 + 23 1.01789693397072e+01 -4.03158773588289e-02 + 24 1.01909269850700e+01 -4.03637079402800e-02 + 25 1.02018206324370e+01 -4.04072825297481e-02 + 26 1.02113074874510e+01 -4.04452299498039e-02 + 27 1.02191274692122e+01 -4.04765098768487e-02 + 28 1.02251046838367e+01 -4.05004187353467e-02 + 29 1.02291462120943e+01 -4.05165848483772e-02 + 30 1.02312399806787e+01 -4.05249599227147e-02 + 31 1.02314518085137e+01 -4.05258072340550e-02 + 32 1.02299198117186e+01 -4.05196792468743e-02 + 33 1.02268443901165e+01 -4.05073775604658e-02 + 34 1.02224730705855e+01 -4.04898922823419e-02 + 35 1.02170817744726e+01 -4.04683270978904e-02 + 36 1.02109552433282e+01 -4.04438209733127e-02 + 37 1.02043693133334e+01 -4.04174772533334e-02 + 38 1.01975763279845e+01 -4.03903053119382e-02 + 39 1.01907933844900e+01 -4.03631735379599e-02 + 40 1.01841922784258e+01 -4.03367691137030e-02 diff --git a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt index 157cac038..b2949c9aa 100644 --- a/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum-pairlist_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-05-08. +colvars: Using NAMD interface, version 2018-04-29. diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out index 28e8e90b2..5f1b09b7b 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,26 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped index bf985d8ad..4b97c242b 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01997380115249e+01 + x 1.01997380106663e+01 } restraint { diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj index 35e491d82..8cadeb993 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.02066554836313e+01 -4.04266219345253e-02 - 1 1.02128103525242e+01 -4.04512414100967e-02 - 2 1.02163905908650e+01 -4.04655623634601e-02 - 3 1.02173205792671e+01 -4.04692823170684e-02 - 4 1.02156993030364e+01 -4.04627972121458e-02 - 5 1.02117868890088e+01 -4.04471475560353e-02 - 6 1.02059806949699e+01 -4.04239227798795e-02 - 7 1.01987849183460e+01 -4.03951396733840e-02 - 8 1.01907770135508e+01 -4.03631080542033e-02 - 9 1.01825727800619e+01 -4.03302911202475e-02 - 10 1.01747908474213e+01 -4.02991633896850e-02 - 11 1.01680172849785e+01 -4.02720691399141e-02 - 12 1.01627718762492e+01 -4.02510875049969e-02 - 13 1.01594784287899e+01 -4.02379137151595e-02 - 14 1.01584416411835e+01 -4.02337665647338e-02 - 15 1.01598322600926e+01 -4.02393290403704e-02 - 16 1.01636811698822e+01 -4.02547246795287e-02 - 17 1.01698820348244e+01 -4.02795281392977e-02 - 18 1.01782016103793e+01 -4.03128064415171e-02 - 19 1.01882968442993e+01 -4.03531873771971e-02 - 20 1.01997380115249e+01 -4.03989520460994e-02 + 1 1.02128103525226e+01 -4.04512414100905e-02 + 2 1.02163905908367e+01 -4.04655623633469e-02 + 3 1.02173205792556e+01 -4.04692823170224e-02 + 4 1.02156993029853e+01 -4.04627972119410e-02 + 5 1.02117868889625e+01 -4.04471475558502e-02 + 6 1.02059806948824e+01 -4.04239227795298e-02 + 7 1.01987849182097e+01 -4.03951396728390e-02 + 8 1.01907770133593e+01 -4.03631080534371e-02 + 9 1.01825727798096e+01 -4.03302911192384e-02 + 10 1.01747908471046e+01 -4.02991633884182e-02 + 11 1.01680172845955e+01 -4.02720691383820e-02 + 12 1.01627718757998e+01 -4.02510875031993e-02 + 13 1.01594784282758e+01 -4.02379137131030e-02 + 14 1.01584416406077e+01 -4.02337665624308e-02 + 15 1.01598322594592e+01 -4.02393290378370e-02 + 16 1.01636811691959e+01 -4.02547246767837e-02 + 17 1.01698820340975e+01 -4.02795281363899e-02 + 18 1.01782016096006e+01 -4.03128064384024e-02 + 19 1.01882968434774e+01 -4.03531873739095e-02 + 20 1.01997380106663e+01 -4.03989520426651e-02 diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out index 56dfff67d..b16bdc9b4 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,31 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - coordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 10.1997 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 047e1a4b2..845030b9e 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.02422968531579e+01 + x 1.02422968511954e+01 } restraint { diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 5d7023dd8..d5957567b 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.01997380115249e+01 -4.03989520460994e-02 - 21 1.02120369506585e+01 -4.04481478026342e-02 - 22 1.02246788006083e+01 -4.04987152024332e-02 - 23 1.02371545609629e+01 -4.05486182438517e-02 - 24 1.02489909366769e+01 -4.05959637467076e-02 - 25 1.02597739407961e+01 -4.06390957631846e-02 - 26 1.02691642113129e+01 -4.06766568452516e-02 - 27 1.02769042725010e+01 -4.07076170900039e-02 - 28 1.02828199936102e+01 -4.07312799744409e-02 - 29 1.02868193884911e+01 -4.07472775539644e-02 - 30 1.02888905080147e+01 -4.07555620320589e-02 - 31 1.02890985157159e+01 -4.07563940628635e-02 - 32 1.02875801485946e+01 -4.07503205943785e-02 - 33 1.02845338037653e+01 -4.07381352150613e-02 - 34 1.02802045334771e+01 -4.07208181339083e-02 - 35 1.02748654999713e+01 -4.06994619998850e-02 - 36 1.02687985973514e+01 -4.06751943894056e-02 - 37 1.02622769033932e+01 -4.06491076135727e-02 - 38 1.02555502383063e+01 -4.06222009532253e-02 - 39 1.02488335287781e+01 -4.05953341151125e-02 - 40 1.02422968531579e+01 -4.05691874126314e-02 + 20 1.01997380106663e+01 -4.03989520426651e-02 + 21 1.02120369497625e+01 -4.04481477990502e-02 + 22 1.02246787996745e+01 -4.04987151986978e-02 + 23 1.02371545599893e+01 -4.05486182399573e-02 + 24 1.02489909356603e+01 -4.05959637426412e-02 + 25 1.02597739397322e+01 -4.06390957589289e-02 + 26 1.02691642101966e+01 -4.06766568407865e-02 + 27 1.02769042713270e+01 -4.07076170853082e-02 + 28 1.02828199923736e+01 -4.07312799694943e-02 + 29 1.02868193871873e+01 -4.07472775487492e-02 + 30 1.02888905066404e+01 -4.07555620265616e-02 + 31 1.02890985142689e+01 -4.07563940570755e-02 + 32 1.02875801470742e+01 -4.07503205882967e-02 + 33 1.02845338021721e+01 -4.07381352086885e-02 + 34 1.02802045318133e+01 -4.07208181272531e-02 + 35 1.02748654982405e+01 -4.06994619929619e-02 + 36 1.02687985955587e+01 -4.06751943822348e-02 + 37 1.02622769015451e+01 -4.06491076061802e-02 + 38 1.02555502364106e+01 -4.06222009456423e-02 + 39 1.02488335268439e+01 -4.05953341073754e-02 + 40 1.02422968511954e+01 -4.05691874047814e-02 diff --git a/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt b/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_coordnum_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out index 0267e6c70..66c642d91 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,51 +1,48 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Writing to colvar trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] -colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). colvars: # smp = on [default] +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,32 +56,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: Initializing a new "distanceVec" component. @@ -97,45 +94,39 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. -colvars: Warning: Variable r1 is absent from expression "x". -colvars: Warning: Variable r2 is absent from expression "x". -colvars: Warning: Variable r3 is absent from expression "x". -colvars: Warning: Variable r2 is absent from expression "cos(x) + r1 + r3". colvars: Expecting colvar value of type n-dimensional vector of size 2. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -143,17 +134,13 @@ colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] -colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] @@ -161,9 +148,7 @@ colvars: # centers = { ( 20 , -5 ) } colvars: # targetCenters = { ( 20 , -5 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] -colvars: The force constant for colvar "one" will be rescaled to 1 according to the specified width (1). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -172,39 +157,16 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:1/0. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:1/1. 4 atoms: total mass = 54.028. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 318d67a54..0383e1a55 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.25547985268017e+00 , -5.47738843838940e+00 ) + x ( 3.25547985288590e+00 , -5.47738843832200e+00 ) } restraint { diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj index 1e5db1022..4339c71c0 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one 0 ( 3.20554673468334e+00 , -5.48239480832893e+00 ) - 1 ( 3.20450053401175e+00 , -5.47990257545904e+00 ) - 2 ( 3.20435467486190e+00 , -5.47779766549469e+00 ) - 3 ( 3.20511804594360e+00 , -5.47623313988655e+00 ) - 4 ( 3.20675835825949e+00 , -5.47530637697672e+00 ) - 5 ( 3.20920474891228e+00 , -5.47505494785335e+00 ) - 6 ( 3.21235235535399e+00 , -5.47545779404383e+00 ) - 7 ( 3.21606826728072e+00 , -5.47644105785056e+00 ) - 8 ( 3.22019856588528e+00 , -5.47788745971868e+00 ) - 9 ( 3.22457647532480e+00 , -5.47964779043341e+00 ) - 10 ( 3.22903171994837e+00 , -5.48155318035299e+00 ) - 11 ( 3.23340084473853e+00 , -5.48342703484804e+00 ) - 12 ( 3.23753771524510e+00 , -5.48509601107600e+00 ) - 13 ( 3.24132302074078e+00 , -5.48639968497611e+00 ) - 14 ( 3.24467151148181e+00 , -5.48719873296004e+00 ) - 15 ( 3.24753606965591e+00 , -5.48738134516515e+00 ) - 16 ( 3.24990839058944e+00 , -5.48686751976987e+00 ) - 17 ( 3.25181665212772e+00 , -5.48561085839974e+00 ) - 18 ( 3.25332092184557e+00 , -5.48359768716950e+00 ) - 19 ( 3.25450708223514e+00 , -5.48084366848863e+00 ) - 20 ( 3.25547985268017e+00 , -5.47738843838940e+00 ) + 1 ( 3.20450053401237e+00 , -5.47990257545915e+00 ) + 2 ( 3.20435467486442e+00 , -5.47779766549509e+00 ) + 3 ( 3.20511804594931e+00 , -5.47623313988732e+00 ) + 4 ( 3.20675835826968e+00 , -5.47530637697787e+00 ) + 5 ( 3.20920474892822e+00 , -5.47505494785474e+00 ) + 6 ( 3.21235235537689e+00 , -5.47545779404524e+00 ) + 7 ( 3.21606826731175e+00 , -5.47644105785165e+00 ) + 8 ( 3.22019856592551e+00 , -5.47788745971902e+00 ) + 9 ( 3.22457647537524e+00 , -5.47964779043249e+00 ) + 10 ( 3.22903172000991e+00 , -5.48155318035021e+00 ) + 11 ( 3.23340084481198e+00 , -5.48342703484273e+00 ) + 12 ( 3.23753771533118e+00 , -5.48509601106745e+00 ) + 13 ( 3.24132302084013e+00 , -5.48639968496354e+00 ) + 14 ( 3.24467151159499e+00 , -5.48719873294262e+00 ) + 15 ( 3.24753606978343e+00 , -5.48738134514202e+00 ) + 16 ( 3.24990839073177e+00 , -5.48686751974010e+00 ) + 17 ( 3.25181665228529e+00 , -5.48561085836232e+00 ) + 18 ( 3.25332092201882e+00 , -5.48359768712336e+00 ) + 19 ( 3.25450708242444e+00 , -5.48084366843255e+00 ) + 20 ( 3.25547985288590e+00 , -5.47738843832200e+00 ) diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out index c1e36fd05..f79039b3e 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,51 +1,48 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Writing to colvar trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] -colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). colvars: # smp = on [default] +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,32 +56,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: Initializing a new "distanceVec" component. @@ -97,45 +94,39 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028, total charge = -0.4. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. -colvars: Warning: Variable r1 is absent from expression "x". -colvars: Warning: Variable r2 is absent from expression "x". -colvars: Warning: Variable r3 is absent from expression "x". -colvars: Warning: Variable r2 is absent from expression "cos(x) + r1 + r3". colvars: Expecting colvar value of type n-dimensional vector of size 2. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -143,17 +134,13 @@ colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] -colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] @@ -161,9 +148,7 @@ colvars: # centers = { ( 20 , -5 ) } colvars: # targetCenters = { ( 20 , -5 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] -colvars: The force constant for colvar "one" will be rescaled to 1 according to the specified width (1). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -172,44 +157,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 3.25548 , -5.47739 ) -colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:1/0. 4 atoms: total mass = 54.028. +colvars: Re-initialized atom group one:1/1. 4 atoms: total mass = 54.028. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Saving collective variables state to "test.restart.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Saving collective variables state to "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index c9ce1cfcf..a96c3f221 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.32026945546912e+00 , -5.34818539717392e+00 ) + x ( 3.32026945594503e+00 , -5.34818539676131e+00 ) } restraint { diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj index fd675d4fa..5de5660db 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one - 20 ( 3.25547985268017e+00 , -5.47738843838940e+00 ) - 21 ( 3.25635522894088e+00 , -5.47328901194575e+00 ) - 22 ( 3.25725254105058e+00 , -5.46861283251178e+00 ) - 23 ( 3.25828644104589e+00 , -5.46343113079200e+00 ) - 24 ( 3.25955938734984e+00 , -5.45781309223334e+00 ) - 25 ( 3.26115536827722e+00 , -5.45182122577788e+00 ) - 26 ( 3.26313553184362e+00 , -5.44550828313081e+00 ) - 27 ( 3.26553608582059e+00 , -5.43891612738297e+00 ) - 28 ( 3.26836835302064e+00 , -5.43207683690314e+00 ) - 29 ( 3.27162052061137e+00 , -5.42501611673935e+00 ) - 30 ( 3.27526059063876e+00 , -5.41775865711888e+00 ) - 31 ( 3.27924018683827e+00 , -5.41033456569601e+00 ) - 32 ( 3.28349904494989e+00 , -5.40278559130820e+00 ) - 33 ( 3.28797000642183e+00 , -5.39516984655777e+00 ) - 34 ( 3.29258420352640e+00 , -5.38756403133415e+00 ) - 35 ( 3.29727601922130e+00 , -5.38006282914348e+00 ) - 36 ( 3.30198732290916e+00 , -5.37277582372652e+00 ) - 37 ( 3.30667059698468e+00 , -5.36582266902454e+00 ) - 38 ( 3.31129085392325e+00 , -5.35932721129127e+00 ) - 39 ( 3.31582650736369e+00 , -5.35341088175048e+00 ) - 40 ( 3.32026945546912e+00 , -5.34818539717392e+00 ) + 20 ( 3.25547985288590e+00 , -5.47738843832200e+00 ) + 21 ( 3.25635522916335e+00 , -5.47328901186553e+00 ) + 22 ( 3.25725254129003e+00 , -5.46861283241705e+00 ) + 23 ( 3.25828644130248e+00 , -5.46343113068098e+00 ) + 24 ( 3.25955938762362e+00 , -5.45781309210418e+00 ) + 25 ( 3.26115536856813e+00 , -5.45182122562873e+00 ) + 26 ( 3.26313553215147e+00 , -5.44550828295996e+00 ) + 27 ( 3.26553608614507e+00 , -5.43891612718894e+00 ) + 28 ( 3.26836835336136e+00 , -5.43207683668482e+00 ) + 29 ( 3.27162052096783e+00 , -5.42501611649609e+00 ) + 30 ( 3.27526059101041e+00 , -5.41775865685059e+00 ) + 31 ( 3.27924018722449e+00 , -5.41033456540318e+00 ) + 32 ( 3.28349904535004e+00 , -5.40278559099195e+00 ) + 33 ( 3.28797000683518e+00 , -5.39516984621977e+00 ) + 34 ( 3.29258420395217e+00 , -5.38756403097662e+00 ) + 35 ( 3.29727601965859e+00 , -5.38006282876905e+00 ) + 36 ( 3.30198732335696e+00 , -5.37277582333816e+00 ) + 37 ( 3.30667059744180e+00 , -5.36582266862542e+00 ) + 38 ( 3.31129085438830e+00 , -5.35932721088458e+00 ) + 39 ( 3.31582650783507e+00 , -5.35341088133938e+00 ) + 40 ( 3.32026945594503e+00 , -5.34818539676131e+00 ) diff --git a/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt b/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt index 157cac038..b7bf5455c 100644 --- a/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_customfunction_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-10-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt b/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt +++ b/namd/tests/library/000_dihedralPC_abf2d/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out index 2695e4d53..2176b6914 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/AutoDiff/test.restart.colvars.out @@ -192,7 +192,7 @@ colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -1.07139 colvars: Restarting collective variable "two" from value: -2.07997 -colvars: Restarting metadynamics bias "metadynamics1" from step number 20. +colvars: Restarting metadynamics bias "metadynamics1" from step number 0. colvars: read biasing energy and forces from grids. colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- diff --git a/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt b/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt +++ b/namd/tests/library/000_dihedralPC_metadynamics-2d/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out index 9ad41eda8..e7f89a4ff 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,56 +55,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -118,10 +114,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -147,7 +143,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -158,27 +153,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 3d5bd5995..66b27ad46 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.98300515486710e+01 + x 5.98300515592260e+01 } restraint { diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj index 1c292a5fb..b78cecb35 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 6.31129478791928e+01 -2.52051791516771e-01 - 1 6.30779645383122e+01 -2.51911858153249e-01 - 2 6.30166636721089e+01 -2.51666654688436e-01 - 3 6.29277968203376e+01 -2.51311187281350e-01 - 4 6.28110919635306e+01 -2.50844367854122e-01 - 5 6.26673366019378e+01 -2.50269346407751e-01 - 6 6.24983825380393e+01 -2.49593530152157e-01 - 7 6.23070775463950e+01 -2.48828310185580e-01 - 8 6.20971375561705e+01 -2.47988550224682e-01 - 9 6.18729765854906e+01 -2.47091906341962e-01 - 10 6.16395107158807e+01 -2.46158042863523e-01 - 11 6.14019498452446e+01 -2.45207799380978e-01 - 12 6.11655875894309e+01 -2.44262350357724e-01 - 13 6.09355955346581e+01 -2.43342382138632e-01 - 14 6.07168266139377e+01 -2.42467306455751e-01 - 15 6.05136310205547e+01 -2.41654524082219e-01 - 16 6.03296902153746e+01 -2.40918760861498e-01 - 17 6.01678777158193e+01 -2.40271510863277e-01 - 18 6.00301578158095e+01 -2.39720631263238e-01 - 19 5.99175335696155e+01 -2.39270134278462e-01 - 20 5.98300515486710e+01 -2.38920206194684e-01 + 0 6.31129478791929e+01 -2.52051791516771e-01 + 1 6.30779645383520e+01 -2.51911858153408e-01 + 2 6.30166636722659e+01 -2.51666654689064e-01 + 3 6.29277968222057e+01 -2.51311187288823e-01 + 4 6.28110919641768e+01 -2.50844367856707e-01 + 5 6.26673366028881e+01 -2.50269346411552e-01 + 6 6.24983825393602e+01 -2.49593530157441e-01 + 7 6.23070775481485e+01 -2.48828310192594e-01 + 8 6.20971375584149e+01 -2.47988550233660e-01 + 9 6.18729765882759e+01 -2.47091906353104e-01 + 10 6.16395107192542e+01 -2.46158042877017e-01 + 11 6.14019498492506e+01 -2.45207799397002e-01 + 12 6.11655875941102e+01 -2.44262350376441e-01 + 13 6.09355955400464e+01 -2.43342382160186e-01 + 14 6.07168266200639e+01 -2.42467306480256e-01 + 15 6.05136310274090e+01 -2.41654524109636e-01 + 16 6.03296902229661e+01 -2.40918760891865e-01 + 17 6.01678777239959e+01 -2.40271510895984e-01 + 18 6.00301578248419e+01 -2.39720631299368e-01 + 19 5.99175335802490e+01 -2.39270134320996e-01 + 20 5.98300515592260e+01 -2.38920206236904e-01 diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out index 9ce9a9ef3..237f53c44 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,56 +55,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -118,10 +114,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -147,7 +143,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -158,32 +153,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 59.8301 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 108bc4cd0..44e24f2b2 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.97551054473693e+01 + x 5.97551054664761e+01 } restraint { diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 3cf42a7dc..71d70ae0b 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.98300515486710e+01 -2.38920206194684e-01 - 21 5.97668650394525e+01 -2.38667460157810e-01 - 22 5.97263508192266e+01 -2.38505403276906e-01 - 23 5.97062661536266e+01 -2.38425064614506e-01 - 24 5.97039266347449e+01 -2.38415706538980e-01 - 25 5.97163827891862e+01 -2.38465531156745e-01 - 26 5.97405738612989e+01 -2.38562295445196e-01 - 27 5.97734430366384e+01 -2.38693772146554e-01 - 28 5.98120052955854e+01 -2.38848021182342e-01 - 29 5.98533709544186e+01 -2.39013483817674e-01 - 30 5.98947361572460e+01 -2.39178944628984e-01 - 31 5.99333583402208e+01 -2.39333433360883e-01 - 32 5.99665373878884e+01 -2.39466149551554e-01 - 33 5.99916207519385e+01 -2.39566483007754e-01 - 34 6.00060426921965e+01 -2.39624170768786e-01 - 35 6.00073965333411e+01 -2.39629586133365e-01 - 36 5.99935248947171e+01 -2.39574099578868e-01 - 37 5.99626029530151e+01 -2.39450411812060e-01 - 38 5.99131916781728e+01 -2.39252766712691e-01 - 39 5.98442490681818e+01 -2.38976996272727e-01 - 40 5.97551054473693e+01 -2.38620421789477e-01 + 20 5.98300515592260e+01 -2.38920206236904e-01 + 21 5.97668650506981e+01 -2.38667460202792e-01 + 22 5.97263508310798e+01 -2.38505403324319e-01 + 23 5.97062661660438e+01 -2.38425064664175e-01 + 24 5.97039266476832e+01 -2.38415706590733e-01 + 25 5.97163828026047e+01 -2.38465531210419e-01 + 26 5.97405738751603e+01 -2.38562295500641e-01 + 27 5.97734430509102e+01 -2.38693772203641e-01 + 28 5.98120053098547e+01 -2.38848021239419e-01 + 29 5.98533709694021e+01 -2.39013483877608e-01 + 30 5.98947361725041e+01 -2.39178944690016e-01 + 31 5.99333583559336e+01 -2.39333433423734e-01 + 32 5.99665374039350e+01 -2.39466149615740e-01 + 33 5.99916207683209e+01 -2.39566483073283e-01 + 34 6.00060427089216e+01 -2.39624170835686e-01 + 35 6.00073965504200e+01 -2.39629586201680e-01 + 36 5.99935249121635e+01 -2.39574099648654e-01 + 37 5.99626029708492e+01 -2.39450411883397e-01 + 38 5.99131916964115e+01 -2.39252766785646e-01 + 39 5.98442490868439e+01 -2.38976996347376e-01 + 40 5.97551054664761e+01 -2.38620421865904e-01 diff --git a/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt b/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_dihedral_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out index f460ff36e..da0de3420 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.out @@ -4,9 +4,10 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -170,12 +170,10 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj index 222745310..e603d2abe 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.colvars.traj @@ -16,7 +16,7 @@ 14 6.09757828886766e+01 0.00000000000000e+00 15 6.08031168275266e+01 0.00000000000000e+00 16 6.06502098430779e+01 0.00000000000000e+00 - 17 6.05198025267682e+01 0.00000000000000e+00 + 17 6.05198025267681e+01 0.00000000000000e+00 18 6.04137510819450e+01 0.00000000000000e+00 19 6.03329740983039e+01 0.00000000000000e+00 20 6.02774557419409e+01 0.00000000000000e+00 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat index 29c2e88d8..add429103 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.histogram1.dat @@ -1,75 +1,75 @@ # 1 -# -6.00000000000000e+01 5.00000000000000e+00 72 1 +# -60 5 72 1 - -5.75000000000000e+01 0.00000000000000e+00 - -5.25000000000000e+01 0.00000000000000e+00 - -4.75000000000000e+01 0.00000000000000e+00 - -4.25000000000000e+01 0.00000000000000e+00 - -3.75000000000000e+01 0.00000000000000e+00 - -3.25000000000000e+01 0.00000000000000e+00 - -2.75000000000000e+01 0.00000000000000e+00 - -2.25000000000000e+01 0.00000000000000e+00 - -1.75000000000000e+01 0.00000000000000e+00 - -1.25000000000000e+01 0.00000000000000e+00 - -7.50000000000000e+00 0.00000000000000e+00 - -2.50000000000000e+00 0.00000000000000e+00 - 2.50000000000000e+00 0.00000000000000e+00 - 7.50000000000000e+00 0.00000000000000e+00 - 1.25000000000000e+01 0.00000000000000e+00 - 1.75000000000000e+01 0.00000000000000e+00 - 2.25000000000000e+01 0.00000000000000e+00 - 2.75000000000000e+01 0.00000000000000e+00 - 3.25000000000000e+01 0.00000000000000e+00 - 3.75000000000000e+01 0.00000000000000e+00 - 4.25000000000000e+01 0.00000000000000e+00 - 4.75000000000000e+01 0.00000000000000e+00 - 5.25000000000000e+01 0.00000000000000e+00 - 5.75000000000000e+01 0.00000000000000e+00 - 6.25000000000000e+01 2.00000000000000e+01 - 6.75000000000000e+01 0.00000000000000e+00 - 7.25000000000000e+01 0.00000000000000e+00 - 7.75000000000000e+01 0.00000000000000e+00 - 8.25000000000000e+01 0.00000000000000e+00 - 8.75000000000000e+01 0.00000000000000e+00 - 9.25000000000000e+01 0.00000000000000e+00 - 9.75000000000000e+01 0.00000000000000e+00 - 1.02500000000000e+02 0.00000000000000e+00 - 1.07500000000000e+02 0.00000000000000e+00 - 1.12500000000000e+02 0.00000000000000e+00 - 1.17500000000000e+02 0.00000000000000e+00 - 1.22500000000000e+02 0.00000000000000e+00 - 1.27500000000000e+02 0.00000000000000e+00 - 1.32500000000000e+02 0.00000000000000e+00 - 1.37500000000000e+02 0.00000000000000e+00 - 1.42500000000000e+02 0.00000000000000e+00 - 1.47500000000000e+02 0.00000000000000e+00 - 1.52500000000000e+02 0.00000000000000e+00 - 1.57500000000000e+02 0.00000000000000e+00 - 1.62500000000000e+02 0.00000000000000e+00 - 1.67500000000000e+02 0.00000000000000e+00 - 1.72500000000000e+02 0.00000000000000e+00 - 1.77500000000000e+02 0.00000000000000e+00 - 1.82500000000000e+02 0.00000000000000e+00 - 1.87500000000000e+02 0.00000000000000e+00 - 1.92500000000000e+02 0.00000000000000e+00 - 1.97500000000000e+02 0.00000000000000e+00 - 2.02500000000000e+02 0.00000000000000e+00 - 2.07500000000000e+02 0.00000000000000e+00 - 2.12500000000000e+02 0.00000000000000e+00 - 2.17500000000000e+02 0.00000000000000e+00 - 2.22500000000000e+02 0.00000000000000e+00 - 2.27500000000000e+02 0.00000000000000e+00 - 2.32500000000000e+02 0.00000000000000e+00 - 2.37500000000000e+02 0.00000000000000e+00 - 2.42500000000000e+02 0.00000000000000e+00 - 2.47500000000000e+02 0.00000000000000e+00 - 2.52500000000000e+02 0.00000000000000e+00 - 2.57500000000000e+02 0.00000000000000e+00 - 2.62500000000000e+02 0.00000000000000e+00 - 2.67500000000000e+02 0.00000000000000e+00 - 2.72500000000000e+02 0.00000000000000e+00 - 2.77500000000000e+02 0.00000000000000e+00 - 2.82500000000000e+02 0.00000000000000e+00 - 2.87500000000000e+02 0.00000000000000e+00 - 2.92500000000000e+02 0.00000000000000e+00 - 2.97500000000000e+02 0.00000000000000e+00 + -57.5 0 + -52.5 0 + -47.5 0 + -42.5 0 + -37.5 0 + -32.5 0 + -27.5 0 + -22.5 0 + -17.5 0 + -12.5 0 + -7.5 0 + -2.5 0 + 2.5 0 + 7.5 0 + 12.5 0 + 17.5 0 + 22.5 0 + 27.5 0 + 32.5 0 + 37.5 0 + 42.5 0 + 47.5 0 + 52.5 0 + 57.5 0 + 62.5 20 + 67.5 0 + 72.5 0 + 77.5 0 + 82.5 0 + 87.5 0 + 92.5 0 + 97.5 0 + 102.5 0 + 107.5 0 + 112.5 0 + 117.5 0 + 122.5 0 + 127.5 0 + 132.5 0 + 137.5 0 + 142.5 0 + 147.5 0 + 152.5 0 + 157.5 0 + 162.5 0 + 167.5 0 + 172.5 0 + 177.5 0 + 182.5 0 + 187.5 0 + 192.5 0 + 197.5 0 + 202.5 0 + 207.5 0 + 212.5 0 + 217.5 0 + 222.5 0 + 227.5 0 + 232.5 0 + 237.5 0 + 242.5 0 + 247.5 0 + 252.5 0 + 257.5 0 + 262.5 0 + 267.5 0 + 272.5 0 + 277.5 0 + 282.5 0 + 287.5 0 + 292.5 0 + 297.5 0 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out index b917756f8..6b4f434fe 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.out @@ -4,9 +4,10 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -170,7 +170,6 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 60.2775 @@ -180,7 +179,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped index 0871d37c1..801e6d28b 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.08972121817132e+01 + x 6.08972121817133e+01 } histogram { diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj index 309eb03b3..26132495a 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.colvars.traj @@ -10,13 +10,13 @@ 28 6.05174152507232e+01 0.00000000000000e+00 29 6.05916134367745e+01 0.00000000000000e+00 30 6.06661106175895e+01 0.00000000000000e+00 - 31 6.07382493916987e+01 0.00000000000000e+00 + 31 6.07382493916988e+01 0.00000000000000e+00 32 6.08054278361141e+01 0.00000000000000e+00 - 33 6.08651028913518e+01 0.00000000000000e+00 - 34 6.09148265769850e+01 0.00000000000000e+00 - 35 6.09523144047667e+01 0.00000000000000e+00 - 36 6.09755306486176e+01 0.00000000000000e+00 - 37 6.09827676263964e+01 0.00000000000000e+00 - 38 6.09726956103267e+01 0.00000000000000e+00 - 39 6.09443715231751e+01 0.00000000000000e+00 - 40 6.08972121817132e+01 0.00000000000000e+00 + 33 6.08651028913519e+01 0.00000000000000e+00 + 34 6.09148265769852e+01 0.00000000000000e+00 + 35 6.09523144047668e+01 0.00000000000000e+00 + 36 6.09755306486177e+01 0.00000000000000e+00 + 37 6.09827676263966e+01 0.00000000000000e+00 + 38 6.09726956103268e+01 0.00000000000000e+00 + 39 6.09443715231752e+01 0.00000000000000e+00 + 40 6.08972121817133e+01 0.00000000000000e+00 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat index 7d3ef8bb5..44f8e383f 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/AutoDiff/test.restart.histogram1.dat @@ -1,75 +1,75 @@ # 1 -# -6.00000000000000e+01 5.00000000000000e+00 72 1 +# -60 5 72 1 - -5.75000000000000e+01 0.00000000000000e+00 - -5.25000000000000e+01 0.00000000000000e+00 - -4.75000000000000e+01 0.00000000000000e+00 - -4.25000000000000e+01 0.00000000000000e+00 - -3.75000000000000e+01 0.00000000000000e+00 - -3.25000000000000e+01 0.00000000000000e+00 - -2.75000000000000e+01 0.00000000000000e+00 - -2.25000000000000e+01 0.00000000000000e+00 - -1.75000000000000e+01 0.00000000000000e+00 - -1.25000000000000e+01 0.00000000000000e+00 - -7.50000000000000e+00 0.00000000000000e+00 - -2.50000000000000e+00 0.00000000000000e+00 - 2.50000000000000e+00 0.00000000000000e+00 - 7.50000000000000e+00 0.00000000000000e+00 - 1.25000000000000e+01 0.00000000000000e+00 - 1.75000000000000e+01 0.00000000000000e+00 - 2.25000000000000e+01 0.00000000000000e+00 - 2.75000000000000e+01 0.00000000000000e+00 - 3.25000000000000e+01 0.00000000000000e+00 - 3.75000000000000e+01 0.00000000000000e+00 - 4.25000000000000e+01 0.00000000000000e+00 - 4.75000000000000e+01 0.00000000000000e+00 - 5.25000000000000e+01 0.00000000000000e+00 - 5.75000000000000e+01 0.00000000000000e+00 - 6.25000000000000e+01 4.00000000000000e+01 - 6.75000000000000e+01 0.00000000000000e+00 - 7.25000000000000e+01 0.00000000000000e+00 - 7.75000000000000e+01 0.00000000000000e+00 - 8.25000000000000e+01 0.00000000000000e+00 - 8.75000000000000e+01 0.00000000000000e+00 - 9.25000000000000e+01 0.00000000000000e+00 - 9.75000000000000e+01 0.00000000000000e+00 - 1.02500000000000e+02 0.00000000000000e+00 - 1.07500000000000e+02 0.00000000000000e+00 - 1.12500000000000e+02 0.00000000000000e+00 - 1.17500000000000e+02 0.00000000000000e+00 - 1.22500000000000e+02 0.00000000000000e+00 - 1.27500000000000e+02 0.00000000000000e+00 - 1.32500000000000e+02 0.00000000000000e+00 - 1.37500000000000e+02 0.00000000000000e+00 - 1.42500000000000e+02 0.00000000000000e+00 - 1.47500000000000e+02 0.00000000000000e+00 - 1.52500000000000e+02 0.00000000000000e+00 - 1.57500000000000e+02 0.00000000000000e+00 - 1.62500000000000e+02 0.00000000000000e+00 - 1.67500000000000e+02 0.00000000000000e+00 - 1.72500000000000e+02 0.00000000000000e+00 - 1.77500000000000e+02 0.00000000000000e+00 - 1.82500000000000e+02 0.00000000000000e+00 - 1.87500000000000e+02 0.00000000000000e+00 - 1.92500000000000e+02 0.00000000000000e+00 - 1.97500000000000e+02 0.00000000000000e+00 - 2.02500000000000e+02 0.00000000000000e+00 - 2.07500000000000e+02 0.00000000000000e+00 - 2.12500000000000e+02 0.00000000000000e+00 - 2.17500000000000e+02 0.00000000000000e+00 - 2.22500000000000e+02 0.00000000000000e+00 - 2.27500000000000e+02 0.00000000000000e+00 - 2.32500000000000e+02 0.00000000000000e+00 - 2.37500000000000e+02 0.00000000000000e+00 - 2.42500000000000e+02 0.00000000000000e+00 - 2.47500000000000e+02 0.00000000000000e+00 - 2.52500000000000e+02 0.00000000000000e+00 - 2.57500000000000e+02 0.00000000000000e+00 - 2.62500000000000e+02 0.00000000000000e+00 - 2.67500000000000e+02 0.00000000000000e+00 - 2.72500000000000e+02 0.00000000000000e+00 - 2.77500000000000e+02 0.00000000000000e+00 - 2.82500000000000e+02 0.00000000000000e+00 - 2.87500000000000e+02 0.00000000000000e+00 - 2.92500000000000e+02 0.00000000000000e+00 - 2.97500000000000e+02 0.00000000000000e+00 + -57.5 0 + -52.5 0 + -47.5 0 + -42.5 0 + -37.5 0 + -32.5 0 + -27.5 0 + -22.5 0 + -17.5 0 + -12.5 0 + -7.5 0 + -2.5 0 + 2.5 0 + 7.5 0 + 12.5 0 + 17.5 0 + 22.5 0 + 27.5 0 + 32.5 0 + 37.5 0 + 42.5 0 + 47.5 0 + 52.5 0 + 57.5 0 + 62.5 40 + 67.5 0 + 72.5 0 + 77.5 0 + 82.5 0 + 87.5 0 + 92.5 0 + 97.5 0 + 102.5 0 + 107.5 0 + 112.5 0 + 117.5 0 + 122.5 0 + 127.5 0 + 132.5 0 + 137.5 0 + 142.5 0 + 147.5 0 + 152.5 0 + 157.5 0 + 162.5 0 + 167.5 0 + 172.5 0 + 177.5 0 + 182.5 0 + 187.5 0 + 192.5 0 + 197.5 0 + 202.5 0 + 207.5 0 + 212.5 0 + 217.5 0 + 222.5 0 + 227.5 0 + 232.5 0 + 237.5 0 + 242.5 0 + 247.5 0 + 252.5 0 + 257.5 0 + 262.5 0 + 267.5 0 + 272.5 0 + 277.5 0 + 282.5 0 + 287.5 0 + 292.5 0 + 297.5 0 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt index 157cac038..2c2fdb849 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2021-10-13. +colvars: Using NAMD interface, version "2021-10-13". diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out index 50378ec14..1218eda97 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,56 +55,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -118,10 +114,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -144,7 +140,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { -10 } colvars: # upperWalls = { 10 } @@ -160,27 +155,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped index 84a539af0..e98cccfbb 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.99015240062048e+01 + x 5.99015240169243e+01 } restraint { diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj index bf8a645ef..f83c37fda 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 0 6.31129478791928e+01 -2.12451791516771e-01 - 1 6.30782207430228e+01 -2.12312882972091e-01 - 2 6.30176844597210e+01 -2.12070737838884e-01 - 3 6.29300795604372e+01 -2.11720318241749e-01 - 4 6.28151165875842e+01 -2.11260466350337e-01 - 5 6.26735597681268e+01 -2.10694239072507e-01 - 6 6.25072326023818e+01 -2.10028930409527e-01 - 7 6.23189505052794e+01 -2.09275802021118e-01 - 8 6.21123940675534e+01 -2.08449576270213e-01 - 9 6.18919401201661e+01 -2.07567760480665e-01 - 10 6.16624668323414e+01 -2.06649867329365e-01 - 11 6.14291465328002e+01 -2.05716586131201e-01 - 12 6.11972365829090e+01 -2.04788946331636e-01 - 13 6.09718744707731e+01 -2.03887497883092e-01 - 14 6.07578818481667e+01 -2.03031527392667e-01 - 15 6.05595809269580e+01 -2.02238323707832e-01 - 16 6.03806287731779e+01 -2.01522515092712e-01 - 17 6.02238782127047e+01 -2.00895512850819e-01 - 18 6.00912764804658e+01 -2.00365105921863e-01 - 19 5.99838130196557e+01 -1.99935252078623e-01 - 20 5.99015240062048e+01 -1.99606096024819e-01 +# step one fa_one + 0 6.31129478791929e+01 -2.12451791516771e-01 + 1 6.30782207430626e+01 -2.12312882972251e-01 + 2 6.30176844598780e+01 -2.12070737839512e-01 + 3 6.29300795621464e+01 -2.11720318248586e-01 + 4 6.28151165882276e+01 -2.11260466352910e-01 + 5 6.26735597690779e+01 -2.10694239076312e-01 + 6 6.25072326037074e+01 -2.10028930414830e-01 + 7 6.23189505070414e+01 -2.09275802028166e-01 + 8 6.21123940698095e+01 -2.08449576279238e-01 + 9 6.18919401229661e+01 -2.07567760491865e-01 + 10 6.16624668357318e+01 -2.06649867342927e-01 + 11 6.14291465368246e+01 -2.05716586147298e-01 + 12 6.11972365876074e+01 -2.04788946350430e-01 + 13 6.09718744761807e+01 -2.03887497904723e-01 + 14 6.07578818543115e+01 -2.03031527417246e-01 + 15 6.05595809338303e+01 -2.02238323735321e-01 + 16 6.03806287808051e+01 -2.01522515123221e-01 + 17 6.02238782208511e+01 -2.00895512883405e-01 + 18 6.00912764895398e+01 -2.00365105958159e-01 + 19 5.99838130302367e+01 -1.99935252120947e-01 + 20 5.99015240167765e+01 -1.99606096067106e-01 diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out index 03cf0c9a7..2b1dab030 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,56 +55,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -118,10 +114,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -144,7 +140,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { -10 } colvars: # upperWalls = { 10 } @@ -160,32 +155,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 59.9015 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped index 77bac4e9f..203f4469d 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 5.99403692539448e+01 + x 5.99403692730741e+01 } diff --git a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj index 5b3f70be7..9c2977f98 100644 --- a/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 20 5.99015240062048e+01 -1.99606096024819e-01 - 21 5.98435552188444e+01 -1.99374220875378e-01 - 22 5.98082785181930e+01 -1.99233114072772e-01 - 23 5.97934484948365e+01 -1.99173793979346e-01 - 24 5.97963800349839e+01 -1.99185520139936e-01 - 25 5.98141247089905e+01 -1.99256498835962e-01 - 26 5.98436244176440e+01 -1.99374497670576e-01 - 27 5.98818266354142e+01 -1.99527306541657e-01 - 28 5.99257523474475e+01 -1.99703009389790e-01 - 29 5.99725198410855e+01 -1.99890079364342e-01 - 30 6.00193353623784e+01 -2.00077341449514e-01 - 31 6.00634687212219e+01 -2.00253874884888e-01 - 32 6.01022344101259e+01 -2.00408937640504e-01 - 33 6.01329964922276e+01 -2.00531985968910e-01 - 34 6.01532073938345e+01 -2.00612829575338e-01 - 35 6.01604795350481e+01 -2.00641918140193e-01 - 36 6.01526748742382e+01 -2.00610699496953e-01 - 37 6.01279874115193e+01 -2.00511949646077e-01 - 38 6.00849959389077e+01 -2.00339983755631e-01 - 39 6.00226748752046e+01 -2.00090699500818e-01 - 40 5.99403692539448e+01 -1.99761477015779e-01 +# step one fa_one + 20 5.99015240167765e+01 -1.99606096067106e-01 + 21 5.98435552301064e+01 -1.99374220920425e-01 + 22 5.98082785300632e+01 -1.99233114120253e-01 + 23 5.97934485072713e+01 -1.99173794029085e-01 + 24 5.97963800479404e+01 -1.99185520191762e-01 + 25 5.98141247224277e+01 -1.99256498889711e-01 + 26 5.98436244315244e+01 -1.99374497726098e-01 + 27 5.98818266497052e+01 -1.99527306598821e-01 + 28 5.99257523617425e+01 -1.99703009446970e-01 + 29 5.99725198560893e+01 -1.99890079424357e-01 + 30 6.00193353776544e+01 -2.00077341510617e-01 + 31 6.00634687369522e+01 -2.00253874947809e-01 + 32 6.01022344261894e+01 -2.00408937704758e-01 + 33 6.01329965086264e+01 -2.00531986034505e-01 + 34 6.01532074105757e+01 -2.00612829642303e-01 + 35 6.01604795521431e+01 -2.00641918208573e-01 + 36 6.01526748917010e+01 -2.00610699566804e-01 + 37 6.01279874293707e+01 -2.00511949717483e-01 + 38 6.00849959571649e+01 -2.00339983828660e-01 + 39 6.00226748938869e+01 -2.00090699575548e-01 + 40 5.99403692730741e+01 -1.99761477092296e-01 diff --git a/namd/tests/library/000_dihedralwalls/namd-version.txt b/namd/tests/library/000_dihedralwalls/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_dihedralwalls/namd-version.txt +++ b/namd/tests/library/000_dihedralwalls/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out index c512baba0..c0fccf38e 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,40 +55,40 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -130,7 +126,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -141,28 +136,16 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - dipoleAngle colvar component: -colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 9f4d54156..291b73e90 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.36349055389455e+01 + x 9.36349055337838e+01 } restraint { diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj index 44c231c6c..336b7c00f 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 8.97962480697652e+01 -3.58784992279061e-01 - 1 9.00687365881581e+01 -3.59874946352633e-01 - 2 9.03696531716400e+01 -3.61078612686560e-01 - 3 9.06810803337954e+01 -3.62324321335182e-01 - 4 9.09847043036197e+01 -3.63538817214479e-01 - 5 9.12638043504929e+01 -3.64655217401972e-01 - 6 9.15051697825636e+01 -3.65620679130254e-01 - 7 9.17006524157741e+01 -3.66402609663097e-01 - 8 9.18480994678579e+01 -3.66992397871432e-01 - 9 9.19515174516923e+01 -3.67406069806769e-01 - 10 9.20204550855094e+01 -3.67681820342038e-01 - 11 9.20687188119887e+01 -3.67874875247955e-01 - 12 9.21126240131068e+01 -3.68050496052427e-01 - 13 9.21690190327914e+01 -3.68276076131166e-01 - 14 9.22533018510856e+01 -3.68613207404342e-01 - 15 9.23775997129957e+01 -3.69110398851983e-01 - 16 9.25492271314794e+01 -3.69796908525918e-01 - 17 9.27695098407462e+01 -3.70678039362985e-01 - 18 9.30330692776144e+01 -3.71732277110457e-01 - 19 9.33276898533472e+01 -3.72910759413389e-01 - 20 9.36349055389455e+01 -3.74139622155782e-01 + 1 9.00687365880860e+01 -3.59874946352344e-01 + 2 9.03696531713662e+01 -3.61078612685465e-01 + 3 9.06810803332082e+01 -3.62324321332833e-01 + 4 9.09847043026283e+01 -3.63538817210513e-01 + 5 9.12638043490304e+01 -3.64655217396121e-01 + 6 9.15051697805885e+01 -3.65620679122354e-01 + 7 9.17006524132711e+01 -3.66402609653084e-01 + 8 9.18480994648365e+01 -3.66992397859346e-01 + 9 9.19515174481835e+01 -3.67406069792734e-01 + 10 9.20204550815615e+01 -3.67681820326246e-01 + 11 9.20687188076611e+01 -3.67874875230645e-01 + 12 9.21126240084645e+01 -3.68050496033858e-01 + 13 9.21690190278993e+01 -3.68276076111597e-01 + 14 9.22533018460045e+01 -3.68613207384018e-01 + 15 9.23775997077804e+01 -3.69110398831122e-01 + 16 9.25492271261785e+01 -3.69796908504714e-01 + 17 9.27695098354046e+01 -3.70678039341619e-01 + 18 9.30330692722776e+01 -3.71732277089110e-01 + 19 9.33276898480665e+01 -3.72910759392266e-01 + 20 9.36349055337838e+01 -3.74139622135135e-01 diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 48c3860e5..99d488573 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,40 +55,40 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -130,7 +126,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -141,33 +136,21 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - dipoleAngle colvar component: -colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 93.6349 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (12 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 651e66dc5..4da36d6f0 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.01098741923154e+01 + x 9.01098742103920e+01 } restraint { diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index ee86202c8..7e403dd06 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.36349055389455e+01 -3.74139622155782e-01 - 21 9.39314096608430e+01 -3.75325638643372e-01 - 22 9.41912842268812e+01 -3.76365136907525e-01 - 23 9.43888705891540e+01 -3.77155482356616e-01 - 24 9.45019115137236e+01 -3.77607646054895e-01 - 25 9.45144559381111e+01 -3.77657823752444e-01 - 26 9.44189957511575e+01 -3.77275983004630e-01 - 27 9.42174306917003e+01 -3.76469722766801e-01 - 28 9.39206949360476e+01 -3.75282779744190e-01 - 29 9.35471730241369e+01 -3.73788692096548e-01 - 30 9.31202694745324e+01 -3.72081077898130e-01 - 31 9.26656093089659e+01 -3.70262437235864e-01 - 32 9.22083464020604e+01 -3.68433385608242e-01 - 33 9.17709340560258e+01 -3.66683736224103e-01 - 34 9.13715370422709e+01 -3.65086148169084e-01 - 35 9.10230941262197e+01 -3.63692376504879e-01 - 36 9.07329203680483e+01 -3.62531681472193e-01 - 37 9.05026913412928e+01 -3.61610765365171e-01 - 38 9.03286700254905e+01 -3.60914680101962e-01 - 39 9.02021116805683e+01 -3.60408446722273e-01 - 40 9.01098741923154e+01 -3.60039496769262e-01 + 20 9.36349055337838e+01 -3.74139622135135e-01 + 21 9.39314096558801e+01 -3.75325638623520e-01 + 22 9.41912842222173e+01 -3.76365136888869e-01 + 23 9.43888705849112e+01 -3.77155482339645e-01 + 24 9.45019115100439e+01 -3.77607646040175e-01 + 25 9.45144559351512e+01 -3.77657823740605e-01 + 26 9.44189957490813e+01 -3.77275982996325e-01 + 27 9.42174306906690e+01 -3.76469722762676e-01 + 28 9.39206949362101e+01 -3.75282779744841e-01 + 29 9.35471730256220e+01 -3.73788692102488e-01 + 30 9.31202694774434e+01 -3.72081077909774e-01 + 31 9.26656093133783e+01 -3.70262437253513e-01 + 32 9.22083464080232e+01 -3.68433385632093e-01 + 33 9.17709340635645e+01 -3.66683736254258e-01 + 34 9.13715370513921e+01 -3.65086148205568e-01 + 35 9.10230941369154e+01 -3.63692376547662e-01 + 36 9.07329203802995e+01 -3.62531681521198e-01 + 37 9.05026913550711e+01 -3.61610765420284e-01 + 38 9.03286700407576e+01 -3.60914680163030e-01 + 39 9.02021116972737e+01 -3.60408446789095e-01 + 40 9.01098742103920e+01 -3.60039496841568e-01 diff --git a/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_dipoleangle_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out index 20f72749d..eb22b6e44 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -76,7 +72,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -104,7 +100,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -115,28 +110,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - dipoleMagnitude colvar component: -colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 9fd17e29c..e17335d86 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.25718680414489e+00 + x 1.25718680414711e+00 } restraint { diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj index 8a5faec6e..897dd65db 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.27248491620818e+00 -4.68993966483274e-03 - 1 1.27180733121966e+00 -4.68722932487864e-03 - 2 1.27112801338785e+00 -4.68451205355138e-03 - 3 1.27047853507381e+00 -4.68191414029525e-03 - 4 1.26988621687599e+00 -4.67954486750395e-03 - 5 1.26936978124289e+00 -4.67747912497155e-03 - 6 1.26893615427592e+00 -4.67574461710367e-03 - 7 1.26857880872927e+00 -4.67431523491708e-03 - 8 1.26827782880240e+00 -4.67311131520959e-03 - 9 1.26800167045610e+00 -4.67200668182440e-03 - 10 1.26771038149395e+00 -4.67084152597581e-03 - 11 1.26735983259476e+00 -4.66943933037905e-03 - 12 1.26690635771585e+00 -4.66762543086338e-03 - 13 1.26631116924668e+00 -4.66524467698671e-03 - 14 1.26554403807739e+00 -4.66217615230955e-03 - 15 1.26458596330156e+00 -4.65834385320625e-03 - 16 1.26343080408206e+00 -4.65372321632822e-03 - 17 1.26208600681132e+00 -4.64834402724529e-03 - 18 1.26057258581588e+00 -4.64229034326350e-03 - 19 1.25892442269974e+00 -4.63569769079898e-03 - 20 1.25718680414489e+00 -4.62874721657957e-03 + 1 1.27180733121971e+00 -4.68722932487885e-03 + 2 1.27112801338806e+00 -4.68451205355224e-03 + 3 1.27047853507430e+00 -4.68191414029720e-03 + 4 1.26988621687686e+00 -4.67954486750746e-03 + 5 1.26936978124426e+00 -4.67747912497706e-03 + 6 1.26893615427789e+00 -4.67574461711154e-03 + 7 1.26857880873190e+00 -4.67431523492760e-03 + 8 1.26827782880573e+00 -4.67311131522291e-03 + 9 1.26800167046013e+00 -4.67200668184053e-03 + 10 1.26771038149865e+00 -4.67084152599461e-03 + 11 1.26735983260005e+00 -4.66943933040020e-03 + 12 1.26690635772161e+00 -4.66762543088644e-03 + 13 1.26631116925277e+00 -4.66524467701107e-03 + 14 1.26554403808362e+00 -4.66217615233448e-03 + 15 1.26458596330773e+00 -4.65834385323092e-03 + 16 1.26343080408792e+00 -4.65372321635169e-03 + 17 1.26208600681664e+00 -4.64834402726657e-03 + 18 1.26057258582039e+00 -4.64229034328157e-03 + 19 1.25892442270322e+00 -4.63569769081287e-03 + 20 1.25718680414711e+00 -4.62874721658843e-03 diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out index 4e9d16093..c8da2f965 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -76,7 +72,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -104,7 +100,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -115,33 +110,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - dipoleMagnitude colvar component: -colvars: Garate2019 https://doi.org/10.1021/acs.jpcb.8b09374 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 1.25719 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 3e1eeb606..51fc5108c 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.23965387203052e+00 + x 1.23965387204761e+00 } restraint { diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj index f3b3820c2..b874d05f4 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.25718680414489e+00 -4.62874721657957e-03 - 21 1.25541401041628e+00 -4.62165604166510e-03 - 22 1.25366577392698e+00 -4.61466309570791e-03 - 23 1.25200261425621e+00 -4.60801045702483e-03 - 24 1.25048035908344e+00 -4.60192143633375e-03 - 25 1.24914448989145e+00 -4.59657795956581e-03 - 26 1.24802517146902e+00 -4.59210068587607e-03 - 27 1.24713379713557e+00 -4.58853518854227e-03 - 28 1.24646162388823e+00 -4.58584649555294e-03 - 29 1.24598068902163e+00 -4.58392275608653e-03 - 30 1.24564683483206e+00 -4.58258733932823e-03 - 31 1.24540441093114e+00 -4.58161764372455e-03 - 32 1.24519207689764e+00 -4.58076830759057e-03 - 33 1.24494905239874e+00 -4.57979620959498e-03 - 34 1.24462113711495e+00 -4.57848454845980e-03 - 35 1.24416586580795e+00 -4.57666346323180e-03 - 36 1.24355630165299e+00 -4.57422520661195e-03 - 37 1.24278318451547e+00 -4.57113273806189e-03 - 38 1.24185538438953e+00 -4.56742153755813e-03 - 39 1.24079879240046e+00 -4.56319516960184e-03 - 40 1.23965387203052e+00 -4.55861548812208e-03 + 20 1.25718680414711e+00 -4.62874721658843e-03 + 21 1.25541401041707e+00 -4.62165604166829e-03 + 22 1.25366577392626e+00 -4.61466309570505e-03 + 23 1.25200261425396e+00 -4.60801045701586e-03 + 24 1.25048035907975e+00 -4.60192143631898e-03 + 25 1.24914448988648e+00 -4.59657795954592e-03 + 26 1.24802517146302e+00 -4.59210068585208e-03 + 27 1.24713379712889e+00 -4.58853518851555e-03 + 28 1.24646162388128e+00 -4.58584649552511e-03 + 29 1.24598068901487e+00 -4.58392275605946e-03 + 30 1.24564683482598e+00 -4.58258733930391e-03 + 31 1.24540441092625e+00 -4.58161764370501e-03 + 32 1.24519207689444e+00 -4.58076830757776e-03 + 33 1.24494905239767e+00 -4.57979620959067e-03 + 34 1.24462113711636e+00 -4.57848454846545e-03 + 35 1.24416586581212e+00 -4.57666346324848e-03 + 36 1.24355630166006e+00 -4.57422520664022e-03 + 37 1.24278318452544e+00 -4.57113273810176e-03 + 38 1.24185538440224e+00 -4.56742153760896e-03 + 39 1.24079879241559e+00 -4.56319516966238e-03 + 40 1.23965387204761e+00 -4.55861548819043e-03 diff --git a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_dipolemagnitude_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out index 6de123229..0c998afc9 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -120,26 +116,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped index 5268daf85..c1e336541 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253464583e+00 } diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj index 9f55268e7..787f78aa5 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 0.00000000000000e+00 + 11 3.21950367383415e+00 0.00000000000000e+00 + 12 3.22130499858006e+00 0.00000000000000e+00 + 13 3.22263479496347e+00 0.00000000000000e+00 + 14 3.22341769665784e+00 0.00000000000000e+00 + 15 3.22361473677138e+00 0.00000000000000e+00 + 16 3.22322417514557e+00 0.00000000000000e+00 + 17 3.22227942564879e+00 0.00000000000000e+00 + 18 3.22084479803044e+00 0.00000000000000e+00 + 19 3.21900979846930e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat index 23457f54b..54058e8f8 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.one.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.94036329632288e-01 - 4 5.63764173125217e-01 - 6 8.25197122357662e-02 - 8 -4.33277918980290e-01 - 10 -8.58922880671951e-01 + 2 8.94036335239450e-01 + 4 5.63764182658574e-01 + 6 8.25197229800656e-02 + 8 -4.33277910141469e-01 + 10 -8.58922876516564e-01 diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out index effa805d2..923c7f755 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -120,30 +116,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped index b307ede0d..139366ade 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878547144e+00 } diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj index 177b1bbb8..3b596ebde 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253444007e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 + 21 3.21458253157603e+00 0.00000000000000e+00 + 22 3.21223315254029e+00 0.00000000000000e+00 + 23 3.20995392032979e+00 0.00000000000000e+00 + 24 3.20785326966943e+00 0.00000000000000e+00 + 25 3.20602244845117e+00 0.00000000000000e+00 + 26 3.20453120146139e+00 0.00000000000000e+00 + 27 3.20342556480347e+00 0.00000000000000e+00 + 28 3.20272769852622e+00 0.00000000000000e+00 + 29 3.20243730776714e+00 0.00000000000000e+00 + 30 3.20253423308456e+00 0.00000000000000e+00 + 31 3.20298183362156e+00 0.00000000000000e+00 + 32 3.20373100914607e+00 0.00000000000000e+00 + 33 3.20472468746373e+00 0.00000000000000e+00 + 34 3.20590256221113e+00 0.00000000000000e+00 + 35 3.20720566184671e+00 0.00000000000000e+00 + 36 3.20858030459458e+00 0.00000000000000e+00 + 37 3.20998111854285e+00 0.00000000000000e+00 + 38 3.21137308334419e+00 0.00000000000000e+00 + 39 3.21273274315657e+00 0.00000000000000e+00 + 40 3.21404878547144e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat index 702a517c3..b55885c02 100644 --- a/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat +++ b/namd/tests/library/000_distance-autocorrfunc/AutoDiff/test.restart.one.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.20806872403133e-01 - 4 4.95149534314936e-01 - 6 3.29843583885573e-02 - 8 -5.10193956226866e-01 - 10 -1.03852681816246e+00 + 2 8.20806874278982e-01 + 4 4.95149538768788e-01 + 6 3.29843664998698e-02 + 8 -5.10193943420893e-01 + 10 -1.03852680015666e+00 diff --git a/namd/tests/library/000_distance-autocorrfunc/namd-version.txt b/namd/tests/library/000_distance-autocorrfunc/namd-version.txt index 157cac038..b7bf5455c 100644 --- a/namd/tests/library/000_distance-autocorrfunc/namd-version.txt +++ b/namd/tests/library/000_distance-autocorrfunc/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-10-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out index 9a7a8d5d0..c89a0b8e7 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -97,28 +93,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -129,7 +125,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -157,7 +153,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -168,28 +163,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Linear and polynomial combination of colvar components: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped index ae9aba124..eb4ad3fa9 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.04350737604756e+01 + x 1.04350737609886e+01 } restraint { diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj index d89de7465..31f5eef44 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.04177432613594e+01 -4.12709730454376e-02 - 1 1.04084193931719e+01 -4.12336775726876e-02 - 2 1.04020579749793e+01 -4.12082318999174e-02 - 3 1.03989629510900e+01 -4.11958518043599e-02 - 4 1.03992141619813e+01 -4.11968566479251e-02 - 5 1.04026682614922e+01 -4.12106730459687e-02 - 6 1.04089744651595e+01 -4.12358978606380e-02 - 7 1.04176020660190e+01 -4.12704082640760e-02 - 8 1.04278769153472e+01 -4.13115076613887e-02 - 9 1.04390245452438e+01 -4.13560981809752e-02 - 10 1.04502182762425e+01 -4.14008731049699e-02 - 11 1.04606302346439e+01 -4.14425209385756e-02 - 12 1.04694824773729e+01 -4.14779299094914e-02 - 13 1.04760942601681e+01 -4.15043770406723e-02 - 14 1.04799211557593e+01 -4.15196846230373e-02 - 15 1.04805822766537e+01 -4.15223291066147e-02 - 16 1.04778735079711e+01 -4.15114940318845e-02 - 17 1.04717666626334e+01 -4.14870666505335e-02 - 18 1.04623962952111e+01 -4.14495851808446e-02 - 19 1.04500369407186e+01 -4.14001477628744e-02 - 20 1.04350737604756e+01 -4.13402950419026e-02 + 1 1.04084193931741e+01 -4.12336775726963e-02 + 2 1.04020579749880e+01 -4.12082318999518e-02 + 3 1.03989629511090e+01 -4.11958518044361e-02 + 4 1.03992141620145e+01 -4.11968566480581e-02 + 5 1.04026682615430e+01 -4.12106730461720e-02 + 6 1.04089744652310e+01 -4.12358978609239e-02 + 7 1.04176020661138e+01 -4.12704082644551e-02 + 8 1.04278769154677e+01 -4.13115076618707e-02 + 9 1.04390245453922e+01 -4.13560981815686e-02 + 10 1.04502182764206e+01 -4.14008731056823e-02 + 11 1.04606302348533e+01 -4.14425209394133e-02 + 12 1.04694824776150e+01 -4.14779299104599e-02 + 13 1.04760942604439e+01 -4.15043770417758e-02 + 14 1.04799211560697e+01 -4.15196846242787e-02 + 15 1.04805822769989e+01 -4.15223291079955e-02 + 16 1.04778735083513e+01 -4.15114940334051e-02 + 17 1.04717666630482e+01 -4.14870666521928e-02 + 18 1.04623962956600e+01 -4.14495851826398e-02 + 19 1.04500369412003e+01 -4.14001477648012e-02 + 20 1.04350737609886e+01 -4.13402950439545e-02 diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out index e7657a286..1bd56dbf9 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -97,28 +93,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -129,7 +125,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -157,7 +153,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -168,33 +163,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Linear and polynomial combination of colvar components: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":1/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 10.4351 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":1/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 11055164f..b8451d7e6 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.01168439967474e+01 + x 1.01168439975032e+01 } restraint { diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj index ee78c4b0f..94f67cf85 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.04350737604756e+01 -4.13402950419026e-02 - 21 1.04179692237962e+01 -4.12718768951847e-02 - 22 1.03992281886028e+01 -4.11969127544111e-02 - 23 1.03793633975077e+01 -4.11174535900307e-02 - 24 1.03588635763992e+01 -4.10354543055969e-02 - 25 1.03381666080959e+01 -4.09526664323835e-02 - 26 1.03176399245696e+01 -4.08705596982785e-02 - 27 1.02975696738682e+01 -4.07902786954729e-02 - 28 1.02781591058678e+01 -4.07126364234711e-02 - 29 1.02595353407094e+01 -4.06381413628374e-02 - 30 1.02417631913002e+01 -4.05670527652007e-02 - 31 1.02248638710941e+01 -4.04994554843765e-02 - 32 1.02088361338553e+01 -4.04353445354210e-02 - 33 1.01936770388753e+01 -4.03747081555012e-02 - 34 1.01793996403201e+01 -4.03175985612803e-02 - 35 1.01660453820078e+01 -4.02641815280313e-02 - 36 1.01536901423957e+01 -4.02147605695830e-02 - 37 1.01424440834353e+01 -4.01697763337413e-02 - 38 1.01324465159344e+01 -4.01297860637376e-02 - 39 1.01238570537632e+01 -4.00954282150527e-02 - 40 1.01168439967474e+01 -4.00673759869896e-02 + 20 1.04350737609886e+01 -4.13402950439545e-02 + 21 1.04179692243383e+01 -4.12718768973531e-02 + 22 1.03992281891713e+01 -4.11969127566851e-02 + 23 1.03793633980993e+01 -4.11174535923974e-02 + 24 1.03588635770104e+01 -4.10354543080416e-02 + 25 1.03381666087226e+01 -4.09526664348903e-02 + 26 1.03176399252079e+01 -4.08705597008314e-02 + 27 1.02975696745142e+01 -4.07902786980569e-02 + 28 1.02781591065183e+01 -4.07126364260730e-02 + 29 1.02595353413618e+01 -4.06381413654473e-02 + 30 1.02417631919532e+01 -4.05670527678126e-02 + 31 1.02248638717473e+01 -4.04994554869891e-02 + 32 1.02088361345094e+01 -4.04353445380376e-02 + 33 1.01936770395323e+01 -4.03747081581293e-02 + 34 1.01793996409827e+01 -4.03175985639309e-02 + 35 1.01660453826794e+01 -4.02641815307176e-02 + 36 1.01536901430796e+01 -4.02147605723186e-02 + 37 1.01424440841347e+01 -4.01697763365387e-02 + 38 1.01324465166516e+01 -4.01297860666066e-02 + 39 1.01238570544997e+01 -4.00954282179988e-02 + 40 1.01168439975032e+01 -4.00673759900128e-02 diff --git a/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt index 157cac038..fc4f9e327 100644 --- a/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distance-coeffs_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. +colvars: Using NAMD interface, version 2016-11-23. diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out index 139d30fdd..a8e792240 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,28 +112,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -148,7 +144,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -177,26 +173,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped index b28d17171..7aec83be0 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.state.stripped @@ -5,11 +5,11 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253464583e+00 } colvar { name two - x 3.24433794495372e+00 + x 3.24433794490785e+00 } diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj index 0cd566be4..5633fa456 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one two fa_two 0 3.20554673468334e+00 0.00000000000000e+00 3.24960869251665e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 3.24790015328133e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 3.24647131781360e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 3.24540254817793e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 3.24474238725799e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 3.24450566303529e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 3.24467445105563e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 3.24520145991688e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 3.24601517427588e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 3.24702592907485e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 3.24813222716439e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 3.24922681805867e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 3.25020238551676e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 3.25095679939459e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 3.25139788925691e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 3.25144751335969e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 3.25104460693083e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 3.25014688214290e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 3.24873101651643e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 3.24679142393386e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 3.24433794495372e+00 0.00000000000000e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 3.24790015328139e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 3.24647131781376e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 3.24540254817816e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 3.24474238725816e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 3.24450566303520e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 3.24467445105498e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 3.24520145991536e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 3.24601517427313e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 3.24702592907053e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 0.00000000000000e+00 3.24813222715817e+00 0.00000000000000e+00 + 11 3.21950367383415e+00 0.00000000000000e+00 3.24922681805023e+00 0.00000000000000e+00 + 12 3.22130499858006e+00 0.00000000000000e+00 3.25020238550581e+00 0.00000000000000e+00 + 13 3.22263479496347e+00 0.00000000000000e+00 3.25095679938081e+00 0.00000000000000e+00 + 14 3.22341769665784e+00 0.00000000000000e+00 3.25139788923999e+00 0.00000000000000e+00 + 15 3.22361473677138e+00 0.00000000000000e+00 3.25144751333927e+00 0.00000000000000e+00 + 16 3.22322417514557e+00 0.00000000000000e+00 3.25104460690651e+00 0.00000000000000e+00 + 17 3.22227942564879e+00 0.00000000000000e+00 3.25014688211417e+00 0.00000000000000e+00 + 18 3.22084479803044e+00 0.00000000000000e+00 3.24873101648273e+00 0.00000000000000e+00 + 19 3.21900979846930e+00 0.00000000000000e+00 3.24679142389449e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 3.24433794490785e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out index ce5cb44d2..0fdca4e94 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,28 +112,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -148,7 +144,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -177,31 +173,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting collective variable "two" from value: 3.24434 colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped index 68f23fd0a..d4fe5f034 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.state.stripped @@ -5,11 +5,11 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878547144e+00 } colvar { name two - x 3.14863335183754e+00 + x 3.14863335158646e+00 } diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj index af3ea4517..a61269b0f 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one two fa_two - 20 3.21688253444007e+00 0.00000000000000e+00 3.24433794495372e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 3.24139291297126e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 3.23798808487052e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 3.23416173175576e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 3.22995602396352e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 3.22541476812382e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 3.22058155457121e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 3.21549850220181e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 3.21020584536443e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 3.20474257688878e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 3.19914817079401e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 3.19346509302453e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 3.18774148383751e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 3.18203328876528e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 3.17640518192333e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 3.17092997382502e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 3.16568658639959e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 3.16075695183232e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 3.15622225136581e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 3.15215875153341e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 3.14863335183754e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 3.24433794490785e+00 0.00000000000000e+00 + 21 3.21458253157603e+00 0.00000000000000e+00 3.24139291291795e+00 0.00000000000000e+00 + 22 3.21223315254029e+00 0.00000000000000e+00 3.23798808480870e+00 0.00000000000000e+00 + 23 3.20995392032979e+00 0.00000000000000e+00 3.23416173168426e+00 0.00000000000000e+00 + 24 3.20785326966943e+00 0.00000000000000e+00 3.22995602388112e+00 0.00000000000000e+00 + 25 3.20602244845117e+00 0.00000000000000e+00 3.22541476802931e+00 0.00000000000000e+00 + 26 3.20453120146139e+00 0.00000000000000e+00 3.22058155446344e+00 0.00000000000000e+00 + 27 3.20342556480347e+00 0.00000000000000e+00 3.21549850207982e+00 0.00000000000000e+00 + 28 3.20272769852622e+00 0.00000000000000e+00 3.21020584522746e+00 0.00000000000000e+00 + 29 3.20243730776714e+00 0.00000000000000e+00 3.20474257673639e+00 0.00000000000000e+00 + 30 3.20253423308456e+00 0.00000000000000e+00 3.19914817062614e+00 0.00000000000000e+00 + 31 3.20298183362156e+00 0.00000000000000e+00 3.19346509284150e+00 0.00000000000000e+00 + 32 3.20373100914607e+00 0.00000000000000e+00 3.18774148364007e+00 0.00000000000000e+00 + 33 3.20472468746373e+00 0.00000000000000e+00 3.18203328855458e+00 0.00000000000000e+00 + 34 3.20590256221113e+00 0.00000000000000e+00 3.17640518170088e+00 0.00000000000000e+00 + 35 3.20720566184671e+00 0.00000000000000e+00 3.17092997359260e+00 0.00000000000000e+00 + 36 3.20858030459458e+00 0.00000000000000e+00 3.16568658615923e+00 0.00000000000000e+00 + 37 3.20998111854285e+00 0.00000000000000e+00 3.16075695158616e+00 0.00000000000000e+00 + 38 3.21137308334419e+00 0.00000000000000e+00 3.15622225111600e+00 0.00000000000000e+00 + 39 3.21273274315657e+00 0.00000000000000e+00 3.15215875128202e+00 0.00000000000000e+00 + 40 3.21404878547144e+00 0.00000000000000e+00 3.14863335158646e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat index c212baec7..82ce99983 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.restart.two.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.20806872403133e-01 - 4 4.95149534314936e-01 - 6 3.29843583885573e-02 - 8 -5.10193956226866e-01 - 10 -1.03852681816246e+00 + 2 8.20806874278982e-01 + 4 4.95149538768788e-01 + 6 3.29843664998698e-02 + 8 -5.10193943420893e-01 + 10 -1.03852680015666e+00 diff --git a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat index aafb87afd..d0534bfc8 100644 --- a/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat +++ b/namd/tests/library/000_distance-corrfunc/AutoDiff/test.two.corrfunc.dat @@ -2,8 +2,8 @@ # Number of samples = 9 (one DoF is used for normalization) # step corrfunc(step) 0 1.00000000000000e+00 - 2 8.94036329632288e-01 - 4 5.63764173125217e-01 - 6 8.25197122357662e-02 - 8 -4.33277918980290e-01 - 10 -8.58922880671951e-01 + 2 8.94036335239450e-01 + 4 5.63764182658574e-01 + 6 8.25197229800656e-02 + 8 -4.33277910141469e-01 + 10 -8.58922876516564e-01 diff --git a/namd/tests/library/000_distance-corrfunc/namd-version.txt b/namd/tests/library/000_distance-corrfunc/namd-version.txt index 157cac038..b7bf5455c 100644 --- a/namd/tests/library/000_distance-corrfunc/namd-version.txt +++ b/namd/tests/library/000_distance-corrfunc/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-10-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out index 8acf9d14a..b48697538 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -228,12 +229,10 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped index 41807dd58..39cdbdd58 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21688253444007e+00 + x 3.21688253464583e+00 } colvar { name phi - x 6.02774557419409e+01 + x 6.02774557527018e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj index 19662210d..0d258d955 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step r phi 0 3.20554673468334e+00 6.31129478791928e+01 - 1 3.20437148316484e+00 6.30795952608635e+01 - 2 3.20384028588952e+00 6.30231590815800e+01 - 3 3.20396721186862e+00 6.29423176376863e+01 - 4 3.20472817286016e+00 6.28366833855655e+01 - 5 3.20606308065050e+00 6.27068898711517e+01 - 6 3.20787989000757e+00 6.25546017852999e+01 - 7 3.21005997940810e+00 6.23824530243513e+01 - 8 3.21246460651160e+00 6.21939260028577e+01 - 9 3.21494247383722e+00 6.19931890890363e+01 - 10 3.21733851230199e+00 6.17849080653709e+01 - 11 3.21950367376059e+00 6.15740450203887e+01 - 12 3.22130499849384e+00 6.13656547612945e+01 - 13 3.22263479486396e+00 6.11646847382338e+01 - 14 3.22341769654449e+00 6.09757828886766e+01 - 15 3.22361473664369e+00 6.08031168275266e+01 - 16 3.22322417500307e+00 6.06502098430779e+01 - 17 3.22227942549106e+00 6.05198025267682e+01 - 18 3.22084479785707e+00 6.04137510819450e+01 - 19 3.21900979827991e+00 6.03329740983039e+01 - 20 3.21688253444007e+00 6.02774557419409e+01 + 1 3.20437148316546e+00 6.30795952609024e+01 + 2 3.20384028589204e+00 6.30231590817356e+01 + 3 3.20396721187433e+00 6.29423176380356e+01 + 4 3.20472817287036e+00 6.28366833861828e+01 + 5 3.20606308066645e+00 6.27068898721072e+01 + 6 3.20787989003051e+00 6.25546017866590e+01 + 7 3.21005997943917e+00 6.23824530261739e+01 + 8 3.21246460655188e+00 6.21939260051983e+01 + 9 3.21494247388772e+00 6.19931890919450e+01 + 10 3.21733851236362e+00 6.17849080688927e+01 + 11 3.21950367383415e+00 6.15740450245643e+01 + 12 3.22130499858006e+00 6.13656547661594e+01 + 13 3.22263479496346e+00 6.11646847438178e+01 + 14 3.22341769665784e+00 6.09757828950022e+01 + 15 3.22361473677138e+00 6.08031168346083e+01 + 16 3.22322417514557e+00 6.06502098509209e+01 + 17 3.22227942564879e+00 6.05198025353684e+01 + 18 3.22084479803044e+00 6.04137510912894e+01 + 19 3.21900979846930e+00 6.03329741083708e+01 + 20 3.21688253464583e+00 6.02774557527018e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat index 337d77a7b..4ca2d87c5 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat @@ -1,3053 +1,3053 @@ # 2 -# 0.00000000000000e+00 2.00000000000000e-01 50 0 -# 0.00000000000000e+00 6.00000000000000e+00 60 1 +# 0 0.2 50 0 +# 0 6 60 1 - 1.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 - 1.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 - 1.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 3.30000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 3.90000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 4.50000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 5.10000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 5.70000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 6.30000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 6.90000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 7.50000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 8.10000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 8.70000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 9.30000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 9.90000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 1.05000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.11000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.17000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.23000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.29000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.35000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.41000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.47000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.53000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.59000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.65000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.71000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.77000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.83000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.89000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.95000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.01000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.07000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.13000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.19000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.25000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.31000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.37000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.43000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.49000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.55000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.61000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.67000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.73000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.79000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.85000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.91000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.97000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.03000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.09000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.15000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.21000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.27000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.33000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.39000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.45000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.51000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.57000000000000e+02 0.00000000000000e+00 + 0.1 3 0 + 0.1 9 0 + 0.1 15 0 + 0.1 21 0 + 0.1 27 0 + 0.1 33 0 + 0.1 39 0 + 0.1 45 0 + 0.1 51 0 + 0.1 57 0 + 0.1 63 0 + 0.1 69 0 + 0.1 75 0 + 0.1 81 0 + 0.1 87 0 + 0.1 93 0 + 0.1 99 0 + 0.1 105 0 + 0.1 111 0 + 0.1 117 0 + 0.1 123 0 + 0.1 129 0 + 0.1 135 0 + 0.1 141 0 + 0.1 147 0 + 0.1 153 0 + 0.1 159 0 + 0.1 165 0 + 0.1 171 0 + 0.1 177 0 + 0.1 183 0 + 0.1 189 0 + 0.1 195 0 + 0.1 201 0 + 0.1 207 0 + 0.1 213 0 + 0.1 219 0 + 0.1 225 0 + 0.1 231 0 + 0.1 237 0 + 0.1 243 0 + 0.1 249 0 + 0.1 255 0 + 0.1 261 0 + 0.1 267 0 + 0.1 273 0 + 0.1 279 0 + 0.1 285 0 + 0.1 291 0 + 0.1 297 0 + 0.1 303 0 + 0.1 309 0 + 0.1 315 0 + 0.1 321 0 + 0.1 327 0 + 0.1 333 0 + 0.1 339 0 + 0.1 345 0 + 0.1 351 0 + 0.1 357 0 - 3.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 - 3.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 - 3.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 3.30000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 3.90000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 4.50000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 5.10000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 5.70000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 6.30000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 6.90000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 7.50000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 8.10000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 8.70000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 9.30000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 9.90000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 1.05000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.11000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.17000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.23000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.29000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.35000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.41000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.47000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.53000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.59000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.65000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.71000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.77000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.83000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.89000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.95000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.01000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.07000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.13000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.19000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.25000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.31000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.37000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.43000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.49000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.55000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.61000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.67000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.73000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.79000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.85000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.91000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.97000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.03000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.09000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.15000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.21000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.27000000000000e+02 0.00000000000000e+00 - 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9.90000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 - 9.90000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 + 9.9 3 0 + 9.9 9 0 + 9.9 15 0 + 9.9 21 0 + 9.9 27 0 + 9.9 33 0 + 9.9 39 0 + 9.9 45 0 + 9.9 51 0 + 9.9 57 0 + 9.9 63 0 + 9.9 69 0 + 9.9 75 0 + 9.9 81 0 + 9.9 87 0 + 9.9 93 0 + 9.9 99 0 + 9.9 105 0 + 9.9 111 0 + 9.9 117 0 + 9.9 123 0 + 9.9 129 0 + 9.9 135 0 + 9.9 141 0 + 9.9 147 0 + 9.9 153 0 + 9.9 159 0 + 9.9 165 0 + 9.9 171 0 + 9.9 177 0 + 9.9 183 0 + 9.9 189 0 + 9.9 195 0 + 9.9 201 0 + 9.9 207 0 + 9.9 213 0 + 9.9 219 0 + 9.9 225 0 + 9.9 231 0 + 9.9 237 0 + 9.9 243 0 + 9.9 249 0 + 9.9 255 0 + 9.9 261 0 + 9.9 267 0 + 9.9 273 0 + 9.9 279 0 + 9.9 285 0 + 9.9 291 0 + 9.9 297 0 + 9.9 303 0 + 9.9 309 0 + 9.9 315 0 + 9.9 321 0 + 9.9 327 0 + 9.9 333 0 + 9.9 339 0 + 9.9 345 0 + 9.9 351 0 + 9.9 357 0 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out index 7e5cda273..5c3fb9114 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -228,7 +229,6 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "r" from value: 3.21688 @@ -239,7 +239,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped index ff6d40c16..16d91a903 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21404878499019e+00 + x 3.21404878547144e+00 } colvar { name phi - x 6.08972121817132e+01 + x 6.08972122017851e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj index 00a61ca9a..6e6a9d108 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step r phi - 20 3.21688253444007e+00 6.02774557419409e+01 - 21 3.21458253135360e+00 6.02463068586077e+01 - 22 3.21223315230095e+00 6.02378794547663e+01 - 23 3.20995392007338e+00 6.02499213666401e+01 - 24 3.20785326939589e+00 6.02797520443280e+01 - 25 3.20602244816055e+00 6.03244374884686e+01 - 26 3.20453120115385e+00 6.03809430381167e+01 - 27 3.20342556447929e+00 6.04462482226441e+01 - 28 3.20272769818575e+00 6.05174152507232e+01 - 29 3.20243730741081e+00 6.05916134367745e+01 - 30 3.20253423271288e+00 6.06661106175895e+01 - 31 3.20298183323508e+00 6.07382493916987e+01 - 32 3.20373100874536e+00 6.08054278361141e+01 - 33 3.20472468704943e+00 6.08651028913518e+01 - 34 3.20590256178394e+00 6.09148265769850e+01 - 35 3.20720566140745e+00 6.09523144047667e+01 - 36 3.20858030414420e+00 6.09755306486176e+01 - 37 3.20998111808250e+00 6.09827676263964e+01 - 38 3.21137308287521e+00 6.09726956103267e+01 - 39 3.21273274268056e+00 6.09443715231751e+01 - 40 3.21404878499019e+00 6.08972121817132e+01 + 20 3.21688253464583e+00 6.02774557527018e+01 + 21 3.21458253157603e+00 6.02463068700288e+01 + 22 3.21223315254029e+00 6.02378794668108e+01 + 23 3.20995392032979e+00 6.02499213792704e+01 + 24 3.20785326966943e+00 6.02797520575071e+01 + 25 3.20602244845117e+00 6.03244375021622e+01 + 26 3.20453120146139e+00 6.03809430522940e+01 + 27 3.20342556480347e+00 6.04462482372788e+01 + 28 3.20272769852622e+00 6.05174152657937e+01 + 29 3.20243730776714e+00 6.05916134522643e+01 + 30 3.20253423308456e+00 6.06661106334871e+01 + 31 3.20298183362156e+00 6.07382494079973e+01 + 32 3.20373100914607e+00 6.08054278528112e+01 + 33 3.20472468746373e+00 6.08651029084488e+01 + 34 3.20590256221113e+00 6.09148265944857e+01 + 35 3.20720566184671e+00 6.09523144226767e+01 + 36 3.20858030459458e+00 6.09755306669437e+01 + 37 3.20998111854285e+00 6.09827676451462e+01 + 38 3.21137308334418e+00 6.09726956295080e+01 + 39 3.21273274315657e+00 6.09443715427968e+01 + 40 3.21404878547144e+00 6.08972122017851e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat index 60d272104..bcd93aff0 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat @@ -1,3053 +1,3053 @@ # 2 -# 0.00000000000000e+00 2.00000000000000e-01 50 0 -# 0.00000000000000e+00 6.00000000000000e+00 60 1 +# 0 0.2 50 0 +# 0 6 60 1 - 1.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 - 1.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 - 1.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 3.30000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 3.90000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 4.50000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 5.10000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 5.70000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 6.30000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 6.90000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 7.50000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 8.10000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 8.70000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 9.30000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 9.90000000000000e+01 0.00000000000000e+00 - 1.00000000000000e-01 1.05000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.11000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.17000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.23000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.29000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.35000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.41000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.47000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.53000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.59000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.65000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.71000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.77000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.83000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.89000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 1.95000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.01000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.07000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.13000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.19000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.25000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.31000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.37000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.43000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.49000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.55000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.61000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.67000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.73000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.79000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.85000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.91000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 2.97000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.03000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.09000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.15000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.21000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.27000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.33000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.39000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.45000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.51000000000000e+02 0.00000000000000e+00 - 1.00000000000000e-01 3.57000000000000e+02 0.00000000000000e+00 + 0.1 3 0 + 0.1 9 0 + 0.1 15 0 + 0.1 21 0 + 0.1 27 0 + 0.1 33 0 + 0.1 39 0 + 0.1 45 0 + 0.1 51 0 + 0.1 57 0 + 0.1 63 0 + 0.1 69 0 + 0.1 75 0 + 0.1 81 0 + 0.1 87 0 + 0.1 93 0 + 0.1 99 0 + 0.1 105 0 + 0.1 111 0 + 0.1 117 0 + 0.1 123 0 + 0.1 129 0 + 0.1 135 0 + 0.1 141 0 + 0.1 147 0 + 0.1 153 0 + 0.1 159 0 + 0.1 165 0 + 0.1 171 0 + 0.1 177 0 + 0.1 183 0 + 0.1 189 0 + 0.1 195 0 + 0.1 201 0 + 0.1 207 0 + 0.1 213 0 + 0.1 219 0 + 0.1 225 0 + 0.1 231 0 + 0.1 237 0 + 0.1 243 0 + 0.1 249 0 + 0.1 255 0 + 0.1 261 0 + 0.1 267 0 + 0.1 273 0 + 0.1 279 0 + 0.1 285 0 + 0.1 291 0 + 0.1 297 0 + 0.1 303 0 + 0.1 309 0 + 0.1 315 0 + 0.1 321 0 + 0.1 327 0 + 0.1 333 0 + 0.1 339 0 + 0.1 345 0 + 0.1 351 0 + 0.1 357 0 - 3.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 - 3.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 - 3.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 3.30000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 3.90000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 4.50000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 5.10000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 5.70000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 6.30000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 6.90000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 7.50000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 8.10000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 8.70000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 9.30000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 9.90000000000000e+01 0.00000000000000e+00 - 3.00000000000000e-01 1.05000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.11000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.17000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.23000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.29000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.35000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.41000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.47000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.53000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.59000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.65000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.71000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.77000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.83000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.89000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 1.95000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.01000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.07000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.13000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.19000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.25000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.31000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.37000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.43000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.49000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.55000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.61000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.67000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.73000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.79000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.85000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.91000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 2.97000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.03000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.09000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.15000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.21000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.27000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.33000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.39000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.45000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.51000000000000e+02 0.00000000000000e+00 - 3.00000000000000e-01 3.57000000000000e+02 0.00000000000000e+00 + 0.3 3 0 + 0.3 9 0 + 0.3 15 0 + 0.3 21 0 + 0.3 27 0 + 0.3 33 0 + 0.3 39 0 + 0.3 45 0 + 0.3 51 0 + 0.3 57 0 + 0.3 63 0 + 0.3 69 0 + 0.3 75 0 + 0.3 81 0 + 0.3 87 0 + 0.3 93 0 + 0.3 99 0 + 0.3 105 0 + 0.3 111 0 + 0.3 117 0 + 0.3 123 0 + 0.3 129 0 + 0.3 135 0 + 0.3 141 0 + 0.3 147 0 + 0.3 153 0 + 0.3 159 0 + 0.3 165 0 + 0.3 171 0 + 0.3 177 0 + 0.3 183 0 + 0.3 189 0 + 0.3 195 0 + 0.3 201 0 + 0.3 207 0 + 0.3 213 0 + 0.3 219 0 + 0.3 225 0 + 0.3 231 0 + 0.3 237 0 + 0.3 243 0 + 0.3 249 0 + 0.3 255 0 + 0.3 261 0 + 0.3 267 0 + 0.3 273 0 + 0.3 279 0 + 0.3 285 0 + 0.3 291 0 + 0.3 297 0 + 0.3 303 0 + 0.3 309 0 + 0.3 315 0 + 0.3 321 0 + 0.3 327 0 + 0.3 333 0 + 0.3 339 0 + 0.3 345 0 + 0.3 351 0 + 0.3 357 0 - 5.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 - 5.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 - 5.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 - 5.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 - 5.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 - 5.00000000000000e-01 3.30000000000000e+01 0.00000000000000e+00 - 5.00000000000000e-01 3.90000000000000e+01 0.00000000000000e+00 - 5.00000000000000e-01 4.50000000000000e+01 0.00000000000000e+00 - 5.00000000000000e-01 5.10000000000000e+01 0.00000000000000e+00 - 5.00000000000000e-01 5.70000000000000e+01 0.00000000000000e+00 - 5.00000000000000e-01 6.30000000000000e+01 0.00000000000000e+00 - 5.00000000000000e-01 6.90000000000000e+01 0.00000000000000e+00 - 5.00000000000000e-01 7.50000000000000e+01 0.00000000000000e+00 - 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9.9 327 0 + 9.9 333 0 + 9.9 339 0 + 9.9 345 0 + 9.9 351 0 + 9.9 357 0 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt index 157cac038..017b69b3a 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2022-04-14. +colvars: Using NAMD interface, version "2022-04-06". diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out index a28b5f43d..0254b6e28 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -225,12 +226,10 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped index 3008cc63c..b2dc7dab5 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21688253444007e+00 + x 3.21688253464583e+00 } colvar { name phi - x 6.02774557419409e+01 + x 6.02774557527018e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj index 19662210d..0d258d955 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step r phi 0 3.20554673468334e+00 6.31129478791928e+01 - 1 3.20437148316484e+00 6.30795952608635e+01 - 2 3.20384028588952e+00 6.30231590815800e+01 - 3 3.20396721186862e+00 6.29423176376863e+01 - 4 3.20472817286016e+00 6.28366833855655e+01 - 5 3.20606308065050e+00 6.27068898711517e+01 - 6 3.20787989000757e+00 6.25546017852999e+01 - 7 3.21005997940810e+00 6.23824530243513e+01 - 8 3.21246460651160e+00 6.21939260028577e+01 - 9 3.21494247383722e+00 6.19931890890363e+01 - 10 3.21733851230199e+00 6.17849080653709e+01 - 11 3.21950367376059e+00 6.15740450203887e+01 - 12 3.22130499849384e+00 6.13656547612945e+01 - 13 3.22263479486396e+00 6.11646847382338e+01 - 14 3.22341769654449e+00 6.09757828886766e+01 - 15 3.22361473664369e+00 6.08031168275266e+01 - 16 3.22322417500307e+00 6.06502098430779e+01 - 17 3.22227942549106e+00 6.05198025267682e+01 - 18 3.22084479785707e+00 6.04137510819450e+01 - 19 3.21900979827991e+00 6.03329740983039e+01 - 20 3.21688253444007e+00 6.02774557419409e+01 + 1 3.20437148316546e+00 6.30795952609024e+01 + 2 3.20384028589204e+00 6.30231590817356e+01 + 3 3.20396721187433e+00 6.29423176380356e+01 + 4 3.20472817287036e+00 6.28366833861828e+01 + 5 3.20606308066645e+00 6.27068898721072e+01 + 6 3.20787989003051e+00 6.25546017866590e+01 + 7 3.21005997943917e+00 6.23824530261739e+01 + 8 3.21246460655188e+00 6.21939260051983e+01 + 9 3.21494247388772e+00 6.19931890919450e+01 + 10 3.21733851236362e+00 6.17849080688927e+01 + 11 3.21950367383415e+00 6.15740450245643e+01 + 12 3.22130499858006e+00 6.13656547661594e+01 + 13 3.22263479496346e+00 6.11646847438178e+01 + 14 3.22341769665784e+00 6.09757828950022e+01 + 15 3.22361473677138e+00 6.08031168346083e+01 + 16 3.22322417514557e+00 6.06502098509209e+01 + 17 3.22227942564879e+00 6.05198025353684e+01 + 18 3.22084479803044e+00 6.04137510912894e+01 + 19 3.21900979846930e+00 6.03329741083708e+01 + 20 3.21688253464583e+00 6.02774557527018e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat index 560cfda3e..d42b8f708 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.histogram1.dat @@ -1,7223 +1,7223 @@ # 2 -# 0.00000000000000e+00 1.00000000000000e+00 20 0 -# -1.80000000000000e+02 1.00000000000000e+00 360 1 +# 0 1 20 0 +# -180 1 360 1 - 5.00000000000000e-01 -1.79500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.78500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.77500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.76500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.75500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.74500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.73500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.72500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.71500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.70500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.69500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 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74614ceb4..43174e795 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -225,7 +226,6 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "r" from value: 3.21688 @@ -236,7 +236,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped index 51260c395..1d0bd953f 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21404878499019e+00 + x 3.21404878547144e+00 } colvar { name phi - x 6.08972121817132e+01 + x 6.08972122017851e+01 } histogram { diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj index 00a61ca9a..6e6a9d108 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step r phi - 20 3.21688253444007e+00 6.02774557419409e+01 - 21 3.21458253135360e+00 6.02463068586077e+01 - 22 3.21223315230095e+00 6.02378794547663e+01 - 23 3.20995392007338e+00 6.02499213666401e+01 - 24 3.20785326939589e+00 6.02797520443280e+01 - 25 3.20602244816055e+00 6.03244374884686e+01 - 26 3.20453120115385e+00 6.03809430381167e+01 - 27 3.20342556447929e+00 6.04462482226441e+01 - 28 3.20272769818575e+00 6.05174152507232e+01 - 29 3.20243730741081e+00 6.05916134367745e+01 - 30 3.20253423271288e+00 6.06661106175895e+01 - 31 3.20298183323508e+00 6.07382493916987e+01 - 32 3.20373100874536e+00 6.08054278361141e+01 - 33 3.20472468704943e+00 6.08651028913518e+01 - 34 3.20590256178394e+00 6.09148265769850e+01 - 35 3.20720566140745e+00 6.09523144047667e+01 - 36 3.20858030414420e+00 6.09755306486176e+01 - 37 3.20998111808250e+00 6.09827676263964e+01 - 38 3.21137308287521e+00 6.09726956103267e+01 - 39 3.21273274268056e+00 6.09443715231751e+01 - 40 3.21404878499019e+00 6.08972121817132e+01 + 20 3.21688253464583e+00 6.02774557527018e+01 + 21 3.21458253157603e+00 6.02463068700288e+01 + 22 3.21223315254029e+00 6.02378794668108e+01 + 23 3.20995392032979e+00 6.02499213792704e+01 + 24 3.20785326966943e+00 6.02797520575071e+01 + 25 3.20602244845117e+00 6.03244375021622e+01 + 26 3.20453120146139e+00 6.03809430522940e+01 + 27 3.20342556480347e+00 6.04462482372788e+01 + 28 3.20272769852622e+00 6.05174152657937e+01 + 29 3.20243730776714e+00 6.05916134522643e+01 + 30 3.20253423308456e+00 6.06661106334871e+01 + 31 3.20298183362156e+00 6.07382494079973e+01 + 32 3.20373100914607e+00 6.08054278528112e+01 + 33 3.20472468746373e+00 6.08651029084488e+01 + 34 3.20590256221113e+00 6.09148265944857e+01 + 35 3.20720566184671e+00 6.09523144226767e+01 + 36 3.20858030459458e+00 6.09755306669437e+01 + 37 3.20998111854285e+00 6.09827676451462e+01 + 38 3.21137308334418e+00 6.09726956295080e+01 + 39 3.21273274315657e+00 6.09443715427968e+01 + 40 3.21404878547144e+00 6.08972122017851e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat index 4d18e65a0..3099652d8 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/test.restart.histogram1.dat @@ -1,7223 +1,7223 @@ # 2 -# 0.00000000000000e+00 1.00000000000000e+00 20 0 -# -1.80000000000000e+02 1.00000000000000e+00 360 1 +# 0 1 20 0 +# -180 1 360 1 - 5.00000000000000e-01 -1.79500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.78500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.77500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.76500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.75500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.74500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.73500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.72500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.71500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.70500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.69500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.68500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.67500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.66500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.65500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.64500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.63500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.62500000000000e+02 0.00000000000000e+00 - 5.00000000000000e-01 -1.61500000000000e+02 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19.5 160.5 0 + 19.5 161.5 0 + 19.5 162.5 0 + 19.5 163.5 0 + 19.5 164.5 0 + 19.5 165.5 0 + 19.5 166.5 0 + 19.5 167.5 0 + 19.5 168.5 0 + 19.5 169.5 0 + 19.5 170.5 0 + 19.5 171.5 0 + 19.5 172.5 0 + 19.5 173.5 0 + 19.5 174.5 0 + 19.5 175.5 0 + 19.5 176.5 0 + 19.5 177.5 0 + 19.5 178.5 0 + 19.5 179.5 0 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt index 157cac038..017b69b3a 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2022-04-14. +colvars: Using NAMD interface, version "2022-04-06". diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out index fd1bac75c..cdf554a37 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/AutoDiff/test.restart.colvars.out @@ -154,7 +154,7 @@ colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.2155 -colvars: Restarting histogram bias "histogram1" from step number 20. +colvars: Restarting histogram bias "histogram1" from step number 0. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). diff --git a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt +++ b/namd/tests/library/000_distance-extended-grid_histogram-bypassExtended/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out index b5dee23d8..89726d6e4 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-extended-grid_histogram/AutoDiff/test.restart.colvars.out @@ -153,7 +153,7 @@ colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.2155 -colvars: Restarting histogram bias "histogram1" from step number 20. +colvars: Restarting histogram bias "histogram1" from step number 0. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). diff --git a/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt b/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt +++ b/namd/tests/library/000_distance-extended-grid_histogram/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-extended/namd-version.txt b/namd/tests/library/000_distance-extended/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_distance-extended/namd-version.txt +++ b/namd/tests/library/000_distance-extended/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out index 04c1af77b..d0cd986cf 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -90,7 +86,7 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 -colvars: # lowerBoundary = 0 [default] +colvars: # lowerBoundary = 0 colvars: # upperBoundary = 0.1 colvars: # hardLowerBoundary = on colvars: # hardUpperBoundary = off [default] @@ -141,27 +137,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped index 10c1037b0..21d01f18d 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688804951235e+00 + x 3.21688804971810e+00 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 2.26845126752189e-07 - 5.71217598091379e-05 1.12710965943565e-03 1.74270241892652e-03 - 2.11141093140343e-04 2.00454018061483e-06 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 2.26845124673292e-07 + 5.71217594827238e-05 1.12710965685979e-03 1.74270242088282e-03 + 2.11141094092476e-04 2.00454019640119e-06 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients grid_parameters { @@ -51,9 +51,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 1.54297695614713e-05 - 2.43078780370765e-03 1.92623445129830e-02 -1.45941325629368e-02 - -7.14477980575610e-03 -1.18875947897555e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.54297694279170e-05 + 2.43078779178197e-03 1.92623445074912e-02 -1.45941325201129e-02 + -7.14477983084629e-03 -1.18875948766480e-04 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj index 06d632fae..f51a5d30c 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 7.26085413750919e-03 - 11 3.21950378525805e+00 7.26085413750919e-03 - 12 3.22130533160336e+00 7.26085413750919e-03 - 13 3.22263545689569e+00 7.26085413750919e-03 - 14 3.22341879070410e+00 7.26085413750919e-03 - 15 3.22361636091569e+00 7.26085413750919e-03 - 16 3.22322642126644e+00 7.26085413750919e-03 - 17 3.22228237889954e+00 7.26085413750919e-03 - 18 3.22084853649908e+00 7.26085413750919e-03 - 19 3.21901439311712e+00 7.26085413750919e-03 - 20 3.21688804951235e+00 1.45941325629368e-02 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 7.26085412753031e-03 + 11 3.21950378533161e+00 7.26085412753031e-03 + 12 3.22130533168958e+00 7.26085412753031e-03 + 13 3.22263545699519e+00 7.26085412753031e-03 + 14 3.22341879081745e+00 7.26085412753031e-03 + 15 3.22361636104338e+00 7.26085412753031e-03 + 16 3.22322642140893e+00 7.26085412753031e-03 + 17 3.22228237905726e+00 7.26085412753031e-03 + 18 3.22084853667244e+00 7.26085412753031e-03 + 19 3.21901439330651e+00 7.26085412753031e-03 + 20 3.21688804971810e+00 1.45941325201129e-02 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf index 80c051dc8..dc034b29d 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.pmf @@ -1,40 +1,40 @@ # 1 # 0.00000000000000e+00 1.00000000000000e-01 37 0 - 5.00000000000000e-02 1.74270241892652e-03 - 1.50000000000000e-01 1.74270241892652e-03 - 2.50000000000000e-01 1.74270241892652e-03 - 3.50000000000000e-01 1.74270241892652e-03 - 4.50000000000000e-01 1.74270241892652e-03 - 5.50000000000000e-01 1.74270241892652e-03 - 6.50000000000000e-01 1.74270241892652e-03 - 7.50000000000000e-01 1.74270241892652e-03 - 8.50000000000000e-01 1.74270241892652e-03 - 9.50000000000000e-01 1.74270241892652e-03 - 1.05000000000000e+00 1.74270241892652e-03 - 1.15000000000000e+00 1.74270241892652e-03 - 1.25000000000000e+00 1.74270241892652e-03 - 1.35000000000000e+00 1.74270241892652e-03 - 1.45000000000000e+00 1.74270241892652e-03 - 1.55000000000000e+00 1.74270241892652e-03 - 1.65000000000000e+00 1.74270241892652e-03 - 1.75000000000000e+00 1.74270241892652e-03 - 1.85000000000000e+00 1.74270241892652e-03 - 1.95000000000000e+00 1.74270241892652e-03 - 2.05000000000000e+00 1.74270241892652e-03 - 2.15000000000000e+00 1.74270241892652e-03 - 2.25000000000000e+00 1.74270241892652e-03 - 2.35000000000000e+00 1.74270241892652e-03 - 2.45000000000000e+00 1.74270241892652e-03 - 2.55000000000000e+00 1.74270241892652e-03 - 2.65000000000000e+00 1.74270241892652e-03 - 2.75000000000000e+00 1.74270241892652e-03 - 2.85000000000000e+00 1.74270241892652e-03 - 2.95000000000000e+00 1.74247557379976e-03 - 3.05000000000000e+00 1.68558065911738e-03 - 3.15000000000000e+00 6.15592759490865e-04 + 5.00000000000000e-02 1.74270242088282e-03 + 1.50000000000000e-01 1.74270242088282e-03 + 2.50000000000000e-01 1.74270242088282e-03 + 3.50000000000000e-01 1.74270242088282e-03 + 4.50000000000000e-01 1.74270242088282e-03 + 5.50000000000000e-01 1.74270242088282e-03 + 6.50000000000000e-01 1.74270242088282e-03 + 7.50000000000000e-01 1.74270242088282e-03 + 8.50000000000000e-01 1.74270242088282e-03 + 9.50000000000000e-01 1.74270242088282e-03 + 1.05000000000000e+00 1.74270242088282e-03 + 1.15000000000000e+00 1.74270242088282e-03 + 1.25000000000000e+00 1.74270242088282e-03 + 1.35000000000000e+00 1.74270242088282e-03 + 1.45000000000000e+00 1.74270242088282e-03 + 1.55000000000000e+00 1.74270242088282e-03 + 1.65000000000000e+00 1.74270242088282e-03 + 1.75000000000000e+00 1.74270242088282e-03 + 1.85000000000000e+00 1.74270242088282e-03 + 1.95000000000000e+00 1.74270242088282e-03 + 2.05000000000000e+00 1.74270242088282e-03 + 2.15000000000000e+00 1.74270242088282e-03 + 2.25000000000000e+00 1.74270242088282e-03 + 2.35000000000000e+00 1.74270242088282e-03 + 2.45000000000000e+00 1.74270242088282e-03 + 2.55000000000000e+00 1.74270242088282e-03 + 2.65000000000000e+00 1.74270242088282e-03 + 2.75000000000000e+00 1.74270242088282e-03 + 2.85000000000000e+00 1.74270242088282e-03 + 2.95000000000000e+00 1.74247557575815e-03 + 3.05000000000000e+00 1.68558066140010e-03 + 3.15000000000000e+00 6.15592764023032e-04 3.25000000000000e+00 -0.00000000000000e+00 - 3.35000000000000e+00 1.53156132578617e-03 - 3.45000000000000e+00 1.74069787874590e-03 - 3.55000000000000e+00 1.74270241892652e-03 - 3.65000000000000e+00 1.74270241892652e-03 + 3.35000000000000e+00 1.53156132679035e-03 + 3.45000000000000e+00 1.74069788068642e-03 + 3.55000000000000e+00 1.74270242088282e-03 + 3.65000000000000e+00 1.74270242088282e-03 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out index e41a5cf1c..5813ff1d2 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -90,7 +86,7 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.1 -colvars: # lowerBoundary = 0 [default] +colvars: # lowerBoundary = 0 colvars: # upperBoundary = 0.1 colvars: # hardLowerBoundary = on colvars: # hardUpperBoundary = off [default] @@ -141,34 +137,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21689 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped index 16770ad61..34fd5ad0c 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21410417583007e+00 + x 3.21410417631119e+00 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 6.62978157520071e-07 - 1.41194487892242e-04 2.42321240493645e-03 3.34221726380270e-03 - 3.69169353864755e-04 3.25342737556381e-06 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 6.62978143841745e-07 + 1.41194486168262e-04 2.42321239420736e-03 3.34221727286243e-03 + 3.69169357278679e-04 3.25342742518778e-06 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients grid_parameters { @@ -51,9 +51,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 4.38875870035617e-05 - 5.79221287439899e-03 3.83513133503907e-02 -3.14227499478963e-02 - -1.27980744195482e-02 -1.95106962739560e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 4.38875861559355e-05 + 5.79221281512363e-03 3.83513133612739e-02 -3.14227498048830e-02 + -1.27980745147960e-02 -1.95106965527919e-04 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj index bc03d36a4..6941fb0a6 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688804951235e+00 1.45941325629368e-02 - 21 3.21458913699124e+00 1.45941325629368e-02 - 22 3.21224101139884e+00 1.45941325629368e-02 - 23 3.20996318736015e+00 1.45941325629368e-02 - 24 3.20786409091340e+00 1.45941325629368e-02 - 25 3.20603496093235e+00 1.45941325629368e-02 - 26 3.20454553304178e+00 1.45941325629368e-02 - 27 3.20344183417990e+00 1.45941325629368e-02 - 28 3.20274601535548e+00 1.45941325629368e-02 - 29 3.20245777287417e+00 1.45941325629368e-02 - 30 3.20255693872927e+00 2.36650234045914e-02 - 31 3.20300700313402e+00 2.36650234045914e-02 - 32 3.20375885604914e+00 2.36650234045914e-02 - 33 3.20475541396031e+00 2.36650234045914e-02 - 34 3.20593635782781e+00 2.36650234045914e-02 - 35 3.20724270238762e+00 2.36650234045914e-02 - 36 3.20862075136558e+00 2.36650234045914e-02 - 37 3.21002511802444e+00 2.36650234045914e-02 - 38 3.21142076721680e+00 2.36650234045914e-02 - 39 3.21278422862637e+00 2.36650234045914e-02 - 40 3.21410417583007e+00 3.14227499478963e-02 + 20 3.21688804971810e+00 1.45941325201129e-02 + 21 3.21458913721366e+00 1.45941325201129e-02 + 22 3.21224101163817e+00 1.45941325201129e-02 + 23 3.20996318761655e+00 1.45941325201129e-02 + 24 3.20786409118692e+00 1.45941325201129e-02 + 25 3.20603496122295e+00 1.45941325201129e-02 + 26 3.20454553334930e+00 1.45941325201129e-02 + 27 3.20344183450406e+00 1.45941325201129e-02 + 28 3.20274601569592e+00 1.45941325201129e-02 + 29 3.20245777323046e+00 1.45941325201129e-02 + 30 3.20255693910090e+00 2.36650233314395e-02 + 31 3.20300700352046e+00 2.36650233314395e-02 + 32 3.20375885644980e+00 2.36650233314395e-02 + 33 3.20475541437456e+00 2.36650233314395e-02 + 34 3.20593635825493e+00 2.36650233314395e-02 + 35 3.20724270282681e+00 2.36650233314395e-02 + 36 3.20862075181587e+00 2.36650233314395e-02 + 37 3.21002511848469e+00 2.36650233314395e-02 + 38 3.21142076768566e+00 2.36650233314395e-02 + 39 3.21278422910227e+00 2.36650233314395e-02 + 40 3.21410417631119e+00 3.14227498048830e-02 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf index 63d82cbc3..dd7b19d0a 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/test.restart.pmf @@ -1,40 +1,40 @@ # 1 # 0.00000000000000e+00 1.00000000000000e-01 37 0 - 5.00000000000000e-02 3.34221726380270e-03 - 1.50000000000000e-01 3.34221726380270e-03 - 2.50000000000000e-01 3.34221726380270e-03 - 3.50000000000000e-01 3.34221726380270e-03 - 4.50000000000000e-01 3.34221726380270e-03 - 5.50000000000000e-01 3.34221726380270e-03 - 6.50000000000000e-01 3.34221726380270e-03 - 7.50000000000000e-01 3.34221726380270e-03 - 8.50000000000000e-01 3.34221726380270e-03 - 9.50000000000000e-01 3.34221726380270e-03 - 1.05000000000000e+00 3.34221726380270e-03 - 1.15000000000000e+00 3.34221726380270e-03 - 1.25000000000000e+00 3.34221726380270e-03 - 1.35000000000000e+00 3.34221726380270e-03 - 1.45000000000000e+00 3.34221726380270e-03 - 1.55000000000000e+00 3.34221726380270e-03 - 1.65000000000000e+00 3.34221726380270e-03 - 1.75000000000000e+00 3.34221726380270e-03 - 1.85000000000000e+00 3.34221726380270e-03 - 1.95000000000000e+00 3.34221726380270e-03 - 2.05000000000000e+00 3.34221726380270e-03 - 2.15000000000000e+00 3.34221726380270e-03 - 2.25000000000000e+00 3.34221726380270e-03 - 2.35000000000000e+00 3.34221726380270e-03 - 2.45000000000000e+00 3.34221726380270e-03 - 2.55000000000000e+00 3.34221726380270e-03 - 2.65000000000000e+00 3.34221726380270e-03 - 2.75000000000000e+00 3.34221726380270e-03 - 2.85000000000000e+00 3.34221726380270e-03 - 2.95000000000000e+00 3.34155428564518e-03 - 3.05000000000000e+00 3.20102277591046e-03 - 3.15000000000000e+00 9.19004858866248e-04 + 5.00000000000000e-02 3.34221727286243e-03 + 1.50000000000000e-01 3.34221727286243e-03 + 2.50000000000000e-01 3.34221727286243e-03 + 3.50000000000000e-01 3.34221727286243e-03 + 4.50000000000000e-01 3.34221727286243e-03 + 5.50000000000000e-01 3.34221727286243e-03 + 6.50000000000000e-01 3.34221727286243e-03 + 7.50000000000000e-01 3.34221727286243e-03 + 8.50000000000000e-01 3.34221727286243e-03 + 9.50000000000000e-01 3.34221727286243e-03 + 1.05000000000000e+00 3.34221727286243e-03 + 1.15000000000000e+00 3.34221727286243e-03 + 1.25000000000000e+00 3.34221727286243e-03 + 1.35000000000000e+00 3.34221727286243e-03 + 1.45000000000000e+00 3.34221727286243e-03 + 1.55000000000000e+00 3.34221727286243e-03 + 1.65000000000000e+00 3.34221727286243e-03 + 1.75000000000000e+00 3.34221727286243e-03 + 1.85000000000000e+00 3.34221727286243e-03 + 1.95000000000000e+00 3.34221727286243e-03 + 2.05000000000000e+00 3.34221727286243e-03 + 2.15000000000000e+00 3.34221727286243e-03 + 2.25000000000000e+00 3.34221727286243e-03 + 2.35000000000000e+00 3.34221727286243e-03 + 2.45000000000000e+00 3.34221727286243e-03 + 2.55000000000000e+00 3.34221727286243e-03 + 2.65000000000000e+00 3.34221727286243e-03 + 2.75000000000000e+00 3.34221727286243e-03 + 2.85000000000000e+00 3.34221727286243e-03 + 2.95000000000000e+00 3.34155429471859e-03 + 3.05000000000000e+00 3.20102278669417e-03 + 3.15000000000000e+00 9.19004878655076e-04 3.25000000000000e+00 -0.00000000000000e+00 - 3.35000000000000e+00 2.97304790993794e-03 - 3.45000000000000e+00 3.33896383642714e-03 - 3.55000000000000e+00 3.34221726380270e-03 - 3.65000000000000e+00 3.34221726380270e-03 + 3.35000000000000e+00 2.97304791558375e-03 + 3.45000000000000e+00 3.33896384543724e-03 + 3.55000000000000e+00 3.34221727286243e-03 + 3.65000000000000e+00 3.34221727286243e-03 diff --git a/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt b/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt +++ b/namd/tests/library/000_distance-grid-expand_metadynamics/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out index 49233a154..7522b04bf 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -133,30 +129,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped index dd78a9c08..20f2914d8 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.19500142870476e+00 + x 3.19500142883077e+00 } abf { @@ -20,7 +20,7 @@ samples 0 0 0 0 gradient - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -2.00127620028148e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -2.00127627059354e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj index 5cab1a630..c883ca64b 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 -7.68950954395538e+00 - 7 3.20994206782701e+00 -1.45081021954275e+01 - 8 3.21200777962688e+00 -2.01168223029416e+01 - 9 3.21384392079195e+00 -2.42708474851834e+01 - 10 3.21523959933526e+00 -2.68357715832755e+01 - 11 3.21601851659179e+00 -2.31658530843961e+01 - 12 3.21612044367303e+00 -1.94776790572418e+01 - 13 3.21551354957116e+00 -1.59170233488103e+01 - 14 3.21419762164954e+00 -1.26130067638535e+01 - 15 3.21220454729786e+00 -9.67058885249113e+00 - 16 3.20959604449940e+00 -7.16540382727106e+00 - 17 3.20645917266472e+00 -5.14219076042560e+00 - 18 3.20290044125515e+00 -3.61665560433892e+00 - 19 3.19903928567179e+00 -2.57951937903240e+00 - 20 3.19500142870476e+00 -2.00127620028148e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 -7.68950956048151e+00 + 7 3.20994206785783e+00 -1.45081022282339e+01 + 8 3.21200777966617e+00 -2.01168223516023e+01 + 9 3.21384392083996e+00 -2.42708475491531e+01 + 10 3.21523959939197e+00 -2.68357716619527e+01 + 11 3.21601851665685e+00 -2.31658531617215e+01 + 12 3.21612044374608e+00 -1.94776791332188e+01 + 13 3.21551354965183e+00 -1.59170234235171e+01 + 14 3.21419762173747e+00 -1.26130068374289e+01 + 15 3.21220454739271e+00 -9.67058892511207e+00 + 16 3.20959604460089e+00 -7.16540389913541e+00 + 17 3.20645917277260e+00 -5.14219083172278e+00 + 18 3.20290044136922e+00 -3.61665567522571e+00 + 19 3.19903928579189e+00 -2.57951944961151e+00 + 20 3.19500142883077e+00 -2.00127627059354e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad index f1d0f6536..a9d8b5547 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -2.00127620028148e+00 + 3.25000000000000e+00 -2.00127627059354e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf index 46f65d7e5..a9c224cc4 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 1.00063810014074e+00 - 5.00000000000000e-01 1.00063810014074e+00 - 1.00000000000000e+00 1.00063810014074e+00 - 1.50000000000000e+00 1.00063810014074e+00 - 2.00000000000000e+00 1.00063810014074e+00 - 2.50000000000000e+00 1.00063810014074e+00 - 3.00000000000000e+00 1.00063810014074e+00 + 0.00000000000000e+00 1.00063813529677e+00 + 5.00000000000000e-01 1.00063813529677e+00 + 1.00000000000000e+00 1.00063813529677e+00 + 1.50000000000000e+00 1.00063813529677e+00 + 2.00000000000000e+00 1.00063813529677e+00 + 2.50000000000000e+00 1.00063813529677e+00 + 3.00000000000000e+00 1.00063813529677e+00 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out index e69be3fb4..1fa514166 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -133,35 +129,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.195 colvars: Restarting abf bias "abf1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped index cf3a7c63e..5ddfe2247 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.16157768304247e+00 + x 3.16157768320120e+00 } abf { @@ -20,7 +20,7 @@ samples 0 0 0 0 gradient - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -1.06018968543260e+01 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -1.06018969033008e+01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj index 790f5da38..6b2274e24 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.19500142870476e+00 -2.00127620028148e+00 - 21 3.19091235913242e+00 -1.83655671092344e+00 - 22 3.18689102863460e+00 -2.02779464964507e+00 - 23 3.18304398632164e+00 -2.50868594751815e+00 - 24 3.17946034157703e+00 -3.20793281356371e+00 - 25 3.17620810280522e+00 -4.05360356466712e+00 - 26 3.17333232267116e+00 -4.97767848574970e+00 - 27 3.17085517066390e+00 -5.92001155007172e+00 - 28 3.16877768256299e+00 -6.83099312723649e+00 - 29 3.16708266039313e+00 -7.67258378612514e+00 - 30 3.16573827065657e+00 -8.41821673794446e+00 - 31 3.16470189524569e+00 -9.05180799754020e+00 - 32 3.16392411278234e+00 -9.56669436325192e+00 - 33 3.16335264543312e+00 -9.96442495777829e+00 - 34 3.16293610801839e+00 -1.02534301314753e+01 - 35 3.16262726153762e+00 -1.04473358447738e+01 - 36 3.16238550229189e+00 -1.05630325935795e+01 - 37 3.16217843203474e+00 -1.06187380623063e+01 - 38 3.16198265878694e+00 -1.06325725153697e+01 - 39 3.16178405667746e+00 -1.06216993194485e+01 - 40 3.16157768304247e+00 -1.06018968543260e+01 + 20 3.19500142883077e+00 -2.00127627059354e+00 + 21 3.19091235926421e+00 -1.83655678093969e+00 + 22 3.18689102877202e+00 -2.02779471927389e+00 + 23 3.18304398646448e+00 -2.50868601661760e+00 + 24 3.17946034172504e+00 -3.20793288196262e+00 + 25 3.17620810295805e+00 -4.05360363219171e+00 + 26 3.17333232282842e+00 -4.97767855224492e+00 + 27 3.17085517082510e+00 -5.92001161542199e+00 + 28 3.16877768272762e+00 -6.83099319137926e+00 + 29 3.16708266056064e+00 -7.67258384905857e+00 + 30 3.16573827082641e+00 -8.41821679971556e+00 + 31 3.16470189541734e+00 -9.05180805822893e+00 + 32 3.16392411295527e+00 -9.56669442294402e+00 + 33 3.16335264560683e+00 -9.96442501653096e+00 + 34 3.16293610819235e+00 -1.02534301892968e+01 + 35 3.16262726171125e+00 -1.04473359016060e+01 + 36 3.16238550246452e+00 -1.05630326492936e+01 + 37 3.16217843220556e+00 -1.06187381167053e+01 + 38 3.16198265895496e+00 -1.06325725682142e+01 + 39 3.16178405684152e+00 -1.06216993704827e+01 + 40 3.16157768320120e+00 -1.06018969033008e+01 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad index be93459e2..9b2cd506d 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.06018968543260e+01 + 3.25000000000000e+00 -1.06018969033008e+01 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf index 34e7b0c50..0ddef6258 100644 --- a/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 5.30094842716302e+00 - 5.00000000000000e-01 5.30094842716302e+00 - 1.00000000000000e+00 5.30094842716302e+00 - 1.50000000000000e+00 5.30094842716302e+00 - 2.00000000000000e+00 5.30094842716302e+00 - 2.50000000000000e+00 5.30094842716302e+00 - 3.00000000000000e+00 5.30094842716302e+00 + 0.00000000000000e+00 5.30094845165041e+00 + 5.00000000000000e-01 5.30094845165041e+00 + 1.00000000000000e+00 5.30094845165041e+00 + 1.50000000000000e+00 5.30094845165041e+00 + 2.00000000000000e+00 5.30094845165041e+00 + 2.50000000000000e+00 5.30094845165041e+00 + 3.00000000000000e+00 5.30094845165041e+00 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf/namd-version.txt b/namd/tests/library/000_distance-grid_abf/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_abf/namd-version.txt +++ b/namd/tests/library/000_distance-grid_abf/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out index 143074633..61f53d955 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,30 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped index 72e414d40..e48d1c4ec 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685457618647e+00 + x 3.21685457639221e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } histogram @@ -29,7 +29,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -1.45777482050594e+00 0.00000000000000e+00 0.00000000000000e+00 + -1.45777476148254e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj index 5eec6dc1f..c0e02c1fa 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788600e+00 -1.23774855515440e-02 1.91502685723351e-02 1.10000000000000e-01 -1.23774855515440e-04 - 2 3.20383990680414e+00 -1.23353596272166e-02 1.90201371415956e-02 1.20000000000000e-01 -2.47128451787606e-04 - 3 3.20396636491103e+00 -1.22958654596441e-02 1.88985384252087e-02 1.30000000000000e-01 -3.70087106384047e-04 - 4 3.20472668059564e+00 -1.22589067223826e-02 1.87850992535096e-02 1.40000000000000e-01 -4.92676173607873e-04 - 5 3.20606077411088e+00 -1.22242430964435e-02 1.86790149101184e-02 1.50000000000000e-01 -6.14918604572308e-04 - 6 3.20787661013578e+00 -1.21915064405431e-02 1.85791036612255e-02 1.60000000000000e-01 -7.36833668977739e-04 - 7 3.21005557808631e+00 -1.21602223123453e-02 1.84838758357074e-02 1.70000000000000e-01 -8.58435892101191e-04 - 8 3.21245894716580e+00 -1.21298357886632e-02 1.83916145324919e-02 1.80000000000000e-01 -9.79734249987824e-04 - 9 3.21493543162121e+00 -1.20997417264848e-02 1.83004687309548e-02 1.90000000000000e-01 -1.10073166725267e-03 - 10 3.21732997387476e+00 -1.20693198954990e-02 1.82085603424861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 11 3.21949353668785e+00 -1.20779741467514e-02 1.82346824361994e-02 2.00000000000000e-01 -1.22142486620766e-03 - 12 3.22129316973139e+00 -1.20851726789256e-02 1.82564248349311e-02 2.00000000000000e-01 -1.22142486620766e-03 - 13 3.22262118961603e+00 -1.20904847584641e-02 1.82724777118316e-02 2.00000000000000e-01 -1.22142486620766e-03 - 14 3.22340223703211e+00 -1.20936089481284e-02 1.82819221737815e-02 2.00000000000000e-01 -1.22142486620766e-03 - 15 3.22359735089020e+00 -1.20943894035608e-02 1.82842818806205e-02 2.00000000000000e-01 -1.22142486620766e-03 - 16 3.22320479573201e+00 -1.20928191829280e-02 1.82795344738740e-02 2.00000000000000e-01 -1.22142486620766e-03 - 17 3.22225798922225e+00 -1.20890319568890e-02 1.82680867068354e-02 2.00000000000000e-01 -1.22142486620766e-03 - 18 3.22082124425633e+00 -1.20832849770253e-02 1.82507219795008e-02 2.00000000000000e-01 -1.22142486620766e-03 - 19 3.21898406979118e+00 -1.20759362791647e-02 1.82285296273058e-02 2.00000000000000e-01 -1.22142486620766e-03 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 + 1 3.20437138788663e+00 -1.23774855515465e-02 1.91502685723428e-02 1.10000000000000e-01 -1.23774855515465e-04 + 2 3.20383990680667e+00 -1.23353596272267e-02 1.90201371416267e-02 1.20000000000000e-01 -2.47128451787732e-04 + 3 3.20396636491675e+00 -1.22958654596670e-02 1.88985384252790e-02 1.30000000000000e-01 -3.70087106384402e-04 + 4 3.20472668060584e+00 -1.22589067224234e-02 1.87850992536346e-02 1.40000000000000e-01 -4.92676173608635e-04 + 5 3.20606077412683e+00 -1.22242430965073e-02 1.86790149103134e-02 1.50000000000000e-01 -6.14918604573709e-04 + 6 3.20787661015870e+00 -1.21915064406348e-02 1.85791036615050e-02 1.60000000000000e-01 -7.36833668980057e-04 + 7 3.21005557811738e+00 -1.21602223124695e-02 1.84838758360852e-02 1.70000000000000e-01 -8.58435892104752e-04 + 8 3.21245894720608e+00 -1.21298357888243e-02 1.83916145329805e-02 1.80000000000000e-01 -9.79734249992995e-04 + 9 3.21493543167171e+00 -1.20997417266868e-02 1.83004687315658e-02 1.90000000000000e-01 -1.10073166725986e-03 + 10 3.21732997393638e+00 -1.20693198957455e-02 1.82085603432298e-02 2.00000000000000e-01 -1.22142486621732e-03 + 11 3.21949353676140e+00 -1.20779741470456e-02 1.82346824370878e-02 2.00000000000000e-01 -1.22142486621732e-03 + 12 3.22129316981759e+00 -1.20851726792704e-02 1.82564248359729e-02 2.00000000000000e-01 -1.22142486621732e-03 + 13 3.22262118971552e+00 -1.20904847588621e-02 1.82724777130345e-02 2.00000000000000e-01 -1.22142486621732e-03 + 14 3.22340223714544e+00 -1.20936089485818e-02 1.82819221751521e-02 2.00000000000000e-01 -1.22142486621732e-03 + 15 3.22359735101788e+00 -1.20943894040715e-02 1.82842818821647e-02 2.00000000000000e-01 -1.22142486621732e-03 + 16 3.22320479587449e+00 -1.20928191834980e-02 1.82795344755970e-02 2.00000000000000e-01 -1.22142486621732e-03 + 17 3.22225798937996e+00 -1.20890319575198e-02 1.82680867087420e-02 2.00000000000000e-01 -1.22142486621732e-03 + 18 3.22082124442969e+00 -1.20832849777187e-02 1.82507219815954e-02 2.00000000000000e-01 -1.22142486621732e-03 + 19 3.21898406998055e+00 -1.20759362799222e-02 1.82285296295926e-02 2.00000000000000e-01 -1.22142486621732e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force index f26fbcd58..29f1a8c10 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.45777482050594e+00 + 3.25000000000000e+00 -1.45777476148234e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf index 34593c780..f89ed6bc3 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.harmonic1.ti.pmf @@ -6,17 +6,17 @@ 2 0 2.5 0 3 0 - 3.5 0.72888741025297 - 4 0.72888741025297 - 4.5 0.72888741025297 - 5 0.72888741025297 - 5.5 0.72888741025297 - 6 0.72888741025297 - 6.5 0.72888741025297 - 7 0.72888741025297 - 7.5 0.72888741025297 - 8 0.72888741025297 - 8.5 0.72888741025297 - 9 0.72888741025297 - 9.5 0.72888741025297 - 10 0.72888741025297 + 3.5 0.72888738074127 + 4 0.72888738074127 + 4.5 0.72888738074127 + 5 0.72888738074127 + 5.5 0.72888738074127 + 6 0.72888738074127 + 6.5 0.72888738074127 + 7 0.72888738074127 + 7.5 0.72888738074127 + 8 0.72888738074127 + 8.5 0.72888738074127 + 9 0.72888738074127 + 9.5 0.72888738074127 + 10 0.72888738074127 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out index 496158813..2a03c4ebb 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,35 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped index f5fbca6c7..e3d52dfab 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397324438969e+00 + x 3.21397324487089e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } histogram @@ -29,7 +29,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 4.72492117878643e+00 0.00000000000000e+00 0.00000000000000e+00 + 4.72492119104379e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj index 9592912c4..82871cb9e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 - 21 3.21455229130029e+00 -1.20582091652012e-02 1.81750510339676e-02 2.00000000000000e-01 -1.22142486620766e-03 - 22 3.21220058167135e+00 -1.20488023266854e-02 1.81467046884425e-02 2.00000000000000e-01 -1.22142486620766e-03 - 23 3.20991897400811e+00 -1.20396758960324e-02 1.81192244601880e-02 2.00000000000000e-01 -1.22142486620766e-03 - 24 3.20781590778578e+00 -1.20312636311431e-02 1.80939130702584e-02 2.00000000000000e-01 -1.22142486620766e-03 - 25 3.20598263662306e+00 -1.20239305464922e-02 1.80718632233586e-02 2.00000000000000e-01 -1.22142486620766e-03 - 26 3.20448891199500e+00 -1.20179556479800e-02 1.80539072446018e-02 2.00000000000000e-01 -1.22142486620766e-03 - 27 3.20338077760483e+00 -1.20135231104193e-02 1.80405921905723e-02 2.00000000000000e-01 -1.22142486620766e-03 - 28 3.20268040182054e+00 -1.20107216072822e-02 1.80321791909543e-02 2.00000000000000e-01 -1.22142486620766e-03 - 29 3.20238749862618e+00 -1.20095499945047e-02 1.80286613838135e-02 2.00000000000000e-01 -1.22142486620766e-03 - 30 3.20248191768589e+00 -1.20099276707435e-02 1.80297953320614e-02 2.00000000000000e-01 -1.22142486620766e-03 - 31 3.20292702714129e+00 -1.20117081085652e-02 1.80351414606713e-02 2.00000000000000e-01 -1.22142486620766e-03 - 32 3.20367373527010e+00 -1.20146949410804e-02 1.80441118159029e-02 2.00000000000000e-01 -1.22142486620766e-03 - 33 3.20466497756289e+00 -1.20186599102516e-02 1.80560232547861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 34 3.20584045419353e+00 -1.20233618167741e-02 1.80701536721327e-02 2.00000000000000e-01 -1.22142486620766e-03 - 35 3.20714119860834e+00 -1.20285647944334e-02 1.80857963767352e-02 2.00000000000000e-01 -1.22142486620766e-03 - 36 3.20851353235803e+00 -1.20340541294321e-02 1.81023073487628e-02 2.00000000000000e-01 -1.22142486620766e-03 - 37 3.20991208499767e+00 -1.20396483399907e-02 1.81191415188300e-02 2.00000000000000e-01 -1.22142486620766e-03 - 38 3.21130183589808e+00 -1.20452073435923e-02 1.81358774937663e-02 2.00000000000000e-01 -1.22142486620766e-03 - 39 3.21265932746957e+00 -1.20506373098783e-02 1.81522324467788e-02 2.00000000000000e-01 -1.22142486620766e-03 - 40 3.21397324438969e+00 -1.20558929775587e-02 1.81680694357938e-02 2.00000000000000e-01 -1.22142486620766e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 + 21 3.21455229152270e+00 -1.20582091660908e-02 1.81750510366495e-02 2.00000000000000e-01 -1.22142486621732e-03 + 22 3.21220058191067e+00 -1.20488023276427e-02 1.81467046913260e-02 2.00000000000000e-01 -1.22142486621732e-03 + 23 3.20991897426449e+00 -1.20396758970580e-02 1.81192244632749e-02 2.00000000000000e-01 -1.22142486621732e-03 + 24 3.20781590805930e+00 -1.20312636322372e-02 1.80939130735492e-02 2.00000000000000e-01 -1.22142486621732e-03 + 25 3.20598263691365e+00 -1.20239305476546e-02 1.80718632268527e-02 2.00000000000000e-01 -1.22142486621732e-03 + 26 3.20448891230251e+00 -1.20179556492100e-02 1.80539072482974e-02 2.00000000000000e-01 -1.22142486621732e-03 + 27 3.20338077792898e+00 -1.20135231117159e-02 1.80405921944666e-02 2.00000000000000e-01 -1.22142486621732e-03 + 28 3.20268040216098e+00 -1.20107216086439e-02 1.80321791950433e-02 2.00000000000000e-01 -1.22142486621732e-03 + 29 3.20238749898247e+00 -1.20095499959299e-02 1.80286613880924e-02 2.00000000000000e-01 -1.22142486621732e-03 + 30 3.20248191805753e+00 -1.20099276722301e-02 1.80297953365248e-02 2.00000000000000e-01 -1.22142486621732e-03 + 31 3.20292702752774e+00 -1.20117081101110e-02 1.80351414653132e-02 2.00000000000000e-01 -1.22142486621732e-03 + 32 3.20367373567078e+00 -1.20146949426831e-02 1.80441118207169e-02 2.00000000000000e-01 -1.22142486621732e-03 + 33 3.20466497797716e+00 -1.20186599119087e-02 1.80560232597650e-02 2.00000000000000e-01 -1.22142486621732e-03 + 34 3.20584045462068e+00 -1.20233618184827e-02 1.80701536772685e-02 2.00000000000000e-01 -1.22142486621732e-03 + 35 3.20714119904756e+00 -1.20285647961903e-02 1.80857963820184e-02 2.00000000000000e-01 -1.22142486621732e-03 + 36 3.20851353280837e+00 -1.20340541312335e-02 1.81023073541822e-02 2.00000000000000e-01 -1.22142486621732e-03 + 37 3.20991208545797e+00 -1.20396483418319e-02 1.81191415243719e-02 2.00000000000000e-01 -1.22142486621732e-03 + 38 3.21130183636701e+00 -1.20452073454680e-02 1.81358774994146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 39 3.21265932794554e+00 -1.20506373117822e-02 1.81522324525146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 40 3.21397324487089e+00 -1.20558929794836e-02 1.81680694415952e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force index 1c62523ef..f7701bacb 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 4.72492117878643e+00 + 3.25000000000000e+00 4.72492119104315e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf index d82c0a308..19f56570c 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.harmonic1.ti.pmf @@ -1,11 +1,11 @@ # xi A(xi) - 0 2.3624605893932 - 0.5 2.3624605893932 - 1 2.3624605893932 - 1.5 2.3624605893932 - 2 2.3624605893932 - 2.5 2.3624605893932 - 3 2.3624605893932 + 0 2.3624605955218 + 0.5 2.3624605955218 + 1 2.3624605955218 + 1.5 2.3624605955218 + 2 2.3624605955218 + 2.5 2.3624605955218 + 3 2.3624605955218 3.5 0 4 0 4.5 0 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving-ti/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out index b95774d40..4054ca6f6 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,27 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped index 5ef095f44..4109af1f5 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685457618647e+00 + x 3.21685457639221e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } } diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj index 5eec6dc1f..c0e02c1fa 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788600e+00 -1.23774855515440e-02 1.91502685723351e-02 1.10000000000000e-01 -1.23774855515440e-04 - 2 3.20383990680414e+00 -1.23353596272166e-02 1.90201371415956e-02 1.20000000000000e-01 -2.47128451787606e-04 - 3 3.20396636491103e+00 -1.22958654596441e-02 1.88985384252087e-02 1.30000000000000e-01 -3.70087106384047e-04 - 4 3.20472668059564e+00 -1.22589067223826e-02 1.87850992535096e-02 1.40000000000000e-01 -4.92676173607873e-04 - 5 3.20606077411088e+00 -1.22242430964435e-02 1.86790149101184e-02 1.50000000000000e-01 -6.14918604572308e-04 - 6 3.20787661013578e+00 -1.21915064405431e-02 1.85791036612255e-02 1.60000000000000e-01 -7.36833668977739e-04 - 7 3.21005557808631e+00 -1.21602223123453e-02 1.84838758357074e-02 1.70000000000000e-01 -8.58435892101191e-04 - 8 3.21245894716580e+00 -1.21298357886632e-02 1.83916145324919e-02 1.80000000000000e-01 -9.79734249987824e-04 - 9 3.21493543162121e+00 -1.20997417264848e-02 1.83004687309548e-02 1.90000000000000e-01 -1.10073166725267e-03 - 10 3.21732997387476e+00 -1.20693198954990e-02 1.82085603424861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 11 3.21949353668785e+00 -1.20779741467514e-02 1.82346824361994e-02 2.00000000000000e-01 -1.22142486620766e-03 - 12 3.22129316973139e+00 -1.20851726789256e-02 1.82564248349311e-02 2.00000000000000e-01 -1.22142486620766e-03 - 13 3.22262118961603e+00 -1.20904847584641e-02 1.82724777118316e-02 2.00000000000000e-01 -1.22142486620766e-03 - 14 3.22340223703211e+00 -1.20936089481284e-02 1.82819221737815e-02 2.00000000000000e-01 -1.22142486620766e-03 - 15 3.22359735089020e+00 -1.20943894035608e-02 1.82842818806205e-02 2.00000000000000e-01 -1.22142486620766e-03 - 16 3.22320479573201e+00 -1.20928191829280e-02 1.82795344738740e-02 2.00000000000000e-01 -1.22142486620766e-03 - 17 3.22225798922225e+00 -1.20890319568890e-02 1.82680867068354e-02 2.00000000000000e-01 -1.22142486620766e-03 - 18 3.22082124425633e+00 -1.20832849770253e-02 1.82507219795008e-02 2.00000000000000e-01 -1.22142486620766e-03 - 19 3.21898406979118e+00 -1.20759362791647e-02 1.82285296273058e-02 2.00000000000000e-01 -1.22142486620766e-03 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 + 1 3.20437138788663e+00 -1.23774855515465e-02 1.91502685723428e-02 1.10000000000000e-01 -1.23774855515465e-04 + 2 3.20383990680667e+00 -1.23353596272267e-02 1.90201371416267e-02 1.20000000000000e-01 -2.47128451787732e-04 + 3 3.20396636491675e+00 -1.22958654596670e-02 1.88985384252790e-02 1.30000000000000e-01 -3.70087106384402e-04 + 4 3.20472668060584e+00 -1.22589067224234e-02 1.87850992536346e-02 1.40000000000000e-01 -4.92676173608635e-04 + 5 3.20606077412683e+00 -1.22242430965073e-02 1.86790149103134e-02 1.50000000000000e-01 -6.14918604573709e-04 + 6 3.20787661015870e+00 -1.21915064406348e-02 1.85791036615050e-02 1.60000000000000e-01 -7.36833668980057e-04 + 7 3.21005557811738e+00 -1.21602223124695e-02 1.84838758360852e-02 1.70000000000000e-01 -8.58435892104752e-04 + 8 3.21245894720608e+00 -1.21298357888243e-02 1.83916145329805e-02 1.80000000000000e-01 -9.79734249992995e-04 + 9 3.21493543167171e+00 -1.20997417266868e-02 1.83004687315658e-02 1.90000000000000e-01 -1.10073166725986e-03 + 10 3.21732997393638e+00 -1.20693198957455e-02 1.82085603432298e-02 2.00000000000000e-01 -1.22142486621732e-03 + 11 3.21949353676140e+00 -1.20779741470456e-02 1.82346824370878e-02 2.00000000000000e-01 -1.22142486621732e-03 + 12 3.22129316981759e+00 -1.20851726792704e-02 1.82564248359729e-02 2.00000000000000e-01 -1.22142486621732e-03 + 13 3.22262118971552e+00 -1.20904847588621e-02 1.82724777130345e-02 2.00000000000000e-01 -1.22142486621732e-03 + 14 3.22340223714544e+00 -1.20936089485818e-02 1.82819221751521e-02 2.00000000000000e-01 -1.22142486621732e-03 + 15 3.22359735101788e+00 -1.20943894040715e-02 1.82842818821647e-02 2.00000000000000e-01 -1.22142486621732e-03 + 16 3.22320479587449e+00 -1.20928191834980e-02 1.82795344755970e-02 2.00000000000000e-01 -1.22142486621732e-03 + 17 3.22225798937996e+00 -1.20890319575198e-02 1.82680867087420e-02 2.00000000000000e-01 -1.22142486621732e-03 + 18 3.22082124442969e+00 -1.20832849777187e-02 1.82507219815954e-02 2.00000000000000e-01 -1.22142486621732e-03 + 19 3.21898406998055e+00 -1.20759362799222e-02 1.82285296295926e-02 2.00000000000000e-01 -1.22142486621732e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out index 40e76217d..88405593c 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,32 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped index a27db3dc3..100eebdff 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397324438969e+00 + x 3.21397324487089e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } } diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj index 9592912c4..82871cb9e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 - 21 3.21455229130029e+00 -1.20582091652012e-02 1.81750510339676e-02 2.00000000000000e-01 -1.22142486620766e-03 - 22 3.21220058167135e+00 -1.20488023266854e-02 1.81467046884425e-02 2.00000000000000e-01 -1.22142486620766e-03 - 23 3.20991897400811e+00 -1.20396758960324e-02 1.81192244601880e-02 2.00000000000000e-01 -1.22142486620766e-03 - 24 3.20781590778578e+00 -1.20312636311431e-02 1.80939130702584e-02 2.00000000000000e-01 -1.22142486620766e-03 - 25 3.20598263662306e+00 -1.20239305464922e-02 1.80718632233586e-02 2.00000000000000e-01 -1.22142486620766e-03 - 26 3.20448891199500e+00 -1.20179556479800e-02 1.80539072446018e-02 2.00000000000000e-01 -1.22142486620766e-03 - 27 3.20338077760483e+00 -1.20135231104193e-02 1.80405921905723e-02 2.00000000000000e-01 -1.22142486620766e-03 - 28 3.20268040182054e+00 -1.20107216072822e-02 1.80321791909543e-02 2.00000000000000e-01 -1.22142486620766e-03 - 29 3.20238749862618e+00 -1.20095499945047e-02 1.80286613838135e-02 2.00000000000000e-01 -1.22142486620766e-03 - 30 3.20248191768589e+00 -1.20099276707435e-02 1.80297953320614e-02 2.00000000000000e-01 -1.22142486620766e-03 - 31 3.20292702714129e+00 -1.20117081085652e-02 1.80351414606713e-02 2.00000000000000e-01 -1.22142486620766e-03 - 32 3.20367373527010e+00 -1.20146949410804e-02 1.80441118159029e-02 2.00000000000000e-01 -1.22142486620766e-03 - 33 3.20466497756289e+00 -1.20186599102516e-02 1.80560232547861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 34 3.20584045419353e+00 -1.20233618167741e-02 1.80701536721327e-02 2.00000000000000e-01 -1.22142486620766e-03 - 35 3.20714119860834e+00 -1.20285647944334e-02 1.80857963767352e-02 2.00000000000000e-01 -1.22142486620766e-03 - 36 3.20851353235803e+00 -1.20340541294321e-02 1.81023073487628e-02 2.00000000000000e-01 -1.22142486620766e-03 - 37 3.20991208499767e+00 -1.20396483399907e-02 1.81191415188300e-02 2.00000000000000e-01 -1.22142486620766e-03 - 38 3.21130183589808e+00 -1.20452073435923e-02 1.81358774937663e-02 2.00000000000000e-01 -1.22142486620766e-03 - 39 3.21265932746957e+00 -1.20506373098783e-02 1.81522324467788e-02 2.00000000000000e-01 -1.22142486620766e-03 - 40 3.21397324438969e+00 -1.20558929775587e-02 1.81680694357938e-02 2.00000000000000e-01 -1.22142486620766e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 + 21 3.21455229152270e+00 -1.20582091660908e-02 1.81750510366495e-02 2.00000000000000e-01 -1.22142486621732e-03 + 22 3.21220058191067e+00 -1.20488023276427e-02 1.81467046913260e-02 2.00000000000000e-01 -1.22142486621732e-03 + 23 3.20991897426449e+00 -1.20396758970580e-02 1.81192244632749e-02 2.00000000000000e-01 -1.22142486621732e-03 + 24 3.20781590805930e+00 -1.20312636322372e-02 1.80939130735492e-02 2.00000000000000e-01 -1.22142486621732e-03 + 25 3.20598263691365e+00 -1.20239305476546e-02 1.80718632268527e-02 2.00000000000000e-01 -1.22142486621732e-03 + 26 3.20448891230251e+00 -1.20179556492100e-02 1.80539072482974e-02 2.00000000000000e-01 -1.22142486621732e-03 + 27 3.20338077792898e+00 -1.20135231117159e-02 1.80405921944666e-02 2.00000000000000e-01 -1.22142486621732e-03 + 28 3.20268040216098e+00 -1.20107216086439e-02 1.80321791950433e-02 2.00000000000000e-01 -1.22142486621732e-03 + 29 3.20238749898247e+00 -1.20095499959299e-02 1.80286613880924e-02 2.00000000000000e-01 -1.22142486621732e-03 + 30 3.20248191805753e+00 -1.20099276722301e-02 1.80297953365248e-02 2.00000000000000e-01 -1.22142486621732e-03 + 31 3.20292702752774e+00 -1.20117081101110e-02 1.80351414653132e-02 2.00000000000000e-01 -1.22142486621732e-03 + 32 3.20367373567078e+00 -1.20146949426831e-02 1.80441118207169e-02 2.00000000000000e-01 -1.22142486621732e-03 + 33 3.20466497797716e+00 -1.20186599119087e-02 1.80560232597650e-02 2.00000000000000e-01 -1.22142486621732e-03 + 34 3.20584045462068e+00 -1.20233618184827e-02 1.80701536772685e-02 2.00000000000000e-01 -1.22142486621732e-03 + 35 3.20714119904756e+00 -1.20285647961903e-02 1.80857963820184e-02 2.00000000000000e-01 -1.22142486621732e-03 + 36 3.20851353280837e+00 -1.20340541312335e-02 1.81023073541822e-02 2.00000000000000e-01 -1.22142486621732e-03 + 37 3.20991208545797e+00 -1.20396483418319e-02 1.81191415243719e-02 2.00000000000000e-01 -1.22142486621732e-03 + 38 3.21130183636701e+00 -1.20452073454680e-02 1.81358774994146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 39 3.21265932794554e+00 -1.20506373117822e-02 1.81522324525146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 40 3.21397324487089e+00 -1.20558929794836e-02 1.81680694415952e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-centers-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out index 3d0f629a2..9b0d8d5c9 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,30 +125,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped index 301b9ace6..3f9b13bdc 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685399817416e+00 + x 3.21685399837991e+00 } restraint { @@ -26,7 +26,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -1.45768708516242e+00 0.00000000000000e+00 0.00000000000000e+00 + -1.45768702613562e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj index 2cd06ea2b..ccbac37f2 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.24221869387334e-02 - 1 3.20437138788600e+00 -1.24174855515440e-02 - 2 3.20383990619069e+00 -1.24153596247627e-02 - 3 3.20396636246577e+00 -1.24158654498631e-02 - 4 3.20472667451135e+00 -1.24189066980454e-02 - 5 3.20606076201392e+00 -1.24242430480557e-02 - 6 3.20787658911377e+00 -1.24315063564551e-02 - 7 3.21005554471991e+00 -1.24402221788797e-02 - 8 3.21245889756338e+00 -1.24498355902535e-02 - 9 3.21493536145531e+00 -1.24597414458212e-02 - 10 3.21732987841907e+00 -1.24693195136763e-02 - 11 3.21949341085340e+00 -1.24779736434136e-02 - 12 3.22129300871542e+00 -1.24851720348617e-02 - 13 3.22262098892565e+00 -1.24904839557026e-02 - 14 3.22340199249676e+00 -1.24936079699870e-02 - 15 3.22359705866319e+00 -1.24943882346527e-02 - 16 3.22320445228234e+00 -1.24928178091294e-02 - 17 3.22225759131848e+00 -1.24890303652739e-02 - 18 3.22082078894448e+00 -1.24832831557779e-02 - 19 3.21898355436871e+00 -1.24759342174748e-02 - 20 3.21685399817416e+00 -1.24674159926967e-02 + 1 3.20437138788663e+00 -1.24174855515465e-02 + 2 3.20383990619321e+00 -1.24153596247728e-02 + 3 3.20396636247149e+00 -1.24158654498859e-02 + 4 3.20472667452156e+00 -1.24189066980862e-02 + 5 3.20606076202988e+00 -1.24242430481195e-02 + 6 3.20787658913670e+00 -1.24315063565468e-02 + 7 3.21005554475098e+00 -1.24402221790039e-02 + 8 3.21245889760366e+00 -1.24498355904146e-02 + 9 3.21493536150581e+00 -1.24597414460232e-02 + 10 3.21732987848069e+00 -1.24693195139228e-02 + 11 3.21949341092696e+00 -1.24779736437079e-02 + 12 3.22129300880163e+00 -1.24851720352065e-02 + 13 3.22262098902515e+00 -1.24904839561006e-02 + 14 3.22340199261010e+00 -1.24936079704404e-02 + 15 3.22359705879087e+00 -1.24943882351635e-02 + 16 3.22320445242483e+00 -1.24928178096993e-02 + 17 3.22225759147620e+00 -1.24890303659048e-02 + 18 3.22082078911784e+00 -1.24832831564713e-02 + 19 3.21898355455808e+00 -1.24759342182323e-02 + 20 3.21685399837991e+00 -1.24674159935196e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force index 640855ec6..1b3e03edb 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.45768708516242e+00 + 3.25000000000000e+00 -1.45768702613609e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf index 270f05c0e..af50b46fb 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.harmonic1.ti.pmf @@ -6,17 +6,17 @@ 2 0 2.5 0 3 0 - 3.5 0.72884354258121 - 4 0.72884354258121 - 4.5 0.72884354258121 - 5 0.72884354258121 - 5.5 0.72884354258121 - 6 0.72884354258121 - 6.5 0.72884354258121 - 7 0.72884354258121 - 7.5 0.72884354258121 - 8 0.72884354258121 - 8.5 0.72884354258121 - 9 0.72884354258121 - 9.5 0.72884354258121 - 10 0.72884354258121 + 3.5 0.72884351306783 + 4 0.72884351306783 + 4.5 0.72884351306783 + 5 0.72884351306783 + 5.5 0.72884351306783 + 6 0.72884351306783 + 6.5 0.72884351306783 + 7 0.72884351306783 + 7.5 0.72884351306783 + 8 0.72884351306783 + 8.5 0.72884351306783 + 9 0.72884351306783 + 9.5 0.72884351306783 + 10 0.72884351306783 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out index 618f855ff..d2b2d5ed3 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,35 +125,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped index 17f669708..4f7e0b7d8 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397114716924e+00 + x 3.21397114765047e+00 } restraint { @@ -26,7 +26,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 4.72514253816199e+00 0.00000000000000e+00 0.00000000000000e+00 + 4.72514255041894e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj index 8924671f5..47d79951b 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685399817416e+00 -1.24674159926967e-02 - 21 3.21455164841394e+00 -1.24582065936557e-02 - 22 3.21219987179556e+00 -1.24487994871822e-02 - 23 3.20991819517487e+00 -1.24396727806995e-02 - 24 3.20781505815938e+00 -1.24312602326375e-02 - 25 3.20598171449351e+00 -1.24239268579740e-02 - 26 3.20448791577891e+00 -1.24179516631157e-02 - 27 3.20337970585434e+00 -1.24135188234173e-02 - 28 3.20267925323760e+00 -1.24107170129504e-02 - 29 3.20238627208178e+00 -1.24095450883271e-02 - 30 3.20248061224166e+00 -1.24099224489666e-02 - 31 3.20292564206961e+00 -1.24117025682784e-02 - 32 3.20367227007056e+00 -1.24146890802823e-02 - 33 3.20466343197421e+00 -1.24186537278969e-02 - 34 3.20583882819824e+00 -1.24233553127930e-02 - 35 3.20713949242506e+00 -1.24285579697002e-02 - 36 3.20851174642574e+00 -1.24340469857030e-02 - 37 3.20991021994729e+00 -1.24396408797892e-02 - 38 3.21129989251817e+00 -1.24451995700727e-02 - 39 3.21265730667037e+00 -1.24506292266815e-02 - 40 3.21397114716924e+00 -1.24558845886769e-02 + 20 3.21685399837991e+00 -1.24674159935196e-02 + 21 3.21455164863636e+00 -1.24582065945454e-02 + 22 3.21219987203489e+00 -1.24487994881395e-02 + 23 3.20991819543127e+00 -1.24396727817251e-02 + 24 3.20781505843291e+00 -1.24312602337316e-02 + 25 3.20598171478412e+00 -1.24239268591365e-02 + 26 3.20448791608644e+00 -1.24179516643458e-02 + 27 3.20337970617851e+00 -1.24135188247141e-02 + 28 3.20267925357806e+00 -1.24107170143122e-02 + 29 3.20238627243809e+00 -1.24095450897524e-02 + 30 3.20248061261333e+00 -1.24099224504533e-02 + 31 3.20292564245608e+00 -1.24117025698243e-02 + 32 3.20367227047127e+00 -1.24146890818851e-02 + 33 3.20466343238851e+00 -1.24186537295541e-02 + 34 3.20583882862542e+00 -1.24233553145017e-02 + 35 3.20713949286431e+00 -1.24285579714572e-02 + 36 3.20851174687611e+00 -1.24340469875045e-02 + 37 3.20991022040763e+00 -1.24396408816305e-02 + 38 3.21129989298713e+00 -1.24451995719485e-02 + 39 3.21265730714637e+00 -1.24506292285855e-02 + 40 3.21397114765047e+00 -1.24558845906019e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force index ac92ca14c..1a0e24a9e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.force @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 4.72514253816199e+00 + 3.25000000000000e+00 4.72514255041972e+00 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf index 9c98fb5a6..8cf383c9e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.harmonic1.ti.pmf @@ -1,11 +1,11 @@ # xi A(xi) - 0 2.362571269081 - 0.5 2.362571269081 - 1 2.362571269081 - 1.5 2.362571269081 - 2 2.362571269081 - 2.5 2.362571269081 - 3 2.362571269081 + 0 2.3625712752095 + 0.5 2.3625712752095 + 1 2.3625712752095 + 1.5 2.3625712752095 + 2 2.3625712752095 + 2.5 2.3625712752095 + 3 2.3625712752095 3.5 0 4 0 4.5 0 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-fixed-ti/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out index 001440131..71d7e2285 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,27 +125,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped index fec1e803e..9eef8b44e 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685399817416e+00 + x 3.21685399835649e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj index 2cd06ea2b..5a6aa23cd 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.24221869387334e-02 - 1 3.20437138788600e+00 -1.24174855515440e-02 - 2 3.20383990619069e+00 -1.24153596247627e-02 - 3 3.20396636246577e+00 -1.24158654498631e-02 - 4 3.20472667451135e+00 -1.24189066980454e-02 - 5 3.20606076201392e+00 -1.24242430480557e-02 - 6 3.20787658911377e+00 -1.24315063564551e-02 - 7 3.21005554471991e+00 -1.24402221788797e-02 - 8 3.21245889756338e+00 -1.24498355902535e-02 - 9 3.21493536145531e+00 -1.24597414458212e-02 - 10 3.21732987841907e+00 -1.24693195136763e-02 - 11 3.21949341085340e+00 -1.24779736434136e-02 - 12 3.22129300871542e+00 -1.24851720348617e-02 - 13 3.22262098892565e+00 -1.24904839557026e-02 - 14 3.22340199249676e+00 -1.24936079699870e-02 - 15 3.22359705866319e+00 -1.24943882346527e-02 - 16 3.22320445228234e+00 -1.24928178091294e-02 - 17 3.22225759131848e+00 -1.24890303652739e-02 - 18 3.22082078894448e+00 -1.24832831557779e-02 - 19 3.21898355436871e+00 -1.24759342174748e-02 - 20 3.21685399817416e+00 -1.24674159926967e-02 + 1 3.20437138788661e+00 -1.24174855515465e-02 + 2 3.20383990624489e+00 -1.24153596249795e-02 + 3 3.20396636247331e+00 -1.24158654498932e-02 + 4 3.20472667455914e+00 -1.24189066982366e-02 + 5 3.20606076201901e+00 -1.24242430480760e-02 + 6 3.20787658913293e+00 -1.24315063565317e-02 + 7 3.21005554475517e+00 -1.24402221790207e-02 + 8 3.21245889761578e+00 -1.24498355904631e-02 + 9 3.21493536152545e+00 -1.24597414461018e-02 + 10 3.21732987850678e+00 -1.24693195140271e-02 + 11 3.21949341095784e+00 -1.24779736438313e-02 + 12 3.22129300883514e+00 -1.24851720353406e-02 + 13 3.22262098905883e+00 -1.24904839562353e-02 + 14 3.22340199264132e+00 -1.24936079705653e-02 + 15 3.22359705881703e+00 -1.24943882352681e-02 + 16 3.22320445244359e+00 -1.24928178097743e-02 + 17 3.22225759148518e+00 -1.24890303659407e-02 + 18 3.22082078911634e+00 -1.24832831564654e-02 + 19 3.21898355455034e+00 -1.24759342182014e-02 + 20 3.21685399835649e+00 -1.24674159934260e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out index fcf2bfa9e..f795a4bf4 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,32 +125,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 086f80ad0..ba9e5b167 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397114716924e+00 + x 3.21397114764396e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 8924671f5..d18eb0fa7 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685399817416e+00 -1.24674159926967e-02 - 21 3.21455164841394e+00 -1.24582065936557e-02 - 22 3.21219987179556e+00 -1.24487994871822e-02 - 23 3.20991819517487e+00 -1.24396727806995e-02 - 24 3.20781505815938e+00 -1.24312602326375e-02 - 25 3.20598171449351e+00 -1.24239268579740e-02 - 26 3.20448791577891e+00 -1.24179516631157e-02 - 27 3.20337970585434e+00 -1.24135188234173e-02 - 28 3.20267925323760e+00 -1.24107170129504e-02 - 29 3.20238627208178e+00 -1.24095450883271e-02 - 30 3.20248061224166e+00 -1.24099224489666e-02 - 31 3.20292564206961e+00 -1.24117025682784e-02 - 32 3.20367227007056e+00 -1.24146890802823e-02 - 33 3.20466343197421e+00 -1.24186537278969e-02 - 34 3.20583882819824e+00 -1.24233553127930e-02 - 35 3.20713949242506e+00 -1.24285579697002e-02 - 36 3.20851174642574e+00 -1.24340469857030e-02 - 37 3.20991021994729e+00 -1.24396408797892e-02 - 38 3.21129989251817e+00 -1.24451995700727e-02 - 39 3.21265730667037e+00 -1.24506292266815e-02 - 40 3.21397114716924e+00 -1.24558845886769e-02 + 20 3.21685399835649e+00 -1.24674159934260e-02 + 21 3.21455164860269e+00 -1.24582065944107e-02 + 22 3.21219987199261e+00 -1.24487994879705e-02 + 23 3.20991819538261e+00 -1.24396727815305e-02 + 24 3.20781505838050e+00 -1.24312602335220e-02 + 25 3.20598171473079e+00 -1.24239268589232e-02 + 26 3.20448791603500e+00 -1.24179516641400e-02 + 27 3.20337970613153e+00 -1.24135188245261e-02 + 28 3.20267925353770e+00 -1.24107170141508e-02 + 29 3.20238627240592e+00 -1.24095450896237e-02 + 30 3.20248061259023e+00 -1.24099224503609e-02 + 31 3.20292564244219e+00 -1.24117025697688e-02 + 32 3.20367227046597e+00 -1.24146890818639e-02 + 33 3.20466343239054e+00 -1.24186537295621e-02 + 34 3.20583882863293e+00 -1.24233553145317e-02 + 35 3.20713949287508e+00 -1.24285579715003e-02 + 36 3.20851174688770e+00 -1.24340469875508e-02 + 37 3.20991022041763e+00 -1.24396408816705e-02 + 38 3.21129989299330e+00 -1.24451995719732e-02 + 39 3.21265730714688e+00 -1.24506292285875e-02 + 40 3.21397114764396e+00 -1.24558845905758e-02 diff --git a/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out index eebcebec0..f64f6efa8 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,27 +131,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped index 6d65b453d..4507a2d83 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687020497026e+00 + x 3.21687020515258e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj index a79591894..f58ff8ba4 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 - 1 3.20437138788600e+00 -1.12999118519050e-02 1.75395615193440e-02 - 2 3.20383992333029e+00 -1.01805949485234e-02 1.57994685222408e-02 - 3 3.20396643077894e+00 -9.06358197787450e-03 1.40665271009677e-02 - 4 3.20472684448397e+00 -7.94810072187895e-03 1.23383408369400e-02 - 5 3.20606109997218e+00 -6.83333441993879e-03 1.06123771124364e-02 - 6 3.20787717647453e+00 -5.71849400471313e-03 8.88618850052717e-03 - 7 3.21005647713329e+00 -4.60288358615728e-03 7.15761395530948e-03 - 8 3.21246028397626e+00 -3.48595551805342e-03 5.42494905082458e-03 - 9 3.21493732312431e+00 -2.36735236557448e-03 3.68707712025729e-03 - 10 3.21733254790344e+00 -1.24693301916138e-03 1.94355244284363e-03 - 11 3.21949693102052e+00 -1.24779877240821e-03 1.94625222052929e-03 - 12 3.22129751453369e+00 -1.24851900581348e-03 1.94849963484684e-03 - 13 3.22262660677352e+00 -1.24905064270941e-03 1.95015938506598e-03 - 14 3.22340883978115e+00 -1.24936353591246e-03 1.95113655608461e-03 - 15 3.22360524373761e+00 -1.24944209749504e-03 1.95138194374102e-03 - 16 3.22321407463655e+00 -1.24928562985462e-03 1.95089323120157e-03 - 17 3.22226874199272e+00 -1.24890749679709e-03 1.94971241944496e-03 - 18 3.22083355111441e+00 -1.24833342044576e-03 1.94792041075227e-03 - 19 3.21899800404481e+00 -1.24759920161792e-03 1.94562970984710e-03 - 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 + 1 3.20437138788661e+00 -1.12999118519073e-02 1.75395615193509e-02 + 2 3.20383992338449e+00 -1.01805949487011e-02 1.57994685227925e-02 + 3 3.20396643078647e+00 -9.06358197789650e-03 1.40665271010360e-02 + 4 3.20472684453174e+00 -7.94810072200125e-03 1.23383408373197e-02 + 5 3.20606109997726e+00 -6.83333441994998e-03 1.06123771124712e-02 + 6 3.20787717649369e+00 -5.71849400474838e-03 8.88618850063674e-03 + 7 3.21005647716855e+00 -4.60288358620946e-03 7.15761395547176e-03 + 8 3.21246028402867e+00 -3.48595551811211e-03 5.42494905100725e-03 + 9 3.21493732319445e+00 -2.36735236562779e-03 3.68707712042334e-03 + 10 3.21733254799115e+00 -1.24693301919646e-03 1.94355244295300e-03 + 11 3.21949693112495e+00 -1.24779877244998e-03 1.94625222065960e-03 + 12 3.22129751465341e+00 -1.24851900586136e-03 1.94849963499631e-03 + 13 3.22262660690669e+00 -1.24905064276268e-03 1.95015938523232e-03 + 14 3.22340883992570e+00 -1.24936353597028e-03 1.95113655626521e-03 + 15 3.22360524389145e+00 -1.24944209755658e-03 1.95138194393324e-03 + 16 3.22321407479779e+00 -1.24928562991912e-03 1.95089323140301e-03 + 17 3.22226874215941e+00 -1.24890749686377e-03 1.94971241965315e-03 + 18 3.22083355128627e+00 -1.24833342051451e-03 1.94792041096681e-03 + 19 3.21899800422646e+00 -1.24759920169058e-03 1.94562971007373e-03 + 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out index 01867c7f6..c2057ff6d 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,32 +131,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped index 226b212c1..32715071f 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21402990668451e+00 + x 3.21402990715919e+00 } restraint { diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj index 2753d1963..0970380b3 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 - 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 - 21 3.21456967632931e+00 -1.24582787053172e-03 1.94010885374201e-03 - 22 3.21221977994646e+00 -1.24488791197858e-03 1.93718239173800e-03 - 23 3.20994003840243e+00 -1.24397601536097e-03 1.93434540849171e-03 - 24 3.20783888746925e+00 -1.24313555498770e-03 1.93173251009322e-03 - 25 3.20600757726167e+00 -1.24240303090467e-03 1.92945661400138e-03 - 26 3.20451585575643e+00 -1.24180634230257e-03 1.92760373972862e-03 - 27 3.20340976294734e+00 -1.24136390517894e-03 1.92623043135138e-03 - 28 3.20271146313867e+00 -1.24108458525547e-03 1.92536368469842e-03 - 29 3.20242066576110e+00 -1.24096826630444e-03 1.92500279746831e-03 - 30 3.20251721536965e+00 -1.24100688614786e-03 1.92512261433301e-03 - 31 3.20296447447623e+00 -1.24118578979049e-03 1.92567770597231e-03 - 32 3.20371334530005e+00 -1.24148533812002e-03 1.92660730595873e-03 - 33 3.20470675696420e+00 -1.24188270278568e-03 1.92784080934784e-03 - 34 3.20588440315285e+00 -1.24235376126114e-03 1.92930358514962e-03 - 35 3.20718731103156e+00 -1.24287492441263e-03 1.93092259716711e-03 - 36 3.20856179628928e+00 -1.24342471851571e-03 1.93263128826985e-03 - 37 3.20996248338009e+00 -1.24398499335204e-03 1.93437332960633e-03 - 38 3.21135434749032e+00 -1.24454173899613e-03 1.93610517512938e-03 - 39 3.21271392780555e+00 -1.24508557112222e-03 1.93779759927093e-03 - 40 3.21402990668451e+00 -1.24561196267380e-03 1.93943645194510e-03 + 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 + 21 3.21456967651805e+00 -1.24582787060722e-03 1.94010885397715e-03 + 22 3.21221978014351e+00 -1.24488791205741e-03 1.93718239198331e-03 + 23 3.20994003861018e+00 -1.24397601544407e-03 1.93434540875013e-03 + 24 3.20783888769037e+00 -1.24313555507615e-03 1.93173251036810e-03 + 25 3.20600757749894e+00 -1.24240303099958e-03 1.92945661429617e-03 + 26 3.20451585601250e+00 -1.24180634240500e-03 1.92760374004661e-03 + 27 3.20340976322452e+00 -1.24136390528981e-03 1.92623043169546e-03 + 28 3.20271146343875e+00 -1.24108458537550e-03 1.92536368507084e-03 + 29 3.20242066608521e+00 -1.24096826643409e-03 1.92500279787052e-03 + 30 3.20251721571819e+00 -1.24100688628728e-03 1.92512261476555e-03 + 31 3.20296447484878e+00 -1.24118578993951e-03 1.92567770643472e-03 + 32 3.20371334569543e+00 -1.24148533827817e-03 1.92660730644958e-03 + 33 3.20470675738049e+00 -1.24188270295219e-03 1.92784080986481e-03 + 34 3.20588440358750e+00 -1.24235376143500e-03 1.92930358568961e-03 + 35 3.20718731148154e+00 -1.24287492459262e-03 1.93092259772638e-03 + 36 3.20856179675119e+00 -1.24342471870048e-03 1.93263128884420e-03 + 37 3.20996248385038e+00 -1.24398499354015e-03 1.93437333019136e-03 + 38 3.21135434796541e+00 -1.24454173918616e-03 1.93610517572065e-03 + 39 3.21271392828201e+00 -1.24508557131280e-03 1.93779759986417e-03 + 40 3.21402990715919e+00 -1.24561196286367e-03 1.93943645253637e-03 diff --git a/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt b/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance-grid_harmonic-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out index 151617c95..2cb8b2826 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -127,27 +123,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Histogram colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped index f1f122306..48987f05a 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253464583e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj index a3529376d..2d1d01de3 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 0.00000000000000e+00 + 11 3.21950367383415e+00 0.00000000000000e+00 + 12 3.22130499858006e+00 0.00000000000000e+00 + 13 3.22263479496346e+00 0.00000000000000e+00 + 14 3.22341769665784e+00 0.00000000000000e+00 + 15 3.22361473677138e+00 0.00000000000000e+00 + 16 3.22322417514557e+00 0.00000000000000e+00 + 17 3.22227942564879e+00 0.00000000000000e+00 + 18 3.22084479803044e+00 0.00000000000000e+00 + 19 3.21900979846930e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat index 6ff3132f9..1b0ff42d4 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 6.00000000000000e-01 2.00000000000000e-01 24 0 +# 0.6 0.2 24 0 - 7.00000000000000e-01 0.00000000000000e+00 - 9.00000000000000e-01 0.00000000000000e+00 - 1.10000000000000e+00 0.00000000000000e+00 - 1.30000000000000e+00 0.00000000000000e+00 - 1.50000000000000e+00 0.00000000000000e+00 - 1.70000000000000e+00 0.00000000000000e+00 - 1.90000000000000e+00 0.00000000000000e+00 - 2.10000000000000e+00 0.00000000000000e+00 - 2.30000000000000e+00 0.00000000000000e+00 - 2.50000000000000e+00 0.00000000000000e+00 - 2.70000000000000e+00 0.00000000000000e+00 - 2.90000000000000e+00 0.00000000000000e+00 - 3.10000000000000e+00 0.00000000000000e+00 - 3.30000000000000e+00 2.00000000000000e+01 - 3.50000000000000e+00 0.00000000000000e+00 - 3.70000000000000e+00 0.00000000000000e+00 - 3.90000000000000e+00 0.00000000000000e+00 - 4.10000000000000e+00 0.00000000000000e+00 - 4.30000000000000e+00 0.00000000000000e+00 - 4.50000000000000e+00 0.00000000000000e+00 - 4.70000000000000e+00 0.00000000000000e+00 - 4.90000000000000e+00 0.00000000000000e+00 - 5.10000000000000e+00 0.00000000000000e+00 - 5.30000000000000e+00 0.00000000000000e+00 + 0.7 0 + 0.9 0 + 1.1 0 + 1.3 0 + 1.5 0 + 1.7 0 + 1.9 0 + 2.1 0 + 2.3 0 + 2.5 0 + 2.7 0 + 2.9 0 + 3.1 0 + 3.3 20 + 3.5 0 + 3.7 0 + 3.9 0 + 4.1 0 + 4.3 0 + 4.5 0 + 4.7 0 + 4.9 0 + 5.1 0 + 5.3 0 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out index a72b72b3d..231ed2e71 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -127,32 +123,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Histogram colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting histogram bias "histogram1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped index 7ca010783..35abb4af3 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878547144e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj index 9c9860479..58d908160 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253444007e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 + 21 3.21458253157603e+00 0.00000000000000e+00 + 22 3.21223315254029e+00 0.00000000000000e+00 + 23 3.20995392032979e+00 0.00000000000000e+00 + 24 3.20785326966943e+00 0.00000000000000e+00 + 25 3.20602244845117e+00 0.00000000000000e+00 + 26 3.20453120146139e+00 0.00000000000000e+00 + 27 3.20342556480347e+00 0.00000000000000e+00 + 28 3.20272769852622e+00 0.00000000000000e+00 + 29 3.20243730776714e+00 0.00000000000000e+00 + 30 3.20253423308456e+00 0.00000000000000e+00 + 31 3.20298183362156e+00 0.00000000000000e+00 + 32 3.20373100914607e+00 0.00000000000000e+00 + 33 3.20472468746373e+00 0.00000000000000e+00 + 34 3.20590256221113e+00 0.00000000000000e+00 + 35 3.20720566184671e+00 0.00000000000000e+00 + 36 3.20858030459458e+00 0.00000000000000e+00 + 37 3.20998111854285e+00 0.00000000000000e+00 + 38 3.21137308334418e+00 0.00000000000000e+00 + 39 3.21273274315657e+00 0.00000000000000e+00 + 40 3.21404878547144e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat index 686fae912..2a16dc5f6 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 6.00000000000000e-01 2.00000000000000e-01 24 0 +# 0.6 0.2 24 0 - 7.00000000000000e-01 0.00000000000000e+00 - 9.00000000000000e-01 0.00000000000000e+00 - 1.10000000000000e+00 0.00000000000000e+00 - 1.30000000000000e+00 0.00000000000000e+00 - 1.50000000000000e+00 0.00000000000000e+00 - 1.70000000000000e+00 0.00000000000000e+00 - 1.90000000000000e+00 0.00000000000000e+00 - 2.10000000000000e+00 0.00000000000000e+00 - 2.30000000000000e+00 0.00000000000000e+00 - 2.50000000000000e+00 0.00000000000000e+00 - 2.70000000000000e+00 0.00000000000000e+00 - 2.90000000000000e+00 0.00000000000000e+00 - 3.10000000000000e+00 0.00000000000000e+00 - 3.30000000000000e+00 4.00000000000000e+01 - 3.50000000000000e+00 0.00000000000000e+00 - 3.70000000000000e+00 0.00000000000000e+00 - 3.90000000000000e+00 0.00000000000000e+00 - 4.10000000000000e+00 0.00000000000000e+00 - 4.30000000000000e+00 0.00000000000000e+00 - 4.50000000000000e+00 0.00000000000000e+00 - 4.70000000000000e+00 0.00000000000000e+00 - 4.90000000000000e+00 0.00000000000000e+00 - 5.10000000000000e+00 0.00000000000000e+00 - 5.30000000000000e+00 0.00000000000000e+00 + 0.7 0 + 0.9 0 + 1.1 0 + 1.3 0 + 1.5 0 + 1.7 0 + 1.9 0 + 2.1 0 + 2.3 0 + 2.5 0 + 2.7 0 + 2.9 0 + 3.1 0 + 3.3 40 + 3.5 0 + 3.7 0 + 3.9 0 + 4.1 0 + 4.3 0 + 4.5 0 + 4.7 0 + 4.9 0 + 5.1 0 + 5.3 0 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt b/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out index d6add8f3d..5d2854533 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -124,27 +120,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Histogram colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped index ccbc01c61..a717bee50 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253464583e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj index a3529376d..2d1d01de3 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 0.00000000000000e+00 + 11 3.21950367383415e+00 0.00000000000000e+00 + 12 3.22130499858006e+00 0.00000000000000e+00 + 13 3.22263479496346e+00 0.00000000000000e+00 + 14 3.22341769665784e+00 0.00000000000000e+00 + 15 3.22361473677138e+00 0.00000000000000e+00 + 16 3.22322417514557e+00 0.00000000000000e+00 + 17 3.22227942564879e+00 0.00000000000000e+00 + 18 3.22084479803044e+00 0.00000000000000e+00 + 19 3.21900979846930e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat index 69e912676..09d19a2d1 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.histogram1.dat @@ -1,23 +1,23 @@ # 1 -# 0.00000000000000e+00 5.00000000000000e-01 20 0 +# 0 0.5 20 0 - 2.50000000000000e-01 0.00000000000000e+00 - 7.50000000000000e-01 0.00000000000000e+00 - 1.25000000000000e+00 0.00000000000000e+00 - 1.75000000000000e+00 0.00000000000000e+00 - 2.25000000000000e+00 0.00000000000000e+00 - 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 2.00000000000000e+01 - 3.75000000000000e+00 0.00000000000000e+00 - 4.25000000000000e+00 0.00000000000000e+00 - 4.75000000000000e+00 0.00000000000000e+00 - 5.25000000000000e+00 0.00000000000000e+00 - 5.75000000000000e+00 0.00000000000000e+00 - 6.25000000000000e+00 0.00000000000000e+00 - 6.75000000000000e+00 0.00000000000000e+00 - 7.25000000000000e+00 0.00000000000000e+00 - 7.75000000000000e+00 0.00000000000000e+00 - 8.25000000000000e+00 0.00000000000000e+00 - 8.75000000000000e+00 0.00000000000000e+00 - 9.25000000000000e+00 0.00000000000000e+00 - 9.75000000000000e+00 0.00000000000000e+00 + 0.25 0 + 0.75 0 + 1.25 0 + 1.75 0 + 2.25 0 + 2.75 0 + 3.25 20 + 3.75 0 + 4.25 0 + 4.75 0 + 5.25 0 + 5.75 0 + 6.25 0 + 6.75 0 + 7.25 0 + 7.75 0 + 8.25 0 + 8.75 0 + 9.25 0 + 9.75 0 diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out index a9d49b469..091d85f52 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -124,32 +120,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Histogram colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting histogram bias "histogram1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped index 0a3fe4f9c..6df06ad1d 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878547144e+00 } histogram { diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj index 9c9860479..58d908160 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253444007e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 + 21 3.21458253157603e+00 0.00000000000000e+00 + 22 3.21223315254029e+00 0.00000000000000e+00 + 23 3.20995392032979e+00 0.00000000000000e+00 + 24 3.20785326966943e+00 0.00000000000000e+00 + 25 3.20602244845117e+00 0.00000000000000e+00 + 26 3.20453120146139e+00 0.00000000000000e+00 + 27 3.20342556480347e+00 0.00000000000000e+00 + 28 3.20272769852622e+00 0.00000000000000e+00 + 29 3.20243730776714e+00 0.00000000000000e+00 + 30 3.20253423308456e+00 0.00000000000000e+00 + 31 3.20298183362156e+00 0.00000000000000e+00 + 32 3.20373100914607e+00 0.00000000000000e+00 + 33 3.20472468746373e+00 0.00000000000000e+00 + 34 3.20590256221113e+00 0.00000000000000e+00 + 35 3.20720566184671e+00 0.00000000000000e+00 + 36 3.20858030459458e+00 0.00000000000000e+00 + 37 3.20998111854285e+00 0.00000000000000e+00 + 38 3.21137308334418e+00 0.00000000000000e+00 + 39 3.21273274315657e+00 0.00000000000000e+00 + 40 3.21404878547144e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat index fe4ddc2fd..544c0ba33 100644 --- a/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram/AutoDiff/test.restart.histogram1.dat @@ -1,23 +1,23 @@ # 1 -# 0.00000000000000e+00 5.00000000000000e-01 20 0 +# 0 0.5 20 0 - 2.50000000000000e-01 0.00000000000000e+00 - 7.50000000000000e-01 0.00000000000000e+00 - 1.25000000000000e+00 0.00000000000000e+00 - 1.75000000000000e+00 0.00000000000000e+00 - 2.25000000000000e+00 0.00000000000000e+00 - 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 4.00000000000000e+01 - 3.75000000000000e+00 0.00000000000000e+00 - 4.25000000000000e+00 0.00000000000000e+00 - 4.75000000000000e+00 0.00000000000000e+00 - 5.25000000000000e+00 0.00000000000000e+00 - 5.75000000000000e+00 0.00000000000000e+00 - 6.25000000000000e+00 0.00000000000000e+00 - 6.75000000000000e+00 0.00000000000000e+00 - 7.25000000000000e+00 0.00000000000000e+00 - 7.75000000000000e+00 0.00000000000000e+00 - 8.25000000000000e+00 0.00000000000000e+00 - 8.75000000000000e+00 0.00000000000000e+00 - 9.25000000000000e+00 0.00000000000000e+00 - 9.75000000000000e+00 0.00000000000000e+00 + 0.25 0 + 0.75 0 + 1.25 0 + 1.75 0 + 2.25 0 + 2.75 0 + 3.25 40 + 3.75 0 + 4.25 0 + 4.75 0 + 5.25 0 + 5.75 0 + 6.25 0 + 6.75 0 + 7.25 0 + 7.75 0 + 8.25 0 + 8.75 0 + 9.25 0 + 9.75 0 diff --git a/namd/tests/library/000_distance-grid_histogram/namd-version.txt b/namd/tests/library/000_distance-grid_histogram/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_histogram/namd-version.txt +++ b/namd/tests/library/000_distance-grid_histogram/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj index dd7940783..6a779c875 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.metadynamics1.hills.traj @@ -1,2 +1,2 @@ - 10 3.21733851230199e+00 7.50000000000000e-01 1.00000000000000e-02 - 20 3.21688297506098e+00 7.50000000000000e-01 1.00000000000000e-02 + 10 3.21733851236362e+00 7.50000000000000e-01 1.00000000000000e-02 + 20 3.21688297526674e+00 7.50000000000000e-01 1.00000000000000e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out index 2c566b0cb..2404d2e37 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -141,26 +141,10 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped index e88987e94..908bf7241 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688297506098e+00 + x 3.21688297526674e+00 } metadynamics { @@ -22,11 +22,11 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 7.98796537769059e-06 8.94022105552033e-05 6.41564889800856e-04 - 2.95197835228273e-03 8.70895398689607e-03 1.64740003814156e-02 - 1.99807780437246e-02 1.55383881988653e-02 7.74782472299776e-03 - 2.47704476502647e-03 5.07771324547938e-04 6.67394672185917e-05 - 5.62441745710086e-06 3.03915330422993e-07 0.00000000000000e+00 + 7.98796537205394e-06 8.94022105027543e-05 6.41564889500790e-04 + 2.95197835125314e-03 8.70895398489406e-03 1.64740003795870e-02 + 1.99807780438813e-02 1.55383882008336e-02 7.74782472489960e-03 + 2.47704476592871e-03 5.07771324793184e-04 6.67394672587493e-05 + 5.62441746115269e-06 3.03915330677999e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients @@ -37,23 +37,23 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 4.21354234780051e-05 3.92115793470621e-04 2.24360723751294e-03 - 7.69934001123311e-03 1.49733727825032e-02 1.36803233064121e-02 - -1.16827176873810e-03 -1.47204255431243e-02 -1.42269229833801e-02 - -6.75028436894966e-03 -1.83509826691184e-03 -3.00522069155109e-04 - -3.03257488096648e-05 -1.90879841183335e-06 0.00000000000000e+00 + 4.21354234501736e-05 3.92115793261853e-04 2.24360723661620e-03 + 7.69934000924979e-03 1.49733727811320e-02 1.36803233088098e-02 + -1.16827176399835e-03 -1.47204255412967e-02 -1.42269229850317e-02 + -6.75028437082004e-03 -1.83509826767759e-03 -3.00522069320091e-04 + -3.03257488301764e-05 -1.90879841336284e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 hill { step 10 weight 1.00000000000000e-02 - centers 3.21733851230199e+00 + centers 3.21733851236362e+00 widths 1.50000000000000e+00 } hill { step 20 weight 1.00000000000000e-02 - centers 3.21688297506098e+00 + centers 3.21688297526674e+00 widths 1.50000000000000e+00 } } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj index dedaa4935..5824ebe05 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 5.80098335424304e-04 - 11 3.21950368266856e+00 5.80098335424304e-04 - 12 3.22130502510728e+00 5.80098335424304e-04 - 13 3.22263484775629e+00 5.80098335424304e-04 - 14 3.22341778396123e+00 5.80098335424304e-04 - 15 3.22361486641320e+00 5.80098335424304e-04 - 16 3.22322435446593e+00 5.80098335424304e-04 - 17 3.22227966145053e+00 5.80098335424304e-04 - 18 3.22084509655195e+00 5.80098335424304e-04 - 19 3.21901016537961e+00 5.80098335424304e-04 - 20 3.21688297506098e+00 1.16827176873810e-03 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 5.80098334331777e-04 + 11 3.21950368274213e+00 5.80098334331777e-04 + 12 3.22130502519349e+00 5.80098334331777e-04 + 13 3.22263484785580e+00 5.80098334331777e-04 + 14 3.22341778407457e+00 5.80098334331777e-04 + 15 3.22361486654089e+00 5.80098334331777e-04 + 16 3.22322435460843e+00 5.80098334331777e-04 + 17 3.22227966160826e+00 5.80098334331777e-04 + 18 3.22084509672532e+00 5.80098334331777e-04 + 19 3.21901016556900e+00 5.80098334331777e-04 + 20 3.21688297526674e+00 1.16827176399835e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf index 9d98a1715..9da766ced 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.99727900783469e-02 - 7.50000000000000e-01 1.98913758331694e-02 - 1.25000000000000e+00 1.93392131539237e-02 - 1.75000000000000e+00 1.70287996914418e-02 - 2.25000000000000e+00 1.12718240568285e-02 - 2.75000000000000e+00 3.50677766230894e-03 + 2.50000000000000e-01 1.99727900785093e-02 + 7.50000000000000e-01 1.98913758333786e-02 + 1.25000000000000e+00 1.93392131543806e-02 + 1.75000000000000e+00 1.70287996926282e-02 + 2.25000000000000e+00 1.12718240589873e-02 + 2.75000000000000e+00 3.50677766429439e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 4.44238984485923e-03 - 4.25000000000000e+00 1.22329533207268e-02 - 4.75000000000000e+00 1.75037332786981e-02 - 5.25000000000000e+00 1.94730067191766e-02 - 5.75000000000000e+00 1.99140385765060e-02 - 6.25000000000000e+00 1.99751536262675e-02 - 6.75000000000000e+00 1.99804741283941e-02 - 7.25000000000000e+00 1.99807780437246e-02 - 7.75000000000000e+00 1.99807780437246e-02 - 8.25000000000000e+00 1.99807780437246e-02 - 8.75000000000000e+00 1.99807780437246e-02 - 9.25000000000000e+00 1.99807780437246e-02 - 9.75000000000000e+00 1.99807780437246e-02 + 3.75000000000000e+00 4.44238984304775e-03 + 4.25000000000000e+00 1.22329533189817e-02 + 4.75000000000000e+00 1.75037332779526e-02 + 5.25000000000000e+00 1.94730067190882e-02 + 5.75000000000000e+00 1.99140385766226e-02 + 6.25000000000000e+00 1.99751536264202e-02 + 6.75000000000000e+00 1.99804741285507e-02 + 7.25000000000000e+00 1.99807780438813e-02 + 7.75000000000000e+00 1.99807780438813e-02 + 8.25000000000000e+00 1.99807780438813e-02 + 8.75000000000000e+00 1.99807780438813e-02 + 9.25000000000000e+00 1.99807780438813e-02 + 9.75000000000000e+00 1.99807780438813e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj index bf802816e..d357d6751 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.metadynamics1.hills.traj @@ -1,2 +1,2 @@ - 30 3.20253726770953e+00 2.00000000000000e+00 1.00000000000000e-14 - 40 3.21405662873448e+00 2.00000000000000e+00 1.00000000000000e-14 + 30 3.20253726808121e+00 2.00000000000000e+00 1.00000000000000e-14 + 40 3.21405662921571e+00 2.00000000000000e+00 1.00000000000000e-14 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out index 25e53b613..3b6b317a8 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.restart.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -139,28 +139,12 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: This state file/stream contains explicit hills. colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 2 additional explicit hills. +colvars: Read 2 hills. colvars: Rebinning the energy and forces grids from 2 hills (this may take a while)... colvars: 0.00% done. colvars: 100.00% done. @@ -170,7 +154,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped index f3ae76614..23fdc9ae2 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405662873448e+00 + x 3.21405662921571e+00 } metadynamics { @@ -22,25 +22,25 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 3.72168800988033e-04 7.62454155222791e-04 1.45480353465099e-03 - 2.58530507810761e-03 4.27893895388223e-03 6.59594797702447e-03 - 9.46967757657534e-03 1.26622243130771e-02 1.57689092191951e-02 - 1.82898499605756e-02 1.97576583941589e-02 1.98782268062245e-02 - 1.86267313298802e-02 1.62559553963231e-02 1.32131141593403e-02 - 1.00026417641938e-02 7.05246732783860e-03 4.63110140045852e-03 - 2.83233316189597e-03 1.61332262367653e-03 8.55884084142272e-04 - 4.22888150792485e-04 1.94604519590907e-04 8.34059758230608e-05 - 3.32934080094220e-05 1.23775924288879e-05 4.28579055102484e-06 - 1.38210980597084e-06 4.15117455025274e-07 3.64063576668077e-15 - 3.01191095861938e-15 2.46697141353276e-15 2.00052137786274e-15 - 1.60612509381090e-15 1.27665229269180e-15 1.00466895561231e-15 - 7.82763248881975e-16 6.03802577686049e-16 4.61122792884764e-16 - 3.48654526190564e-16 2.60994356544342e-16 1.93430082535114e-16 - 1.41929936582350e-16 1.03105324043511e-16 7.41558240772166e-17 - 5.28039645304659e-17 3.72258726281876e-17 2.59824640226949e-17 - 1.79544817286721e-17 1.22835105542170e-17 8.32011299530226e-18 - 5.57947115673577e-18 3.70436643439502e-18 2.43496058203075e-18 - 1.58462688892833e-18 + 3.72168800800684e-04 7.62454154875249e-04 1.45480353405707e-03 + 2.58530507717515e-03 4.27893895254244e-03 6.59594797527291e-03 + 9.46967757451101e-03 1.26622243109190e-02 1.57689092172573e-02 + 1.82898499591976e-02 1.97576583936095e-02 1.98782268066167e-02 + 1.86267313311331e-02 1.62559553981891e-02 1.32131141614850e-02 + 1.00026417662927e-02 7.05246732965355e-03 4.63110140187036e-03 + 2.83233316289399e-03 1.61332262432165e-03 8.55884084525168e-04 + 4.22888151001758e-04 1.94604519696452e-04 8.34059758722572e-05 + 3.32934080306407e-05 1.23775924373641e-05 4.28579055416322e-06 + 1.38210980704854e-06 4.15117455368664e-07 3.64063576811435e-15 + 3.01191095986970e-15 2.46697141460954e-15 2.00052137877865e-15 + 1.60612509458054e-15 1.27665229333083e-15 1.00466895613666e-15 + 7.82763249307229e-16 6.03802578026978e-16 4.61122793154982e-16 + 3.48654526402326e-16 2.60994356708439e-16 1.93430082660864e-16 + 1.41929936677652e-16 1.03105324114947e-16 7.41558241301806e-17 + 5.28039645693086e-17 3.72258726563668e-17 2.59824640429186e-17 + 1.79544817430310e-17 1.22835105643033e-17 8.32011300231200e-18 + 5.57947116155582e-18 3.70436643767441e-18 2.43496058423845e-18 + 1.58462689039896e-18 hills_energy_gradients grid_parameters { n_colvars 1 @@ -49,47 +49,47 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 1.40075110105780e-03 2.59859363148452e-03 4.44099297579070e-03 - 6.97278888521528e-03 1.00192639073998e-02 1.30993843027639e-02 - 1.54395417665452e-02 1.61426066779483e-02 1.44964828823443e-02 - 1.03109464673752e-02 4.11348240807316e-03 -2.92922895099231e-03 - -9.36764744456861e-03 -1.39552453121627e-02 -1.60410539906239e-02 - -1.56999540158312e-02 -1.35769607030841e-02 -1.05621149930753e-02 - -7.46673071770275e-03 -4.82674321766440e-03 -2.86495075206286e-03 - -1.56591840826989e-03 -7.89796490686730e-04 -3.68156057181895e-04 - -1.58795588263100e-04 -6.34368443091680e-05 -2.34890958399494e-05 - -8.06633422230724e-06 -2.57032529393441e-06 -3.36000867643381e-15 - -2.93034146466045e-15 -2.52350768675858e-15 -2.14639312464089e-15 - -1.80354428877811e-15 -1.49740594580019e-15 -1.22862535955312e-15 - -9.96391242316789e-16 -7.98779361165857e-16 -6.33082111844533e-16 - -4.96105393301648e-16 -3.84422123590172e-16 -2.94577212993405e-16 - -2.23243402354083e-16 -1.67330898960416e-16 -1.24056159737195e-16 - -9.09765563814143e-17 -6.59981612906651e-17 -4.73637102529462e-17 - -3.36271325125033e-17 -2.36200830178057e-17 -1.64148291477159e-17 - -1.12867623434892e-17 -7.67881293566128e-18 -5.16919768249119e-18 - -3.44324803635265e-18 + 1.40075110044120e-03 2.59859363048141e-03 4.44099297432371e-03 + 6.97278888331524e-03 1.00192639052802e-02 1.30993843008538e-02 + 1.54395417654311e-02 1.61426066782075e-02 1.44964828843116e-02 + 1.03109464709461e-02 4.11348241265501e-03 -2.92922894632563e-03 + -9.36764744077205e-03 -1.39552453099017e-02 -1.60410539900880e-02 + -1.56999540167490e-02 -1.35769607049026e-02 -1.05621149951951e-02 + -7.46673071966103e-03 -4.82674321921130e-03 -2.86495075314130e-03 + -1.56591840894438e-03 -7.89796491068873e-04 -3.68156057379246e-04 + -1.58795588356400e-04 -6.34368443496714e-05 -2.34890958561326e-05 + -8.06633422826891e-06 -2.57032529596210e-06 -3.36000867736823e-15 + -2.93034146555533e-15 -2.52350768759663e-15 -2.14639312540996e-15 + -1.80354428947083e-15 -1.49740594641337e-15 -1.22862536008705e-15 + -9.96391242774491e-16 -7.98779361552378e-16 -6.33082112166259e-16 + -4.96105393565718e-16 -3.84422123803986e-16 -2.94577213164243e-16 + -2.23243402488820e-16 -1.67330899065332e-16 -1.24056159817874e-16 + -9.09765564426929e-17 -6.59981613366451e-17 -4.73637102870346e-17 + -3.36271325374767e-17 -2.36200830358874e-17 -1.64148291606559e-17 + -1.12867623526432e-17 -7.67881294206302e-18 -5.16919768691752e-18 + -3.44324803937870e-18 hill { step 10 weight 1.00000000000000e-02 - centers 3.21733851230199e+00 + centers 3.21733851236362e+00 widths 1.50000000000000e+00 } hill { step 20 weight 1.00000000000000e-02 - centers 3.21688297506098e+00 + centers 3.21688297526674e+00 widths 1.50000000000000e+00 } hill { step 30 weight 1.00000000000000e-14 - centers 3.20253726770953e+00 + centers 3.20253726808121e+00 widths 4.00000000000000e+00 } hill { step 40 weight 1.00000000000000e-14 - centers 3.21405662873448e+00 + centers 3.21405662921571e+00 widths 4.00000000000000e+00 } } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj index b775fab7c..05c21c5c1 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688297506098e+00 2.92922895099185e-03 - 21 3.21458307267896e+00 2.92922895099185e-03 - 22 3.21223383426493e+00 2.92922895099185e-03 - 23 3.20995478139232e+00 2.92922895099185e-03 - 24 3.20785434718462e+00 2.92922895099185e-03 - 25 3.20602377760800e+00 2.92922895099185e-03 - 26 3.20453281527191e+00 2.92922895099185e-03 - 27 3.20342749392972e+00 2.92922895099185e-03 - 28 3.20272997118845e+00 2.92922895099185e-03 - 29 3.20243994972914e+00 2.92922895099185e-03 - 30 3.20253726770953e+00 2.92922895099210e-03 - 31 3.20298528199370e+00 2.92922895099210e-03 - 32 3.20373489024518e+00 2.92922895099210e-03 - 33 3.20472901837284e+00 2.92922895099210e-03 - 34 3.20590735833942e+00 2.92922895099210e-03 - 35 3.20721093715982e+00 2.92922895099210e-03 - 36 3.20858607182116e+00 2.92922895099210e-03 - 37 3.20998738936608e+00 2.92922895099210e-03 - 38 3.21137986855483e+00 2.92922895099210e-03 - 39 3.21274005275856e+00 2.92922895099210e-03 - 40 3.21405662873448e+00 2.92922895099231e-03 + 20 3.21688297526674e+00 2.92922894632517e-03 + 21 3.21458307290139e+00 2.92922894632517e-03 + 22 3.21223383450427e+00 2.92922894632517e-03 + 23 3.20995478164873e+00 2.92922894632517e-03 + 24 3.20785434745816e+00 2.92922894632517e-03 + 25 3.20602377789862e+00 2.92922894632517e-03 + 26 3.20453281557945e+00 2.92922894632517e-03 + 27 3.20342749425391e+00 2.92922894632517e-03 + 28 3.20272997152892e+00 2.92922894632517e-03 + 29 3.20243995008546e+00 2.92922894632517e-03 + 30 3.20253726808121e+00 2.92922894632541e-03 + 31 3.20298528238019e+00 2.92922894632541e-03 + 32 3.20373489064589e+00 2.92922894632541e-03 + 33 3.20472901878714e+00 2.92922894632541e-03 + 34 3.20590735876660e+00 2.92922894632541e-03 + 35 3.20721093759908e+00 2.92922894632541e-03 + 36 3.20858607227153e+00 2.92922894632541e-03 + 37 3.20998738982642e+00 2.92922894632541e-03 + 38 3.21137986902379e+00 2.92922894632541e-03 + 39 3.21274005323456e+00 2.92922894632541e-03 + 40 3.21405662921571e+00 2.92922894632563e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf index 775f05da1..35289f537 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/AutoDiff/test.restart.pmf @@ -1,58 +1,58 @@ # 1 # 1.00000000000000e+00 2.00000000000000e-01 55 0 - 1.10000000000000e+00 1.95060580052365e-02 - 1.30000000000000e+00 1.91157726510017e-02 - 1.50000000000000e+00 1.84234232715735e-02 - 1.70000000000000e+00 1.72929217281169e-02 - 1.90000000000000e+00 1.55992878523423e-02 - 2.10000000000000e+00 1.32822788292000e-02 - 2.30000000000000e+00 1.04085492296491e-02 - 2.50000000000000e+00 7.21600249314737e-03 - 2.70000000000000e+00 4.10931758702936e-03 - 2.90000000000000e+00 1.58837684564884e-03 - 3.10000000000000e+00 1.20568412065550e-04 + 1.10000000000000e+00 1.95060580058160e-02 + 1.30000000000000e+00 1.91157726517414e-02 + 1.50000000000000e+00 1.84234232725596e-02 + 1.70000000000000e+00 1.72929217294415e-02 + 1.90000000000000e+00 1.55992878540742e-02 + 2.10000000000000e+00 1.32822788313438e-02 + 2.30000000000000e+00 1.04085492321057e-02 + 2.50000000000000e+00 7.21600249569771e-03 + 2.70000000000000e+00 4.10931758935941e-03 + 2.90000000000000e+00 1.58837684741911e-03 + 3.10000000000000e+00 1.20568413007130e-04 3.30000000000000e+00 -0.00000000000000e+00 - 3.50000000000000e+00 1.25149547634431e-03 - 3.70000000000000e+00 3.62227140990143e-03 - 3.90000000000000e+00 6.66511264688419e-03 - 4.10000000000000e+00 9.87558504203071e-03 - 4.30000000000000e+00 1.28257594783859e-02 - 4.50000000000000e+00 1.52471254057660e-02 - 4.70000000000000e+00 1.70458936443285e-02 - 4.90000000000000e+00 1.82649041825480e-02 - 5.10000000000000e+00 1.90223427220822e-02 - 5.30000000000000e+00 1.94553386554320e-02 - 5.50000000000000e+00 1.96836222866336e-02 - 5.70000000000000e+00 1.97948208304014e-02 - 5.90000000000000e+00 1.98449333982151e-02 - 6.10000000000000e+00 1.98658492137956e-02 - 6.30000000000000e+00 1.98739410156735e-02 - 6.50000000000000e+00 1.98768446964185e-02 - 6.70000000000000e+00 1.98778116887695e-02 - 6.90000000000000e+00 1.98782268062208e-02 - 7.10000000000000e+00 1.98782268062215e-02 - 7.30000000000000e+00 1.98782268062220e-02 - 7.50000000000000e+00 1.98782268062225e-02 - 7.70000000000000e+00 1.98782268062229e-02 - 7.90000000000000e+00 1.98782268062232e-02 - 8.10000000000000e+00 1.98782268062235e-02 - 8.30000000000000e+00 1.98782268062237e-02 - 8.50000000000000e+00 1.98782268062239e-02 - 8.70000000000000e+00 1.98782268062240e-02 - 8.90000000000000e+00 1.98782268062241e-02 - 9.10000000000000e+00 1.98782268062242e-02 - 9.30000000000000e+00 1.98782268062243e-02 - 9.50000000000000e+00 1.98782268062243e-02 - 9.70000000000000e+00 1.98782268062244e-02 - 9.90000000000000e+00 1.98782268062244e-02 - 1.01000000000000e+01 1.98782268062244e-02 - 1.03000000000000e+01 1.98782268062244e-02 - 1.05000000000000e+01 1.98782268062245e-02 - 1.07000000000000e+01 1.98782268062245e-02 - 1.09000000000000e+01 1.98782268062245e-02 - 1.11000000000000e+01 1.98782268062245e-02 - 1.13000000000000e+01 1.98782268062245e-02 - 1.15000000000000e+01 1.98782268062245e-02 - 1.17000000000000e+01 1.98782268062245e-02 - 1.19000000000000e+01 1.98782268062245e-02 + 3.50000000000000e+00 1.25149547548363e-03 + 3.70000000000000e+00 3.62227140842760e-03 + 3.90000000000000e+00 6.66511264513171e-03 + 4.10000000000000e+00 9.87558504032401e-03 + 4.30000000000000e+00 1.28257594769631e-02 + 4.50000000000000e+00 1.52471254047463e-02 + 4.70000000000000e+00 1.70458936437227e-02 + 4.90000000000000e+00 1.82649041822950e-02 + 5.10000000000000e+00 1.90223427220915e-02 + 5.30000000000000e+00 1.94553386556149e-02 + 5.50000000000000e+00 1.96836222869202e-02 + 5.70000000000000e+00 1.97948208307444e-02 + 5.90000000000000e+00 1.98449333985860e-02 + 6.10000000000000e+00 1.98658492141793e-02 + 6.30000000000000e+00 1.98739410160625e-02 + 6.50000000000000e+00 1.98768446968096e-02 + 6.70000000000000e+00 1.98778116891613e-02 + 6.90000000000000e+00 1.98782268066130e-02 + 7.10000000000000e+00 1.98782268066137e-02 + 7.30000000000000e+00 1.98782268066142e-02 + 7.50000000000000e+00 1.98782268066147e-02 + 7.70000000000000e+00 1.98782268066151e-02 + 7.90000000000000e+00 1.98782268066154e-02 + 8.10000000000000e+00 1.98782268066157e-02 + 8.30000000000000e+00 1.98782268066159e-02 + 8.50000000000000e+00 1.98782268066161e-02 + 8.70000000000000e+00 1.98782268066162e-02 + 8.90000000000000e+00 1.98782268066163e-02 + 9.10000000000000e+00 1.98782268066164e-02 + 9.30000000000000e+00 1.98782268066165e-02 + 9.50000000000000e+00 1.98782268066165e-02 + 9.70000000000000e+00 1.98782268066166e-02 + 9.90000000000000e+00 1.98782268066166e-02 + 1.01000000000000e+01 1.98782268066166e-02 + 1.03000000000000e+01 1.98782268066166e-02 + 1.05000000000000e+01 1.98782268066167e-02 + 1.07000000000000e+01 1.98782268066167e-02 + 1.09000000000000e+01 1.98782268066167e-02 + 1.11000000000000e+01 1.98782268066167e-02 + 1.13000000000000e+01 1.98782268066167e-02 + 1.15000000000000e+01 1.98782268066167e-02 + 1.17000000000000e+01 1.98782268066167e-02 + 1.19000000000000e+01 1.98782268066167e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt index 157cac038..49dcaf892 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-rebin/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2021-03-09. +colvars: Using NAMD interface, version "2021-03-02". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out index 25ec7c329..3b35ba0c9 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -139,26 +139,10 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped index a9f5cad12..24be7d8f2 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688254064136e+00 + x 3.21688254084712e+00 } metadynamics { @@ -21,13 +21,13 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 6.65430605259840e-04 9.34557513055957e-04 1.23300798770362e-03 - 1.52820755424302e-03 1.77932544550601e-03 1.94618908285837e-03 - 1.99972957592583e-03 1.93025240787750e-03 1.75030418482405e-03 - 1.49097223014520e-03 1.19311463635811e-03 8.96915206801889e-04 - 6.33398742101442e-04 4.20203437622546e-04 2.61877749852370e-04 - 1.53318370754311e-04 8.43230653239168e-05 4.35667507513804e-05 - 2.11456262451310e-05 9.64145386575516e-06 + 6.65430605193845e-04 9.34557512978891e-04 1.23300798762255e-03 + 1.52820755416809e-03 1.77932544544850e-03 1.94618908282799e-03 + 1.99972957592804e-03 1.93025240791188e-03 1.75030418488448e-03 + 1.49097223022159e-03 1.19311463643918e-03 8.96915206877818e-04 + 6.33398742165647e-04 4.20203437672161e-04 2.61877749887666e-04 + 1.53318370777537e-04 8.43230653380996e-05 4.35667507594360e-05 + 2.11456262493941e-05 9.64145386786002e-06 hills_energy_gradients grid_parameters { n_colvars 1 @@ -36,12 +36,12 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 4.93601531961674e-04 5.76414162023237e-04 6.06365740079512e-04 - 5.60512340082354e-04 4.30201086501742e-04 2.27271348823597e-04 - -1.64425130241460e-05 -2.57152794011114e-04 -4.51967686121292e-04 - -5.71373901803506e-04 -6.06367538361871e-04 -5.67946764108878e-04 - -4.80257088125742e-04 -3.71133070556632e-04 -2.64031001751807e-04 - -1.73743804964989e-04 -1.06097165582428e-04 -6.02625033739621e-05 - -3.18923060819328e-05 -1.57466379126574e-05 + 4.93601531934965e-04 5.76414162006946e-04 6.06365740080861e-04 + 5.60512340105952e-04 4.30201086547313e-04 2.27271348885101e-04 + -1.64425129573257e-05 -2.57152793951181e-04 -4.51967686078399e-04 + -5.71373901782952e-04 -6.06367538363199e-04 -5.67946764126985e-04 + -4.80257088153256e-04 -3.71133070586411e-04 -2.64031001778642e-04 + -1.73743804986186e-04 -1.06097165597456e-04 -6.02625033836491e-05 + -3.18923060876561e-05 -1.57466379157729e-05 } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj index 0738ec8f1..372662fa9 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 8.16428317253262e-06 - 11 3.21950367388596e+00 8.16428317253262e-06 - 12 3.22130499886840e+00 8.16428317253262e-06 - 13 3.22263479560837e+00 8.16428317253262e-06 - 14 3.22341769777479e+00 8.16428317253262e-06 - 15 3.22361473847006e+00 8.16428317253262e-06 - 16 3.22322417752882e+00 8.16428317253262e-06 - 17 3.22227942881194e+00 8.16428317253262e-06 - 18 3.22084480206089e+00 8.16428317253262e-06 - 19 3.21900980344646e+00 8.16428317253262e-06 - 20 3.21688254064136e+00 1.64425130241460e-05 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 8.16428315713133e-06 + 11 3.21950367395952e+00 8.16428315713133e-06 + 12 3.22130499895462e+00 8.16428315713133e-06 + 13 3.22263479570787e+00 8.16428315713133e-06 + 14 3.22341769788814e+00 8.16428315713133e-06 + 15 3.22361473859775e+00 8.16428315713133e-06 + 16 3.22322417767132e+00 8.16428315713133e-06 + 17 3.22227942896967e+00 8.16428315713133e-06 + 18 3.22084480223426e+00 8.16428315713133e-06 + 19 3.21900980363585e+00 8.16428315713133e-06 + 20 3.21688254084712e+00 1.64425129573257e-05 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf index bcac69118..67c5801c2 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.33429897066599e-03 - 7.50000000000000e-01 1.06517206286987e-03 - 1.25000000000000e+00 7.66721588222210e-04 - 1.75000000000000e+00 4.71522021682808e-04 - 2.25000000000000e+00 2.20404130419819e-04 - 2.75000000000000e+00 5.35404930674629e-05 + 2.50000000000000e-01 1.33429897073419e-03 + 7.50000000000000e-01 1.06517206294915e-03 + 1.25000000000000e+00 7.66721588305484e-04 + 1.75000000000000e+00 4.71522021759950e-04 + 2.25000000000000e+00 2.20404130479536e-04 + 2.75000000000000e+00 5.35404931000470e-05 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 6.94771680483336e-05 - 4.25000000000000e+00 2.49425391101783e-04 - 4.75000000000000e+00 5.08757345780628e-04 - 5.25000000000000e+00 8.06614939567721e-04 - 5.75000000000000e+00 1.10281436912394e-03 - 6.25000000000000e+00 1.36633083382439e-03 - 6.75000000000000e+00 1.57952613830328e-03 - 7.25000000000000e+00 1.73785182607346e-03 - 7.75000000000000e+00 1.84641120517152e-03 - 8.25000000000000e+00 1.91540651060191e-03 - 8.75000000000000e+00 1.95616282517445e-03 - 9.25000000000000e+00 1.97858394968070e-03 - 9.75000000000000e+00 1.99008812206007e-03 + 3.75000000000000e+00 6.94771680161525e-05 + 4.25000000000000e+00 2.49425391043558e-04 + 4.75000000000000e+00 5.08757345706442e-04 + 5.25000000000000e+00 8.06614939488859e-04 + 5.75000000000000e+00 1.10281436905022e-03 + 6.25000000000000e+00 1.36633083376239e-03 + 6.75000000000000e+00 1.57952613825587e-03 + 7.25000000000000e+00 1.73785182604037e-03 + 7.75000000000000e+00 1.84641120515050e-03 + 8.25000000000000e+00 1.91540651058994e-03 + 8.75000000000000e+00 1.95616282516860e-03 + 9.25000000000000e+00 1.97858394967864e-03 + 9.75000000000000e+00 1.99008812206018e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out index f80dd081e..2a87d0982 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.restart.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -139,34 +139,17 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. +colvars: Read 0 hills. colvars: Rebinning the energy and forces grids from the grids in the restart file. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped index 81421cf45..ce121d56f 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21404883965667e+00 + x 3.21404884013792e+00 } metadynamics { @@ -21,25 +21,25 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 1.23300798771509e-03 1.23300798771631e-03 1.52820755425691e-03 - 1.52820755425807e-03 1.52820755425917e-03 1.77932544552316e-03 - 1.77932544552405e-03 1.94618908287715e-03 1.94618908287773e-03 - 1.94618908287813e-03 1.99972957594580e-03 1.99972957594581e-03 - 1.93025240789729e-03 1.93025240789690e-03 1.93025240789634e-03 - 1.75030418484216e-03 1.75030418484128e-03 1.49097223016143e-03 - 1.49097223016034e-03 1.49097223015919e-03 1.19311463637090e-03 - 1.19311463636968e-03 8.96915206812262e-04 8.96915206811093e-04 - 8.96915206809974e-04 6.33398742108474e-04 6.33398742107497e-04 - 4.20203437627708e-04 4.20203437626903e-04 4.20203437626187e-04 - 2.61877749855382e-04 2.61877749854837e-04 1.53318370756312e-04 - 1.53318370755917e-04 1.53318370755588e-04 8.43230653249215e-05 - 8.43230653246995e-05 4.35667507519842e-05 4.35667507518415e-05 - 4.35667507517290e-05 2.11456262453920e-05 2.11456262453244e-05 - 9.64145386589709e-06 9.64145386585826e-06 9.64145386582932e-06 - 5.28034713511762e-17 3.72255148064365e-17 2.59822071961412e-17 - 1.79542993629898e-17 1.22833824411128e-17 8.32002395079111e-18 - 5.57940992188942e-18 3.70432476841225e-18 2.43493252970905e-18 - 1.58460820053553e-18 + 1.23300798763402e-03 1.23300798763524e-03 1.52820755418198e-03 + 1.52820755418314e-03 1.52820755418424e-03 1.77932544546565e-03 + 1.77932544546654e-03 1.94618908284677e-03 1.94618908284735e-03 + 1.94618908284775e-03 1.99972957594801e-03 1.99972957594802e-03 + 1.93025240793167e-03 1.93025240793128e-03 1.93025240793072e-03 + 1.75030418490259e-03 1.75030418490171e-03 1.49097223023783e-03 + 1.49097223023673e-03 1.49097223023558e-03 1.19311463645197e-03 + 1.19311463645075e-03 8.96915206888191e-04 8.96915206887022e-04 + 8.96915206885903e-04 6.33398742172679e-04 6.33398742171702e-04 + 4.20203437677323e-04 4.20203437676518e-04 4.20203437675802e-04 + 2.61877749890678e-04 2.61877749890133e-04 1.53318370779538e-04 + 1.53318370779143e-04 1.53318370778814e-04 8.43230653391043e-05 + 8.43230653388823e-05 4.35667507600398e-05 4.35667507598971e-05 + 4.35667507597847e-05 2.11456262496551e-05 2.11456262495875e-05 + 9.64145386800195e-06 9.64145386796312e-06 9.64145386793418e-06 + 5.28034713900195e-17 3.72255148346162e-17 2.59822072163652e-17 + 1.79542993773489e-17 1.22833824511992e-17 8.32002395780095e-18 + 5.57940992670954e-18 3.70432477169169e-18 2.43493253191679e-18 + 1.58460820200618e-18 hills_energy_gradients grid_parameters { n_colvars 1 @@ -48,24 +48,24 @@ grid_parameters { widths 2.00000000000000e-01 sizes 55 } - 6.06365740085560e-04 6.06365740085564e-04 5.60512340088285e-04 - 5.60512340088029e-04 5.60512340087635e-04 4.30201086506495e-04 - 4.30201086505838e-04 2.27271348826923e-04 2.27271348826058e-04 - 2.27271348825120e-04 -1.64425130236053e-05 -1.64425130246041e-05 - -2.57152794012557e-04 -2.57152794013499e-04 -2.57152794014372e-04 - -4.51967686125329e-04 -4.51967686125995e-04 -5.71373901808749e-04 - -5.71373901809154e-04 -5.71373901809421e-04 -6.06367538367918e-04 - -6.06367538367924e-04 -5.67946764114821e-04 -5.67946764114611e-04 - -5.67946764114319e-04 -4.80257088130826e-04 -4.80257088130422e-04 - -3.71133070560880e-04 -3.71133070560435e-04 -3.71133070559992e-04 - -2.64031001754737e-04 -2.64031001754330e-04 -1.73743804967135e-04 - -1.73743804966793e-04 -1.73743804966486e-04 -1.06097165583657e-04 - -1.06097165583424e-04 -6.02625033747609e-05 -6.02625033745952e-05 - -6.02625033744582e-05 -3.18923060823172e-05 -3.18923060822274e-05 - -1.57466379128806e-05 -1.57466379128247e-05 -1.57466379127815e-05 - -9.09757785774318e-17 -6.59975776057536e-17 -4.73632774778447e-17 - -3.36268154240955e-17 -2.36198534105275e-17 -1.64146648142998e-17 - -1.12866460797317e-17 -7.67873161883127e-18 -5.16914145223437e-18 - -3.44320959079916e-18 + 6.06365740086909e-04 6.06365740086913e-04 5.60512340111883e-04 + 5.60512340111627e-04 5.60512340111233e-04 4.30201086552066e-04 + 4.30201086551409e-04 2.27271348888427e-04 2.27271348887562e-04 + 2.27271348886624e-04 -1.64425129567850e-05 -1.64425129577838e-05 + -2.57152793952624e-04 -2.57152793953566e-04 -2.57152793954439e-04 + -4.51967686082436e-04 -4.51967686083102e-04 -5.71373901788195e-04 + -5.71373901788600e-04 -5.71373901788867e-04 -6.06367538369246e-04 + -6.06367538369252e-04 -5.67946764132928e-04 -5.67946764132719e-04 + -5.67946764132426e-04 -4.80257088158340e-04 -4.80257088157936e-04 + -3.71133070590659e-04 -3.71133070590214e-04 -3.71133070589771e-04 + -2.64031001781572e-04 -2.64031001781165e-04 -1.73743804988332e-04 + -1.73743804987990e-04 -1.73743804987683e-04 -1.06097165598685e-04 + -1.06097165598452e-04 -6.02625033844479e-05 -6.02625033842822e-05 + -6.02625033841452e-05 -3.18923060880405e-05 -3.18923060879507e-05 + -1.57466379159961e-05 -1.57466379159402e-05 -1.57466379158970e-05 + -9.09757786387114e-17 -6.59975776517344e-17 -4.73632775119337e-17 + -3.36268154490693e-17 -2.36198534286094e-17 -1.64146648272399e-17 + -1.12866460888857e-17 -7.67873162523311e-18 -5.16914145666077e-18 + -3.44320959382525e-18 } diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj index 509a07520..fb142e4f6 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688254064136e+00 1.64425130241460e-05 - 21 3.21458253878164e+00 1.64425130241460e-05 - 22 3.21223316113940e+00 1.64425130241460e-05 - 23 3.20995393049671e+00 1.64425130241460e-05 - 24 3.20785328156876e+00 1.64425130241460e-05 - 25 3.20602246223748e+00 1.64425130241460e-05 - 26 3.20453121727901e+00 1.64425130241460e-05 - 27 3.20342558278651e+00 1.64425130241460e-05 - 28 3.20272771879869e+00 1.64425130241460e-05 - 29 3.20243733044315e+00 1.64425130241460e-05 - 30 3.20253425826863e+00 1.64425130243894e-05 - 31 3.20298186140896e+00 1.64425130243894e-05 - 32 3.20373103962324e+00 1.64425130243894e-05 - 33 3.20472472070871e+00 1.64425130243894e-05 - 34 3.20590259829393e+00 1.64425130243894e-05 - 35 3.20720570082978e+00 1.64425130243894e-05 - 36 3.20858034653318e+00 1.64425130243894e-05 - 37 3.20998116348556e+00 1.64425130243894e-05 - 38 3.21137313133328e+00 1.64425130243894e-05 - 39 3.21273279422841e+00 1.64425130243894e-05 - 40 3.21404883965667e+00 1.64425130246041e-05 + 20 3.21688254084712e+00 1.64425129573257e-05 + 21 3.21458253900407e+00 1.64425129573257e-05 + 22 3.21223316137874e+00 1.64425129573257e-05 + 23 3.20995393075312e+00 1.64425129573257e-05 + 24 3.20785328184230e+00 1.64425129573257e-05 + 25 3.20602246252810e+00 1.64425129573257e-05 + 26 3.20453121758655e+00 1.64425129573257e-05 + 27 3.20342558311071e+00 1.64425129573257e-05 + 28 3.20272771913917e+00 1.64425129573257e-05 + 29 3.20243733079947e+00 1.64425129573257e-05 + 30 3.20253425864031e+00 1.64425129575691e-05 + 31 3.20298186179545e+00 1.64425129575691e-05 + 32 3.20373104002396e+00 1.64425129575691e-05 + 33 3.20472472112302e+00 1.64425129575691e-05 + 34 3.20590259872112e+00 1.64425129575691e-05 + 35 3.20720570126905e+00 1.64425129575691e-05 + 36 3.20858034698356e+00 1.64425129575691e-05 + 37 3.20998116394591e+00 1.64425129575691e-05 + 38 3.21137313180225e+00 1.64425129575691e-05 + 39 3.21273279470442e+00 1.64425129575691e-05 + 40 3.21404884013792e+00 1.64425129577838e-05 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf index 9054286e1..225f83d93 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/AutoDiff/test.restart.pmf @@ -1,58 +1,58 @@ # 1 # 1.00000000000000e+00 2.00000000000000e-01 55 0 - 1.10000000000000e+00 7.66721588230714e-04 - 1.30000000000000e+00 7.66721588229502e-04 - 1.50000000000000e+00 4.71522021688902e-04 - 1.70000000000000e+00 4.71522021687739e-04 - 1.90000000000000e+00 4.71522021686641e-04 - 2.10000000000000e+00 2.20404130422646e-04 - 2.30000000000000e+00 2.20404130421759e-04 - 2.50000000000000e+00 5.35404930686546e-05 - 2.70000000000000e+00 5.35404930680746e-05 - 2.90000000000000e+00 5.35404930676752e-05 + 1.10000000000000e+00 7.66721588313994e-04 + 1.30000000000000e+00 7.66721588312782e-04 + 1.50000000000000e+00 4.71522021766042e-04 + 1.70000000000000e+00 4.71522021764879e-04 + 1.90000000000000e+00 4.71522021763781e-04 + 2.10000000000000e+00 2.20404130482366e-04 + 2.30000000000000e+00 2.20404130481479e-04 + 2.50000000000000e+00 5.35404931012447e-05 + 2.70000000000000e+00 5.35404931006646e-05 + 2.90000000000000e+00 5.35404931002652e-05 3.10000000000000e+00 8.23993651088983e-18 3.30000000000000e+00 -0.00000000000000e+00 - 3.50000000000000e+00 6.94771680485205e-05 - 3.70000000000000e+00 6.94771680489045e-05 - 3.90000000000000e+00 6.94771680494700e-05 - 4.10000000000000e+00 2.49425391103651e-04 - 4.30000000000000e+00 2.49425391104527e-04 - 4.50000000000000e+00 5.08757345784374e-04 - 4.70000000000000e+00 5.08757345785465e-04 - 4.90000000000000e+00 5.08757345786624e-04 - 5.10000000000000e+00 8.06614939574912e-04 - 5.30000000000000e+00 8.06614939576124e-04 - 5.50000000000000e+00 1.10281436913355e-03 - 5.70000000000000e+00 1.10281436913472e-03 - 5.90000000000000e+00 1.10281436913583e-03 - 6.10000000000000e+00 1.36633083383733e-03 - 6.30000000000000e+00 1.36633083383831e-03 - 6.50000000000000e+00 1.57952613831810e-03 - 6.70000000000000e+00 1.57952613831891e-03 - 6.90000000000000e+00 1.57952613831962e-03 - 7.10000000000000e+00 1.73785182609043e-03 - 7.30000000000000e+00 1.73785182609097e-03 - 7.50000000000000e+00 1.84641120518950e-03 - 7.70000000000000e+00 1.84641120518989e-03 - 7.90000000000000e+00 1.84641120519022e-03 - 8.10000000000000e+00 1.91540651062089e-03 - 8.30000000000000e+00 1.91540651062111e-03 - 8.50000000000000e+00 1.95616282519382e-03 - 8.70000000000000e+00 1.95616282519397e-03 - 8.90000000000000e+00 1.95616282519408e-03 - 9.10000000000000e+00 1.97858394970042e-03 - 9.30000000000000e+00 1.97858394970048e-03 - 9.50000000000000e+00 1.99008812207991e-03 - 9.70000000000000e+00 1.99008812207995e-03 - 9.90000000000000e+00 1.99008812207998e-03 - 1.01000000000000e+01 1.99972957594576e-03 - 1.03000000000000e+01 1.99972957594577e-03 - 1.05000000000000e+01 1.99972957594578e-03 - 1.07000000000000e+01 1.99972957594579e-03 - 1.09000000000000e+01 1.99972957594580e-03 - 1.11000000000000e+01 1.99972957594580e-03 - 1.13000000000000e+01 1.99972957594580e-03 - 1.15000000000000e+01 1.99972957594580e-03 - 1.17000000000000e+01 1.99972957594581e-03 - 1.19000000000000e+01 1.99972957594581e-03 + 3.50000000000000e+00 6.94771680163505e-05 + 3.70000000000000e+00 6.94771680167345e-05 + 3.90000000000000e+00 6.94771680173000e-05 + 4.10000000000000e+00 2.49425391045431e-04 + 4.30000000000000e+00 2.49425391046307e-04 + 4.50000000000000e+00 5.08757345710194e-04 + 4.70000000000000e+00 5.08757345711285e-04 + 4.90000000000000e+00 5.08757345712444e-04 + 5.10000000000000e+00 8.06614939496052e-04 + 5.30000000000000e+00 8.06614939497264e-04 + 5.50000000000000e+00 1.10281436905983e-03 + 5.70000000000000e+00 1.10281436906100e-03 + 5.90000000000000e+00 1.10281436906212e-03 + 6.10000000000000e+00 1.36633083377534e-03 + 6.30000000000000e+00 1.36633083377632e-03 + 6.50000000000000e+00 1.57952613827070e-03 + 6.70000000000000e+00 1.57952613827150e-03 + 6.90000000000000e+00 1.57952613827222e-03 + 7.10000000000000e+00 1.73785182605734e-03 + 7.30000000000000e+00 1.73785182605789e-03 + 7.50000000000000e+00 1.84641120516848e-03 + 7.70000000000000e+00 1.84641120516888e-03 + 7.90000000000000e+00 1.84641120516921e-03 + 8.10000000000000e+00 1.91540651060891e-03 + 8.30000000000000e+00 1.91540651060914e-03 + 8.50000000000000e+00 1.95616282518798e-03 + 8.70000000000000e+00 1.95616282518812e-03 + 8.90000000000000e+00 1.95616282518823e-03 + 9.10000000000000e+00 1.97858394969836e-03 + 9.30000000000000e+00 1.97858394969843e-03 + 9.50000000000000e+00 1.99008812208002e-03 + 9.70000000000000e+00 1.99008812208006e-03 + 9.90000000000000e+00 1.99008812208008e-03 + 1.01000000000000e+01 1.99972957594797e-03 + 1.03000000000000e+01 1.99972957594798e-03 + 1.05000000000000e+01 1.99972957594799e-03 + 1.07000000000000e+01 1.99972957594800e-03 + 1.09000000000000e+01 1.99972957594801e-03 + 1.11000000000000e+01 1.99972957594801e-03 + 1.13000000000000e+01 1.99972957594801e-03 + 1.15000000000000e+01 1.99972957594801e-03 + 1.17000000000000e+01 1.99972957594802e-03 + 1.19000000000000e+01 1.99972957594802e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt index 157cac038..49dcaf892 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-rebinfromgrids/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2021-03-09. +colvars: Using NAMD interface, version "2021-03-02". diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out index caed7f14e..a5e27860c 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -138,27 +134,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped index ab45cb882..6de09bffd 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688278576757e+00 + x 3.21688278597333e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.46920493464415e-08 1.70721010337625e-05 6.58298335707084e-04 - 1.98901157282260e-03 4.70902104095221e-04 8.73580075153432e-06 + 3.46920492770083e-08 1.70721010112539e-05 6.58298335288197e-04 + 1.98901157291202e-03 4.70902104436801e-04 8.73580076380761e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 5.18433074964325e-07 1.68175610778412e-04 3.13214891049980e-03 - -6.66334790621162e-04 -2.55603942662786e-03 -9.19086518597186e-05 + 5.18433073974142e-07 1.68175610579987e-04 3.13214890940428e-03 + -6.66334787942696e-04 -2.55603942784152e-03 -9.19086519769792e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj index 56616ce4c..3ac32bb03 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 3.30884583877525e-04 - 11 3.21950367884164e+00 3.30884583877525e-04 - 12 3.22130501367398e+00 3.30884583877525e-04 - 13 3.22263482503343e+00 3.30884583877525e-04 - 14 3.22341774640647e+00 3.30884583877525e-04 - 15 3.22361481066343e+00 3.30884583877525e-04 - 16 3.22322427736760e+00 3.30884583877525e-04 - 17 3.22227956008091e+00 3.30884583877525e-04 - 18 3.22084496823082e+00 3.30884583877525e-04 - 19 3.21901000767136e+00 3.30884583877525e-04 - 20 3.21688278576757e+00 6.66334790621162e-04 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 3.30884583259955e-04 + 11 3.21950367891521e+00 3.30884583259955e-04 + 12 3.22130501376020e+00 3.30884583259955e-04 + 13 3.22263482513293e+00 3.30884583259955e-04 + 14 3.22341774651982e+00 3.30884583259955e-04 + 15 3.22361481079113e+00 3.30884583259955e-04 + 16 3.22322427751010e+00 3.30884583259955e-04 + 17 3.22227956023865e+00 3.30884583259955e-04 + 18 3.22084496840419e+00 3.30884583259955e-04 + 19 3.21901000786075e+00 3.30884583259955e-04 + 20 3.21688278597333e+00 6.66334787942696e-04 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf index 7a24c6664..3a05a7c71 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.98901157282260e-03 - 7.50000000000000e-01 1.98901157282260e-03 - 1.25000000000000e+00 1.98901157282260e-03 - 1.75000000000000e+00 1.98897688077326e-03 - 2.25000000000000e+00 1.97193947178884e-03 - 2.75000000000000e+00 1.33071323711552e-03 + 2.50000000000000e-01 1.98901157291202e-03 + 7.50000000000000e-01 1.98901157291202e-03 + 1.25000000000000e+00 1.98901157291202e-03 + 1.75000000000000e+00 1.98897688086274e-03 + 2.25000000000000e+00 1.97193947190077e-03 + 2.75000000000000e+00 1.33071323762382e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.51810946872738e-03 - 4.25000000000000e+00 1.98027577207107e-03 - 4.75000000000000e+00 1.98901157282260e-03 - 5.25000000000000e+00 1.98901157282260e-03 - 5.75000000000000e+00 1.98901157282260e-03 - 6.25000000000000e+00 1.98901157282260e-03 - 6.75000000000000e+00 1.98901157282260e-03 - 7.25000000000000e+00 1.98901157282260e-03 - 7.75000000000000e+00 1.98901157282260e-03 - 8.25000000000000e+00 1.98901157282260e-03 - 8.75000000000000e+00 1.98901157282260e-03 - 9.25000000000000e+00 1.98901157282260e-03 - 9.75000000000000e+00 1.98901157282260e-03 + 3.75000000000000e+00 1.51810946847522e-03 + 4.25000000000000e+00 1.98027577214821e-03 + 4.75000000000000e+00 1.98901157291202e-03 + 5.25000000000000e+00 1.98901157291202e-03 + 5.75000000000000e+00 1.98901157291202e-03 + 6.25000000000000e+00 1.98901157291202e-03 + 6.75000000000000e+00 1.98901157291202e-03 + 7.25000000000000e+00 1.98901157291202e-03 + 7.75000000000000e+00 1.98901157291202e-03 + 8.25000000000000e+00 1.98901157291202e-03 + 8.75000000000000e+00 1.98901157291202e-03 + 9.25000000000000e+00 1.98901157291202e-03 + 9.75000000000000e+00 1.98901157291202e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out index 2bb4389fd..adabe2e3d 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -138,34 +134,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped index 5f97bd617..235b1896e 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405136086868e+00 + x 3.21405136134992e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 7.43923406409864e-08 3.57122156643391e-05 1.34466139863962e-03 - 3.97104317611064e-03 9.19770326015385e-04 1.67080044137238e-05 + 7.43923403227782e-08 3.57122155647627e-05 1.34466139685731e-03 + 3.97104317655277e-03 9.19770327415716e-04 1.67080044623168e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1.10794466506920e-06 3.50062168801214e-04 6.33510418316085e-03 - -1.50805870086533e-03 -5.03195891344979e-03 -1.76471077412228e-04 + 1.10794466055357e-06 3.50062167930554e-04 6.33510417866273e-03 + -1.50805868972440e-03 -5.03195891853835e-03 -1.76471077879577e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj index e23343a0c..6b959f565 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688278576757e+00 6.66334790621162e-04 - 21 3.21458283239873e+00 6.66334790621162e-04 - 22 3.21223351050617e+00 6.66334790621162e-04 - 23 3.20995434250849e+00 6.66334790621162e-04 - 24 3.20785376273403e+00 6.66334790621162e-04 - 25 3.20602301866294e+00 6.66334790621162e-04 - 26 3.20453185466307e+00 6.66334790621162e-04 - 27 3.20342630641905e+00 6.66334790621162e-04 - 28 3.20272853356652e+00 6.66334790621162e-04 - 29 3.20243824083933e+00 6.66334790621162e-04 - 30 3.20253526840434e+00 1.14429095893840e-03 - 31 3.20298298236841e+00 1.14429095893840e-03 - 32 3.20373228203772e+00 1.14429095893840e-03 - 33 3.20472609467411e+00 1.14429095893840e-03 - 34 3.20590411329665e+00 1.14429095893840e-03 - 35 3.20720736568876e+00 1.14429095893840e-03 - 36 3.20858216935653e+00 1.14429095893840e-03 - 37 3.20998315165031e+00 1.14429095893840e-03 - 38 3.21137529148386e+00 1.14429095893840e-03 - 39 3.21273513229142e+00 1.14429095893840e-03 - 40 3.21405136086868e+00 1.50805870086533e-03 + 20 3.21688278597333e+00 6.66334787942696e-04 + 21 3.21458283262116e+00 6.66334787942696e-04 + 22 3.21223351074552e+00 6.66334787942696e-04 + 23 3.20995434276490e+00 6.66334787942696e-04 + 24 3.20785376300757e+00 6.66334787942696e-04 + 25 3.20602301895356e+00 6.66334787942696e-04 + 26 3.20453185497061e+00 6.66334787942696e-04 + 27 3.20342630674324e+00 6.66334787942696e-04 + 28 3.20272853390700e+00 6.66334787942696e-04 + 29 3.20243824119566e+00 6.66334787942696e-04 + 30 3.20253526877602e+00 1.14429095260314e-03 + 31 3.20298298275490e+00 1.14429095260314e-03 + 32 3.20373228243844e+00 1.14429095260314e-03 + 33 3.20472609508842e+00 1.14429095260314e-03 + 34 3.20590411372385e+00 1.14429095260314e-03 + 35 3.20720736612802e+00 1.14429095260314e-03 + 36 3.20858216980690e+00 1.14429095260314e-03 + 37 3.20998315211066e+00 1.14429095260314e-03 + 38 3.21137529195283e+00 1.14429095260314e-03 + 39 3.21273513276742e+00 1.14429095260314e-03 + 40 3.21405136134992e+00 1.50805868972440e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf index 38a897e10..051812fec 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.97104317611064e-03 - 7.50000000000000e-01 3.97104317611064e-03 - 1.25000000000000e+00 3.97104317611064e-03 - 1.75000000000000e+00 3.97096878377000e-03 - 2.25000000000000e+00 3.93533096044630e-03 - 2.75000000000000e+00 2.62638177747102e-03 + 2.50000000000000e-01 3.97104317655277e-03 + 7.50000000000000e-01 3.97104317655277e-03 + 1.25000000000000e+00 3.97104317655277e-03 + 1.75000000000000e+00 3.97096878421245e-03 + 2.25000000000000e+00 3.93533096098801e-03 + 2.75000000000000e+00 2.62638177969546e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 3.05127285009526e-03 - 4.25000000000000e+00 3.95433517169692e-03 - 4.75000000000000e+00 3.97104317611064e-03 - 5.25000000000000e+00 3.97104317611064e-03 - 5.75000000000000e+00 3.97104317611064e-03 - 6.25000000000000e+00 3.97104317611064e-03 - 6.75000000000000e+00 3.97104317611064e-03 - 7.25000000000000e+00 3.97104317611064e-03 - 7.75000000000000e+00 3.97104317611064e-03 - 8.25000000000000e+00 3.97104317611064e-03 - 8.75000000000000e+00 3.97104317611064e-03 - 9.25000000000000e+00 3.97104317611064e-03 - 9.75000000000000e+00 3.97104317611064e-03 + 3.75000000000000e+00 3.05127284913705e-03 + 4.25000000000000e+00 3.95433517209045e-03 + 4.75000000000000e+00 3.97104317655277e-03 + 5.25000000000000e+00 3.97104317655277e-03 + 5.75000000000000e+00 3.97104317655277e-03 + 6.25000000000000e+00 3.97104317655277e-03 + 6.75000000000000e+00 3.97104317655277e-03 + 7.25000000000000e+00 3.97104317655277e-03 + 7.75000000000000e+00 3.97104317655277e-03 + 8.25000000000000e+00 3.97104317655277e-03 + 8.75000000000000e+00 3.97104317655277e-03 + 9.25000000000000e+00 3.97104317655277e-03 + 9.75000000000000e+00 3.97104317655277e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-sigmas/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out index 60aee7ad6..5fcb5a777 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -140,30 +136,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped index 7dc8c95f8..2e2ab665b 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688278576757e+00 + x 3.21688278597333e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.46920493464415e-08 1.70721010337625e-05 6.58298335707084e-04 - 1.98901157282260e-03 4.70902104095221e-04 8.73580075153432e-06 + 3.46920492770083e-08 1.70721010112539e-05 6.58298335288197e-04 + 1.98901157291202e-03 4.70902104436801e-04 8.73580076380761e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 5.18433074964325e-07 1.68175610778412e-04 3.13214891049980e-03 - -6.66334790621162e-04 -2.55603942662786e-03 -9.19086518597186e-05 + 5.18433073974142e-07 1.68175610579987e-04 3.13214890940428e-03 + -6.66334787942696e-04 -2.55603942784152e-03 -9.19086519769792e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -56,7 +56,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - -1.46245128120959e+00 0.00000000000000e+00 0.00000000000000e+00 + -1.46245122218042e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj index 56616ce4c..3ac32bb03 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 3.30884583877525e-04 - 11 3.21950367884164e+00 3.30884583877525e-04 - 12 3.22130501367398e+00 3.30884583877525e-04 - 13 3.22263482503343e+00 3.30884583877525e-04 - 14 3.22341774640647e+00 3.30884583877525e-04 - 15 3.22361481066343e+00 3.30884583877525e-04 - 16 3.22322427736760e+00 3.30884583877525e-04 - 17 3.22227956008091e+00 3.30884583877525e-04 - 18 3.22084496823082e+00 3.30884583877525e-04 - 19 3.21901000767136e+00 3.30884583877525e-04 - 20 3.21688278576757e+00 6.66334790621162e-04 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 3.30884583259955e-04 + 11 3.21950367891521e+00 3.30884583259955e-04 + 12 3.22130501376020e+00 3.30884583259955e-04 + 13 3.22263482513293e+00 3.30884583259955e-04 + 14 3.22341774651982e+00 3.30884583259955e-04 + 15 3.22361481079113e+00 3.30884583259955e-04 + 16 3.22322427751010e+00 3.30884583259955e-04 + 17 3.22227956023865e+00 3.30884583259955e-04 + 18 3.22084496840419e+00 3.30884583259955e-04 + 19 3.21901000786075e+00 3.30884583259955e-04 + 20 3.21688278597333e+00 6.66334787942696e-04 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf index 7a24c6664..3a05a7c71 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.98901157282260e-03 - 7.50000000000000e-01 1.98901157282260e-03 - 1.25000000000000e+00 1.98901157282260e-03 - 1.75000000000000e+00 1.98897688077326e-03 - 2.25000000000000e+00 1.97193947178884e-03 - 2.75000000000000e+00 1.33071323711552e-03 + 2.50000000000000e-01 1.98901157291202e-03 + 7.50000000000000e-01 1.98901157291202e-03 + 1.25000000000000e+00 1.98901157291202e-03 + 1.75000000000000e+00 1.98897688086274e-03 + 2.25000000000000e+00 1.97193947190077e-03 + 2.75000000000000e+00 1.33071323762382e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.51810946872738e-03 - 4.25000000000000e+00 1.98027577207107e-03 - 4.75000000000000e+00 1.98901157282260e-03 - 5.25000000000000e+00 1.98901157282260e-03 - 5.75000000000000e+00 1.98901157282260e-03 - 6.25000000000000e+00 1.98901157282260e-03 - 6.75000000000000e+00 1.98901157282260e-03 - 7.25000000000000e+00 1.98901157282260e-03 - 7.75000000000000e+00 1.98901157282260e-03 - 8.25000000000000e+00 1.98901157282260e-03 - 8.75000000000000e+00 1.98901157282260e-03 - 9.25000000000000e+00 1.98901157282260e-03 - 9.75000000000000e+00 1.98901157282260e-03 + 3.75000000000000e+00 1.51810946847522e-03 + 4.25000000000000e+00 1.98027577214821e-03 + 4.75000000000000e+00 1.98901157291202e-03 + 5.25000000000000e+00 1.98901157291202e-03 + 5.75000000000000e+00 1.98901157291202e-03 + 6.25000000000000e+00 1.98901157291202e-03 + 6.75000000000000e+00 1.98901157291202e-03 + 7.25000000000000e+00 1.98901157291202e-03 + 7.75000000000000e+00 1.98901157291202e-03 + 8.25000000000000e+00 1.98901157291202e-03 + 8.75000000000000e+00 1.98901157291202e-03 + 9.25000000000000e+00 1.98901157291202e-03 + 9.75000000000000e+00 1.98901157291202e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out index 60a73ce49..8704eef89 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -140,37 +136,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped index c9a85fb5b..d3e71c6bd 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405136086868e+00 + x 3.21405136134992e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 7.43923406409864e-08 3.57122156643391e-05 1.34466139863962e-03 - 3.97104317611064e-03 9.19770326015385e-04 1.67080044137238e-05 + 7.43923403227782e-08 3.57122155647627e-05 1.34466139685731e-03 + 3.97104317655277e-03 9.19770327415716e-04 1.67080044623168e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1.10794466506920e-06 3.50062168801214e-04 6.33510418316085e-03 - -1.50805870086533e-03 -5.03195891344979e-03 -1.76471077412228e-04 + 1.10794466055357e-06 3.50062167930554e-04 6.33510417866273e-03 + -1.50805868972440e-03 -5.03195891853835e-03 -1.76471077879577e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -56,7 +56,7 @@ histogram system_forces 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 4.71618560685502e+00 0.00000000000000e+00 0.00000000000000e+00 + 4.71618561911262e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj index e23343a0c..6b959f565 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688278576757e+00 6.66334790621162e-04 - 21 3.21458283239873e+00 6.66334790621162e-04 - 22 3.21223351050617e+00 6.66334790621162e-04 - 23 3.20995434250849e+00 6.66334790621162e-04 - 24 3.20785376273403e+00 6.66334790621162e-04 - 25 3.20602301866294e+00 6.66334790621162e-04 - 26 3.20453185466307e+00 6.66334790621162e-04 - 27 3.20342630641905e+00 6.66334790621162e-04 - 28 3.20272853356652e+00 6.66334790621162e-04 - 29 3.20243824083933e+00 6.66334790621162e-04 - 30 3.20253526840434e+00 1.14429095893840e-03 - 31 3.20298298236841e+00 1.14429095893840e-03 - 32 3.20373228203772e+00 1.14429095893840e-03 - 33 3.20472609467411e+00 1.14429095893840e-03 - 34 3.20590411329665e+00 1.14429095893840e-03 - 35 3.20720736568876e+00 1.14429095893840e-03 - 36 3.20858216935653e+00 1.14429095893840e-03 - 37 3.20998315165031e+00 1.14429095893840e-03 - 38 3.21137529148386e+00 1.14429095893840e-03 - 39 3.21273513229142e+00 1.14429095893840e-03 - 40 3.21405136086868e+00 1.50805870086533e-03 + 20 3.21688278597333e+00 6.66334787942696e-04 + 21 3.21458283262116e+00 6.66334787942696e-04 + 22 3.21223351074552e+00 6.66334787942696e-04 + 23 3.20995434276490e+00 6.66334787942696e-04 + 24 3.20785376300757e+00 6.66334787942696e-04 + 25 3.20602301895356e+00 6.66334787942696e-04 + 26 3.20453185497061e+00 6.66334787942696e-04 + 27 3.20342630674324e+00 6.66334787942696e-04 + 28 3.20272853390700e+00 6.66334787942696e-04 + 29 3.20243824119566e+00 6.66334787942696e-04 + 30 3.20253526877602e+00 1.14429095260314e-03 + 31 3.20298298275490e+00 1.14429095260314e-03 + 32 3.20373228243844e+00 1.14429095260314e-03 + 33 3.20472609508842e+00 1.14429095260314e-03 + 34 3.20590411372385e+00 1.14429095260314e-03 + 35 3.20720736612802e+00 1.14429095260314e-03 + 36 3.20858216980690e+00 1.14429095260314e-03 + 37 3.20998315211066e+00 1.14429095260314e-03 + 38 3.21137529195283e+00 1.14429095260314e-03 + 39 3.21273513276742e+00 1.14429095260314e-03 + 40 3.21405136134992e+00 1.50805868972440e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf index 38a897e10..051812fec 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.97104317611064e-03 - 7.50000000000000e-01 3.97104317611064e-03 - 1.25000000000000e+00 3.97104317611064e-03 - 1.75000000000000e+00 3.97096878377000e-03 - 2.25000000000000e+00 3.93533096044630e-03 - 2.75000000000000e+00 2.62638177747102e-03 + 2.50000000000000e-01 3.97104317655277e-03 + 7.50000000000000e-01 3.97104317655277e-03 + 1.25000000000000e+00 3.97104317655277e-03 + 1.75000000000000e+00 3.97096878421245e-03 + 2.25000000000000e+00 3.93533096098801e-03 + 2.75000000000000e+00 2.62638177969546e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 3.05127285009526e-03 - 4.25000000000000e+00 3.95433517169692e-03 - 4.75000000000000e+00 3.97104317611064e-03 - 5.25000000000000e+00 3.97104317611064e-03 - 5.75000000000000e+00 3.97104317611064e-03 - 6.25000000000000e+00 3.97104317611064e-03 - 6.75000000000000e+00 3.97104317611064e-03 - 7.25000000000000e+00 3.97104317611064e-03 - 7.75000000000000e+00 3.97104317611064e-03 - 8.25000000000000e+00 3.97104317611064e-03 - 8.75000000000000e+00 3.97104317611064e-03 - 9.25000000000000e+00 3.97104317611064e-03 - 9.75000000000000e+00 3.97104317611064e-03 + 3.75000000000000e+00 3.05127284913705e-03 + 4.25000000000000e+00 3.95433517209045e-03 + 4.75000000000000e+00 3.97104317655277e-03 + 5.25000000000000e+00 3.97104317655277e-03 + 5.75000000000000e+00 3.97104317655277e-03 + 6.25000000000000e+00 3.97104317655277e-03 + 6.75000000000000e+00 3.97104317655277e-03 + 7.25000000000000e+00 3.97104317655277e-03 + 7.75000000000000e+00 3.97104317655277e-03 + 8.25000000000000e+00 3.97104317655277e-03 + 8.75000000000000e+00 3.97104317655277e-03 + 9.25000000000000e+00 3.97104317655277e-03 + 9.75000000000000e+00 3.97104317655277e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-ti/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj index fa1b525d4..a66046fd3 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.metadynamics1.hills.traj @@ -1,4 +1,4 @@ 5 3.20606308065050e+00 5.00000000000000e-01 1.00000000000000e-01 10 3.21734242206787e+00 5.00000000000000e-01 8.46119581367384e-02 - 15 3.22363050330140e+00 5.00000000000000e-01 7.34385578106080e-02 + 15 3.22363050330139e+00 5.00000000000000e-01 7.34385578106080e-02 20 3.21691895295305e+00 5.00000000000000e-01 6.49380514240066e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out index 689bb1bf4..8e00aed34 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -143,26 +139,16 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped index 87801e244..2b4ef2420 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.state.stripped @@ -21,10 +21,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.42973919084568e-04 - 4.41360461286583e-03 5.01317117210112e-02 2.09514390772553e-01 - 3.22178897971626e-01 1.82289606890753e-01 3.79496667604973e-02 - 2.90693223696987e-03 8.19298874561864e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.42973919084570e-04 + 4.41360461286586e-03 5.01317117210114e-02 2.09514390772554e-01 + 3.22178897971626e-01 1.82289606890752e-01 3.79496667604971e-02 + 2.90693223696984e-03 8.19298874561855e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -36,10 +36,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.12368805589937e-03 - 2.58626065712127e-02 1.93513466997635e-01 3.89791769357681e-01 - -4.48458537631413e-02 -3.89889393515630e-01 -1.57054622900226e-01 - -1.78431915109616e-02 -6.66729644383008e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.12368805589938e-03 + 2.58626065712129e-02 1.93513466997636e-01 3.89791769357681e-01 + -4.48458537631430e-02 -3.89889393515630e-01 -1.57054622900226e-01 + -1.78431915109615e-02 -6.66729644383001e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj index 89043bf99..b0936f14b 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.colvars.traj @@ -4,19 +4,19 @@ 2 3.20384028588952e+00 0.00000000000000e+00 3 3.20396721186862e+00 0.00000000000000e+00 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 1.75070440392767e-02 - 6 3.20788015841690e+00 1.75070440392767e-02 - 7 3.21006078117990e+00 1.75070440392767e-02 - 8 3.21246619986317e+00 1.75070440392767e-02 - 9 3.21494510727501e+00 1.75070440392767e-02 - 10 3.21734242206787e+00 2.85363794417937e-02 - 11 3.21950925117359e+00 2.85363794417937e-02 - 12 3.22131261706854e+00 2.85363794417937e-02 - 13 3.22264480741010e+00 2.85363794417937e-02 - 14 3.22343043310305e+00 2.85363794417937e-02 - 15 3.22363050330140e+00 3.62717655819525e-02 - 16 3.22324337253598e+00 3.62717655819525e-02 - 17 3.22230242928906e+00 3.62717655819525e-02 - 18 3.22087195749114e+00 3.62717655819525e-02 - 19 3.21904143773479e+00 3.62717655819525e-02 - 20 3.21691895295305e+00 4.48458537631413e-02 + 5 3.20606308065050e+00 1.75070440392768e-02 + 6 3.20788015841690e+00 1.75070440392768e-02 + 7 3.21006078117990e+00 1.75070440392768e-02 + 8 3.21246619986317e+00 1.75070440392768e-02 + 9 3.21494510727501e+00 1.75070440392768e-02 + 10 3.21734242206787e+00 2.85363794417943e-02 + 11 3.21950925117359e+00 2.85363794417943e-02 + 12 3.22131261706854e+00 2.85363794417943e-02 + 13 3.22264480741010e+00 2.85363794417943e-02 + 14 3.22343043310305e+00 2.85363794417943e-02 + 15 3.22363050330139e+00 3.62717655819535e-02 + 16 3.22324337253598e+00 3.62717655819535e-02 + 17 3.22230242928906e+00 3.62717655819535e-02 + 18 3.22087195749114e+00 3.62717655819535e-02 + 19 3.21904143773479e+00 3.62717655819535e-02 + 20 3.21691895295305e+00 4.48458537631430e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf index a4a179906..1433280e7 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.22178897971626e-01 - 7.50000000000000e-01 3.22178897971626e-01 - 1.25000000000000e+00 3.22035924052542e-01 - 1.75000000000000e+00 3.17765293358761e-01 - 2.25000000000000e+00 2.72047186250615e-01 - 2.75000000000000e+00 1.12664507199074e-01 + 2.50000000000000e-01 3.22178897974989e-01 + 7.50000000000000e-01 3.22178897974989e-01 + 1.25000000000000e+00 3.22035924056005e-01 + 1.75000000000000e+00 3.17765293364453e-01 + 2.25000000000000e+00 2.72047186271566e-01 + 2.75000000000000e+00 1.12664507238354e-01 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.39889291080873e-01 - 4.25000000000000e+00 2.84229231211129e-01 - 4.75000000000000e+00 3.19271965734657e-01 - 5.25000000000000e+00 3.22096968084170e-01 - 5.75000000000000e+00 3.22178897971626e-01 - 6.25000000000000e+00 3.22178897971626e-01 - 6.75000000000000e+00 3.22178897971626e-01 - 7.25000000000000e+00 3.22178897971626e-01 - 7.75000000000000e+00 3.22178897971626e-01 - 8.25000000000000e+00 3.22178897971626e-01 - 8.75000000000000e+00 3.22178897971626e-01 - 9.25000000000000e+00 3.22178897971626e-01 - 9.75000000000000e+00 3.22178897971626e-01 + 3.75000000000000e+00 1.39889291048735e-01 + 4.25000000000000e+00 2.84229231200015e-01 + 4.75000000000000e+00 3.19271965736361e-01 + 5.25000000000000e+00 3.22096968087471e-01 + 5.75000000000000e+00 3.22178897974989e-01 + 6.25000000000000e+00 3.22178897974989e-01 + 6.75000000000000e+00 3.22178897974989e-01 + 7.25000000000000e+00 3.22178897974989e-01 + 7.75000000000000e+00 3.22178897974989e-01 + 8.25000000000000e+00 3.22178897974989e-01 + 8.75000000000000e+00 3.22178897974989e-01 + 9.25000000000000e+00 3.22178897974989e-01 + 9.75000000000000e+00 3.22178897974989e-01 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out index 857505a84..817eae3a8 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -143,33 +139,21 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21692 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped index 37445afe6..86220cc57 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.state.stripped @@ -21,10 +21,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 2.39032008958370e-04 - 7.33347556564710e-03 8.27850280039973e-02 3.43860479556675e-01 - 5.25534912996650e-01 2.95535757364180e-01 6.11516158055121e-02 - 4.65581319200507e-03 1.30428682628954e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 2.39032008958375e-04 + 7.33347556564719e-03 8.27850280039980e-02 3.43860479556677e-01 + 5.25534912996650e-01 2.95535757364178e-01 6.11516158055115e-02 + 4.65581319200500e-03 1.30428682628952e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -36,10 +36,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.87569014992071e-03 - 4.28817998866071e-02 3.18539085938462e-01 6.35512332470773e-01 - -7.95903631638424e-02 -6.35715309684715e-01 -2.53820387793996e-01 - -2.86345787796512e-02 -1.06298017276162e-03 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.87569014992074e-03 + 4.28817998866076e-02 3.18539085938464e-01 6.35512332470772e-01 + -7.95903631638470e-02 -6.35715309684715e-01 -2.53820387793995e-01 + -2.86345787796509e-02 -1.06298017276160e-03 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj index f184c4075..dba722227 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21691895295305e+00 4.48458537631413e-02 - 21 3.21462413660772e+00 4.48458537631413e-02 - 22 3.21228032841215e+00 4.48458537631413e-02 - 23 3.21000702769477e+00 4.48458537631413e-02 - 24 3.20791264597674e+00 4.48458537631413e-02 - 25 3.20608840817769e+00 5.50378747704764e-02 - 26 3.20460419289259e+00 5.50378747704764e-02 - 27 3.20350601131064e+00 5.50378747704764e-02 - 28 3.20281599649048e+00 5.50378747704764e-02 - 29 3.20253382453620e+00 5.50378747704764e-02 - 30 3.20263930510781e+00 6.50046475230887e-02 - 31 3.20309591808115e+00 6.50046475230887e-02 - 32 3.20385452785452e+00 6.50046475230887e-02 - 33 3.20485802441983e+00 6.50046475230887e-02 - 34 3.20604606196811e+00 6.50046475230887e-02 - 35 3.20735962915093e+00 7.32270721427094e-02 - 36 3.20874513121416e+00 7.32270721427094e-02 - 37 3.21015715709204e+00 7.32270721427094e-02 - 38 3.21156064829882e+00 7.32270721427094e-02 - 39 3.21293211249028e+00 7.32270721427094e-02 - 40 3.21426020264931e+00 7.95903631638424e-02 + 20 3.21691895295305e+00 4.48458537631430e-02 + 21 3.21462413660771e+00 4.48458537631430e-02 + 22 3.21228032841214e+00 4.48458537631430e-02 + 23 3.21000702769477e+00 4.48458537631430e-02 + 24 3.20791264597674e+00 4.48458537631430e-02 + 25 3.20608840817769e+00 5.50378747704786e-02 + 26 3.20460419289258e+00 5.50378747704786e-02 + 27 3.20350601131064e+00 5.50378747704786e-02 + 28 3.20281599649047e+00 5.50378747704786e-02 + 29 3.20253382453620e+00 5.50378747704786e-02 + 30 3.20263930510781e+00 6.50046475230917e-02 + 31 3.20309591808115e+00 6.50046475230917e-02 + 32 3.20385452785452e+00 6.50046475230917e-02 + 33 3.20485802441983e+00 6.50046475230917e-02 + 34 3.20604606196811e+00 6.50046475230917e-02 + 35 3.20735962915093e+00 7.32270721427131e-02 + 36 3.20874513121416e+00 7.32270721427131e-02 + 37 3.21015715709204e+00 7.32270721427131e-02 + 38 3.21156064829882e+00 7.32270721427131e-02 + 39 3.21293211249027e+00 7.32270721427131e-02 + 40 3.21426020264931e+00 7.95903631638470e-02 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf index 29265ec37..f2f4c584a 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 5.25534912996650e-01 - 7.50000000000000e-01 5.25534912996650e-01 - 1.25000000000000e+00 5.25295880987692e-01 - 1.75000000000000e+00 5.18201437431003e-01 - 2.25000000000000e+00 4.42749884992653e-01 - 2.75000000000000e+00 1.81674433439975e-01 + 2.50000000000000e-01 5.25534913010848e-01 + 7.50000000000000e-01 5.25534913010848e-01 + 1.25000000000000e+00 5.25295881002282e-01 + 1.75000000000000e+00 5.18201437454156e-01 + 2.25000000000000e+00 4.42749885073309e-01 + 2.75000000000000e+00 1.81674433587149e-01 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 2.29999155632470e-01 - 4.25000000000000e+00 4.64383297191138e-01 - 4.75000000000000e+00 5.20879099804645e-01 - 5.25000000000000e+00 5.25404484314022e-01 - 5.75000000000000e+00 5.25534912996650e-01 - 6.25000000000000e+00 5.25534912996650e-01 - 6.75000000000000e+00 5.25534912996650e-01 - 7.25000000000000e+00 5.25534912996650e-01 - 7.75000000000000e+00 5.25534912996650e-01 - 8.25000000000000e+00 5.25534912996650e-01 - 8.75000000000000e+00 5.25534912996650e-01 - 9.25000000000000e+00 5.25534912996650e-01 - 9.75000000000000e+00 5.25534912996650e-01 + 3.75000000000000e+00 2.29999155517106e-01 + 4.25000000000000e+00 4.64383297153516e-01 + 4.75000000000000e+00 5.20879099813004e-01 + 5.25000000000000e+00 5.25404484328003e-01 + 5.75000000000000e+00 5.25534913010848e-01 + 6.25000000000000e+00 5.25534913010848e-01 + 6.75000000000000e+00 5.25534913010848e-01 + 7.25000000000000e+00 5.25534913010848e-01 + 7.75000000000000e+00 5.25534913010848e-01 + 8.25000000000000e+00 5.25534913010848e-01 + 8.75000000000000e+00 5.25534913010848e-01 + 9.25000000000000e+00 5.25534913010848e-01 + 9.75000000000000e+00 5.25534913010848e-01 diff --git a/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt index 157cac038..617210efd 100644 --- a/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics-wt/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-07-07". +colvars: Using NAMD interface, version "2020-05-04". diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out index bc1e4dfcd..0343b9172 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -140,27 +136,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped index ab45cb882..6de09bffd 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688278576757e+00 + x 3.21688278597333e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 3.46920493464415e-08 1.70721010337625e-05 6.58298335707084e-04 - 1.98901157282260e-03 4.70902104095221e-04 8.73580075153432e-06 + 3.46920492770083e-08 1.70721010112539e-05 6.58298335288197e-04 + 1.98901157291202e-03 4.70902104436801e-04 8.73580076380761e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 5.18433074964325e-07 1.68175610778412e-04 3.13214891049980e-03 - -6.66334790621162e-04 -2.55603942662786e-03 -9.19086518597186e-05 + 5.18433073974142e-07 1.68175610579987e-04 3.13214890940428e-03 + -6.66334787942696e-04 -2.55603942784152e-03 -9.19086519769792e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj index 56616ce4c..3ac32bb03 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 3.30884583877525e-04 - 11 3.21950367884164e+00 3.30884583877525e-04 - 12 3.22130501367398e+00 3.30884583877525e-04 - 13 3.22263482503343e+00 3.30884583877525e-04 - 14 3.22341774640647e+00 3.30884583877525e-04 - 15 3.22361481066343e+00 3.30884583877525e-04 - 16 3.22322427736760e+00 3.30884583877525e-04 - 17 3.22227956008091e+00 3.30884583877525e-04 - 18 3.22084496823082e+00 3.30884583877525e-04 - 19 3.21901000767136e+00 3.30884583877525e-04 - 20 3.21688278576757e+00 6.66334790621162e-04 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 3.30884583259955e-04 + 11 3.21950367891521e+00 3.30884583259955e-04 + 12 3.22130501376020e+00 3.30884583259955e-04 + 13 3.22263482513293e+00 3.30884583259955e-04 + 14 3.22341774651982e+00 3.30884583259955e-04 + 15 3.22361481079113e+00 3.30884583259955e-04 + 16 3.22322427751010e+00 3.30884583259955e-04 + 17 3.22227956023865e+00 3.30884583259955e-04 + 18 3.22084496840419e+00 3.30884583259955e-04 + 19 3.21901000786075e+00 3.30884583259955e-04 + 20 3.21688278597333e+00 6.66334787942696e-04 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf index 7a24c6664..3a05a7c71 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 1.98901157282260e-03 - 7.50000000000000e-01 1.98901157282260e-03 - 1.25000000000000e+00 1.98901157282260e-03 - 1.75000000000000e+00 1.98897688077326e-03 - 2.25000000000000e+00 1.97193947178884e-03 - 2.75000000000000e+00 1.33071323711552e-03 + 2.50000000000000e-01 1.98901157291202e-03 + 7.50000000000000e-01 1.98901157291202e-03 + 1.25000000000000e+00 1.98901157291202e-03 + 1.75000000000000e+00 1.98897688086274e-03 + 2.25000000000000e+00 1.97193947190077e-03 + 2.75000000000000e+00 1.33071323762382e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.51810946872738e-03 - 4.25000000000000e+00 1.98027577207107e-03 - 4.75000000000000e+00 1.98901157282260e-03 - 5.25000000000000e+00 1.98901157282260e-03 - 5.75000000000000e+00 1.98901157282260e-03 - 6.25000000000000e+00 1.98901157282260e-03 - 6.75000000000000e+00 1.98901157282260e-03 - 7.25000000000000e+00 1.98901157282260e-03 - 7.75000000000000e+00 1.98901157282260e-03 - 8.25000000000000e+00 1.98901157282260e-03 - 8.75000000000000e+00 1.98901157282260e-03 - 9.25000000000000e+00 1.98901157282260e-03 - 9.75000000000000e+00 1.98901157282260e-03 + 3.75000000000000e+00 1.51810946847522e-03 + 4.25000000000000e+00 1.98027577214821e-03 + 4.75000000000000e+00 1.98901157291202e-03 + 5.25000000000000e+00 1.98901157291202e-03 + 5.75000000000000e+00 1.98901157291202e-03 + 6.25000000000000e+00 1.98901157291202e-03 + 6.75000000000000e+00 1.98901157291202e-03 + 7.25000000000000e+00 1.98901157291202e-03 + 7.75000000000000e+00 1.98901157291202e-03 + 8.25000000000000e+00 1.98901157291202e-03 + 8.75000000000000e+00 1.98901157291202e-03 + 9.25000000000000e+00 1.98901157291202e-03 + 9.75000000000000e+00 1.98901157291202e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out index 625d7c300..1c3db0232 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -140,34 +136,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting metadynamics bias "metadynamics1" from step number 20. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped index 5f97bd617..235b1896e 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21405136086868e+00 + x 3.21405136134992e+00 } metadynamics { @@ -22,8 +22,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 7.43923406409864e-08 3.57122156643391e-05 1.34466139863962e-03 - 3.97104317611064e-03 9.19770326015385e-04 1.67080044137238e-05 + 7.43923403227782e-08 3.57122155647627e-05 1.34466139685731e-03 + 3.97104317655277e-03 9.19770327415716e-04 1.67080044623168e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -37,8 +37,8 @@ grid_parameters { sizes 20 } 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 1.10794466506920e-06 3.50062168801214e-04 6.33510418316085e-03 - -1.50805870086533e-03 -5.03195891344979e-03 -1.76471077412228e-04 + 1.10794466055357e-06 3.50062167930554e-04 6.33510417866273e-03 + -1.50805868972440e-03 -5.03195891853835e-03 -1.76471077879577e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj index e23343a0c..6b959f565 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688278576757e+00 6.66334790621162e-04 - 21 3.21458283239873e+00 6.66334790621162e-04 - 22 3.21223351050617e+00 6.66334790621162e-04 - 23 3.20995434250849e+00 6.66334790621162e-04 - 24 3.20785376273403e+00 6.66334790621162e-04 - 25 3.20602301866294e+00 6.66334790621162e-04 - 26 3.20453185466307e+00 6.66334790621162e-04 - 27 3.20342630641905e+00 6.66334790621162e-04 - 28 3.20272853356652e+00 6.66334790621162e-04 - 29 3.20243824083933e+00 6.66334790621162e-04 - 30 3.20253526840434e+00 1.14429095893840e-03 - 31 3.20298298236841e+00 1.14429095893840e-03 - 32 3.20373228203772e+00 1.14429095893840e-03 - 33 3.20472609467411e+00 1.14429095893840e-03 - 34 3.20590411329665e+00 1.14429095893840e-03 - 35 3.20720736568876e+00 1.14429095893840e-03 - 36 3.20858216935653e+00 1.14429095893840e-03 - 37 3.20998315165031e+00 1.14429095893840e-03 - 38 3.21137529148386e+00 1.14429095893840e-03 - 39 3.21273513229142e+00 1.14429095893840e-03 - 40 3.21405136086868e+00 1.50805870086533e-03 + 20 3.21688278597333e+00 6.66334787942696e-04 + 21 3.21458283262116e+00 6.66334787942696e-04 + 22 3.21223351074552e+00 6.66334787942696e-04 + 23 3.20995434276490e+00 6.66334787942696e-04 + 24 3.20785376300757e+00 6.66334787942696e-04 + 25 3.20602301895356e+00 6.66334787942696e-04 + 26 3.20453185497061e+00 6.66334787942696e-04 + 27 3.20342630674324e+00 6.66334787942696e-04 + 28 3.20272853390700e+00 6.66334787942696e-04 + 29 3.20243824119566e+00 6.66334787942696e-04 + 30 3.20253526877602e+00 1.14429095260314e-03 + 31 3.20298298275490e+00 1.14429095260314e-03 + 32 3.20373228243844e+00 1.14429095260314e-03 + 33 3.20472609508842e+00 1.14429095260314e-03 + 34 3.20590411372385e+00 1.14429095260314e-03 + 35 3.20720736612802e+00 1.14429095260314e-03 + 36 3.20858216980690e+00 1.14429095260314e-03 + 37 3.20998315211066e+00 1.14429095260314e-03 + 38 3.21137529195283e+00 1.14429095260314e-03 + 39 3.21273513276742e+00 1.14429095260314e-03 + 40 3.21405136134992e+00 1.50805868972440e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf index 38a897e10..051812fec 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf +++ b/namd/tests/library/000_distance-grid_metadynamics/AutoDiff/test.restart.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.97104317611064e-03 - 7.50000000000000e-01 3.97104317611064e-03 - 1.25000000000000e+00 3.97104317611064e-03 - 1.75000000000000e+00 3.97096878377000e-03 - 2.25000000000000e+00 3.93533096044630e-03 - 2.75000000000000e+00 2.62638177747102e-03 + 2.50000000000000e-01 3.97104317655277e-03 + 7.50000000000000e-01 3.97104317655277e-03 + 1.25000000000000e+00 3.97104317655277e-03 + 1.75000000000000e+00 3.97096878421245e-03 + 2.25000000000000e+00 3.93533096098801e-03 + 2.75000000000000e+00 2.62638177969546e-03 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 3.05127285009526e-03 - 4.25000000000000e+00 3.95433517169692e-03 - 4.75000000000000e+00 3.97104317611064e-03 - 5.25000000000000e+00 3.97104317611064e-03 - 5.75000000000000e+00 3.97104317611064e-03 - 6.25000000000000e+00 3.97104317611064e-03 - 6.75000000000000e+00 3.97104317611064e-03 - 7.25000000000000e+00 3.97104317611064e-03 - 7.75000000000000e+00 3.97104317611064e-03 - 8.25000000000000e+00 3.97104317611064e-03 - 8.75000000000000e+00 3.97104317611064e-03 - 9.25000000000000e+00 3.97104317611064e-03 - 9.75000000000000e+00 3.97104317611064e-03 + 3.75000000000000e+00 3.05127284913705e-03 + 4.25000000000000e+00 3.95433517209045e-03 + 4.75000000000000e+00 3.97104317655277e-03 + 5.25000000000000e+00 3.97104317655277e-03 + 5.75000000000000e+00 3.97104317655277e-03 + 6.25000000000000e+00 3.97104317655277e-03 + 6.75000000000000e+00 3.97104317655277e-03 + 7.25000000000000e+00 3.97104317655277e-03 + 7.75000000000000e+00 3.97104317655277e-03 + 8.25000000000000e+00 3.97104317655277e-03 + 8.75000000000000e+00 3.97104317655277e-03 + 9.25000000000000e+00 3.97104317655277e-03 + 9.75000000000000e+00 3.97104317655277e-03 diff --git a/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt b/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt +++ b/namd/tests/library/000_distance-grid_metadynamics/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out index dbedf374d..2fccbc3b5 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,26 +111,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped index 5268daf85..c1e336541 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253464583e+00 } diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj index 9f55268e7..787f78aa5 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 0.00000000000000e+00 + 11 3.21950367383415e+00 0.00000000000000e+00 + 12 3.22130499858006e+00 0.00000000000000e+00 + 13 3.22263479496347e+00 0.00000000000000e+00 + 14 3.22341769665784e+00 0.00000000000000e+00 + 15 3.22361473677138e+00 0.00000000000000e+00 + 16 3.22322417514557e+00 0.00000000000000e+00 + 17 3.22227942564879e+00 0.00000000000000e+00 + 18 3.22084479803044e+00 0.00000000000000e+00 + 19 3.21900979846930e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj b/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj index 31a359570..1a1e986ed 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.one.runave.traj @@ -1,8 +1,8 @@ # step running average running stddev - 8 3.20722823881721e+00 7.80321480520572e-03 - 10 4.01156286689271e+00 4.58710790766007e-01 - 12 4.01592904504379e+00 4.58975774808969e-01 - 14 4.02060142596487e+00 4.60400083999393e-01 - 16 4.02443749721375e+00 4.62636256583393e-01 - 18 4.02653254505012e+00 4.65172918760069e-01 - 20 4.02641855058464e+00 4.67427978018598e-01 + 8 3.20722823883620e+00 7.80321483722600e-03 + 10 4.01156286692710e+00 4.58710790751680e-01 + 12 4.01592904509911e+00 4.58975774793035e-01 + 14 4.02060142604598e+00 4.60400083982649e-01 + 16 4.02443749732474e+00 4.62636256566416e-01 + 18 4.02653254519438e+00 4.65172918743354e-01 + 20 4.02641855076493e+00 4.67427978002713e-01 diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out index 33058590a..98b6025c4 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,30 +111,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped index b307ede0d..139366ade 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878547144e+00 } diff --git a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj index 177b1bbb8..3b596ebde 100644 --- a/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-runave/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253444007e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 + 20 3.21688253464583e+00 0.00000000000000e+00 + 21 3.21458253157603e+00 0.00000000000000e+00 + 22 3.21223315254029e+00 0.00000000000000e+00 + 23 3.20995392032979e+00 0.00000000000000e+00 + 24 3.20785326966943e+00 0.00000000000000e+00 + 25 3.20602244845117e+00 0.00000000000000e+00 + 26 3.20453120146139e+00 0.00000000000000e+00 + 27 3.20342556480347e+00 0.00000000000000e+00 + 28 3.20272769852622e+00 0.00000000000000e+00 + 29 3.20243730776714e+00 0.00000000000000e+00 + 30 3.20253423308456e+00 0.00000000000000e+00 + 31 3.20298183362156e+00 0.00000000000000e+00 + 32 3.20373100914607e+00 0.00000000000000e+00 + 33 3.20472468746373e+00 0.00000000000000e+00 + 34 3.20590256221113e+00 0.00000000000000e+00 + 35 3.20720566184671e+00 0.00000000000000e+00 + 36 3.20858030459458e+00 0.00000000000000e+00 + 37 3.20998111854285e+00 0.00000000000000e+00 + 38 3.21137308334419e+00 0.00000000000000e+00 + 39 3.21273274315657e+00 0.00000000000000e+00 + 40 3.21404878547144e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-runave/namd-version.txt b/namd/tests/library/000_distance-runave/namd-version.txt index 157cac038..b7bf5455c 100644 --- a/namd/tests/library/000_distance-runave/namd-version.txt +++ b/namd/tests/library/000_distance-runave/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-10-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out index ec75406ef..5b1c03881 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out @@ -130,7 +130,7 @@ colvars: # forceConstant = 0.001 colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } -colvars: # upperWalls = { 0.3 } +colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.001 [default] colvars: # upperWallConstant = 0.001 [default] colvars: The lower wall force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped index 868eb59c6..83b0d62b7 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21549621301549e+00 - v 1.63839888121770e-04 - extended_x 3.20653095017852e+00 - extended_v 1.63839888121770e-04 + x 3.21549617587205e+00 + v 1.63765399419808e-04 + extended_x 3.20653014354441e+00 + extended_v 1.63765399419808e-04 } restraint { diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj index 64538e290..ea3cb4584 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 -1.16221869387334e-02 - 1 3.20437148316484e+00 3.20554661923758e+00 -1.17525151850328e-03 -1.15445759728991e-07 -1.16221864769503e-02 - 2 3.20384207658804e+00 3.20554522853325e+00 -5.29406576805336e-04 -1.39070433041396e-06 -1.16221809141330e-02 - 3 3.20397336375347e+00 3.20554204143963e+00 1.31287165431537e-04 -3.18709362372464e-06 -1.16221681657585e-02 - 4 3.20474099381307e+00 3.20553719067761e+00 7.67630059602453e-04 -4.85076201650243e-06 -1.16221487627105e-02 - 5 3.20608361746435e+00 3.20553143865541e+00 1.34262365128279e-03 -5.75202220486511e-06 -1.16221257546216e-02 - 6 3.20790704408264e+00 3.20552611616669e+00 1.82342661828994e-03 -5.32248871654545e-06 -1.16221044646668e-02 - 7 3.21008979782599e+00 3.20552302811470e+00 2.18275374334675e-03 -3.08805199324812e-06 -1.16220921124588e-02 - 8 3.21248979814124e+00 3.20552433183893e+00 2.40000031525378e-03 1.30372423308412e-06 -1.16220973273557e-02 - 9 3.21495218657788e+00 3.20553239475798e+00 2.46238843663571e-03 8.06291905077686e-06 -1.16221295790319e-02 - 10 3.21731839169077e+00 3.20554963919372e+00 2.36620511289365e-03 1.72444357411129e-05 -1.16221985567749e-02 - 11 3.21943620459394e+00 3.20557838347673e+00 2.11781290316582e-03 2.87442830099992e-05 -1.16223135339069e-02 - 12 3.22117011052185e+00 3.20562068943396e+00 1.73390592791511e-03 4.23059572215591e-05 -1.16224827577358e-02 - 13 3.22241069262564e+00 3.20567822660596e+00 1.24058210378664e-03 5.75371720037448e-05 -1.16227129064238e-02 - 14 3.22308185566108e+00 3.20575216260901e+00 6.71163035445232e-04 7.39360030463537e-05 -1.16230086504360e-02 - 15 3.22314499588221e+00 3.20584308687961e+00 6.31402211261900e-05 9.09242706060132e-05 -1.16233723475184e-02 - 16 3.22259984691011e+00 3.20595097199241e+00 -5.45148972103338e-04 1.07885112795286e-04 -1.16238038879696e-02 - 17 3.22148234906601e+00 3.20607517342430e+00 -1.11749784410220e-03 1.24201431890135e-04 -1.16243006936972e-02 - 18 3.21986026327429e+00 3.20621446566228e+00 -1.62208579171264e-03 1.39292237986185e-04 -1.16248578626491e-02 - 19 3.21782728428053e+00 3.20636711029040e+00 -2.03297899376365e-03 1.52644628112363e-04 -1.16254684411616e-02 - 20 3.21549621301549e+00 3.20653095017852e+00 -2.33107126504306e-03 1.63839888121770e-04 -1.16261238007141e-02 + 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 -1.20221869387334e-02 + 1 3.20437148316484e+00 3.20554661526430e+00 -1.17525151850328e-03 -1.19419048416827e-07 -1.20221864610572e-02 + 2 3.20384207658198e+00 3.20554521661731e+00 -5.29406582859160e-04 -1.39864698615333e-06 -1.20221808664692e-02 + 3 3.20397336372329e+00 3.20554201761950e+00 1.31287141313052e-04 -3.19899781308815e-06 -1.20221680704780e-02 + 4 3.20474099372294e+00 3.20553715100348e+00 7.67629999647745e-04 -4.86661601385684e-06 -1.20221486040139e-02 + 5 3.20608361725515e+00 3.20553137919306e+00 1.34262353221182e-03 -5.77181042148448e-06 -1.20221255167722e-02 + 6 3.20790704366680e+00 3.20552603300132e+00 1.82342641164146e-03 -5.34619173897510e-06 -1.20221041320053e-02 + 7 3.21008979708265e+00 3.20552291735469e+00 2.18275341585361e-03 -3.11564663055446e-06 -1.20220916694188e-02 + 8 3.21248979691190e+00 3.20552418961958e+00 2.39999982925276e-03 1.27226489358961e-06 -1.20220967584783e-02 + 9 3.21495218466242e+00 3.20553221724516e+00 2.46238775052099e-03 8.02762557980444e-06 -1.20221288689807e-02 + 10 3.21731838884401e+00 3.20554942258746e+00 2.36620418158973e-03 1.72053422961567e-05 -1.20221976903498e-02 + 11 3.21943620052261e+00 3.20557812401472e+00 2.11781167860092e-03 2.87014272571360e-05 -1.20223124960589e-02 + 12 3.22117010488210e+00 3.20562038339497e+00 1.73390435948928e-03 4.22593802508272e-05 -1.20224815335799e-02 + 13 3.22241068502092e+00 3.20567787031321e+00 1.24058013882022e-03 5.74869182386481e-05 -1.20227114812528e-02 + 14 3.22308184564051e+00 3.20575175243336e+00 6.71160619590605e-04 7.38821201480224e-05 -1.20230070097334e-02 + 15 3.22314498293928e+00 3.20584261924273e+00 6.31372987673906e-05 9.08668093725243e-05 -1.20233704769709e-02 + 16 3.22259983048180e+00 3.20595044336978e+00 -5.45152457477549e-04 1.07824127056634e-04 -1.20238017734791e-02 + 17 3.22148232853223e+00 3.20607458034818e+00 -1.11750194957105e-03 1.24136978399328e-04 -1.20242983213927e-02 + 18 3.21986023795765e+00 3.20621380472449e+00 -1.62209057458140e-03 1.39224376306895e-04 -1.20248552188980e-02 + 19 3.21782725344634e+00 3.20636637814499e+00 -2.03298451131184e-03 1.52573420503577e-04 -1.20254655125800e-02 + 20 3.21549617587205e+00 3.20653014354441e+00 -2.33107757428819e-03 1.63765399419808e-04 -1.20261205741777e-02 diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out index af642ac95..fd298f3cd 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out @@ -130,7 +130,7 @@ colvars: # forceConstant = 0.001 colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } -colvars: # upperWalls = { 0.3 } +colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.001 [default] colvars: # upperWallConstant = 0.001 [default] colvars: The lower wall force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). @@ -162,7 +162,7 @@ colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.2155 -colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. +colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 0. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped index 67e9debbf..740730ef2 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21130958093225e+00 - v 1.01074979342738e-04 - extended_x 3.20938413437057e+00 - extended_v 1.01074979342738e-04 + x 3.21130917292044e+00 + v 1.00951348854985e-04 + extended_x 3.20938126631322e+00 + extended_v 1.00951348854985e-04 } restraint { diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj index 457fcb155..e35e1b0ba 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 20 3.21549621301549e+00 3.20653095017852e+00 0.00000000000000e+00 1.63839888121770e-04 -1.16261238007141e-02 - 21 3.21299151121102e+00 3.20670352294153e+00 -2.50470180446749e-03 1.72572763011582e-04 -1.16268140917661e-02 - 22 3.21044145238583e+00 3.20688218620849e+00 -2.55005882518766e-03 1.78663266959169e-04 -1.16275287448340e-02 - 23 3.20797018574579e+00 3.20706424683154e+00 -2.47126664004549e-03 1.82060623050948e-04 -1.16282569873262e-02 - 24 3.20569026122289e+00 3.20724708607441e+00 -2.27992452289572e-03 1.82839242865593e-04 -1.16289883442976e-02 - 25 3.20369635095381e+00 3.20742827327941e+00 -1.99391026908335e-03 1.81187205005368e-04 -1.16297130931177e-02 - 26 3.20206080670596e+00 3.20760566170420e+00 -1.63554424784840e-03 1.77388424785744e-04 -1.16304226468168e-02 - 27 3.20083139121777e+00 3.20777746204889e+00 -1.22941548818822e-03 1.71800344689496e-04 -1.16311098481956e-02 - 28 3.20003110175216e+00 3.20794229136206e+00 -8.00289465613613e-04 1.64829313172020e-04 -1.16317691654482e-02 - 29 3.19965963674732e+00 3.20809919710311e+00 -3.71465004831428e-04 1.56905741050733e-04 -1.16323967884124e-02 - 30 3.19969607653556e+00 3.20824765778478e+00 3.64397882326450e-05 1.48460681671230e-04 -1.16329906311391e-02 - 31 3.20010239198518e+00 3.20838756284098e+00 4.06315449623662e-04 1.39905056202667e-04 -1.16335502513639e-02 - 32 3.20082761419017e+00 3.20851917520268e+00 7.25222204989162e-04 1.31612361694413e-04 -1.16340767008107e-02 - 33 3.20181248689262e+00 3.20864308073407e+00 9.84872702445738e-04 1.23905531389011e-04 -1.16345723229363e-02 - 34 3.20299435917704e+00 3.20876012917077e+00 1.18187228442679e-03 1.17048436698551e-04 -1.16350405166831e-02 - 35 3.20431188560568e+00 3.20887137144714e+00 1.31752642863958e-03 1.11242276370810e-04 -1.16354854857885e-02 - 36 3.20570909188769e+00 3.20897799811350e+00 1.39720628201090e-03 1.06626666360912e-04 -1.16359119924540e-02 - 37 3.20713846663531e+00 3.20908128291664e+00 1.42937474761640e-03 1.03284803139886e-04 -1.16363251316666e-02 - 38 3.20856305344034e+00 3.20918253465077e+00 1.42458680502822e-03 1.01251734130282e-04 -1.16367301386031e-02 - 39 3.20995768936497e+00 3.20928305939123e+00 1.39463592463418e-03 1.00524740461639e-04 -1.16371322375649e-02 - 40 3.21130958093225e+00 3.20938413437057e+00 1.35189156727877e-03 1.01074979342738e-04 -1.16375365374823e-02 + 20 3.21549617587205e+00 3.20653014354441e+00 0.00000000000000e+00 1.63765399419808e-04 -1.20261205741776e-02 + 21 3.21299146691002e+00 3.20670263860492e+00 -2.50470896202648e-03 1.72495060509838e-04 -1.20268105544197e-02 + 22 3.21044140002284e+00 3.20688122102521e+00 -2.55006688718051e-03 1.78582420285797e-04 -1.20275248841008e-02 + 23 3.20797012436086e+00 3.20706319772925e+00 -2.47127566198468e-03 1.81976704044760e-04 -1.20282527909170e-02 + 24 3.20569018980129e+00 3.20724595005470e+00 -2.27993455957121e-03 1.82752325450367e-04 -1.20289838002188e-02 + 25 3.20369626842688e+00 3.20742704741977e+00 -1.99392137440801e-03 1.81097365062805e-04 -1.20297081896791e-02 + 26 3.20206071195224e+00 3.20760434315979e+00 -1.63555647464264e-03 1.77295740027368e-04 -1.20304173726392e-02 + 27 3.20083128306446e+00 3.20777604805432e+00 -1.22942888777944e-03 1.71704894527817e-04 -1.20311041922173e-02 + 28 3.20003097897692e+00 3.20794077923291e+00 -8.00304087535064e-04 1.64731178591497e-04 -1.20317631169316e-02 + 29 3.19965949808046e+00 3.20809758423739e+00 -3.71480896461218e-04 1.56805004478955e-04 -1.20323903369496e-02 + 30 3.19969592066247e+00 3.20824594166424e+00 3.64225820090880e-05 1.48357426850803e-04 -1.20329837666570e-02 + 31 3.20010221754926e+00 3.20838574103230e+00 4.06296886787061e-04 1.39799368064253e-04 -1.20335429641292e-02 + 32 3.20082741979556e+00 3.20851724535854e+00 7.25202246302015e-04 1.31504326231438e-04 -1.20340689814341e-02 + 33 3.20181227110765e+00 3.20864104059407e+00 9.84851312094914e-04 1.23795235534061e-04 -1.20345641623763e-02 + 34 3.20299412053733e+00 3.20875797656227e+00 1.18184942967092e-03 1.16935968202223e-04 -1.20350319062491e-02 + 35 3.20431162261699e+00 3.20886910428595e+00 1.31750207966386e-03 1.11127723682791e-04 -1.20354764171438e-02 + 36 3.20570880302891e+00 3.20897561440447e+00 1.39718041191950e-03 1.06510118513249e-04 -1.20359024576179e-02 + 37 3.20713815036053e+00 3.20907878075410e+00 1.42934733162248e-03 1.03166349632568e-04 -1.20363151230164e-02 + 38 3.20856270818102e+00 3.20917991221892e+00 1.42455782049122e-03 1.01131464818439e-04 -1.20367196488757e-02 + 39 3.20995731353255e+00 3.20928031496436e+00 1.39460535153013e-03 1.00402745444511e-04 -1.20371212598575e-02 + 40 3.21130917292044e+00 3.20938126631322e+00 1.35185938788940e-03 1.00951348854985e-04 -1.20375250652529e-02 diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt b/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/test.in b/namd/tests/library/000_distance-wall-bypassExtended-off/test.in index 770d32a5b..5a5def555 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/test.in +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/test.in @@ -30,7 +30,7 @@ colvar { harmonicWalls { colvars one lowerWalls 0.1 - upperWalls 0.3 + upperWalls 0.2 forceConstant 0.001 bypassExtendedLagrangian off } diff --git a/namd/tests/library/000_distance/AutoDiff/test.colvars.out b/namd/tests/library/000_distance/AutoDiff/test.colvars.out index 27f0966fb..1edf5300b 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,26 +108,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped index 5268daf85..283a80870 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance/AutoDiff/test.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21688253444007e+00 + x 3.21688253462243e+00 } diff --git a/namd/tests/library/000_distance/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance/AutoDiff/test.colvars.traj index 9f55268e7..d19a63aaf 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 0.00000000000000e+00 - 11 3.21950367376059e+00 0.00000000000000e+00 - 12 3.22130499849384e+00 0.00000000000000e+00 - 13 3.22263479486396e+00 0.00000000000000e+00 - 14 3.22341769654449e+00 0.00000000000000e+00 - 15 3.22361473664369e+00 0.00000000000000e+00 - 16 3.22322417500307e+00 0.00000000000000e+00 - 17 3.22227942549106e+00 0.00000000000000e+00 - 18 3.22084479785707e+00 0.00000000000000e+00 - 19 3.21900979827991e+00 0.00000000000000e+00 - 20 3.21688253444007e+00 0.00000000000000e+00 + 1 3.20437148316545e+00 0.00000000000000e+00 + 2 3.20384028594369e+00 0.00000000000000e+00 + 3 3.20396721187615e+00 0.00000000000000e+00 + 4 3.20472817290791e+00 0.00000000000000e+00 + 5 3.20606308065559e+00 0.00000000000000e+00 + 6 3.20787989002674e+00 0.00000000000000e+00 + 7 3.21005997944336e+00 0.00000000000000e+00 + 8 3.21246460656400e+00 0.00000000000000e+00 + 9 3.21494247390735e+00 0.00000000000000e+00 + 10 3.21733851238969e+00 0.00000000000000e+00 + 11 3.21950367386500e+00 0.00000000000000e+00 + 12 3.22130499861355e+00 0.00000000000000e+00 + 13 3.22263479499712e+00 0.00000000000000e+00 + 14 3.22341769668903e+00 0.00000000000000e+00 + 15 3.22361473679752e+00 0.00000000000000e+00 + 16 3.22322417516431e+00 0.00000000000000e+00 + 17 3.22227942565775e+00 0.00000000000000e+00 + 18 3.22084479802894e+00 0.00000000000000e+00 + 19 3.21900979846159e+00 0.00000000000000e+00 + 20 3.21688253462243e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out index f4778ef00..3a7264d71 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -112,30 +108,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped index b307ede0d..9b4200d28 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21404878499019e+00 + x 3.21404878546491e+00 } diff --git a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj index 177b1bbb8..2f8dd9cef 100644 --- a/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253444007e+00 0.00000000000000e+00 - 21 3.21458253135360e+00 0.00000000000000e+00 - 22 3.21223315230095e+00 0.00000000000000e+00 - 23 3.20995392007338e+00 0.00000000000000e+00 - 24 3.20785326939589e+00 0.00000000000000e+00 - 25 3.20602244816055e+00 0.00000000000000e+00 - 26 3.20453120115385e+00 0.00000000000000e+00 - 27 3.20342556447929e+00 0.00000000000000e+00 - 28 3.20272769818575e+00 0.00000000000000e+00 - 29 3.20243730741081e+00 0.00000000000000e+00 - 30 3.20253423271288e+00 0.00000000000000e+00 - 31 3.20298183323508e+00 0.00000000000000e+00 - 32 3.20373100874536e+00 0.00000000000000e+00 - 33 3.20472468704943e+00 0.00000000000000e+00 - 34 3.20590256178394e+00 0.00000000000000e+00 - 35 3.20720566140745e+00 0.00000000000000e+00 - 36 3.20858030414420e+00 0.00000000000000e+00 - 37 3.20998111808250e+00 0.00000000000000e+00 - 38 3.21137308287521e+00 0.00000000000000e+00 - 39 3.21273274268056e+00 0.00000000000000e+00 - 40 3.21404878499019e+00 0.00000000000000e+00 + 20 3.21688253462243e+00 0.00000000000000e+00 + 21 3.21458253154238e+00 0.00000000000000e+00 + 22 3.21223315249804e+00 0.00000000000000e+00 + 23 3.20995392028117e+00 0.00000000000000e+00 + 24 3.20785326961705e+00 0.00000000000000e+00 + 25 3.20602244839787e+00 0.00000000000000e+00 + 26 3.20453120140997e+00 0.00000000000000e+00 + 27 3.20342556475651e+00 0.00000000000000e+00 + 28 3.20272769848587e+00 0.00000000000000e+00 + 29 3.20243730773497e+00 0.00000000000000e+00 + 30 3.20253423306146e+00 0.00000000000000e+00 + 31 3.20298183360766e+00 0.00000000000000e+00 + 32 3.20373100914076e+00 0.00000000000000e+00 + 33 3.20472468746573e+00 0.00000000000000e+00 + 34 3.20590256221861e+00 0.00000000000000e+00 + 35 3.20720566185745e+00 0.00000000000000e+00 + 36 3.20858030460613e+00 0.00000000000000e+00 + 37 3.20998111855282e+00 0.00000000000000e+00 + 38 3.21137308335033e+00 0.00000000000000e+00 + 39 3.21273274315706e+00 0.00000000000000e+00 + 40 3.21404878546491e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance/namd-version.txt b/namd/tests/library/000_distance/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance/namd-version.txt +++ b/namd/tests/library/000_distance/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out index aa012e652..3ab6145e8 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,27 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped index 7932133bf..4e365695b 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685433498741e+00 + x 3.21685433519314e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22496300314925e-03 + accumulatedWork -1.22496300318146e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj index 036216748..7f6576778 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788600e+00 -1.23974855515440e-02 1.92122060000928e-02 1.05000000000000e-01 -6.19874277577201e-05 - 2 3.20383990649741e+00 -1.23753596259897e-02 1.91436907340719e-02 1.10000000000000e-01 -1.23864225887668e-04 - 3 3.20396636368840e+00 -1.23558654547536e-02 1.90834263919967e-02 1.15000000000000e-01 -1.85643553161436e-04 - 4 3.20472667755350e+00 -1.23389067102140e-02 1.90310773504205e-02 1.20000000000000e-01 -2.47338086712507e-04 - 5 3.20606076806240e+00 -1.23242430722496e-02 1.89858709129865e-02 1.25000000000000e-01 -3.08959302073754e-04 - 6 3.20787659962477e+00 -1.23115063984991e-02 1.89466487250355e-02 1.30000000000000e-01 -3.70516834066250e-04 - 7 3.21005556140311e+00 -1.23002222456125e-02 1.89119334114324e-02 1.35000000000000e-01 -4.32017945294312e-04 - 8 3.21245892236459e+00 -1.22898356894584e-02 1.88800076592355e-02 1.40000000000000e-01 -4.93467123741604e-04 - 9 3.21493539653826e+00 -1.22797415861530e-02 1.88490066778370e-02 1.45000000000000e-01 -5.54865831672369e-04 - 10 3.21732992614691e+00 -1.22693197045876e-02 1.88170257516728e-02 1.50000000000000e-01 -6.16212430195307e-04 - 11 3.21949347377062e+00 -1.22579738950825e-02 1.87822405015655e-02 1.55000000000000e-01 -6.77502299670720e-04 - 12 3.22129308953064e+00 -1.22451723581226e-02 1.87430307600161e-02 1.60000000000000e-01 -7.38728161461332e-04 - 13 3.22262109049609e+00 -1.22304843619843e-02 1.86980934660929e-02 1.65000000000000e-01 -7.99880583271254e-04 - 14 3.22340211781424e+00 -1.22136084712570e-02 1.86465289861450e-02 1.70000000000000e-01 -8.60948625627539e-04 - 15 3.22359721084197e+00 -1.21943888433679e-02 1.85878899079069e-02 1.75000000000000e-01 -9.21920569844378e-04 - 16 3.22320463454852e+00 -1.21728185381941e-02 1.85221888954752e-02 1.80000000000000e-01 -9.82784662535349e-04 - 17 3.22225780700082e+00 -1.21490312280033e-02 1.84498699723748e-02 1.85000000000000e-01 -1.04352981867537e-03 - 18 3.22082104146627e+00 -1.21232841658651e-02 1.83717523707893e-02 1.90000000000000e-01 -1.10414623950469e-03 - 19 3.21898384724052e+00 -1.20959353889621e-02 1.82889566167431e-02 1.95000000000000e-01 -1.16462591644950e-03 - 20 3.21685433498741e+00 -1.20674173399496e-02 1.82028201570646e-02 2.00000000000000e-01 -1.22496300314925e-03 + 1 3.20437138788663e+00 -1.23974855515465e-02 1.92122060001005e-02 1.05000000000000e-01 -6.19874277577326e-05 + 2 3.20383990649994e+00 -1.23753596259998e-02 1.91436907341031e-02 1.10000000000000e-01 -1.23864225887731e-04 + 3 3.20396636369412e+00 -1.23558654547765e-02 1.90834263920673e-02 1.15000000000000e-01 -1.85643553161614e-04 + 4 3.20472667756370e+00 -1.23389067102548e-02 1.90310773505463e-02 1.20000000000000e-01 -2.47338086712888e-04 + 5 3.20606076807835e+00 -1.23242430723134e-02 1.89858709131831e-02 1.25000000000000e-01 -3.08959302074455e-04 + 6 3.20787659964770e+00 -1.23115063985908e-02 1.89466487253177e-02 1.30000000000000e-01 -3.70516834067408e-04 + 7 3.21005556143417e+00 -1.23002222457367e-02 1.89119334118145e-02 1.35000000000000e-01 -4.32017945296092e-04 + 8 3.21245892240487e+00 -1.22898356896195e-02 1.88800076597306e-02 1.40000000000000e-01 -4.93467123744190e-04 + 9 3.21493539658876e+00 -1.22797415863550e-02 1.88490066784571e-02 1.45000000000000e-01 -5.54865831675965e-04 + 10 3.21732992620853e+00 -1.22693197048341e-02 1.88170257524289e-02 1.50000000000000e-01 -6.16212430200135e-04 + 11 3.21949347384418e+00 -1.22579738953767e-02 1.87822405024671e-02 1.55000000000000e-01 -6.77502299677019e-04 + 12 3.22129308961685e+00 -1.22451723584674e-02 1.87430307610718e-02 1.60000000000000e-01 -7.38728161469356e-04 + 13 3.22262109059558e+00 -1.22304843623823e-02 1.86980934673098e-02 1.65000000000000e-01 -7.99880583281267e-04 + 14 3.22340211792757e+00 -1.22136084717103e-02 1.86465289875292e-02 1.70000000000000e-01 -8.60948625639819e-04 + 15 3.22359721096965e+00 -1.21943888438786e-02 1.85878899094638e-02 1.75000000000000e-01 -9.21920569859212e-04 + 16 3.22320463469100e+00 -1.21728185387640e-02 1.85221888972096e-02 1.80000000000000e-01 -9.82784662553032e-04 + 17 3.22225780715853e+00 -1.21490312286341e-02 1.84498699742909e-02 1.85000000000000e-01 -1.04352981869620e-03 + 18 3.22082104163962e+00 -1.21232841665585e-02 1.83717523728909e-02 1.90000000000000e-01 -1.10414623952900e-03 + 19 3.21898384742989e+00 -1.20959353897195e-02 1.82889566190337e-02 1.95000000000000e-01 -1.16462591647759e-03 + 20 3.21685433519314e+00 -1.20674173407726e-02 1.82028201595473e-02 2.00000000000000e-01 -1.22496300318146e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out index fb727736f..baca0fc5b 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,32 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped index 1f650f086..e0888c9dd 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397283795342e+00 + x 3.21397283843462e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22496300314925e-03 + accumulatedWork -1.22496300318146e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj index ad5f71a3c..d650368f1 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685433498741e+00 -1.20674173399496e-02 1.82028201570646e-02 2.00000000000000e-01 -1.22496300314925e-03 - 21 3.21455203283509e+00 -1.20582081313404e-02 1.81750479173404e-02 2.00000000000000e-01 -1.22496300314925e-03 - 22 3.21220030725328e+00 -1.20488012290131e-02 1.81467013820335e-02 2.00000000000000e-01 -1.22496300314925e-03 - 23 3.20991868485870e+00 -1.20396747394348e-02 1.81192209789231e-02 2.00000000000000e-01 -1.22496300314925e-03 - 24 3.20781560502190e+00 -1.20312624200876e-02 1.80939094276265e-02 2.00000000000000e-01 -1.22496300314925e-03 - 25 3.20598232125433e+00 -1.20239292850173e-02 1.80718594313871e-02 2.00000000000000e-01 -1.22496300314925e-03 - 26 3.20448858493049e+00 -1.20179543397220e-02 1.80539033139553e-02 2.00000000000000e-01 -1.22496300314925e-03 - 27 3.20338043966796e+00 -1.20135217586718e-02 1.80405881307602e-02 2.00000000000000e-01 -1.22496300314925e-03 - 28 3.20268005376972e+00 -1.20107202150789e-02 1.80321750106130e-02 2.00000000000000e-01 -1.22496300314925e-03 - 29 3.20238714117950e+00 -1.20095485647180e-02 1.80286570910400e-02 2.00000000000000e-01 -1.22496300314925e-03 - 30 3.20248155154737e+00 -1.20099262061895e-02 1.80297909347646e-02 2.00000000000000e-01 -1.22496300314925e-03 - 31 3.20292665302594e+00 -1.20117066121038e-02 1.80351369669071e-02 2.00000000000000e-01 -1.22496300314925e-03 - 32 3.20367335392557e+00 -1.20146934157023e-02 1.80441072341650e-02 2.00000000000000e-01 -1.22496300314925e-03 - 33 3.20466458978601e+00 -1.20186583591440e-02 1.80560185942279e-02 2.00000000000000e-01 -1.22496300314925e-03 - 34 3.20584006083970e+00 -1.20233602433588e-02 1.80701489426977e-02 2.00000000000000e-01 -1.22496300314925e-03 - 35 3.20714080059199e+00 -1.20285632023680e-02 1.80857915891700e-02 2.00000000000000e-01 -1.22496300314925e-03 - 36 3.20851313064513e+00 -1.20340525225805e-02 1.81023025145283e-02 2.00000000000000e-01 -1.22496300314925e-03 - 37 3.20991168059037e+00 -1.20396467223615e-02 1.81191366499087e-02 2.00000000000000e-01 -1.22496300314925e-03 - 38 3.21130142981427e+00 -1.20452057192571e-02 1.81358726024029e-02 2.00000000000000e-01 -1.22496300314925e-03 - 39 3.21265892071976e+00 -1.20506356828790e-02 1.81522275451847e-02 2.00000000000000e-01 -1.22496300314925e-03 - 40 3.21397283795342e+00 -1.20558913518137e-02 1.81680645358420e-02 2.00000000000000e-01 -1.22496300314925e-03 + 20 3.21685433519314e+00 -1.20674173407726e-02 1.82028201595473e-02 2.00000000000000e-01 -1.22496300318146e-03 + 21 3.21455203305750e+00 -1.20582081322300e-02 1.81750479200222e-02 2.00000000000000e-01 -1.22496300318146e-03 + 22 3.21220030749260e+00 -1.20488012299704e-02 1.81467013849170e-02 2.00000000000000e-01 -1.22496300318146e-03 + 23 3.20991868511508e+00 -1.20396747404603e-02 1.81192209820098e-02 2.00000000000000e-01 -1.22496300318146e-03 + 24 3.20781560529541e+00 -1.20312624211816e-02 1.80939094309172e-02 2.00000000000000e-01 -1.22496300318146e-03 + 25 3.20598232154492e+00 -1.20239292861797e-02 1.80718594348811e-02 2.00000000000000e-01 -1.22496300318146e-03 + 26 3.20448858523800e+00 -1.20179543409520e-02 1.80539033176509e-02 2.00000000000000e-01 -1.22496300318146e-03 + 27 3.20338043999211e+00 -1.20135217599685e-02 1.80405881346544e-02 2.00000000000000e-01 -1.22496300318146e-03 + 28 3.20268005411016e+00 -1.20107202164406e-02 1.80321750147019e-02 2.00000000000000e-01 -1.22496300318146e-03 + 29 3.20238714153578e+00 -1.20095485661431e-02 1.80286570953188e-02 2.00000000000000e-01 -1.22496300318146e-03 + 30 3.20248155191901e+00 -1.20099262076760e-02 1.80297909392280e-02 2.00000000000000e-01 -1.22496300318146e-03 + 31 3.20292665341239e+00 -1.20117066136495e-02 1.80351369715490e-02 2.00000000000000e-01 -1.22496300318146e-03 + 32 3.20367335432625e+00 -1.20146934173050e-02 1.80441072389790e-02 2.00000000000000e-01 -1.22496300318146e-03 + 33 3.20466459020028e+00 -1.20186583608011e-02 1.80560185992068e-02 2.00000000000000e-01 -1.22496300318146e-03 + 34 3.20584006126686e+00 -1.20233602450674e-02 1.80701489478335e-02 2.00000000000000e-01 -1.22496300318146e-03 + 35 3.20714080103121e+00 -1.20285632041248e-02 1.80857915944533e-02 2.00000000000000e-01 -1.22496300318146e-03 + 36 3.20851313109546e+00 -1.20340525243818e-02 1.81023025199476e-02 2.00000000000000e-01 -1.22496300318146e-03 + 37 3.20991168105067e+00 -1.20396467242027e-02 1.81191366554506e-02 2.00000000000000e-01 -1.22496300318146e-03 + 38 3.21130143028320e+00 -1.20452057211328e-02 1.81358726080512e-02 2.00000000000000e-01 -1.22496300318146e-03 + 39 3.21265892119573e+00 -1.20506356847829e-02 1.81522275509204e-02 2.00000000000000e-01 -1.22496300318146e-03 + 40 3.21397283843462e+00 -1.20558913537385e-02 1.81680645416433e-02 2.00000000000000e-01 -1.22496300318146e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt b/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-centers-moving-full/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out index 2bce89042..9d06eb030 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 4 colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,27 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped index e298649e7..1cf9a8664 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685409675932e+00 + x 3.21685409696506e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj index 5c980cf93..66081f9e6 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 - 1 3.20437138788600e+00 -1.24174855515440e-02 1.92742434278505e-02 1.00000000000000e-01 - 2 3.20383990619069e+00 -1.24153596247627e-02 1.92676443265236e-02 1.00000000000000e-01 - 3 3.20396636246577e+00 -1.24158654498631e-02 1.92692143586380e-02 1.00000000000000e-01 - 4 3.20472667451135e+00 -1.24189066980454e-02 1.92786554468447e-02 1.00000000000000e-01 - 5 3.20606076201392e+00 -1.24242430480557e-02 1.92952269146450e-02 1.00000000000000e-01 - 6 3.20787658911377e+00 -1.24315063564551e-02 1.93177937863229e-02 1.00000000000000e-01 - 7 3.21005554471991e+00 -1.24402221788797e-02 1.93448909824861e-02 1.00000000000000e-01 - 8 3.21245889756338e+00 -1.24498355902535e-02 1.93748007780429e-02 1.00000000000000e-01 - 9 3.21493536145531e+00 -1.23597414458212e-02 1.90954010759439e-02 1.25000000000000e-01 - 10 3.21732987995403e+00 -1.23693195198161e-02 1.91250081729130e-02 1.25000000000000e-01 - 11 3.21949341543930e+00 -1.23779736617572e-02 1.91517789963944e-02 1.25000000000000e-01 - 12 3.22129301782985e+00 -1.23851720713194e-02 1.91740609045237e-02 1.25000000000000e-01 - 13 3.22262100399005e+00 -1.23904840159602e-02 1.91905117687206e-02 1.25000000000000e-01 - 14 3.22340201486115e+00 -1.23936080594446e-02 1.92001900913912e-02 1.25000000000000e-01 - 15 3.22359708959410e+00 -1.23943883583764e-02 1.92026078472821e-02 1.25000000000000e-01 - 16 3.22320449295439e+00 -1.23928179718176e-02 1.91977421603256e-02 1.25000000000000e-01 - 17 3.22225764280973e+00 -1.22890305712389e-02 1.88775340476056e-02 1.50000000000000e-01 - 18 3.22082085377380e+00 -1.22832834150952e-02 1.88598814319441e-02 1.50000000000000e-01 - 19 3.21898363493937e+00 -1.22759345397575e-02 1.88373211030514e-02 1.50000000000000e-01 - 20 3.21685409675932e+00 -1.22674163870373e-02 1.88111881016189e-02 1.50000000000000e-01 + 1 3.20437138788663e+00 -1.24174855515465e-02 1.92742434278583e-02 1.00000000000000e-01 + 2 3.20383990619321e+00 -1.24153596247728e-02 1.92676443265549e-02 1.00000000000000e-01 + 3 3.20396636247149e+00 -1.24158654498859e-02 1.92692143587090e-02 1.00000000000000e-01 + 4 3.20472667452156e+00 -1.24189066980862e-02 1.92786554469713e-02 1.00000000000000e-01 + 5 3.20606076202988e+00 -1.24242430481195e-02 1.92952269148432e-02 1.00000000000000e-01 + 6 3.20787658913670e+00 -1.24315063565468e-02 1.93177937866079e-02 1.00000000000000e-01 + 7 3.21005554475098e+00 -1.24402221790039e-02 1.93448909828726e-02 1.00000000000000e-01 + 8 3.21245889760366e+00 -1.24498355904147e-02 1.93748007785444e-02 1.00000000000000e-01 + 9 3.21493536150581e+00 -1.23597414460232e-02 1.90954010765681e-02 1.25000000000000e-01 + 10 3.21732988001565e+00 -1.23693195200626e-02 1.91250081736752e-02 1.25000000000000e-01 + 11 3.21949341551286e+00 -1.23779736620515e-02 1.91517789973049e-02 1.25000000000000e-01 + 12 3.22129301791606e+00 -1.23851720716642e-02 1.91740609055915e-02 1.25000000000000e-01 + 13 3.22262100408954e+00 -1.23904840163582e-02 1.91905117699534e-02 1.25000000000000e-01 + 14 3.22340201497448e+00 -1.23936080598979e-02 1.92001900927959e-02 1.25000000000000e-01 + 15 3.22359708972178e+00 -1.23943883588871e-02 1.92026078488646e-02 1.25000000000000e-01 + 16 3.22320449309688e+00 -1.23928179723875e-02 1.91977421620913e-02 1.25000000000000e-01 + 17 3.22225764296745e+00 -1.22890305718698e-02 1.88775340495438e-02 1.50000000000000e-01 + 18 3.22082085394715e+00 -1.22832834157886e-02 1.88598814340734e-02 1.50000000000000e-01 + 19 3.21898363512874e+00 -1.22759345405150e-02 1.88373211053761e-02 1.50000000000000e-01 + 20 3.21685409696506e+00 -1.22674163878602e-02 1.88111881041427e-02 1.50000000000000e-01 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out index abea13011..ac78db1f1 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 4 colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,32 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped index 14415afc1..59699cf48 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397207945158e+00 + x 3.21397207993279e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj index c6b191d7a..cb822a1c2 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one - 20 3.21685409675932e+00 -1.22674163870373e-02 1.88111881016189e-02 1.50000000000000e-01 - 21 3.21455176714650e+00 -1.22582070685860e-02 1.87829550670414e-02 1.50000000000000e-01 - 22 3.21220001266275e+00 -1.22488000506510e-02 1.87541378351035e-02 1.50000000000000e-01 - 23 3.20991836001725e+00 -1.22396734400690e-02 1.87262007399414e-02 1.50000000000000e-01 - 24 3.20781524867392e+00 -1.22312609946957e-02 1.87004681900454e-02 1.50000000000000e-01 - 25 3.20598193223964e+00 -1.21239277289585e-02 1.83737029471263e-02 1.75000000000000e-01 - 26 3.20448816372304e+00 -1.21179526548922e-02 1.83555970682760e-02 1.75000000000000e-01 - 27 3.20337998682136e+00 -1.21135199472854e-02 1.83421706891602e-02 1.75000000000000e-01 - 28 3.20267956990048e+00 -1.21107182796019e-02 1.83336871559855e-02 1.75000000000000e-01 - 29 3.20238662695248e+00 -1.21095465078099e-02 1.83301395781014e-02 1.75000000000000e-01 - 30 3.20248100766347e+00 -1.21099240306539e-02 1.83312825035261e-02 1.75000000000000e-01 - 31 3.20292608021181e+00 -1.21117043208472e-02 1.83366726944537e-02 1.75000000000000e-01 - 32 3.20367275292539e+00 -1.21146910117016e-02 1.83457172886253e-02 1.75000000000000e-01 - 33 3.20466396135575e+00 -1.20186558454230e-02 1.80560110413401e-02 2.00000000000000e-01 - 34 3.20583940727948e+00 -1.20233576291179e-02 1.80701410847085e-02 2.00000000000000e-01 - 35 3.20714012418463e+00 -1.20285604967385e-02 1.80857834529623e-02 2.00000000000000e-01 - 36 3.20851243363315e+00 -1.20340497345326e-02 1.81022941266506e-02 2.00000000000000e-01 - 37 3.20991096515382e+00 -1.20396438606153e-02 1.81191280363064e-02 2.00000000000000e-01 - 38 3.21130069805223e+00 -1.20452027922089e-02 1.81358637881797e-02 2.00000000000000e-01 - 39 3.21265817463677e+00 -1.20506326985471e-02 1.81522185544115e-02 2.00000000000000e-01 - 40 3.21397207945158e+00 -1.20558883178063e-02 1.81680553914274e-02 2.00000000000000e-01 + 20 3.21685409696506e+00 -1.22674163878602e-02 1.88111881041427e-02 1.50000000000000e-01 + 21 3.21455176736891e+00 -1.22582070694756e-02 1.87829550697678e-02 1.50000000000000e-01 + 22 3.21220001290207e+00 -1.22488000516083e-02 1.87541378380349e-02 1.50000000000000e-01 + 23 3.20991836027364e+00 -1.22396734410946e-02 1.87262007430795e-02 1.50000000000000e-01 + 24 3.20781524894743e+00 -1.22312609957897e-02 1.87004681933909e-02 1.50000000000000e-01 + 25 3.20598193253024e+00 -1.21239277301209e-02 1.83737029506495e-02 1.75000000000000e-01 + 26 3.20448816403056e+00 -1.21179526561222e-02 1.83555970720025e-02 1.75000000000000e-01 + 27 3.20337998714552e+00 -1.21135199485821e-02 1.83421706930870e-02 1.75000000000000e-01 + 28 3.20267957024093e+00 -1.21107182809637e-02 1.83336871601086e-02 1.75000000000000e-01 + 29 3.20238662730877e+00 -1.21095465092351e-02 1.83301395824160e-02 1.75000000000000e-01 + 30 3.20248100803512e+00 -1.21099240321405e-02 1.83312825080267e-02 1.75000000000000e-01 + 31 3.20292608059827e+00 -1.21117043223931e-02 1.83366726991344e-02 1.75000000000000e-01 + 32 3.20367275332608e+00 -1.21146910133043e-02 1.83457172934795e-02 1.75000000000000e-01 + 33 3.20466396177004e+00 -1.20186558470801e-02 1.80560110463192e-02 2.00000000000000e-01 + 34 3.20583940770664e+00 -1.20233576308266e-02 1.80701410898444e-02 2.00000000000000e-01 + 35 3.20714012462387e+00 -1.20285604984955e-02 1.80857834582457e-02 2.00000000000000e-01 + 36 3.20851243408350e+00 -1.20340497363340e-02 1.81022941320700e-02 2.00000000000000e-01 + 37 3.20991096561413e+00 -1.20396438624565e-02 1.81191280418484e-02 2.00000000000000e-01 + 38 3.21130069852117e+00 -1.20452027940847e-02 1.81358637938281e-02 2.00000000000000e-01 + 39 3.21265817511275e+00 -1.20506327004510e-02 1.81522185601474e-02 2.00000000000000e-01 + 40 3.21397207993279e+00 -1.20558883197312e-02 1.81680553972288e-02 2.00000000000000e-01 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt b/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-centers-moving-stages/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out index c5200e63f..437e26dcb 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,27 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped index 5ef095f44..4109af1f5 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685457618647e+00 + x 3.21685457639221e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj index 5eec6dc1f..c0e02c1fa 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 1.00000000000000e-01 0.00000000000000e+00 - 1 3.20437138788600e+00 -1.23774855515440e-02 1.91502685723351e-02 1.10000000000000e-01 -1.23774855515440e-04 - 2 3.20383990680414e+00 -1.23353596272166e-02 1.90201371415956e-02 1.20000000000000e-01 -2.47128451787606e-04 - 3 3.20396636491103e+00 -1.22958654596441e-02 1.88985384252087e-02 1.30000000000000e-01 -3.70087106384047e-04 - 4 3.20472668059564e+00 -1.22589067223826e-02 1.87850992535096e-02 1.40000000000000e-01 -4.92676173607873e-04 - 5 3.20606077411088e+00 -1.22242430964435e-02 1.86790149101184e-02 1.50000000000000e-01 -6.14918604572308e-04 - 6 3.20787661013578e+00 -1.21915064405431e-02 1.85791036612255e-02 1.60000000000000e-01 -7.36833668977739e-04 - 7 3.21005557808631e+00 -1.21602223123453e-02 1.84838758357074e-02 1.70000000000000e-01 -8.58435892101191e-04 - 8 3.21245894716580e+00 -1.21298357886632e-02 1.83916145324919e-02 1.80000000000000e-01 -9.79734249987824e-04 - 9 3.21493543162121e+00 -1.20997417264848e-02 1.83004687309548e-02 1.90000000000000e-01 -1.10073166725267e-03 - 10 3.21732997387476e+00 -1.20693198954990e-02 1.82085603424861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 11 3.21949353668785e+00 -1.20779741467514e-02 1.82346824361994e-02 2.00000000000000e-01 -1.22142486620766e-03 - 12 3.22129316973139e+00 -1.20851726789256e-02 1.82564248349311e-02 2.00000000000000e-01 -1.22142486620766e-03 - 13 3.22262118961603e+00 -1.20904847584641e-02 1.82724777118316e-02 2.00000000000000e-01 -1.22142486620766e-03 - 14 3.22340223703211e+00 -1.20936089481284e-02 1.82819221737815e-02 2.00000000000000e-01 -1.22142486620766e-03 - 15 3.22359735089020e+00 -1.20943894035608e-02 1.82842818806205e-02 2.00000000000000e-01 -1.22142486620766e-03 - 16 3.22320479573201e+00 -1.20928191829280e-02 1.82795344738740e-02 2.00000000000000e-01 -1.22142486620766e-03 - 17 3.22225798922225e+00 -1.20890319568890e-02 1.82680867068354e-02 2.00000000000000e-01 -1.22142486620766e-03 - 18 3.22082124425633e+00 -1.20832849770253e-02 1.82507219795008e-02 2.00000000000000e-01 -1.22142486620766e-03 - 19 3.21898406979118e+00 -1.20759362791647e-02 1.82285296273058e-02 2.00000000000000e-01 -1.22142486620766e-03 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 + 1 3.20437138788663e+00 -1.23774855515465e-02 1.91502685723428e-02 1.10000000000000e-01 -1.23774855515465e-04 + 2 3.20383990680667e+00 -1.23353596272267e-02 1.90201371416267e-02 1.20000000000000e-01 -2.47128451787732e-04 + 3 3.20396636491675e+00 -1.22958654596670e-02 1.88985384252790e-02 1.30000000000000e-01 -3.70087106384402e-04 + 4 3.20472668060584e+00 -1.22589067224234e-02 1.87850992536346e-02 1.40000000000000e-01 -4.92676173608635e-04 + 5 3.20606077412683e+00 -1.22242430965073e-02 1.86790149103134e-02 1.50000000000000e-01 -6.14918604573709e-04 + 6 3.20787661015870e+00 -1.21915064406348e-02 1.85791036615050e-02 1.60000000000000e-01 -7.36833668980057e-04 + 7 3.21005557811738e+00 -1.21602223124695e-02 1.84838758360852e-02 1.70000000000000e-01 -8.58435892104752e-04 + 8 3.21245894720608e+00 -1.21298357888243e-02 1.83916145329805e-02 1.80000000000000e-01 -9.79734249992995e-04 + 9 3.21493543167171e+00 -1.20997417266868e-02 1.83004687315658e-02 1.90000000000000e-01 -1.10073166725986e-03 + 10 3.21732997393638e+00 -1.20693198957455e-02 1.82085603432298e-02 2.00000000000000e-01 -1.22142486621732e-03 + 11 3.21949353676140e+00 -1.20779741470456e-02 1.82346824370878e-02 2.00000000000000e-01 -1.22142486621732e-03 + 12 3.22129316981759e+00 -1.20851726792704e-02 1.82564248359729e-02 2.00000000000000e-01 -1.22142486621732e-03 + 13 3.22262118971552e+00 -1.20904847588621e-02 1.82724777130345e-02 2.00000000000000e-01 -1.22142486621732e-03 + 14 3.22340223714544e+00 -1.20936089485818e-02 1.82819221751521e-02 2.00000000000000e-01 -1.22142486621732e-03 + 15 3.22359735101788e+00 -1.20943894040715e-02 1.82842818821647e-02 2.00000000000000e-01 -1.22142486621732e-03 + 16 3.22320479587449e+00 -1.20928191834980e-02 1.82795344755970e-02 2.00000000000000e-01 -1.22142486621732e-03 + 17 3.22225798937996e+00 -1.20890319575198e-02 1.82680867087420e-02 2.00000000000000e-01 -1.22142486621732e-03 + 18 3.22082124442969e+00 -1.20832849777187e-02 1.82507219815954e-02 2.00000000000000e-01 -1.22142486621732e-03 + 19 3.21898406998055e+00 -1.20759362799222e-02 1.82285296295926e-02 2.00000000000000e-01 -1.22142486621732e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out index c92a324d4..ec62b7868 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -122,7 +118,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,32 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped index a27db3dc3..100eebdff 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397324438969e+00 + x 3.21397324487089e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -1.22142486620766e-03 + accumulatedWork -1.22142486621732e-03 } } diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj index 9592912c4..82871cb9e 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-centers-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 3.21685457618647e+00 -1.20674183047459e-02 1.82028230677145e-02 2.00000000000000e-01 -1.22142486620766e-03 - 21 3.21455229130029e+00 -1.20582091652012e-02 1.81750510339676e-02 2.00000000000000e-01 -1.22142486620766e-03 - 22 3.21220058167135e+00 -1.20488023266854e-02 1.81467046884425e-02 2.00000000000000e-01 -1.22142486620766e-03 - 23 3.20991897400811e+00 -1.20396758960324e-02 1.81192244601880e-02 2.00000000000000e-01 -1.22142486620766e-03 - 24 3.20781590778578e+00 -1.20312636311431e-02 1.80939130702584e-02 2.00000000000000e-01 -1.22142486620766e-03 - 25 3.20598263662306e+00 -1.20239305464922e-02 1.80718632233586e-02 2.00000000000000e-01 -1.22142486620766e-03 - 26 3.20448891199500e+00 -1.20179556479800e-02 1.80539072446018e-02 2.00000000000000e-01 -1.22142486620766e-03 - 27 3.20338077760483e+00 -1.20135231104193e-02 1.80405921905723e-02 2.00000000000000e-01 -1.22142486620766e-03 - 28 3.20268040182054e+00 -1.20107216072822e-02 1.80321791909543e-02 2.00000000000000e-01 -1.22142486620766e-03 - 29 3.20238749862618e+00 -1.20095499945047e-02 1.80286613838135e-02 2.00000000000000e-01 -1.22142486620766e-03 - 30 3.20248191768589e+00 -1.20099276707435e-02 1.80297953320614e-02 2.00000000000000e-01 -1.22142486620766e-03 - 31 3.20292702714129e+00 -1.20117081085652e-02 1.80351414606713e-02 2.00000000000000e-01 -1.22142486620766e-03 - 32 3.20367373527010e+00 -1.20146949410804e-02 1.80441118159029e-02 2.00000000000000e-01 -1.22142486620766e-03 - 33 3.20466497756289e+00 -1.20186599102516e-02 1.80560232547861e-02 2.00000000000000e-01 -1.22142486620766e-03 - 34 3.20584045419353e+00 -1.20233618167741e-02 1.80701536721327e-02 2.00000000000000e-01 -1.22142486620766e-03 - 35 3.20714119860834e+00 -1.20285647944334e-02 1.80857963767352e-02 2.00000000000000e-01 -1.22142486620766e-03 - 36 3.20851353235803e+00 -1.20340541294321e-02 1.81023073487628e-02 2.00000000000000e-01 -1.22142486620766e-03 - 37 3.20991208499767e+00 -1.20396483399907e-02 1.81191415188300e-02 2.00000000000000e-01 -1.22142486620766e-03 - 38 3.21130183589808e+00 -1.20452073435923e-02 1.81358774937663e-02 2.00000000000000e-01 -1.22142486620766e-03 - 39 3.21265932746957e+00 -1.20506373098783e-02 1.81522324467788e-02 2.00000000000000e-01 -1.22142486620766e-03 - 40 3.21397324438969e+00 -1.20558929775587e-02 1.81680694357938e-02 2.00000000000000e-01 -1.22142486620766e-03 + 20 3.21685457639221e+00 -1.20674183055688e-02 1.82028230701972e-02 2.00000000000000e-01 -1.22142486621732e-03 + 21 3.21455229152270e+00 -1.20582091660908e-02 1.81750510366495e-02 2.00000000000000e-01 -1.22142486621732e-03 + 22 3.21220058191067e+00 -1.20488023276427e-02 1.81467046913260e-02 2.00000000000000e-01 -1.22142486621732e-03 + 23 3.20991897426449e+00 -1.20396758970580e-02 1.81192244632749e-02 2.00000000000000e-01 -1.22142486621732e-03 + 24 3.20781590805930e+00 -1.20312636322372e-02 1.80939130735492e-02 2.00000000000000e-01 -1.22142486621732e-03 + 25 3.20598263691365e+00 -1.20239305476546e-02 1.80718632268527e-02 2.00000000000000e-01 -1.22142486621732e-03 + 26 3.20448891230251e+00 -1.20179556492100e-02 1.80539072482974e-02 2.00000000000000e-01 -1.22142486621732e-03 + 27 3.20338077792898e+00 -1.20135231117159e-02 1.80405921944666e-02 2.00000000000000e-01 -1.22142486621732e-03 + 28 3.20268040216098e+00 -1.20107216086439e-02 1.80321791950433e-02 2.00000000000000e-01 -1.22142486621732e-03 + 29 3.20238749898247e+00 -1.20095499959299e-02 1.80286613880924e-02 2.00000000000000e-01 -1.22142486621732e-03 + 30 3.20248191805753e+00 -1.20099276722301e-02 1.80297953365248e-02 2.00000000000000e-01 -1.22142486621732e-03 + 31 3.20292702752774e+00 -1.20117081101110e-02 1.80351414653132e-02 2.00000000000000e-01 -1.22142486621732e-03 + 32 3.20367373567078e+00 -1.20146949426831e-02 1.80441118207169e-02 2.00000000000000e-01 -1.22142486621732e-03 + 33 3.20466497797716e+00 -1.20186599119087e-02 1.80560232597650e-02 2.00000000000000e-01 -1.22142486621732e-03 + 34 3.20584045462068e+00 -1.20233618184827e-02 1.80701536772685e-02 2.00000000000000e-01 -1.22142486621732e-03 + 35 3.20714119904756e+00 -1.20285647961903e-02 1.80857963820184e-02 2.00000000000000e-01 -1.22142486621732e-03 + 36 3.20851353280837e+00 -1.20340541312335e-02 1.81023073541822e-02 2.00000000000000e-01 -1.22142486621732e-03 + 37 3.20991208545797e+00 -1.20396483418319e-02 1.81191415243719e-02 2.00000000000000e-01 -1.22142486621732e-03 + 38 3.21130183636701e+00 -1.20452073454680e-02 1.81358774994146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 39 3.21265932794554e+00 -1.20506373117822e-02 1.81522324525146e-02 2.00000000000000e-01 -1.22142486621732e-03 + 40 3.21397324487089e+00 -1.20558929794836e-02 1.81680694415952e-02 2.00000000000000e-01 -1.22142486621732e-03 diff --git a/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt b/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-centers-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out index 99cf50a61..908c0f068 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,27 +125,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped index fec1e803e..9eef8b44e 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685399817416e+00 + x 3.21685399835649e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj index 2cd06ea2b..5a6aa23cd 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.24221869387334e-02 - 1 3.20437138788600e+00 -1.24174855515440e-02 - 2 3.20383990619069e+00 -1.24153596247627e-02 - 3 3.20396636246577e+00 -1.24158654498631e-02 - 4 3.20472667451135e+00 -1.24189066980454e-02 - 5 3.20606076201392e+00 -1.24242430480557e-02 - 6 3.20787658911377e+00 -1.24315063564551e-02 - 7 3.21005554471991e+00 -1.24402221788797e-02 - 8 3.21245889756338e+00 -1.24498355902535e-02 - 9 3.21493536145531e+00 -1.24597414458212e-02 - 10 3.21732987841907e+00 -1.24693195136763e-02 - 11 3.21949341085340e+00 -1.24779736434136e-02 - 12 3.22129300871542e+00 -1.24851720348617e-02 - 13 3.22262098892565e+00 -1.24904839557026e-02 - 14 3.22340199249676e+00 -1.24936079699870e-02 - 15 3.22359705866319e+00 -1.24943882346527e-02 - 16 3.22320445228234e+00 -1.24928178091294e-02 - 17 3.22225759131848e+00 -1.24890303652739e-02 - 18 3.22082078894448e+00 -1.24832831557779e-02 - 19 3.21898355436871e+00 -1.24759342174748e-02 - 20 3.21685399817416e+00 -1.24674159926967e-02 + 1 3.20437138788661e+00 -1.24174855515465e-02 + 2 3.20383990624489e+00 -1.24153596249795e-02 + 3 3.20396636247331e+00 -1.24158654498932e-02 + 4 3.20472667455914e+00 -1.24189066982366e-02 + 5 3.20606076201901e+00 -1.24242430480760e-02 + 6 3.20787658913293e+00 -1.24315063565317e-02 + 7 3.21005554475517e+00 -1.24402221790207e-02 + 8 3.21245889761578e+00 -1.24498355904631e-02 + 9 3.21493536152545e+00 -1.24597414461018e-02 + 10 3.21732987850678e+00 -1.24693195140271e-02 + 11 3.21949341095784e+00 -1.24779736438313e-02 + 12 3.22129300883514e+00 -1.24851720353406e-02 + 13 3.22262098905883e+00 -1.24904839562353e-02 + 14 3.22340199264132e+00 -1.24936079705653e-02 + 15 3.22359705881703e+00 -1.24943882352681e-02 + 16 3.22320445244359e+00 -1.24928178097743e-02 + 17 3.22225759148518e+00 -1.24890303659407e-02 + 18 3.22082078911634e+00 -1.24832831564654e-02 + 19 3.21898355455034e+00 -1.24759342182014e-02 + 20 3.21685399835649e+00 -1.24674159934260e-02 diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out index a71fdf83a..8752f5403 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,32 +125,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 086f80ad0..ba9e5b167 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397114716924e+00 + x 3.21397114764396e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 8924671f5..d18eb0fa7 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685399817416e+00 -1.24674159926967e-02 - 21 3.21455164841394e+00 -1.24582065936557e-02 - 22 3.21219987179556e+00 -1.24487994871822e-02 - 23 3.20991819517487e+00 -1.24396727806995e-02 - 24 3.20781505815938e+00 -1.24312602326375e-02 - 25 3.20598171449351e+00 -1.24239268579740e-02 - 26 3.20448791577891e+00 -1.24179516631157e-02 - 27 3.20337970585434e+00 -1.24135188234173e-02 - 28 3.20267925323760e+00 -1.24107170129504e-02 - 29 3.20238627208178e+00 -1.24095450883271e-02 - 30 3.20248061224166e+00 -1.24099224489666e-02 - 31 3.20292564206961e+00 -1.24117025682784e-02 - 32 3.20367227007056e+00 -1.24146890802823e-02 - 33 3.20466343197421e+00 -1.24186537278969e-02 - 34 3.20583882819824e+00 -1.24233553127930e-02 - 35 3.20713949242506e+00 -1.24285579697002e-02 - 36 3.20851174642574e+00 -1.24340469857030e-02 - 37 3.20991021994729e+00 -1.24396408797892e-02 - 38 3.21129989251817e+00 -1.24451995700727e-02 - 39 3.21265730667037e+00 -1.24506292266815e-02 - 40 3.21397114716924e+00 -1.24558845886769e-02 + 20 3.21685399835649e+00 -1.24674159934260e-02 + 21 3.21455164860269e+00 -1.24582065944107e-02 + 22 3.21219987199261e+00 -1.24487994879705e-02 + 23 3.20991819538261e+00 -1.24396727815305e-02 + 24 3.20781505838050e+00 -1.24312602335220e-02 + 25 3.20598171473079e+00 -1.24239268589232e-02 + 26 3.20448791603500e+00 -1.24179516641400e-02 + 27 3.20337970613153e+00 -1.24135188245261e-02 + 28 3.20267925353770e+00 -1.24107170141508e-02 + 29 3.20238627240592e+00 -1.24095450896237e-02 + 30 3.20248061259023e+00 -1.24099224503609e-02 + 31 3.20292564244219e+00 -1.24117025697688e-02 + 32 3.20367227046597e+00 -1.24146890818639e-02 + 33 3.20466343239054e+00 -1.24186537295621e-02 + 34 3.20583882863293e+00 -1.24233553145317e-02 + 35 3.20713949287508e+00 -1.24285579715003e-02 + 36 3.20851174688770e+00 -1.24340469875508e-02 + 37 3.20991022041763e+00 -1.24396408816705e-02 + 38 3.21129989299330e+00 -1.24451995719732e-02 + 39 3.21265730714688e+00 -1.24506292285875e-02 + 40 3.21397114764396e+00 -1.24558845905758e-02 diff --git a/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out index 8085f9903..db180cf49 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.out @@ -1,174 +1,118 @@ colvars: ---------------------------------------------------------------------- -colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] -colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) -colvars: # smp = on [default] +colvars: # indexFile = index.ndx +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 -colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] +colvars: # colvarsTrajAppend = off [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. -colvars: # name = "one" +colvars: # name = one colvars: Initializing a new "distance" component. -colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] -colvars: # scalable = on [default] +colvars: # oneSiteSystemForce = off [default] colvars: Initializing atom group "group1". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] -colvars: # indexGroup = "group1" +colvars: # indexGroup = group1 colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Enabling scalable calculation for group "group1". -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028. colvars: Initializing atom group "group2". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] -colvars: # indexGroup = "group2" +colvars: # indexGroup = group2 colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Enabling scalable calculation for group "group2". -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028. colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerWallConstant = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] -colvars: # outputTotalForce = off [default] +colvars: # outputSystemForce = off [default] colvars: # outputAppliedForce = on -colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = on -colvars: # outputFreq = 10 [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] +colvars: # forceConstant = 0.001 colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] -colvars: # outputCenters = off [default] -colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 -colvars: # targetNumSteps = 8 -colvars: # targetNumStages = 4 -colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). +colvars: # targetNumSteps = 8 +colvars: # targetNumStages = 4 +colvars: # targetForceExponent = 1 [default] +colvars: # outputCenters = off [default] +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- -colvars: Updating NAMD interface: -colvars: updating atomic data (0 atoms). -colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). -colvars: Updating NAMD interface: -colvars: updating atomic data (0 atoms). -colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Restraint harmonic1, stage 0 : lambda = 0, k = 0.001 -colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Restraint harmonic1 Lambda= 0 dA/dLambda= -0.0195425 -colvars: Restraint harmonic1, stage 1 : lambda = 0.25, k = 0.000775 +colvars: Writing to colvar trajectory file "test.colvars.traj". +colvars: Restraint harmonic1, stage 0 : lambda = 0 +colvars: Setting force constant to 0.001 +colvars: Lambda= 0 dA/dLambda= -0.0195425 +colvars: Restraint harmonic1, stage 1 : lambda = 0.25 +colvars: Setting force constant to 0.000775 +colvars: Writing the state file "test.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.tmp.colvars.state". -colvars: Restraint harmonic1 Lambda= 0.25 dA/dLambda= -0.0175302 -colvars: Restraint harmonic1, stage 2 : lambda = 0.5, k = 0.00055 +colvars: Lambda= 0.25 dA/dLambda= -0.0175302 +colvars: Restraint harmonic1, stage 2 : lambda = 0.5 +colvars: Setting force constant to 0.00055 +colvars: Writing the state file "test.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.tmp.colvars.state". colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped index 199ba99ec..57c7b11d1 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685733295311e+00 + x 3.21685733313543e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj index b1edac98e..ec772e9bf 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 - 1 3.20437138788600e+00 -1.24174855515440e-02 1.92742434278505e-02 - 2 3.20383990619069e+00 -1.24153596247627e-02 1.92676443265236e-02 - 3 3.20396636246577e+00 -1.24158654498631e-02 1.92692143586380e-02 - 4 3.20472667451135e+00 -1.24189066980454e-02 1.92786554468447e-02 - 5 3.20606076201392e+00 -1.24242430480557e-02 1.92952269146450e-02 - 6 3.20787658911377e+00 -1.24315063564551e-02 1.93177937863229e-02 - 7 3.21005554471991e+00 -1.24402221788797e-02 1.93448909824861e-02 - 8 3.21245889756338e+00 -9.64862258244647e-03 1.50154706029832e-02 - 9 3.21493540443572e+00 -9.65629975375074e-03 1.50393749894011e-02 - 10 3.21733000686193e+00 -9.66372302127197e-03 1.50625068761068e-02 - 11 3.21949366620235e+00 -9.67043036522729e-03 1.50834231368887e-02 - 12 3.22129343087844e+00 -9.67600963572316e-03 1.51008326565496e-02 - 13 3.22262161584524e+00 -9.68012700912024e-03 1.51136869214031e-02 - 14 3.22340285980675e+00 -9.68254886540093e-03 1.51212504082059e-02 - 15 3.22359819944574e+00 -9.68315441828180e-03 1.51231418529500e-02 - 16 3.22320589693159e+00 -6.87105297324950e-03 1.07298565820911e-02 - 17 3.22225941074492e+00 -6.86897070363883e-03 1.07233542107838e-02 - 18 3.22082305081454e+00 -6.86581071179198e-03 1.07134901659449e-02 - 19 3.21898632267996e+00 -6.86176990989590e-03 1.07008832491711e-02 - 20 3.21685733295311e+00 -6.85708613249684e-03 1.06862795973819e-02 + 1 3.20437138788661e+00 -1.24174855515465e-02 1.92742434278581e-02 + 2 3.20383990624489e+00 -1.24153596249795e-02 1.92676443271965e-02 + 3 3.20396636247331e+00 -1.24158654498932e-02 1.92692143587316e-02 + 4 3.20472667455914e+00 -1.24189066982366e-02 1.92786554474381e-02 + 5 3.20606076201901e+00 -1.24242430480760e-02 1.92952269147082e-02 + 6 3.20787658913293e+00 -1.24315063565317e-02 1.93177937865610e-02 + 7 3.21005554475517e+00 -1.24402221790207e-02 1.93448909829248e-02 + 8 3.21245889761578e+00 -9.64862258260892e-03 1.50154706034888e-02 + 9 3.21493540450586e+00 -9.65629975396818e-03 1.50393749900784e-02 + 10 3.21733000694964e+00 -9.66372302154388e-03 1.50625068769544e-02 + 11 3.21949366630678e+00 -9.67043036555102e-03 1.50834231378986e-02 + 12 3.22129343099816e+00 -9.67600963609430e-03 1.51008326577080e-02 + 13 3.22262161597842e+00 -9.68012700953309e-03 1.51136869226923e-02 + 14 3.22340285995130e+00 -9.68254886584905e-03 1.51212504096056e-02 + 15 3.22359819959959e+00 -9.68315441875872e-03 1.51231418544397e-02 + 16 3.22320589709283e+00 -6.87105297360423e-03 1.07298565831990e-02 + 17 3.22225941091162e+00 -6.86897070400556e-03 1.07233542119288e-02 + 18 3.22082305098640e+00 -6.86581071217007e-03 1.07134901671248e-02 + 19 3.21898632286159e+00 -6.86176991029550e-03 1.07008832504174e-02 + 20 3.21685733313543e+00 -6.85708613289795e-03 1.06862795986321e-02 diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out index e5fe4122e..cd19260d0 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.out @@ -1,179 +1,123 @@ colvars: ---------------------------------------------------------------------- -colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] -colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) -colvars: # smp = on [default] +colvars: # indexFile = index.ndx +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 -colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] +colvars: # colvarsTrajAppend = off [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. -colvars: # name = "one" +colvars: # name = one colvars: Initializing a new "distance" component. -colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] -colvars: # scalable = on [default] +colvars: # oneSiteSystemForce = off [default] colvars: Initializing atom group "group1". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] -colvars: # indexGroup = "group1" +colvars: # indexGroup = group1 colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Enabling scalable calculation for group "group1". -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 54.028. colvars: Initializing atom group "group2". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] -colvars: # indexGroup = "group2" +colvars: # indexGroup = group2 colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Enabling scalable calculation for group "group2". -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 54.028. colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerWallConstant = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] -colvars: # outputTotalForce = off [default] +colvars: # outputSystemForce = off [default] colvars: # outputAppliedForce = on -colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = on -colvars: # outputFreq = 10 [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] +colvars: # forceConstant = 0.001 colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] -colvars: # outputCenters = off [default] -colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 -colvars: # targetNumSteps = 8 -colvars: # targetNumStages = 4 -colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). +colvars: # targetNumSteps = 8 +colvars: # targetNumStages = 4 +colvars: # targetForceExponent = 1 [default] +colvars: # outputCenters = off [default] +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- -colvars: Updating NAMD interface: -colvars: updating atomic data (0 atoms). -colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). -colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21686 -colvars: Restarting harmonic bias "harmonic1" from step number 20. +colvars: Restarting restraint bias "harmonic1". +colvars: # forceConstant = 0.00055 +colvars: # stage = 2 colvars: ---------------------------------------------------------------------- -colvars: Updating NAMD interface: -colvars: updating atomic data (0 atoms). -colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Writing to colvar trajectory file "test.restart.colvars.traj". +colvars: Lambda= 0.5 dA/dLambda= -0.010897 +colvars: Restraint harmonic1, stage 3 : lambda = 0.75 +colvars: Setting force constant to 0.000325 +colvars: Writing the state file "test.restart.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Restraint harmonic1 Lambda= 0.5 dA/dLambda= -0.010897 -colvars: Restraint harmonic1, stage 3 : lambda = 0.75, k = 0.000325 -colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Saving collective variables state to "test.restart.tmp.colvars.state". -colvars: Restraint harmonic1 Lambda= 0.75 dA/dLambda= -0.0173372 -colvars: Restraint harmonic1, stage 4 : lambda = 1, k = 0.0001 -colvars: Restraint harmonic1 Lambda= 1 dA/dLambda= -0.0174016 +colvars: Lambda= 0.75 dA/dLambda= -0.0173372 +colvars: Restraint harmonic1, stage 4 : lambda = 1 +colvars: Setting force constant to 0.0001 +colvars: Lambda= 1 dA/dLambda= -0.0174016 +colvars: Writing the state file "test.restart.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Saving collective variables state to "test.restart.tmp.colvars.state". colvars: Saving collective variables state to "test.restart.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped index 74a01de19..b91f1692e 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21399913220478e+00 + x 3.21399913267948e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj index d899a4145..9b8f32622 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 - 20 3.21685733295311e+00 -6.85708613249684e-03 1.06862795973819e-02 - 21 3.21455560554461e+00 -6.85202233219815e-03 1.06705022820323e-02 - 22 3.21220450297830e+00 -6.84684990655226e-03 1.06543985551943e-02 - 23 3.20992354800290e+00 -6.84183180560639e-03 1.06387869218653e-02 - 24 3.20782117629534e+00 -4.04016752918394e-03 6.27805910148934e-03 - 25 3.20598868088311e+00 -4.03778528514804e-03 6.27065769575309e-03 - 26 3.20449580932365e+00 -4.03584455212074e-03 6.26463124957027e-03 - 27 3.20338860114077e+00 -4.03440518148300e-03 6.26016352629879e-03 - 28 3.20268922031311e+00 -4.03349598640704e-03 6.25734225860066e-03 - 29 3.20239737626966e+00 -4.03311658915055e-03 6.25616516218516e-03 - 30 3.20249291400027e+00 -4.03324078820035e-03 6.25655048292422e-03 - 31 3.20293919691480e+00 -4.03382095598924e-03 6.25835057883767e-03 - 32 3.20368712856237e+00 -1.24147485142495e-03 1.92657475840075e-03 - 33 3.20467968265656e+00 -1.24187187306262e-03 1.92780718638008e-03 - 34 3.20585655419651e+00 -1.24234262167861e-03 1.92926898704909e-03 - 35 3.20715877104842e+00 -1.24286350841937e-03 1.93088712570063e-03 - 36 3.20853264885916e+00 -1.24341305954367e-03 1.93259504580467e-03 - 37 3.20993281112190e+00 -1.24397312444876e-03 1.93433641793852e-03 - 38 3.21132423111018e+00 -1.24452969244407e-03 1.93606769421867e-03 - 39 3.21268344520547e+00 -1.24507337808219e-03 1.93775964601125e-03 - 40 3.21399913220478e+00 -1.24559965288191e-03 1.93939811907443e-03 + 20 3.21685733313543e+00 -6.85708613289795e-03 1.06862795986321e-02 + 21 3.21455560573336e+00 -6.85202233261338e-03 1.06705022833256e-02 + 22 3.21220450317535e+00 -6.84684990698578e-03 1.06543985565434e-02 + 23 3.20992354821064e+00 -6.84183180606342e-03 1.06387869232866e-02 + 24 3.20782117651646e+00 -4.04016752947140e-03 6.27805910238270e-03 + 25 3.20598868112038e+00 -4.03778528545649e-03 6.27065769671115e-03 + 26 3.20449580957973e+00 -4.03584455245364e-03 6.26463125060375e-03 + 27 3.20338860141795e+00 -4.03440518184334e-03 6.26016352741707e-03 + 28 3.20268922061319e+00 -4.03349598679715e-03 6.25734225981105e-03 + 29 3.20239737659378e+00 -4.03311658957192e-03 6.25616516349240e-03 + 30 3.20249291434882e+00 -4.03324078865346e-03 6.25655048433000e-03 + 31 3.20293919728737e+00 -4.03382095647358e-03 6.25835058034053e-03 + 32 3.20368712895776e+00 -1.24147485158310e-03 1.92657475889161e-03 + 33 3.20467968307286e+00 -1.24187187322914e-03 1.92780718689708e-03 + 34 3.20585655463118e+00 -1.24234262185247e-03 1.92926898758910e-03 + 35 3.20715877149842e+00 -1.24286350859937e-03 1.93088712625992e-03 + 36 3.20853264932110e+00 -1.24341305972844e-03 1.93259504637905e-03 + 37 3.20993281159222e+00 -1.24397312463689e-03 1.93433641852358e-03 + 38 3.21132423158529e+00 -1.24452969263412e-03 1.93606769480996e-03 + 39 3.21268344568196e+00 -1.24507337827279e-03 1.93775964660451e-03 + 40 3.21399913267948e+00 -1.24559965307179e-03 1.93939811966572e-03 diff --git a/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt b/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt index 157cac038..494519348 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-k-moving-stages/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2015-09-16. +colvars: Using NAMD interface, version 2015-07-24. diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out index d2be0212a..11f61358e 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,27 +131,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped index 6d65b453d..4507a2d83 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687020497026e+00 + x 3.21687020515258e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj index a79591894..f58ff8ba4 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 - 1 3.20437138788600e+00 -1.12999118519050e-02 1.75395615193440e-02 - 2 3.20383992333029e+00 -1.01805949485234e-02 1.57994685222408e-02 - 3 3.20396643077894e+00 -9.06358197787450e-03 1.40665271009677e-02 - 4 3.20472684448397e+00 -7.94810072187895e-03 1.23383408369400e-02 - 5 3.20606109997218e+00 -6.83333441993879e-03 1.06123771124364e-02 - 6 3.20787717647453e+00 -5.71849400471313e-03 8.88618850052717e-03 - 7 3.21005647713329e+00 -4.60288358615728e-03 7.15761395530948e-03 - 8 3.21246028397626e+00 -3.48595551805342e-03 5.42494905082458e-03 - 9 3.21493732312431e+00 -2.36735236557448e-03 3.68707712025729e-03 - 10 3.21733254790344e+00 -1.24693301916138e-03 1.94355244284363e-03 - 11 3.21949693102052e+00 -1.24779877240821e-03 1.94625222052929e-03 - 12 3.22129751453369e+00 -1.24851900581348e-03 1.94849963484684e-03 - 13 3.22262660677352e+00 -1.24905064270941e-03 1.95015938506598e-03 - 14 3.22340883978115e+00 -1.24936353591246e-03 1.95113655608461e-03 - 15 3.22360524373761e+00 -1.24944209749504e-03 1.95138194374102e-03 - 16 3.22321407463655e+00 -1.24928562985462e-03 1.95089323120157e-03 - 17 3.22226874199272e+00 -1.24890749679709e-03 1.94971241944496e-03 - 18 3.22083355111441e+00 -1.24833342044576e-03 1.94792041075227e-03 - 19 3.21899800404481e+00 -1.24759920161792e-03 1.94562970984710e-03 - 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 + 1 3.20437138788661e+00 -1.12999118519073e-02 1.75395615193509e-02 + 2 3.20383992338449e+00 -1.01805949487011e-02 1.57994685227925e-02 + 3 3.20396643078647e+00 -9.06358197789650e-03 1.40665271010360e-02 + 4 3.20472684453174e+00 -7.94810072200125e-03 1.23383408373197e-02 + 5 3.20606109997726e+00 -6.83333441994998e-03 1.06123771124712e-02 + 6 3.20787717649369e+00 -5.71849400474838e-03 8.88618850063674e-03 + 7 3.21005647716855e+00 -4.60288358620946e-03 7.15761395547176e-03 + 8 3.21246028402867e+00 -3.48595551811211e-03 5.42494905100725e-03 + 9 3.21493732319445e+00 -2.36735236562779e-03 3.68707712042334e-03 + 10 3.21733254799115e+00 -1.24693301919646e-03 1.94355244295300e-03 + 11 3.21949693112495e+00 -1.24779877244998e-03 1.94625222065960e-03 + 12 3.22129751465341e+00 -1.24851900586136e-03 1.94849963499631e-03 + 13 3.22262660690669e+00 -1.24905064276268e-03 1.95015938523232e-03 + 14 3.22340883992570e+00 -1.24936353597028e-03 1.95113655626521e-03 + 15 3.22360524389145e+00 -1.24944209755658e-03 1.95138194393324e-03 + 16 3.22321407479779e+00 -1.24928562991912e-03 1.95089323140301e-03 + 17 3.22226874215941e+00 -1.24890749686377e-03 1.94971241965315e-03 + 18 3.22083355128627e+00 -1.24833342051451e-03 1.94792041096681e-03 + 19 3.21899800422646e+00 -1.24759920169058e-03 1.94562971007373e-03 + 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out index 4e433433c..126710c7e 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,32 +131,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped index 226b212c1..32715071f 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21402990668451e+00 + x 3.21402990715919e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj index 2753d1963..0970380b3 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonic-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 - 20 3.21687020497026e+00 -1.24674808198810e-03 1.94297597492627e-03 - 21 3.21456967632931e+00 -1.24582787053172e-03 1.94010885374201e-03 - 22 3.21221977994646e+00 -1.24488791197858e-03 1.93718239173800e-03 - 23 3.20994003840243e+00 -1.24397601536097e-03 1.93434540849171e-03 - 24 3.20783888746925e+00 -1.24313555498770e-03 1.93173251009322e-03 - 25 3.20600757726167e+00 -1.24240303090467e-03 1.92945661400138e-03 - 26 3.20451585575643e+00 -1.24180634230257e-03 1.92760373972862e-03 - 27 3.20340976294734e+00 -1.24136390517894e-03 1.92623043135138e-03 - 28 3.20271146313867e+00 -1.24108458525547e-03 1.92536368469842e-03 - 29 3.20242066576110e+00 -1.24096826630444e-03 1.92500279746831e-03 - 30 3.20251721536965e+00 -1.24100688614786e-03 1.92512261433301e-03 - 31 3.20296447447623e+00 -1.24118578979049e-03 1.92567770597231e-03 - 32 3.20371334530005e+00 -1.24148533812002e-03 1.92660730595873e-03 - 33 3.20470675696420e+00 -1.24188270278568e-03 1.92784080934784e-03 - 34 3.20588440315285e+00 -1.24235376126114e-03 1.92930358514962e-03 - 35 3.20718731103156e+00 -1.24287492441263e-03 1.93092259716711e-03 - 36 3.20856179628928e+00 -1.24342471851571e-03 1.93263128826985e-03 - 37 3.20996248338009e+00 -1.24398499335204e-03 1.93437332960633e-03 - 38 3.21135434749032e+00 -1.24454173899613e-03 1.93610517512938e-03 - 39 3.21271392780555e+00 -1.24508557112222e-03 1.93779759927093e-03 - 40 3.21402990668451e+00 -1.24561196267380e-03 1.93943645194510e-03 + 20 3.21687020515258e+00 -1.24674808206103e-03 1.94297597515358e-03 + 21 3.21456967651805e+00 -1.24582787060722e-03 1.94010885397715e-03 + 22 3.21221978014351e+00 -1.24488791205741e-03 1.93718239198331e-03 + 23 3.20994003861018e+00 -1.24397601544407e-03 1.93434540875013e-03 + 24 3.20783888769037e+00 -1.24313555507615e-03 1.93173251036810e-03 + 25 3.20600757749894e+00 -1.24240303099958e-03 1.92945661429617e-03 + 26 3.20451585601250e+00 -1.24180634240500e-03 1.92760374004661e-03 + 27 3.20340976322452e+00 -1.24136390528981e-03 1.92623043169546e-03 + 28 3.20271146343875e+00 -1.24108458537550e-03 1.92536368507084e-03 + 29 3.20242066608521e+00 -1.24096826643409e-03 1.92500279787052e-03 + 30 3.20251721571819e+00 -1.24100688628728e-03 1.92512261476555e-03 + 31 3.20296447484878e+00 -1.24118578993951e-03 1.92567770643472e-03 + 32 3.20371334569543e+00 -1.24148533827817e-03 1.92660730644958e-03 + 33 3.20470675738049e+00 -1.24188270295219e-03 1.92784080986481e-03 + 34 3.20588440358750e+00 -1.24235376143500e-03 1.92930358568961e-03 + 35 3.20718731148154e+00 -1.24287492459262e-03 1.93092259772638e-03 + 36 3.20856179675119e+00 -1.24342471870048e-03 1.93263128884420e-03 + 37 3.20996248385038e+00 -1.24398499354015e-03 1.93437333019136e-03 + 38 3.21135434796541e+00 -1.24454173918616e-03 1.93610517572065e-03 + 39 3.21271392828201e+00 -1.24508557131280e-03 1.93779759986417e-03 + 40 3.21402990715919e+00 -1.24561196286367e-03 1.93943645253637e-03 diff --git a/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonic-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out index e8ce74ce1..454648299 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -132,27 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped index a0bbaca3d..ed4ff587f 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491521323e+00 + x 3.21685491541898e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj index d5d525eb6..dfbf0ebd2 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095402e+00 -1.20174855638161e-02 - 2 3.20383991841948e+00 -1.20153596736779e-02 - 3 3.20396638982490e+00 -1.20158655592996e-02 - 4 3.20472672277551e+00 -1.20189068911021e-02 - 5 3.20606083670179e+00 -1.20242433468072e-02 - 6 3.20787669543948e+00 -1.20315067817579e-02 - 7 3.21005568755800e+00 -1.20402227502320e-02 - 8 3.21245908142754e+00 -1.20498363257101e-02 - 9 3.21493559049101e+00 -1.20597423619640e-02 - 10 3.21733015640955e+00 -1.20693206256382e-02 - 11 3.21949374123820e+00 -1.20779749649528e-02 - 12 3.22129339461899e+00 -1.20851735784760e-02 - 13 3.22262143319445e+00 -1.20904857327778e-02 - 14 3.22340249773966e+00 -1.20936099909586e-02 - 15 3.22359762729192e+00 -1.20943905091677e-02 - 16 3.22320508654863e+00 -1.20928203461945e-02 - 17 3.22225829334495e+00 -1.20890331733798e-02 - 18 3.22082156074746e+00 -1.20832862429898e-02 - 19 3.21898439787187e+00 -1.20759375914875e-02 - 20 3.21685491521323e+00 -1.20674196608529e-02 + 1 3.20437139095465e+00 -1.20174855638186e-02 + 2 3.20383991842200e+00 -1.20153596736880e-02 + 3 3.20396638983062e+00 -1.20158655593225e-02 + 4 3.20472672278571e+00 -1.20189068911429e-02 + 5 3.20606083671774e+00 -1.20242433468710e-02 + 6 3.20787669546241e+00 -1.20315067818496e-02 + 7 3.21005568758906e+00 -1.20402227503562e-02 + 8 3.21245908146782e+00 -1.20498363258713e-02 + 9 3.21493559054151e+00 -1.20597423621660e-02 + 10 3.21733015647118e+00 -1.20693206258847e-02 + 11 3.21949374131176e+00 -1.20779749652470e-02 + 12 3.22129339470521e+00 -1.20851735788208e-02 + 13 3.22262143329394e+00 -1.20904857331758e-02 + 14 3.22340249785300e+00 -1.20936099914120e-02 + 15 3.22359762741961e+00 -1.20943905096784e-02 + 16 3.22320508669112e+00 -1.20928203467645e-02 + 17 3.22225829350267e+00 -1.20890331740107e-02 + 18 3.22082156092082e+00 -1.20832862436833e-02 + 19 3.21898439806125e+00 -1.20759375922450e-02 + 20 3.21685491541898e+00 -1.20674196616759e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out index 5da67b4d9..57651fe22 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -132,32 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped index f58df11b7..8719ed7ca 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397364200070e+00 + x 3.21397364248195e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj index 8b5e494a7..fec7bdbdb 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685491521323e+00 -1.20674196608529e-02 - 21 3.21455264073267e+00 -1.20582105629307e-02 - 22 3.21220094103318e+00 -1.20488037641327e-02 - 23 3.20991934284523e+00 -1.20396773713809e-02 - 24 3.20781628562398e+00 -1.20312651424959e-02 - 25 3.20598302292944e+00 -1.20239320917178e-02 - 26 3.20448930614687e+00 -1.20179572245875e-02 - 27 3.20338117886792e+00 -1.20135247154717e-02 - 28 3.20268080933861e+00 -1.20107232373544e-02 - 29 3.20238791142161e+00 -1.20095516456865e-02 - 30 3.20248233467135e+00 -1.20099293386854e-02 - 31 3.20292744714189e+00 -1.20117097885676e-02 - 32 3.20367415705454e+00 -1.20146966282182e-02 - 33 3.20466539988114e+00 -1.20186615995246e-02 - 34 3.20584087581816e+00 -1.20233635032726e-02 - 35 3.20714161837695e+00 -1.20285664735078e-02 - 36 3.20851394921166e+00 -1.20340557968466e-02 - 37 3.20991249801338e+00 -1.20396499920535e-02 - 38 3.21130224431234e+00 -1.20452089772494e-02 - 39 3.21265973069097e+00 -1.20506389227639e-02 - 40 3.21397364200070e+00 -1.20558945680028e-02 + 20 3.21685491541898e+00 -1.20674196616759e-02 + 21 3.21455264095509e+00 -1.20582105638204e-02 + 22 3.21220094127252e+00 -1.20488037650901e-02 + 23 3.20991934310164e+00 -1.20396773724066e-02 + 24 3.20781628589752e+00 -1.20312651435901e-02 + 25 3.20598302322006e+00 -1.20239320928802e-02 + 26 3.20448930645441e+00 -1.20179572258176e-02 + 27 3.20338117919211e+00 -1.20135247167684e-02 + 28 3.20268080967909e+00 -1.20107232387163e-02 + 29 3.20238791177794e+00 -1.20095516471117e-02 + 30 3.20248233504303e+00 -1.20099293401721e-02 + 31 3.20292744752838e+00 -1.20117097901135e-02 + 32 3.20367415745526e+00 -1.20146966298210e-02 + 33 3.20466540029545e+00 -1.20186616011818e-02 + 34 3.20584087624535e+00 -1.20233635049814e-02 + 35 3.20714161881621e+00 -1.20285664752649e-02 + 36 3.20851394966204e+00 -1.20340557986482e-02 + 37 3.20991249847373e+00 -1.20396499938949e-02 + 38 3.21130224478131e+00 -1.20452089791253e-02 + 39 3.21265973116698e+00 -1.20506389246679e-02 + 40 3.21397364248195e+00 -1.20558945699278e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-both-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out index 9064d17fa..a58050110 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.002 @@ -138,27 +133,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped index bf89cca29..75c48b998 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687111229972e+00 + x 3.21687111250546e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.37880405391244e-02 + accumulatedWork -3.37880405409319e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj index dfafafb40..260962906 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 0 3.20554673468334e+00 -1.20221869387334e-02 1.80666223487314e-02 0.00000000000000e+00 - 1 3.20437139095402e+00 -1.09007134627843e-02 1.63748958342883e-02 -1.67759907527770e-03 - 2 3.20383993554679e+00 -9.78221064079167e-03 1.46920974903704e-02 -3.35460468847827e-03 - 3 3.20396645808888e+00 -8.66600108900544e-03 1.30161882985670e-02 -5.03175157650461e-03 - 4 3.20472689262560e+00 -7.55129058412370e-03 1.13447829460735e-02 -6.70974768961999e-03 - 5 3.20606117441688e+00 -6.43724359705212e-03 9.67537402368102e-03 -8.38923439861843e-03 - 6 3.20787728237960e+00 -5.32305735341078e-03 8.00555164306400e-03 -1.00707510400595e-02 - 7 3.21005661930852e+00 -4.20802874840541e-03 6.33320239418913e-03 -1.17547052270162e-02 - 8 3.21246046686444e+00 -3.09161036522795e-03 4.65667700209877e-03 -1.34413501178592e-02 - 9 3.21493755079559e+00 -1.97345282364599e-03 2.97491851136694e-03 -1.51307699355289e-02 - 10 3.21733282406293e+00 -8.53430600396662e-04 1.28754208181829e-03 -1.68228752015806e-02 - 11 3.21949725902808e+00 -8.54042795053181e-04 1.28938993937788e-03 -1.85174089470984e-02 - 12 3.22129789744302e+00 -8.54552092506647e-04 1.29092822017293e-03 -2.02139643220999e-02 - 13 3.22262704736871e+00 -8.54928032876915e-04 1.29206429786374e-03 -2.19120127458105e-02 - 14 3.22340934061631e+00 -8.55149298821016e-04 1.29273318883847e-03 -2.36109402351118e-02 - 15 3.22360580717604e+00 -8.55204867955681e-04 1.29290120253801e-03 -2.53100885302957e-02 - 16 3.22321470288645e+00 -8.55094246957553e-04 1.29256674987784e-03 -2.70087972832577e-02 - 17 3.22226943713660e+00 -8.54826885428858e-04 1.29175858493715e-03 -2.87064439348940e-02 - 18 3.22083431513039e+00 -8.54420971627888e-04 1.29053209533029e-03 -3.04024787172548e-02 - 19 3.21899883881885e+00 -8.53901820529248e-04 1.28896430232155e-03 -3.20964530847806e-02 - 20 3.21687111229972e+00 -8.53300008589174e-04 1.28714807301889e-03 -3.37880405391244e-02 + 1 3.20437139095465e+00 -1.09007134627866e-02 1.63748958342951e-02 -1.67759907527840e-03 + 2 3.20383993554932e+00 -9.78221064079988e-03 1.46920974903951e-02 -3.35460468848178e-03 + 3 3.20396645809459e+00 -8.66600108902194e-03 1.30161882986166e-02 -5.03175157651451e-03 + 4 3.20472689263580e+00 -7.55129058414933e-03 1.13447829461505e-02 -6.70974768964128e-03 + 5 3.20606117443283e+00 -6.43724359708628e-03 9.67537402378371e-03 -8.38923439865754e-03 + 6 3.20787728240253e+00 -5.32305735345136e-03 8.00555164318605e-03 -1.00707510401243e-02 + 7 3.21005661933959e+00 -4.20802874844884e-03 6.33320239431985e-03 -1.17547052271157e-02 + 8 3.21246046690473e+00 -3.09161036526929e-03 4.65667700222331e-03 -1.34413501180038e-02 + 9 3.21493755084609e+00 -1.97345282367904e-03 2.97491851146660e-03 -1.51307699357301e-02 + 10 3.21733282412455e+00 -8.53430600414092e-04 1.28754208187088e-03 -1.68228752018509e-02 + 11 3.21949725910164e+00 -8.54042795073986e-04 1.28938993944070e-03 -1.85174089474513e-02 + 12 3.22129789752922e+00 -8.54552092531030e-04 1.29092822024660e-03 -2.02139643225496e-02 + 13 3.22262704746820e+00 -8.54928032905055e-04 1.29206429794880e-03 -2.19120127463720e-02 + 14 3.22340934072964e+00 -8.55149298853072e-04 1.29273318893539e-03 -2.36109402358007e-02 + 15 3.22360580730372e+00 -8.55204867991794e-04 1.29290120264720e-03 -2.53100885311281e-02 + 16 3.22321470302893e+00 -8.55094246997852e-04 1.29256674999968e-03 -2.70087972842502e-02 + 17 3.22226943729432e+00 -8.54826885473466e-04 1.29175858507197e-03 -2.87064439360637e-02 + 18 3.22083431530374e+00 -8.54420971676919e-04 1.29053209547840e-03 -3.04024787186191e-02 + 19 3.21899883900822e+00 -8.53901820582810e-04 1.28896430248325e-03 -3.20964530863574e-02 + 20 3.21687111250546e+00 -8.53300008647365e-04 1.28714807319445e-03 -3.37880405409319e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out index 9014734ce..942b809b4 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.002 @@ -138,32 +133,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped index fc7a79383..520580d86 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403236488325e+00 + x 3.21403236536445e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.37880405391244e-02 + accumulatedWork -3.37880405409319e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj index d0e1dbfa0..2e304633f 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 - 20 3.21687111229972e+00 -8.53300008589174e-04 1.28714807301889e-03 -3.37880405391244e-02 - 21 3.21457065791810e+00 -8.52649341831951e-04 1.28518584368989e-03 -3.37880405391244e-02 - 22 3.21222083739193e+00 -8.51984712220503e-04 1.28318305164498e-03 -3.37880405391244e-02 - 23 3.20994117317441e+00 -8.51339925809688e-04 1.28124154753091e-03 -3.37880405391244e-02 - 24 3.20784010088332e+00 -8.50745652823771e-04 1.27945344510775e-03 -3.37880405391244e-02 - 25 3.20600887044777e+00 -8.50227702640212e-04 1.27789600801845e-03 -3.37880405391244e-02 - 26 3.20451722962774e+00 -8.49805802904639e-04 1.27662808833231e-03 -3.37880405391244e-02 - 27 3.20341121817082e+00 -8.49492975624134e-04 1.27568836637342e-03 -3.37880405391244e-02 - 28 3.20271300011156e+00 -8.49295489734355e-04 1.27509530398073e-03 -3.37880405391244e-02 - 29 3.20242228459368e+00 -8.49213262968719e-04 1.27484841255490e-03 -3.37880405391244e-02 - 30 3.20251891587653e+00 -8.49240594422870e-04 1.27493047444245e-03 -3.37880405391244e-02 - 31 3.20296625617950e+00 -8.49367121367561e-04 1.27531040228755e-03 -3.37880405391244e-02 - 32 3.20371520744477e+00 -8.49578956774942e-04 1.27594661619498e-03 -3.37880405391244e-02 - 33 3.20470869854482e+00 -8.49859958492498e-04 1.27679080491367e-03 -3.37880405391244e-02 - 34 3.20588642295006e+00 -8.50193069257824e-04 1.27779190188417e-03 -3.37880405391244e-02 - 35 3.20718940766233e+00 -8.50561608988155e-04 1.27889993055670e-03 -3.37880405391244e-02 - 36 3.20856396826048e+00 -8.50950393436199e-04 1.28006934623462e-03 -3.37880405391244e-02 - 37 3.20996472914883e+00 -8.51346588445386e-04 1.28126160175090e-03 -3.37880405391244e-02 - 38 3.21135666552061e+00 -8.51740287504375e-04 1.28244689603437e-03 -3.37880405391244e-02 - 39 3.21271631661605e+00 -8.52124854908226e-04 1.28360522708805e-03 -3.37880405391244e-02 - 40 3.21403236488325e+00 -8.52497089569868e-04 1.28472690946618e-03 -3.37880405391244e-02 + 20 3.21687111250546e+00 -8.53300008647364e-04 1.28714807319444e-03 -3.37880405409319e-02 + 21 3.21457065814050e+00 -8.52649341894857e-04 1.28518584387952e-03 -3.37880405409319e-02 + 22 3.21222083763125e+00 -8.51984712288192e-04 1.28318305184888e-03 -3.37880405409319e-02 + 23 3.20994117343080e+00 -8.51339925882205e-04 1.28124154774919e-03 -3.37880405409319e-02 + 24 3.20784010115684e+00 -8.50745652901133e-04 1.27945344534044e-03 -3.37880405409319e-02 + 25 3.20600887073836e+00 -8.50227702722403e-04 1.27789600826552e-03 -3.37880405409319e-02 + 26 3.20451722993525e+00 -8.49805802991615e-04 1.27662808859363e-03 -3.37880405409319e-02 + 27 3.20341121849498e+00 -8.49492975715819e-04 1.27568836664879e-03 -3.37880405409319e-02 + 28 3.20271300045200e+00 -8.49295489830646e-04 1.27509530426987e-03 -3.37880405409319e-02 + 29 3.20242228494997e+00 -8.49213263069492e-04 1.27484841285746e-03 -3.37880405409319e-02 + 30 3.20251891624817e+00 -8.49240594527986e-04 1.27493047475806e-03 -3.37880405409319e-02 + 31 3.20296625656595e+00 -8.49367121476866e-04 1.27531040261579e-03 -3.37880405409319e-02 + 32 3.20371520784545e+00 -8.49578956888271e-04 1.27594661653539e-03 -3.37880405409319e-02 + 33 3.20470869895909e+00 -8.49859958609671e-04 1.27679080526574e-03 -3.37880405409319e-02 + 34 3.20588642337721e+00 -8.50193069378641e-04 1.27779190224733e-03 -3.37880405409319e-02 + 35 3.20718940810155e+00 -8.50561609112386e-04 1.27889993093029e-03 -3.37880405409319e-02 + 36 3.20856396871082e+00 -8.50950393563573e-04 1.28006934661783e-03 -3.37880405409319e-02 + 37 3.20996472960913e+00 -8.51346588575580e-04 1.28126160214278e-03 -3.37880405409319e-02 + 38 3.21135666598954e+00 -8.51740287637006e-04 1.28244689643377e-03 -3.37880405409319e-02 + 39 3.21271631709201e+00 -8.52124855042849e-04 1.28360522749363e-03 -3.37880405409319e-02 + 40 3.21403236536445e+00 -8.52497089705972e-04 1.28472690987640e-03 -3.37880405409319e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-both-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out index a29b506dc..333ed7f0a 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.001 [default] @@ -138,27 +133,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped index 99d5623d0..af765be67 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687060179954e+00 + x 3.21687060200527e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063080692e-02 + accumulatedWork -3.27231063098198e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj index f2c850ae5..6c0216a7f 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 0 3.20554673468334e+00 -1.20221869387334e-02 1.80666223487314e-02 0.00000000000000e+00 - 1 3.20437139095402e+00 -1.09359118630726e-02 1.64277703677051e-02 -1.62472454186094e-03 - 2 3.20383993500698e+00 -9.85259498682288e-03 1.47978091424340e-02 -3.24887432578663e-03 - 3 3.20396645593733e+00 -8.77158205133702e-03 1.31747691238592e-02 -4.87316093009804e-03 - 4 3.20472688727227e+00 -7.69210083141700e-03 1.15563310938840e-02 -6.49826999017548e-03 - 5 3.20606116377278e+00 -6.61333456030012e-03 9.94004409237728e-03 -8.12482265983721e-03 - 6 3.20787726388044e+00 -5.53449416554000e-03 8.32353958380334e-03 -9.75334127405960e-03 - 7 3.21005658994163e+00 -4.45488375311361e-03 6.70472609924175e-03 -1.13842205954968e-02 - 8 3.21246042319826e+00 -3.37395567398206e-03 5.08195396874809e-03 -1.30177057997372e-02 - 9 3.21493748901074e+00 -2.29135249164817e-03 3.45414226380412e-03 -1.46538784510129e-02 - 10 3.21733273998387e+00 -1.20693309599355e-03 1.82085937275571e-03 -1.62926518864930e-02 - 11 3.21949714815442e+00 -1.20779885926177e-03 1.82347260554254e-03 -1.79337772314813e-02 - 12 3.22129775552305e+00 -1.20851910220922e-03 1.82564802550573e-03 -1.95768604544364e-02 - 13 3.22262687042120e+00 -1.20905074816848e-03 1.82725463955845e-03 -2.12213896300391e-02 - 14 3.22340912494254e+00 -1.20936364997702e-03 1.82820054735717e-03 -2.28667701226605e-02 - 15 3.22360554936245e+00 -1.20944221974498e-03 1.82843810362708e-03 -2.45123644159249e-02 - 16 3.22321439979867e+00 -1.20928575991947e-03 1.82796506143001e-03 -2.61575329712119e-02 - 17 3.22226908590648e+00 -1.20890763436259e-03 1.82682208552520e-03 -2.78016728481846e-02 - 18 3.22083391313757e+00 -1.20833356525503e-03 1.82508750615241e-03 -2.94442516037217e-02 - 19 3.21899838366880e+00 -1.20759935346752e-03 1.82287024811897e-03 -3.10848348270288e-02 - 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 + 1 3.20437139095465e+00 -1.09359118630749e-02 1.64277703677119e-02 -1.62472454186161e-03 + 2 3.20383993500950e+00 -9.85259498683116e-03 1.47978091424589e-02 -3.24887432579003e-03 + 3 3.20396645594305e+00 -8.77158205135371e-03 1.31747691239093e-02 -4.87316093010762e-03 + 4 3.20472688728247e+00 -7.69210083144311e-03 1.15563310939625e-02 -6.49826999019610e-03 + 5 3.20606116378874e+00 -6.61333456033522e-03 9.94004409248278e-03 -8.12482265987509e-03 + 6 3.20787726390336e+00 -5.53449416558219e-03 8.32353958393024e-03 -9.75334127412231e-03 + 7 3.21005658997269e+00 -4.45488375315958e-03 6.70472609938014e-03 -1.13842205955932e-02 + 8 3.21246042323855e+00 -3.37395567402717e-03 5.08195396888400e-03 -1.30177057998773e-02 + 9 3.21493748906124e+00 -2.29135249168655e-03 3.45414226391983e-03 -1.46538784512077e-02 + 10 3.21733274004549e+00 -1.20693309601820e-03 1.82085937283009e-03 -1.62926518867548e-02 + 11 3.21949714822798e+00 -1.20779885929119e-03 1.82347260563138e-03 -1.79337772318231e-02 + 12 3.22129775560926e+00 -1.20851910224370e-03 1.82564802560991e-03 -1.95768604548720e-02 + 13 3.22262687052069e+00 -1.20905074820828e-03 1.82725463967874e-03 -2.12213896305829e-02 + 14 3.22340912505588e+00 -1.20936365002235e-03 1.82820054749423e-03 -2.28667701233277e-02 + 15 3.22360554949013e+00 -1.20944221979605e-03 1.82843810378150e-03 -2.45123644167310e-02 + 16 3.22321439994115e+00 -1.20928575997646e-03 1.82796506160231e-03 -2.61575329721731e-02 + 17 3.22226908606420e+00 -1.20890763442568e-03 1.82682208571586e-03 -2.78016728493174e-02 + 18 3.22083391331092e+00 -1.20833356532437e-03 1.82508750636188e-03 -2.94442516050430e-02 + 19 3.21899838385817e+00 -1.20759935354327e-03 1.82287024834765e-03 -3.10848348285559e-02 + 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out index 959f0c552..35f57cbba 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } colvars: # lowerWallConstant = 0.001 [default] @@ -138,32 +133,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped index a9bad9be9..1cdd044fd 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403051403523e+00 + x 3.21403051451645e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063080692e-02 + accumulatedWork -3.27231063098198e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj index 7cdbd31e7..476fdf462 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 - 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 - 21 3.21457009005187e+00 -1.20582803602075e-03 1.81752656556706e-03 -3.27231063080692e-02 - 22 3.21222021029772e+00 -1.20488808411909e-03 1.81469411906520e-03 -3.27231063080692e-02 - 23 3.20994048512507e+00 -1.20397619405003e-03 1.81194834479899e-03 -3.27231063080692e-02 - 24 3.20783935027265e+00 -1.20313574010906e-03 1.80941951140972e-03 -3.27231063080692e-02 - 25 3.20600805578400e+00 -1.20240322231360e-03 1.80721688628766e-03 -3.27231063080692e-02 - 26 3.20451634953337e+00 -1.20180653981335e-03 1.80542369892267e-03 -3.27231063080692e-02 - 27 3.20341027138948e+00 -1.20136410855579e-03 1.80409465165757e-03 -3.27231063080692e-02 - 28 3.20271198551962e+00 -1.20108479420785e-03 1.80325585359664e-03 -3.27231063080692e-02 - 29 3.20242120121622e+00 -1.20096848048649e-03 1.80290661390253e-03 -3.27231063080692e-02 - 30 3.20251776290552e+00 -1.20100710516221e-03 1.80302258331263e-03 -3.27231063080692e-02 - 31 3.20296503299079e+00 -1.20118601319632e-03 1.80355979787307e-03 -3.27231063080692e-02 - 32 3.20371391361211e+00 -1.20148556544484e-03 1.80445945496540e-03 -3.27231063080692e-02 - 33 3.20470733384994e+00 -1.20188293353998e-03 1.80565323241832e-03 -3.27231063080692e-02 - 34 3.20588498738668e+00 -1.20235399495467e-03 1.80706891147932e-03 -3.27231063080692e-02 - 35 3.20718790142930e+00 -1.20287516057172e-03 1.80863581490056e-03 -3.27231063080692e-02 - 36 3.20856239174816e+00 -1.20342495669926e-03 1.81028953300828e-03 -3.27231063080692e-02 - 37 3.20996308291416e+00 -1.20398523316567e-03 1.81197555210123e-03 -3.27231063080692e-02 - 38 3.21135495025727e+00 -1.20454198010291e-03 1.81365172728779e-03 -3.27231063080692e-02 - 39 3.21271453312301e+00 -1.20508581324920e-03 1.81528977161812e-03 -3.27231063080692e-02 - 40 3.21403051403523e+00 -1.20561220561409e-03 1.81687598790710e-03 -3.27231063080692e-02 + 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 + 21 3.21457009027428e+00 -1.20582803610971e-03 1.81752656583525e-03 -3.27231063098198e-02 + 22 3.21222021053704e+00 -1.20488808421481e-03 1.81469411935356e-03 -3.27231063098198e-02 + 23 3.20994048538146e+00 -1.20397619415258e-03 1.81194834510767e-03 -3.27231063098198e-02 + 24 3.20783935054617e+00 -1.20313574021847e-03 1.80941951173880e-03 -3.27231063098198e-02 + 25 3.20600805607460e+00 -1.20240322242984e-03 1.80721688663708e-03 -3.27231063098198e-02 + 26 3.20451634984089e+00 -1.20180653993636e-03 1.80542369929224e-03 -3.27231063098198e-02 + 27 3.20341027171365e+00 -1.20136410868546e-03 1.80409465204701e-03 -3.27231063098198e-02 + 28 3.20271198586007e+00 -1.20108479434403e-03 1.80325585400555e-03 -3.27231063098198e-02 + 29 3.20242120157252e+00 -1.20096848062901e-03 1.80290661433043e-03 -3.27231063098198e-02 + 30 3.20251776327717e+00 -1.20100710531087e-03 1.80302258375899e-03 -3.27231063098198e-02 + 31 3.20296503337725e+00 -1.20118601335090e-03 1.80355979833728e-03 -3.27231063098198e-02 + 32 3.20371391401280e+00 -1.20148556560512e-03 1.80445945544681e-03 -3.27231063098198e-02 + 33 3.20470733426422e+00 -1.20188293370569e-03 1.80565323291624e-03 -3.27231063098198e-02 + 34 3.20588498781384e+00 -1.20235399512554e-03 1.80706891199292e-03 -3.27231063098198e-02 + 35 3.20718790186854e+00 -1.20287516074742e-03 1.80863581542890e-03 -3.27231063098198e-02 + 36 3.20856239219851e+00 -1.20342495687940e-03 1.81028953355024e-03 -3.27231063098198e-02 + 37 3.20996308337448e+00 -1.20398523334979e-03 1.81197555265544e-03 -3.27231063098198e-02 + 38 3.21135495072621e+00 -1.20454198029048e-03 1.81365172785265e-03 -3.27231063098198e-02 + 39 3.21271453359899e+00 -1.20508581343960e-03 1.81528977219172e-03 -3.27231063098198e-02 + 40 3.21403051451645e+00 -1.20561220580658e-03 1.81687598848726e-03 -3.27231063098198e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out index 29a8ea10b..2432c858b 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -131,27 +126,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped index a0bbaca3d..ed4ff587f 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491521323e+00 + x 3.21685491541898e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj index d5d525eb6..dfbf0ebd2 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095402e+00 -1.20174855638161e-02 - 2 3.20383991841948e+00 -1.20153596736779e-02 - 3 3.20396638982490e+00 -1.20158655592996e-02 - 4 3.20472672277551e+00 -1.20189068911021e-02 - 5 3.20606083670179e+00 -1.20242433468072e-02 - 6 3.20787669543948e+00 -1.20315067817579e-02 - 7 3.21005568755800e+00 -1.20402227502320e-02 - 8 3.21245908142754e+00 -1.20498363257101e-02 - 9 3.21493559049101e+00 -1.20597423619640e-02 - 10 3.21733015640955e+00 -1.20693206256382e-02 - 11 3.21949374123820e+00 -1.20779749649528e-02 - 12 3.22129339461899e+00 -1.20851735784760e-02 - 13 3.22262143319445e+00 -1.20904857327778e-02 - 14 3.22340249773966e+00 -1.20936099909586e-02 - 15 3.22359762729192e+00 -1.20943905091677e-02 - 16 3.22320508654863e+00 -1.20928203461945e-02 - 17 3.22225829334495e+00 -1.20890331733798e-02 - 18 3.22082156074746e+00 -1.20832862429898e-02 - 19 3.21898439787187e+00 -1.20759375914875e-02 - 20 3.21685491521323e+00 -1.20674196608529e-02 + 1 3.20437139095465e+00 -1.20174855638186e-02 + 2 3.20383991842200e+00 -1.20153596736880e-02 + 3 3.20396638983062e+00 -1.20158655593225e-02 + 4 3.20472672278571e+00 -1.20189068911429e-02 + 5 3.20606083671774e+00 -1.20242433468710e-02 + 6 3.20787669546241e+00 -1.20315067818496e-02 + 7 3.21005568758906e+00 -1.20402227503562e-02 + 8 3.21245908146782e+00 -1.20498363258713e-02 + 9 3.21493559054151e+00 -1.20597423621660e-02 + 10 3.21733015647118e+00 -1.20693206258847e-02 + 11 3.21949374131176e+00 -1.20779749652470e-02 + 12 3.22129339470521e+00 -1.20851735788208e-02 + 13 3.22262143329394e+00 -1.20904857331758e-02 + 14 3.22340249785300e+00 -1.20936099914120e-02 + 15 3.22359762741961e+00 -1.20943905096784e-02 + 16 3.22320508669112e+00 -1.20928203467645e-02 + 17 3.22225829350267e+00 -1.20890331740107e-02 + 18 3.22082156092082e+00 -1.20832862436833e-02 + 19 3.21898439806125e+00 -1.20759375922450e-02 + 20 3.21685491541898e+00 -1.20674196616759e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out index 95f077f0b..57b080e73 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -131,32 +126,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped index f58df11b7..8719ed7ca 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397364200070e+00 + x 3.21397364248195e+00 } restraint { diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj index 8b5e494a7..fec7bdbdb 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21685491521323e+00 -1.20674196608529e-02 - 21 3.21455264073267e+00 -1.20582105629307e-02 - 22 3.21220094103318e+00 -1.20488037641327e-02 - 23 3.20991934284523e+00 -1.20396773713809e-02 - 24 3.20781628562398e+00 -1.20312651424959e-02 - 25 3.20598302292944e+00 -1.20239320917178e-02 - 26 3.20448930614687e+00 -1.20179572245875e-02 - 27 3.20338117886792e+00 -1.20135247154717e-02 - 28 3.20268080933861e+00 -1.20107232373544e-02 - 29 3.20238791142161e+00 -1.20095516456865e-02 - 30 3.20248233467135e+00 -1.20099293386854e-02 - 31 3.20292744714189e+00 -1.20117097885676e-02 - 32 3.20367415705454e+00 -1.20146966282182e-02 - 33 3.20466539988114e+00 -1.20186615995246e-02 - 34 3.20584087581816e+00 -1.20233635032726e-02 - 35 3.20714161837695e+00 -1.20285664735078e-02 - 36 3.20851394921166e+00 -1.20340557968466e-02 - 37 3.20991249801338e+00 -1.20396499920535e-02 - 38 3.21130224431234e+00 -1.20452089772494e-02 - 39 3.21265973069097e+00 -1.20506389227639e-02 - 40 3.21397364200070e+00 -1.20558945680028e-02 + 20 3.21685491541898e+00 -1.20674196616759e-02 + 21 3.21455264095509e+00 -1.20582105638204e-02 + 22 3.21220094127252e+00 -1.20488037650901e-02 + 23 3.20991934310164e+00 -1.20396773724066e-02 + 24 3.20781628589752e+00 -1.20312651435901e-02 + 25 3.20598302322006e+00 -1.20239320928802e-02 + 26 3.20448930645441e+00 -1.20179572258176e-02 + 27 3.20338117919211e+00 -1.20135247167684e-02 + 28 3.20268080967909e+00 -1.20107232387163e-02 + 29 3.20238791177794e+00 -1.20095516471117e-02 + 30 3.20248233504303e+00 -1.20099293401721e-02 + 31 3.20292744752838e+00 -1.20117097901135e-02 + 32 3.20367415745526e+00 -1.20146966298210e-02 + 33 3.20466540029545e+00 -1.20186616011818e-02 + 34 3.20584087624535e+00 -1.20233635049814e-02 + 35 3.20714161881621e+00 -1.20285664752649e-02 + 36 3.20851394966204e+00 -1.20340557986482e-02 + 37 3.20991249847373e+00 -1.20396499938949e-02 + 38 3.21130224478131e+00 -1.20452089791253e-02 + 39 3.21265973116698e+00 -1.20506389246679e-02 + 40 3.21397364248195e+00 -1.20558945699278e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-upper-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out index 188ad78a8..be491208e 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -152,12 +153,10 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out index abd39e0f9..27cae7081 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test.restart.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -152,7 +153,6 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.1979 @@ -162,7 +162,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt index 157cac038..d885e1c46 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving-decoupling/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2022-05-24. +colvars: Using NAMD interface, version "2022-05-09". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out index c92a480be..0dd351c58 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. colvars: # upperWalls = { 0.2 } @@ -137,27 +132,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped index 99d5623d0..af765be67 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687060179954e+00 + x 3.21687060200527e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063080692e-02 + accumulatedWork -3.27231063098198e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj index f2c850ae5..6c0216a7f 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 0 3.20554673468334e+00 -1.20221869387334e-02 1.80666223487314e-02 0.00000000000000e+00 - 1 3.20437139095402e+00 -1.09359118630726e-02 1.64277703677051e-02 -1.62472454186094e-03 - 2 3.20383993500698e+00 -9.85259498682288e-03 1.47978091424340e-02 -3.24887432578663e-03 - 3 3.20396645593733e+00 -8.77158205133702e-03 1.31747691238592e-02 -4.87316093009804e-03 - 4 3.20472688727227e+00 -7.69210083141700e-03 1.15563310938840e-02 -6.49826999017548e-03 - 5 3.20606116377278e+00 -6.61333456030012e-03 9.94004409237728e-03 -8.12482265983721e-03 - 6 3.20787726388044e+00 -5.53449416554000e-03 8.32353958380334e-03 -9.75334127405960e-03 - 7 3.21005658994163e+00 -4.45488375311361e-03 6.70472609924175e-03 -1.13842205954968e-02 - 8 3.21246042319826e+00 -3.37395567398206e-03 5.08195396874809e-03 -1.30177057997372e-02 - 9 3.21493748901074e+00 -2.29135249164817e-03 3.45414226380412e-03 -1.46538784510129e-02 - 10 3.21733273998387e+00 -1.20693309599355e-03 1.82085937275571e-03 -1.62926518864930e-02 - 11 3.21949714815442e+00 -1.20779885926177e-03 1.82347260554254e-03 -1.79337772314813e-02 - 12 3.22129775552305e+00 -1.20851910220922e-03 1.82564802550573e-03 -1.95768604544364e-02 - 13 3.22262687042120e+00 -1.20905074816848e-03 1.82725463955845e-03 -2.12213896300391e-02 - 14 3.22340912494254e+00 -1.20936364997702e-03 1.82820054735717e-03 -2.28667701226605e-02 - 15 3.22360554936245e+00 -1.20944221974498e-03 1.82843810362708e-03 -2.45123644159249e-02 - 16 3.22321439979867e+00 -1.20928575991947e-03 1.82796506143001e-03 -2.61575329712119e-02 - 17 3.22226908590648e+00 -1.20890763436259e-03 1.82682208552520e-03 -2.78016728481846e-02 - 18 3.22083391313757e+00 -1.20833356525503e-03 1.82508750615241e-03 -2.94442516037217e-02 - 19 3.21899838366880e+00 -1.20759935346752e-03 1.82287024811897e-03 -3.10848348270288e-02 - 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 + 1 3.20437139095465e+00 -1.09359118630749e-02 1.64277703677119e-02 -1.62472454186161e-03 + 2 3.20383993500950e+00 -9.85259498683116e-03 1.47978091424589e-02 -3.24887432579003e-03 + 3 3.20396645594305e+00 -8.77158205135371e-03 1.31747691239093e-02 -4.87316093010762e-03 + 4 3.20472688728247e+00 -7.69210083144311e-03 1.15563310939625e-02 -6.49826999019610e-03 + 5 3.20606116378874e+00 -6.61333456033522e-03 9.94004409248278e-03 -8.12482265987509e-03 + 6 3.20787726390336e+00 -5.53449416558219e-03 8.32353958393024e-03 -9.75334127412231e-03 + 7 3.21005658997269e+00 -4.45488375315958e-03 6.70472609938014e-03 -1.13842205955932e-02 + 8 3.21246042323855e+00 -3.37395567402717e-03 5.08195396888400e-03 -1.30177057998773e-02 + 9 3.21493748906124e+00 -2.29135249168655e-03 3.45414226391983e-03 -1.46538784512077e-02 + 10 3.21733274004549e+00 -1.20693309601820e-03 1.82085937283009e-03 -1.62926518867548e-02 + 11 3.21949714822798e+00 -1.20779885929119e-03 1.82347260563138e-03 -1.79337772318231e-02 + 12 3.22129775560926e+00 -1.20851910224370e-03 1.82564802560991e-03 -1.95768604548720e-02 + 13 3.22262687052069e+00 -1.20905074820828e-03 1.82725463967874e-03 -2.12213896305829e-02 + 14 3.22340912505588e+00 -1.20936365002235e-03 1.82820054749423e-03 -2.28667701233277e-02 + 15 3.22360554949013e+00 -1.20944221979605e-03 1.82843810378150e-03 -2.45123644167310e-02 + 16 3.22321439994115e+00 -1.20928575997646e-03 1.82796506160231e-03 -2.61575329721731e-02 + 17 3.22226908606420e+00 -1.20890763442568e-03 1.82682208571586e-03 -2.78016728493174e-02 + 18 3.22083391331092e+00 -1.20833356532437e-03 1.82508750636188e-03 -2.94442516050430e-02 + 19 3.21899838385817e+00 -1.20759935354327e-03 1.82287024834765e-03 -3.10848348285559e-02 + 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out index 0187122c8..0bd2a2834 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,14 +112,13 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = 0.0001 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. colvars: # upperWalls = { 0.2 } @@ -137,32 +132,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21687 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped index a9bad9be9..1cdd044fd 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403051403523e+00 + x 3.21403051451645e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonicwalls1 firstStep 0 forceConstant 1.00000000000000e-04 - accumulatedWork -3.27231063080692e-02 + accumulatedWork -3.27231063098198e-02 } } diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj index 7cdbd31e7..476fdf462 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonicwalls1 W_harmonicwalls1 - 20 3.21687060179954e+00 -1.20674824071981e-03 1.82030164560046e-03 -3.27231063080692e-02 - 21 3.21457009005187e+00 -1.20582803602075e-03 1.81752656556706e-03 -3.27231063080692e-02 - 22 3.21222021029772e+00 -1.20488808411909e-03 1.81469411906520e-03 -3.27231063080692e-02 - 23 3.20994048512507e+00 -1.20397619405003e-03 1.81194834479899e-03 -3.27231063080692e-02 - 24 3.20783935027265e+00 -1.20313574010906e-03 1.80941951140972e-03 -3.27231063080692e-02 - 25 3.20600805578400e+00 -1.20240322231360e-03 1.80721688628766e-03 -3.27231063080692e-02 - 26 3.20451634953337e+00 -1.20180653981335e-03 1.80542369892267e-03 -3.27231063080692e-02 - 27 3.20341027138948e+00 -1.20136410855579e-03 1.80409465165757e-03 -3.27231063080692e-02 - 28 3.20271198551962e+00 -1.20108479420785e-03 1.80325585359664e-03 -3.27231063080692e-02 - 29 3.20242120121622e+00 -1.20096848048649e-03 1.80290661390253e-03 -3.27231063080692e-02 - 30 3.20251776290552e+00 -1.20100710516221e-03 1.80302258331263e-03 -3.27231063080692e-02 - 31 3.20296503299079e+00 -1.20118601319632e-03 1.80355979787307e-03 -3.27231063080692e-02 - 32 3.20371391361211e+00 -1.20148556544484e-03 1.80445945496540e-03 -3.27231063080692e-02 - 33 3.20470733384994e+00 -1.20188293353998e-03 1.80565323241832e-03 -3.27231063080692e-02 - 34 3.20588498738668e+00 -1.20235399495467e-03 1.80706891147932e-03 -3.27231063080692e-02 - 35 3.20718790142930e+00 -1.20287516057172e-03 1.80863581490056e-03 -3.27231063080692e-02 - 36 3.20856239174816e+00 -1.20342495669926e-03 1.81028953300828e-03 -3.27231063080692e-02 - 37 3.20996308291416e+00 -1.20398523316567e-03 1.81197555210123e-03 -3.27231063080692e-02 - 38 3.21135495025727e+00 -1.20454198010291e-03 1.81365172728779e-03 -3.27231063080692e-02 - 39 3.21271453312301e+00 -1.20508581324920e-03 1.81528977161812e-03 -3.27231063080692e-02 - 40 3.21403051403523e+00 -1.20561220561409e-03 1.81687598790710e-03 -3.27231063080692e-02 + 20 3.21687060200527e+00 -1.20674824080211e-03 1.82030164584873e-03 -3.27231063098198e-02 + 21 3.21457009027428e+00 -1.20582803610971e-03 1.81752656583525e-03 -3.27231063098198e-02 + 22 3.21222021053704e+00 -1.20488808421481e-03 1.81469411935356e-03 -3.27231063098198e-02 + 23 3.20994048538146e+00 -1.20397619415258e-03 1.81194834510767e-03 -3.27231063098198e-02 + 24 3.20783935054617e+00 -1.20313574021847e-03 1.80941951173880e-03 -3.27231063098198e-02 + 25 3.20600805607460e+00 -1.20240322242984e-03 1.80721688663708e-03 -3.27231063098198e-02 + 26 3.20451634984089e+00 -1.20180653993636e-03 1.80542369929224e-03 -3.27231063098198e-02 + 27 3.20341027171365e+00 -1.20136410868546e-03 1.80409465204701e-03 -3.27231063098198e-02 + 28 3.20271198586007e+00 -1.20108479434403e-03 1.80325585400555e-03 -3.27231063098198e-02 + 29 3.20242120157252e+00 -1.20096848062901e-03 1.80290661433043e-03 -3.27231063098198e-02 + 30 3.20251776327717e+00 -1.20100710531087e-03 1.80302258375899e-03 -3.27231063098198e-02 + 31 3.20296503337725e+00 -1.20118601335090e-03 1.80355979833728e-03 -3.27231063098198e-02 + 32 3.20371391401280e+00 -1.20148556560512e-03 1.80445945544681e-03 -3.27231063098198e-02 + 33 3.20470733426422e+00 -1.20188293370569e-03 1.80565323291624e-03 -3.27231063098198e-02 + 34 3.20588498781384e+00 -1.20235399512554e-03 1.80706891199292e-03 -3.27231063098198e-02 + 35 3.20718790186854e+00 -1.20287516074742e-03 1.80863581542890e-03 -3.27231063098198e-02 + 36 3.20856239219851e+00 -1.20342495687940e-03 1.81028953355024e-03 -3.27231063098198e-02 + 37 3.20996308337448e+00 -1.20398523334979e-03 1.81197555265544e-03 -3.27231063098198e-02 + 38 3.21135495072621e+00 -1.20454198029048e-03 1.81365172785265e-03 -3.27231063098198e-02 + 39 3.21271453359899e+00 -1.20508581343960e-03 1.81528977219172e-03 -3.27231063098198e-02 + 40 3.21403051451645e+00 -1.20561220580658e-03 1.81687598848726e-03 -3.27231063098198e-02 diff --git a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_harmonicwalls-upper-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out index c19bd65ec..a86d5ad83 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out @@ -4,9 +4,10 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -142,12 +142,10 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat index 6ff3132f9..1b0ff42d4 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 6.00000000000000e-01 2.00000000000000e-01 24 0 +# 0.6 0.2 24 0 - 7.00000000000000e-01 0.00000000000000e+00 - 9.00000000000000e-01 0.00000000000000e+00 - 1.10000000000000e+00 0.00000000000000e+00 - 1.30000000000000e+00 0.00000000000000e+00 - 1.50000000000000e+00 0.00000000000000e+00 - 1.70000000000000e+00 0.00000000000000e+00 - 1.90000000000000e+00 0.00000000000000e+00 - 2.10000000000000e+00 0.00000000000000e+00 - 2.30000000000000e+00 0.00000000000000e+00 - 2.50000000000000e+00 0.00000000000000e+00 - 2.70000000000000e+00 0.00000000000000e+00 - 2.90000000000000e+00 0.00000000000000e+00 - 3.10000000000000e+00 0.00000000000000e+00 - 3.30000000000000e+00 2.00000000000000e+01 - 3.50000000000000e+00 0.00000000000000e+00 - 3.70000000000000e+00 0.00000000000000e+00 - 3.90000000000000e+00 0.00000000000000e+00 - 4.10000000000000e+00 0.00000000000000e+00 - 4.30000000000000e+00 0.00000000000000e+00 - 4.50000000000000e+00 0.00000000000000e+00 - 4.70000000000000e+00 0.00000000000000e+00 - 4.90000000000000e+00 0.00000000000000e+00 - 5.10000000000000e+00 0.00000000000000e+00 - 5.30000000000000e+00 0.00000000000000e+00 + 0.7 0 + 0.9 0 + 1.1 0 + 1.3 0 + 1.5 0 + 1.7 0 + 1.9 0 + 2.1 0 + 2.3 0 + 2.5 0 + 2.7 0 + 2.9 0 + 3.1 0 + 3.3 20 + 3.5 0 + 3.7 0 + 3.9 0 + 4.1 0 + 4.3 0 + 4.5 0 + 4.7 0 + 4.9 0 + 5.1 0 + 5.3 0 diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out index a44f3ed1b..cc179e493 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out @@ -4,9 +4,10 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -142,7 +142,6 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 @@ -152,7 +151,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out index 6e8a55a99..2f8db54b9 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,27 +125,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped index e2cb5b6df..54969f08b 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21687794922887e+00 + x 3.21687794941120e+00 } restraint { diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj index 31625d56a..60f1c7042 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 -2.00000000000000e-03 - 1 3.20437146782473e+00 -2.00000000000000e-03 - 2 3.20384022474555e+00 -2.00000000000000e-03 - 3 3.20396707507294e+00 -2.00000000000000e-03 - 4 3.20472793153934e+00 -2.00000000000000e-03 - 5 3.20606270721111e+00 -2.00000000000000e-03 - 6 3.20787935837892e+00 -2.00000000000000e-03 - 7 3.21005926521749e+00 -2.00000000000000e-03 - 8 3.21246368719045e+00 -2.00000000000000e-03 - 9 3.21494132865815e+00 -2.00000000000000e-03 - 10 3.21733712234869e+00 -2.00000000000000e-03 - 11 3.21950202183533e+00 -2.00000000000000e-03 - 12 3.22130306897412e+00 -2.00000000000000e-03 - 13 3.22263257351741e+00 -2.00000000000000e-03 - 14 3.22341517032649e+00 -2.00000000000000e-03 - 15 3.22361189349532e+00 -2.00000000000000e-03 - 16 3.22322100366549e+00 -2.00000000000000e-03 - 17 3.22227591535082e+00 -2.00000000000000e-03 - 18 3.22084093883207e+00 -2.00000000000000e-03 - 19 3.21900558075137e+00 -2.00000000000000e-03 - 20 3.21687794922887e+00 -2.00000000000000e-03 + 1 3.20437146782535e+00 -2.00000000000000e-03 + 2 3.20384022479972e+00 -2.00000000000000e-03 + 3 3.20396707508047e+00 -2.00000000000000e-03 + 4 3.20472793158710e+00 -2.00000000000000e-03 + 5 3.20606270721620e+00 -2.00000000000000e-03 + 6 3.20787935839808e+00 -2.00000000000000e-03 + 7 3.21005926525274e+00 -2.00000000000000e-03 + 8 3.21246368724284e+00 -2.00000000000000e-03 + 9 3.21494132872828e+00 -2.00000000000000e-03 + 10 3.21733712243639e+00 -2.00000000000000e-03 + 11 3.21950202193975e+00 -2.00000000000000e-03 + 12 3.22130306909382e+00 -2.00000000000000e-03 + 13 3.22263257365056e+00 -2.00000000000000e-03 + 14 3.22341517047102e+00 -2.00000000000000e-03 + 15 3.22361189364914e+00 -2.00000000000000e-03 + 16 3.22322100382672e+00 -2.00000000000000e-03 + 17 3.22227591551750e+00 -2.00000000000000e-03 + 18 3.22084093900392e+00 -2.00000000000000e-03 + 19 3.21900558093302e+00 -2.00000000000000e-03 + 20 3.21687794941120e+00 -2.00000000000000e-03 diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out index f25f2a600..ae73096ad 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,32 +125,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 colvars: Restarting linear bias "linear1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped index 8bd282397..7819eca62 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21403631049857e+00 + x 3.21403631097325e+00 } restraint { diff --git a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj index feadd768c..22b58b046 100644 --- a/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_linear-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21687794922887e+00 -2.00000000000000e-03 - 21 3.21457756974034e+00 -2.00000000000000e-03 - 22 3.21222780608884e+00 -2.00000000000000e-03 - 23 3.20994818169250e+00 -2.00000000000000e-03 - 24 3.20784713203794e+00 -2.00000000000000e-03 - 25 3.20601590593918e+00 -2.00000000000000e-03 - 26 3.20452424926460e+00 -2.00000000000000e-03 - 27 3.20341819935304e+00 -2.00000000000000e-03 - 28 3.20271991761219e+00 -2.00000000000000e-03 - 29 3.20242911063155e+00 -2.00000000000000e-03 - 30 3.20252562047120e+00 -2.00000000000000e-03 - 31 3.20297280776558e+00 -2.00000000000000e-03 - 32 3.20372157370085e+00 -2.00000000000000e-03 - 33 3.20471484737174e+00 -2.00000000000000e-03 - 34 3.20589232352072e+00 -2.00000000000000e-03 - 35 3.20719503146155e+00 -2.00000000000000e-03 - 36 3.20856929000306e+00 -2.00000000000000e-03 - 37 3.20996972751317e+00 -2.00000000000000e-03 - 38 3.21136132363592e+00 -2.00000000000000e-03 - 39 3.21272062227744e+00 -2.00000000000000e-03 - 40 3.21403631049857e+00 -2.00000000000000e-03 + 20 3.21687794941120e+00 -2.00000000000000e-03 + 21 3.21457756992910e+00 -2.00000000000000e-03 + 22 3.21222780628590e+00 -2.00000000000000e-03 + 23 3.20994818190026e+00 -2.00000000000000e-03 + 24 3.20784713225907e+00 -2.00000000000000e-03 + 25 3.20601590617646e+00 -2.00000000000000e-03 + 26 3.20452424952068e+00 -2.00000000000000e-03 + 27 3.20341819963022e+00 -2.00000000000000e-03 + 28 3.20271991791227e+00 -2.00000000000000e-03 + 29 3.20242911095567e+00 -2.00000000000000e-03 + 30 3.20252562081973e+00 -2.00000000000000e-03 + 31 3.20297280813812e+00 -2.00000000000000e-03 + 32 3.20372157409621e+00 -2.00000000000000e-03 + 33 3.20471484778801e+00 -2.00000000000000e-03 + 34 3.20589232395536e+00 -2.00000000000000e-03 + 35 3.20719503191152e+00 -2.00000000000000e-03 + 36 3.20856929046496e+00 -2.00000000000000e-03 + 37 3.20996972798345e+00 -2.00000000000000e-03 + 38 3.21136132411101e+00 -2.00000000000000e-03 + 39 3.21272062275390e+00 -2.00000000000000e-03 + 40 3.21403631097325e+00 -2.00000000000000e-03 diff --git a/namd/tests/library/000_distance_linear-fixed/namd-version.txt b/namd/tests/library/000_distance_linear-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distance_linear-fixed/namd-version.txt +++ b/namd/tests/library/000_distance_linear-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out index 3d1d47403..5461163f6 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -0.1 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,27 +131,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped index 7978e66e5..d40e34747 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21716984757735e+00 + x 3.21716984778310e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name linear1 firstStep 0 forceConstant -1.00000000000000e-01 - accumulatedWork -1.25846317029250e+00 + accumulatedWork -1.25846317032503e+00 } } diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj index ab81a1e48..d7a3f40f3 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_linear1 W_linear1 0 3.20554673468334e+00 -2.00000000000000e-03 6.21109346936669e-03 0.00000000000000e+00 - 1 3.20437146782473e+00 1.82000000000000e-02 -5.64995607144102e-02 -6.27083036500596e-02 - 2 3.20384053454173e+00 3.84000000000000e-02 -1.19187476526403e-01 -1.25405882447803e-01 - 3 3.20396830993065e+00 5.86000000000000e-02 -1.81892542961936e-01 -1.88106042308402e-01 - 4 3.20473100410431e+00 7.88000000000000e-02 -2.44652803123419e-01 -2.50821608591309e-01 - 5 3.20606881617484e+00 9.90000000000000e-02 -3.07500812801309e-01 -3.13564198678041e-01 - 6 3.20788997449316e+00 1.19200000000000e-01 -3.70460484959585e-01 -3.76343576162802e-01 - 7 3.21007611525328e+00 1.39400000000000e-01 -4.33544610466307e-01 -4.39167113690919e-01 - 8 3.21248873642126e+00 1.59600000000000e-01 -4.96753202332834e-01 -5.02039386166628e-01 - 9 3.21497676245318e+00 1.79800000000000e-01 -5.60072821889081e-01 -5.64961916768182e-01 - 10 3.21738532749986e+00 2.00000000000000e-01 -6.23477065499971e-01 -6.27933100383679e-01 - 11 3.21956556827726e+00 2.00000000000000e-01 -6.23913113655452e-01 -6.90948324862880e-01 - 12 3.22138438212180e+00 2.00000000000000e-01 -6.24276876424360e-01 -7.54000289381740e-01 - 13 3.22273392229575e+00 2.00000000000000e-01 -6.24546784459149e-01 -8.17079514612114e-01 - 14 3.22353866090033e+00 2.00000000000000e-01 -6.24707732180065e-01 -8.80174995562301e-01 - 15 3.22375946848086e+00 2.00000000000000e-01 -6.24751893696173e-01 -9.43274936825614e-01 - 16 3.22339444626381e+00 2.00000000000000e-01 -6.24678889252761e-01 -1.00636750464014e+00 - 17 3.22247685750743e+00 2.00000000000000e-01 -6.24495371501486e-01 -1.06944153716179e+00 - 18 3.22107087240991e+00 2.00000000000000e-01 -6.24214174481982e-01 -1.13248716878447e+00 - 19 3.21926587064193e+00 2.00000000000000e-01 -6.23853174128386e-01 -1.19549633937144e+00 - 20 3.21716984757735e+00 2.00000000000000e-01 -6.23433969515469e-01 -1.25846317029250e+00 + 1 3.20437146782536e+00 1.82000000000000e-02 -5.64995607144215e-02 -6.27083036500722e-02 + 2 3.20384053454426e+00 3.84000000000000e-02 -1.19187476526499e-01 -1.25405882447866e-01 + 3 3.20396830993637e+00 5.86000000000000e-02 -1.81892542962271e-01 -1.88106042308581e-01 + 4 3.20473100411451e+00 7.88000000000000e-02 -2.44652803124223e-01 -2.50821608591694e-01 + 5 3.20606881619079e+00 9.90000000000000e-02 -3.07500812802888e-01 -3.13564198678748e-01 + 6 3.20788997451609e+00 1.19200000000000e-01 -3.70460484962318e-01 -3.76343576163973e-01 + 7 3.21007611528435e+00 1.39400000000000e-01 -4.33544610470638e-01 -4.39167113692717e-01 + 8 3.21248873646155e+00 1.59600000000000e-01 -4.96753202339263e-01 -5.02039386169240e-01 + 9 3.21497676250368e+00 1.79800000000000e-01 -5.60072821898162e-01 -5.64961916771815e-01 + 10 3.21738532756148e+00 2.00000000000000e-01 -6.23477065512297e-01 -6.27933100388556e-01 + 11 3.21956556835082e+00 2.00000000000000e-01 -6.23913113670165e-01 -6.90948324869243e-01 + 12 3.22138438220801e+00 2.00000000000000e-01 -6.24276876441603e-01 -7.54000289389845e-01 + 13 3.22273392239524e+00 2.00000000000000e-01 -6.24546784479049e-01 -8.17079514622229e-01 + 14 3.22353866101367e+00 2.00000000000000e-01 -6.24707732202734e-01 -8.80174995574705e-01 + 15 3.22375946860855e+00 2.00000000000000e-01 -6.24751893721710e-01 -9.43274936840598e-01 + 16 3.22339444640630e+00 2.00000000000000e-01 -6.24678889281260e-01 -1.00636750465800e+00 + 17 3.22247685766515e+00 2.00000000000000e-01 -6.24495371533031e-01 -1.06944153718284e+00 + 18 3.22107087258327e+00 2.00000000000000e-01 -6.24214174516655e-01 -1.13248716880902e+00 + 19 3.21926587083132e+00 2.00000000000000e-01 -6.23853174166263e-01 -1.19549633939982e+00 + 20 3.21716984778310e+00 2.00000000000000e-01 -6.23433969556620e-01 -1.25846317032503e+00 diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out index 1abc5a030..bffe886e1 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,14 +115,13 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -0.1 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # targetEquilSteps = 0 [default] colvars: # lambdaSchedule = [default] -colvars: # lambdaExponent = 1 [default] +colvars: # targetForceExponent = 1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -136,32 +131,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21717 colvars: Restarting linear bias "linear1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped index 329d673d2..c2d3e24ea 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21509555082278e+00 + x 3.21509555130398e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name linear1 firstStep 0 forceConstant -1.00000000000000e-01 - accumulatedWork -1.25846317029250e+00 + accumulatedWork -1.25846317032503e+00 } } diff --git a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj index cd6a6f61c..105936f55 100644 --- a/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance_linear-k-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_linear1 W_linear1 - 20 3.21716984757735e+00 2.00000000000000e-01 -6.23433969515469e-01 -1.25846317029250e+00 - 21 3.21490223025136e+00 2.00000000000000e-01 -6.22980446050271e-01 -1.25846317029250e+00 - 22 3.21258629724258e+00 2.00000000000000e-01 -6.22517259448516e-01 -1.25846317029250e+00 - 23 3.21034149757330e+00 2.00000000000000e-01 -6.22068299514661e-01 -1.25846317029250e+00 - 24 3.20827619999141e+00 2.00000000000000e-01 -6.21655239998281e-01 -1.25846317029250e+00 - 25 3.20648158985175e+00 2.00000000000000e-01 -6.21296317970351e-01 -1.25846317029250e+00 - 26 3.20502734915530e+00 2.00000000000000e-01 -6.21005469831060e-01 -1.25846317029250e+00 - 27 3.20395944688168e+00 2.00000000000000e-01 -6.20791889376335e-01 -1.25846317029250e+00 - 28 3.20329996891376e+00 2.00000000000000e-01 -6.20659993782751e-01 -1.25846317029250e+00 - 29 3.20304853658376e+00 2.00000000000000e-01 -6.20609707316753e-01 -1.25846317029250e+00 - 30 3.20318489575175e+00 2.00000000000000e-01 -6.20636979150349e-01 -1.25846317029250e+00 - 31 3.20367230075533e+00 2.00000000000000e-01 -6.20734460151066e-01 -1.25846317029250e+00 - 32 3.20446153809111e+00 2.00000000000000e-01 -6.20892307618221e-01 -1.25846317029250e+00 - 33 3.20549541623088e+00 2.00000000000000e-01 -6.21099083246176e-01 -1.25846317029250e+00 - 34 3.20671350699132e+00 2.00000000000000e-01 -6.21342701398263e-01 -1.25846317029250e+00 - 35 3.20805672062037e+00 2.00000000000000e-01 -6.21611344124074e-01 -1.25846317029250e+00 - 36 3.20947126470013e+00 2.00000000000000e-01 -6.21894252940025e-01 -1.25846317029250e+00 - 37 3.21091167068192e+00 2.00000000000000e-01 -6.22182334136383e-01 -1.25846317029250e+00 - 38 3.21234283861993e+00 2.00000000000000e-01 -6.22468567723985e-01 -1.25846317029250e+00 - 39 3.21374125101100e+00 2.00000000000000e-01 -6.22748250202200e-01 -1.25846317029250e+00 - 40 3.21509555082278e+00 2.00000000000000e-01 -6.23019110164555e-01 -1.25846317029250e+00 + 20 3.21716984778310e+00 2.00000000000000e-01 -6.23433969556620e-01 -1.25846317032503e+00 + 21 3.21490223047378e+00 2.00000000000000e-01 -6.22980446094756e-01 -1.25846317032503e+00 + 22 3.21258629748191e+00 2.00000000000000e-01 -6.22517259496383e-01 -1.25846317032503e+00 + 23 3.21034149782971e+00 2.00000000000000e-01 -6.22068299565942e-01 -1.25846317032503e+00 + 24 3.20827620026494e+00 2.00000000000000e-01 -6.21655240052988e-01 -1.25846317032503e+00 + 25 3.20648159014237e+00 2.00000000000000e-01 -6.21296318028474e-01 -1.25846317032503e+00 + 26 3.20502734946283e+00 2.00000000000000e-01 -6.21005469892566e-01 -1.25846317032503e+00 + 27 3.20395944720586e+00 2.00000000000000e-01 -6.20791889441172e-01 -1.25846317032503e+00 + 28 3.20329996925422e+00 2.00000000000000e-01 -6.20659993850845e-01 -1.25846317032503e+00 + 29 3.20304853694008e+00 2.00000000000000e-01 -6.20609707388016e-01 -1.25846317032503e+00 + 30 3.20318489612342e+00 2.00000000000000e-01 -6.20636979224683e-01 -1.25846317032503e+00 + 31 3.20367230114181e+00 2.00000000000000e-01 -6.20734460228362e-01 -1.25846317032503e+00 + 32 3.20446153849181e+00 2.00000000000000e-01 -6.20892307698363e-01 -1.25846317032503e+00 + 33 3.20549541664518e+00 2.00000000000000e-01 -6.21099083329035e-01 -1.25846317032503e+00 + 34 3.20671350741850e+00 2.00000000000000e-01 -6.21342701483699e-01 -1.25846317032503e+00 + 35 3.20805672105962e+00 2.00000000000000e-01 -6.21611344211924e-01 -1.25846317032503e+00 + 36 3.20947126515048e+00 2.00000000000000e-01 -6.21894253030096e-01 -1.25846317032503e+00 + 37 3.21091167114224e+00 2.00000000000000e-01 -6.22182334228447e-01 -1.25846317032503e+00 + 38 3.21234283908886e+00 2.00000000000000e-01 -6.22468567817772e-01 -1.25846317032503e+00 + 39 3.21374125148697e+00 2.00000000000000e-01 -6.22748250297394e-01 -1.25846317032503e+00 + 40 3.21509555130398e+00 2.00000000000000e-01 -6.23019110260796e-01 -1.25846317032503e+00 diff --git a/namd/tests/library/000_distance_linear-k-moving/namd-version.txt b/namd/tests/library/000_distance_linear-k-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distance_linear-k-moving/namd-version.txt +++ b/namd/tests/library/000_distance_linear-k-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out index b7fa6abce..abb32eebd 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -152,7 +148,6 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -163,28 +158,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped index 26945fa08..f4d2ca8a0 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.17274648853048e-01 , -1.89053561545958e-03 , 9.48331810639220e-01 ) + x ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj index 84fccc97a..653638305 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -3.39806527406457e-01 , 7.75672148823424e-03 , 9.40463373664131e-01 ) ( 2.67961305481292e-03 , -1.55134429764685e-05 , -1.88092674732826e-03 ) - 1 ( -3.39402299530748e-01 , 6.96783241211861e-03 , 9.40615505073522e-01 ) ( 2.67880459906150e-03 , -1.39356648242372e-05 , -1.88123101014704e-03 ) - 2 ( -3.38852268621315e-01 , 6.28615128621521e-03 , 9.40818592690533e-01 ) ( 2.67770453724263e-03 , -1.25723025724304e-05 , -1.88163718538107e-03 ) - 3 ( -3.38144430390545e-01 , 5.71702991523034e-03 , 9.41076861773151e-01 ) ( 2.67628886078109e-03 , -1.14340598304607e-05 , -1.88215372354630e-03 ) - 4 ( -3.37272058702922e-01 , 5.26001267429506e-03 , 9.41392527421457e-01 ) ( 2.67454411740584e-03 , -1.05200253485901e-05 , -1.88278505484291e-03 ) - 5 ( -3.36235002706895e-01 , 4.90828501062859e-03 , 9.41765327293880e-01 ) ( 2.67247000541379e-03 , -9.81657002125718e-06 , -1.88353065458776e-03 ) - 6 ( -3.35040319467782e-01 , 4.64847236791525e-03 , 9.42192324334884e-01 ) ( 2.67008063893556e-03 , -9.29694473583050e-06 , -1.88438464866977e-03 ) - 7 ( -3.33702304344449e-01 , 4.46100232397236e-03 , 9.42667954018524e-01 ) ( 2.66740460868890e-03 , -8.92200464794472e-06 , -1.88533590803705e-03 ) - 8 ( -3.32242055264741e-01 , 4.32116578678476e-03 , 9.43184257841332e-01 ) ( 2.66448411052948e-03 , -8.64233157356951e-06 , -1.88636851568266e-03 ) - 9 ( -3.30686722575443e-01 , 4.20085972855961e-03 , 9.43731235198800e-01 ) ( 2.66137344515089e-03 , -8.40171945711923e-06 , -1.88746247039760e-03 ) - 10 ( -3.29068550292791e-01 , 4.07080426882692e-03 , 9.44297261332895e-01 ) ( 2.65813710058558e-03 , -8.14160853765385e-06 , -1.88859452266579e-03 ) - 11 ( -3.27423742833967e-01 , 3.90288351107626e-03 , 9.44869546619476e-01 ) ( 2.65484748566793e-03 , -7.80576702215252e-06 , -1.88973909323895e-03 ) - 12 ( -3.25791132203644e-01 , 3.67221267471163e-03 , 9.45434637101656e-01 ) ( 2.65158226440729e-03 , -7.34442534942325e-06 , -1.89086927420331e-03 ) - 13 ( -3.24210587610799e-01 , 3.35858640839648e-03 , 9.45978971636472e-01 ) ( 2.64842117522160e-03 , -6.71717281679296e-06 , -1.89195794327294e-03 ) - 14 ( -3.22721152621232e-01 , 2.94710471653878e-03 , 9.46489499268013e-01 ) ( 2.64544230524246e-03 , -5.89420943307757e-06 , -1.89297899853603e-03 ) - 15 ( -3.21358984318630e-01 , 2.42796439219500e-03 , 9.46954332682738e-01 ) ( 2.64271796863726e-03 , -4.85592878438999e-06 , -1.89390866536548e-03 ) - 16 ( -3.20155244148942e-01 , 1.79559469694439e-03 , 9.47363391462651e-01 ) ( 2.64031048829788e-03 , -3.59118939388878e-06 , -1.89472678292530e-03 ) - 17 ( -3.19134137387790e-01 , 1.04747308610593e-03 , 9.47708977035611e-01 ) ( 2.63826827477558e-03 , -2.09494617221186e-06 , -1.89541795407122e-03 ) - 18 ( -3.18311310715357e-01 , 1.83029983452565e-04 , 9.47986221403400e-01 ) ( 2.63662262143071e-03 , -3.66059966905130e-07 , -1.89597244280680e-03 ) - 19 ( -3.17692796752311e-01 , -7.96993693460030e-04 , 9.48193361974628e-01 ) ( 2.63538559350462e-03 , 1.59398738692006e-06 , -1.89638672394926e-03 ) - 20 ( -3.17274648853048e-01 , -1.89053561545958e-03 , 9.48331810639220e-01 ) ( 2.63454929770610e-03 , 3.78107123091915e-06 , -1.89666362127844e-03 ) + 0 ( -3.39806527406457e-01 , 7.75672148823417e-03 , 9.40463373664131e-01 ) ( 2.67961305481292e-03 , -1.55134429764683e-05 , -1.88092674732826e-03 ) + 1 ( -3.39402299531197e-01 , 6.96783241200742e-03 , 9.40615505073361e-01 ) ( 2.67880459906239e-03 , -1.39356648240148e-05 , -1.88123101014672e-03 ) + 2 ( -3.38852268623157e-01 , 6.28615128581265e-03 , 9.40818592689872e-01 ) ( 2.67770453724631e-03 , -1.25723025716253e-05 , -1.88163718537974e-03 ) + 3 ( -3.38144430394757e-01 , 5.71702991439356e-03 , 9.41076861771643e-01 ) ( 2.67628886078951e-03 , -1.14340598287871e-05 , -1.88215372354329e-03 ) + 4 ( -3.37272058710501e-01 , 5.26001267291420e-03 , 9.41392527418750e-01 ) ( 2.67454411742100e-03 , -1.05200253458284e-05 , -1.88278505483750e-03 ) + 5 ( -3.36235002718839e-01 , 4.90828500862304e-03 , 9.41765327289626e-01 ) ( 2.67247000543768e-03 , -9.81657001724609e-06 , -1.88353065457925e-03 ) + 6 ( -3.35040319485078e-01 , 4.64847236523130e-03 , 9.42192324328747e-01 ) ( 2.67008063897016e-03 , -9.29694473046260e-06 , -1.88438464865749e-03 ) + 7 ( -3.33702304368059e-01 , 4.46100232057914e-03 , 9.42667954010182e-01 ) ( 2.66740460873612e-03 , -8.92200464115828e-06 , -1.88533590802036e-03 ) + 8 ( -3.32242055295591e-01 , 4.32116578267109e-03 , 9.43184257830484e-01 ) ( 2.66448411059118e-03 , -8.64233156534219e-06 , -1.88636851566097e-03 ) + 9 ( -3.30686722614415e-01 , 4.20085972373069e-03 , 9.43731235185166e-01 ) ( 2.66137344522883e-03 , -8.40171944746138e-06 , -1.88746247037033e-03 ) + 10 ( -3.29068550340716e-01 , 4.07080426330041e-03 , 9.44297261316218e-01 ) ( 2.65813710068143e-03 , -8.14160852660083e-06 , -1.88859452263244e-03 ) + 11 ( -3.27423742891617e-01 , 3.90288350488177e-03 , 9.44869546599525e-01 ) ( 2.65484748578323e-03 , -7.80576700976354e-06 , -1.88973909319905e-03 ) + 12 ( -3.25791132271727e-01 , 3.67221266789039e-03 , 9.45434637078221e-01 ) ( 2.65158226454345e-03 , -7.34442533578077e-06 , -1.89086927415644e-03 ) + 13 ( -3.24210587689955e-01 , 3.35858640100320e-03 , 9.45978971609370e-01 ) ( 2.64842117537991e-03 , -6.71717280200640e-06 , -1.89195794321874e-03 ) + 14 ( -3.22721152712020e-01 , 2.94710470864841e-03 , 9.46489499237081e-01 ) ( 2.64544230542404e-03 , -5.89420941729682e-06 , -1.89297899847416e-03 ) + 15 ( -3.21358984421525e-01 , 2.42796438390647e-03 , 9.46954332647840e-01 ) ( 2.64271796884305e-03 , -4.85592876781293e-06 , -1.89390866529568e-03 ) + 16 ( -3.20155244264332e-01 , 1.79559468838712e-03 , 9.47363391423672e-01 ) ( 2.64031048852866e-03 , -3.59118937677423e-06 , -1.89472678284734e-03 ) + 17 ( -3.19134137515970e-01 , 1.04747307744542e-03 , 9.47708976992457e-01 ) ( 2.63826827503194e-03 , -2.09494615489084e-06 , -1.89541795398491e-03 ) + 18 ( -3.18311310856538e-01 , 1.83029974893031e-04 , 9.47986221355997e-01 ) ( 2.63662262171308e-03 , -3.66059949786063e-07 , -1.89597244271199e-03 ) + 19 ( -3.17692796906620e-01 , -7.96993701676326e-04 , 9.48193361922919e-01 ) ( 2.63538559381324e-03 , 1.59398740335265e-06 , -1.89638672384584e-03 ) + 20 ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) ( 2.63454929804108e-03 , 3.78107124610862e-06 , -1.89666362116634e-03 ) diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out index 6785f7248..9097222e0 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -152,7 +148,6 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -163,33 +158,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -0.317275 , -0.00189054 , 0.948332 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped index 0236b3b01..f3e20f202 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.11598263481038e-01 , -2.44590603951106e-02 , 9.49899087566774e-01 ) + x ( -3.11598263889815e-01 , -2.44590603702029e-02 , 9.49899087433323e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj index 2bb02cd37..7d738d1c8 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -3.17274648853048e-01 , -1.89053561545958e-03 , 9.48331810639220e-01 ) ( 2.63454929770610e-03 , 3.78107123091915e-06 , -1.89666362127844e-03 ) - 21 ( -3.17043326102425e-01 , -3.09358621457674e-03 , 9.48406009627862e-01 ) ( 2.63408665220485e-03 , 6.18717242915348e-06 , -1.89681201925572e-03 ) - 22 ( -3.16976780285387e-01 , -4.39920684988128e-03 , 9.48423095321387e-01 ) ( 2.63395356057077e-03 , 8.79841369976256e-06 , -1.89684619064277e-03 ) - 23 ( -3.17046097459336e-01 , -5.79657340367589e-03 , 9.48392414469127e-01 ) ( 2.63409219491867e-03 , 1.15931468073518e-05 , -1.89678482893825e-03 ) - 24 ( -3.17217482639898e-01 , -7.27041161938927e-03 , 9.48324949488565e-01 ) ( 2.63443496527980e-03 , 1.45408232387785e-05 , -1.89664989897713e-03 ) - 25 ( -3.17454368922200e-01 , -8.80106277368526e-03 , 9.48232706115045e-01 ) ( 2.63490873784440e-03 , 1.76021255473705e-05 , -1.89646541223009e-03 ) - 26 ( -3.17719471221428e-01 , -1.03652349433106e-02 , 9.48128102901367e-01 ) ( 2.63543894244286e-03 , 2.07304698866213e-05 , -1.89625620580273e-03 ) - 27 ( -3.17976645861785e-01 , -1.19373246190291e-02 , 9.48023392626695e-01 ) ( 2.63595329172357e-03 , 2.38746492380582e-05 , -1.89604678525339e-03 ) - 28 ( -3.18192455511519e-01 , -1.34910475095471e-02 , 9.47930141356759e-01 ) ( 2.63638491102304e-03 , 2.69820950190943e-05 , -1.89586028271352e-03 ) - 29 ( -3.18337378603559e-01 , -1.50010625514700e-02 , 9.47858787745380e-01 ) ( 2.63667475720712e-03 , 3.00021251029400e-05 , -1.89571757549076e-03 ) - 30 ( -3.18386627540012e-01 , -1.64443011671489e-02 , 9.47818305564322e-01 ) ( 2.63677325508002e-03 , 3.28886023342977e-05 , -1.89563661112864e-03 ) - 31 ( -3.18320580486092e-01 , -1.78008340716119e-02 , 9.47815983377233e-01 ) ( 2.63664116097219e-03 , 3.56016681432239e-05 , -1.89563196675447e-03 ) - 32 ( -3.18124861284371e-01 , -1.90542515899086e-02 , 9.47857324774751e-01 ) ( 2.63624972256874e-03 , 3.81085031798172e-05 , -1.89571464954950e-03 ) - 33 ( -3.17790139572305e-01 , -2.01916660342723e-02 , 9.47946055328770e-01 ) ( 2.63558027914461e-03 , 4.03833320685447e-05 , -1.89589211065754e-03 ) - 34 ( -3.17311724625781e-01 , -2.12034927642144e-02 , 9.48084216359291e-01 ) ( 2.63462344925156e-03 , 4.24069855284288e-05 , -1.89616843271858e-03 ) - 35 ( -3.16689032700701e-01 , -2.20831582361305e-02 , 9.48272318845917e-01 ) ( 2.63337806540140e-03 , 4.41663164722610e-05 , -1.89654463769183e-03 ) - 36 ( -3.15924961738176e-01 , -2.28268525331288e-02 , 9.48509543101261e-01 ) ( 2.63184992347635e-03 , 4.56537050662576e-05 , -1.89701908620252e-03 ) - 37 ( -3.15025223717057e-01 , -2.34334010090392e-02 , 9.48793962954638e-01 ) ( 2.63005044743411e-03 , 4.68668020180783e-05 , -1.89758792590928e-03 ) - 38 ( -3.13997687895431e-01 , -2.39042792710176e-02 , 9.49122772579426e-01 ) ( 2.62799537579086e-03 , 4.78085585420352e-05 , -1.89824554515885e-03 ) - 39 ( -3.12851812803389e-01 , -2.42437511921662e-02 , 9.49492487465681e-01 ) ( 2.62570362560678e-03 , 4.84875023843323e-05 , -1.89898497493136e-03 ) - 40 ( -3.11598263481038e-01 , -2.44590603951106e-02 , 9.49899087566774e-01 ) ( 2.62319652696208e-03 , 4.89181207902213e-05 , -1.89979817513355e-03 ) + 20 ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) ( 2.63454929804108e-03 , 3.78107124610862e-06 , -1.89666362116634e-03 ) + 21 ( -3.17043326283096e-01 , -3.09358622124357e-03 , 9.48406009567444e-01 ) ( 2.63408665256619e-03 , 6.18717244248714e-06 , -1.89681201913489e-03 ) + 22 ( -3.16976780479176e-01 , -4.39920685529361e-03 , 9.48423095256595e-01 ) ( 2.63395356095835e-03 , 8.79841371058722e-06 , -1.89684619051319e-03 ) + 23 ( -3.17046097666149e-01 , -5.79657340749948e-03 , 9.48392414399967e-01 ) ( 2.63409219533230e-03 , 1.15931468149990e-05 , -1.89678482879993e-03 ) + 24 ( -3.17217482859608e-01 , -7.27041162129638e-03 , 9.48324949415057e-01 ) ( 2.63443496571922e-03 , 1.45408232425928e-05 , -1.89664989883011e-03 ) + 25 ( -3.17454369154660e-01 , -8.80106277336966e-03 , 9.48232706037224e-01 ) ( 2.63490873830932e-03 , 1.76021255467393e-05 , -1.89646541207445e-03 ) + 26 ( -3.17719471466479e-01 , -1.03652349405030e-02 , 9.48128102819281e-01 ) ( 2.63543894293296e-03 , 2.07304698810060e-05 , -1.89625620563856e-03 ) + 27 ( -3.17976646119255e-01 , -1.19373246135143e-02 , 9.48023392540407e-01 ) ( 2.63595329223851e-03 , 2.38746492270286e-05 , -1.89604678508081e-03 ) + 28 ( -3.18192455781236e-01 , -1.34910475011762e-02 , 9.47930141266342e-01 ) ( 2.63638491156247e-03 , 2.69820950023524e-05 , -1.89586028253268e-03 ) + 29 ( -3.18337378885354e-01 , -1.50010625401725e-02 , 9.47858787650918e-01 ) ( 2.63667475777071e-03 , 3.00021250803450e-05 , -1.89571757530184e-03 ) + 30 ( -3.18386627833720e-01 , -1.64443011529380e-02 , 9.47818305465907e-01 ) ( 2.63677325566744e-03 , 3.28886023058761e-05 , -1.89563661093181e-03 ) + 31 ( -3.18320580791560e-01 , -1.78008340545886e-02 , 9.47815983274963e-01 ) ( 2.63664116158312e-03 , 3.56016681091771e-05 , -1.89563196654993e-03 ) + 32 ( -3.18124861601468e-01 , -1.90542515702588e-02 , 9.47857324668720e-01 ) ( 2.63624972320294e-03 , 3.81085031405176e-05 , -1.89571464933744e-03 ) + 33 ( -3.17790139900921e-01 , -2.01916660122652e-02 , 9.47946055219073e-01 ) ( 2.63558027980184e-03 , 4.03833320245304e-05 , -1.89589211043815e-03 ) + 34 ( -3.17311724965833e-01 , -2.12034927401992e-02 , 9.48084216246017e-01 ) ( 2.63462344993167e-03 , 4.24069854803984e-05 , -1.89616843249203e-03 ) + 35 ( -3.16689033052138e-01 , -2.20831582105308e-02 , 9.48272318729146e-01 ) ( 2.63337806610428e-03 , 4.41663164210616e-05 , -1.89654463745829e-03 ) + 36 ( -3.15924962100982e-01 , -2.28268525064398e-02 , 9.48509542981062e-01 ) ( 2.63184992420196e-03 , 4.56537050128795e-05 , -1.89701908596212e-03 ) + 37 ( -3.15025224091246e-01 , -2.34334009818228e-02 , 9.48793962831070e-01 ) ( 2.63005044818249e-03 , 4.68668019636457e-05 , -1.89758792566214e-03 ) + 38 ( -3.13997688281053e-01 , -2.39042792438929e-02 , 9.49122772452534e-01 ) ( 2.62799537656211e-03 , 4.78085584877859e-05 , -1.89824554490507e-03 ) + 39 ( -3.12851813200530e-01 , -2.42437511657998e-02 , 9.49492487335498e-01 ) ( 2.62570362640106e-03 , 4.84875023315996e-05 , -1.89898497467100e-03 ) + 40 ( -3.11598263889815e-01 , -2.44590603702029e-02 , 9.49899087433323e-01 ) ( 2.62319652777963e-03 , 4.89181207404057e-05 , -1.89979817486665e-03 ) diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out index 6d5786be0..1d23f8568 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -117,7 +113,6 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,28 +123,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped index ae8e82001..e64cb9b15 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.10901432109335e-01 , 2.11904534160048e-01 , 9.26518627937279e-01 ) + x ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj index b16b4e9e6..8935a8e9e 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -3.31000066838099e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 2.66200013367620e-03 , -4.30091230223396e-04 , -1.83760097863971e-03 ) - 1 ( -3.30748902386493e-01 , 2.14640582517095e-01 , 9.18985627693302e-01 ) ( 2.66149780477299e-03 , -4.29281165034190e-04 , -1.83797125538660e-03 ) - 2 ( -3.30335278565548e-01 , 2.14351255511183e-01 , 9.19201905457012e-01 ) ( 2.66067055713110e-03 , -4.28702511022365e-04 , -1.83840381091402e-03 ) - 3 ( -3.29748301584291e-01 , 2.14175295386331e-01 , 9.19453642359664e-01 ) ( 2.65949660316858e-03 , -4.28350590772662e-04 , -1.83890728471933e-03 ) - 4 ( -3.28983003247068e-01 , 2.14104941845713e-01 , 9.19744126076260e-01 ) ( 2.65796600649414e-03 , -4.28209883691426e-04 , -1.83948825215252e-03 ) - 5 ( -3.28041624976885e-01 , 2.14126988072693e-01 , 9.20075173701281e-01 ) ( 2.65608324995377e-03 , -4.28253976145385e-04 , -1.84015034740256e-03 ) - 6 ( -3.26934234935534e-01 , 2.14223081735800e-01 , 9.20446889982651e-01 ) ( 2.65386846987107e-03 , -4.28446163471600e-04 , -1.84089377996530e-03 ) - 7 ( -3.25678693135581e-01 , 2.14370527640576e-01 , 9.20857570809189e-01 ) ( 2.65135738627116e-03 , -4.28741055281152e-04 , -1.84171514161838e-03 ) - 8 ( -3.24300051430000e-01 , 2.14543670061471e-01 , 9.21303690581479e-01 ) ( 2.64860010286000e-03 , -4.29087340122942e-04 , -1.84260738116296e-03 ) - 9 ( -3.22829511472042e-01 , 2.14715764661014e-01 , 9.21779934110501e-01 ) ( 2.64565902294409e-03 , -4.29431529322028e-04 , -1.84355986822100e-03 ) - 10 ( -3.21303059745326e-01 , 2.14861065905351e-01 , 9.22279277744170e-01 ) ( 2.64260611949065e-03 , -4.29722131810702e-04 , -1.84455855548834e-03 ) - 11 ( -3.19759878990855e-01 , 2.14956751283305e-01 , 9.22793159307914e-01 ) ( 2.63951975798171e-03 , -4.29913502566610e-04 , -1.84558631861583e-03 ) - 12 ( -3.18240618841290e-01 , 2.14984320901043e-01 , 9.23311783898716e-01 ) ( 2.63648123768258e-03 , -4.29968641802086e-04 , -1.84662356779743e-03 ) - 13 ( -3.16785580563842e-01 , 2.14930240619444e-01 , 9.23824597861573e-01 ) ( 2.63357116112768e-03 , -4.29860481238888e-04 , -1.84764919572315e-03 ) - 14 ( -3.15432869408985e-01 , 2.14785792597053e-01 , 9.24320922729152e-01 ) ( 2.63086573881797e-03 , -4.29571585194106e-04 , -1.84864184545830e-03 ) - 15 ( -3.14216581806419e-01 , 2.14546290789039e-01 , 9.24790694604220e-01 ) ( 2.62843316361284e-03 , -4.29092581578078e-04 , -1.84958138920844e-03 ) - 16 ( -3.13165103198593e-01 , 2.14209940595846e-01 , 9.25225226357636e-01 ) ( 2.62633020639719e-03 , -4.28419881191692e-04 , -1.85045045271527e-03 ) - 17 ( -3.12299612081994e-01 , 2.13776666346595e-01 , 9.25617895904770e-01 ) ( 2.62459922416399e-03 , -4.27553332693190e-04 , -1.85123579180954e-03 ) - 18 ( -3.11632908920174e-01 , 2.13247200166255e-01 , 9.25964665470127e-01 ) ( 2.62326581784035e-03 , -4.26494400332510e-04 , -1.85192933094025e-03 ) - 19 ( -3.11168697452754e-01 , 2.12622637200253e-01 , 9.26264355287175e-01 ) ( 2.62233739490551e-03 , -4.25245274400506e-04 , -1.85252871057435e-03 ) - 20 ( -3.10901432109335e-01 , 2.11904534160048e-01 , 9.26518627937279e-01 ) ( 2.62180286421867e-03 , -4.23809068320096e-04 , -1.85303725587456e-03 ) + 0 ( -3.31000066838100e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 2.66200013367620e-03 , -4.30091230223397e-04 , -1.83760097863971e-03 ) + 1 ( -3.30748902386919e-01 , 2.14640582516973e-01 , 9.18985627693177e-01 ) ( 2.66149780477384e-03 , -4.29281165033946e-04 , -1.83797125538635e-03 ) + 2 ( -3.30335278614263e-01 , 2.14351255518651e-01 , 9.19201905437763e-01 ) ( 2.66067055722853e-03 , -4.28702511037302e-04 , -1.83840381087553e-03 ) + 3 ( -3.29748301598012e-01 , 2.14175295385314e-01 , 9.19453642354981e-01 ) ( 2.65949660319602e-03 , -4.28350590770628e-04 , -1.83890728470996e-03 ) + 4 ( -3.28983003286818e-01 , 2.14104941848711e-01 , 9.19744126061344e-01 ) ( 2.65796600657364e-03 , -4.28209883697422e-04 , -1.83948825212269e-03 ) + 5 ( -3.28041624986510e-01 , 2.14126988066820e-01 , 9.20075173699216e-01 ) ( 2.65608324997302e-03 , -4.28253976133641e-04 , -1.84015034739843e-03 ) + 6 ( -3.26934234947895e-01 , 2.14223081728789e-01 , 9.20446889979892e-01 ) ( 2.65386846989579e-03 , -4.28446163457579e-04 , -1.84089377995978e-03 ) + 7 ( -3.25678693151725e-01 , 2.14370527632503e-01 , 9.20857570805359e-01 ) ( 2.65135738630345e-03 , -4.28741055265006e-04 , -1.84171514161072e-03 ) + 8 ( -3.24300051451023e-01 , 2.14543670052469e-01 , 9.21303690576175e-01 ) ( 2.64860010290205e-03 , -4.29087340104938e-04 , -1.84260738115235e-03 ) + 9 ( -3.22829511499202e-01 , 2.14715764651319e-01 , 9.21779934103247e-01 ) ( 2.64565902299840e-03 , -4.29431529302638e-04 , -1.84355986820649e-03 ) + 10 ( -3.21303059779930e-01 , 2.14861065895251e-01 , 9.22279277734468e-01 ) ( 2.64260611955986e-03 , -4.29722131790503e-04 , -1.84455855546894e-03 ) + 11 ( -3.19759879034225e-01 , 2.14956751273127e-01 , 9.22793159295257e-01 ) ( 2.63951975806845e-03 , -4.29913502546255e-04 , -1.84558631859051e-03 ) + 12 ( -3.18240618894718e-01 , 2.14984320891132e-01 , 9.23311783882609e-01 ) ( 2.63648123778944e-03 , -4.29968641782263e-04 , -1.84662356776522e-03 ) + 13 ( -3.16785580628539e-01 , 2.14930240610141e-01 , 9.23824597841553e-01 ) ( 2.63357116125708e-03 , -4.29860481220281e-04 , -1.84764919568311e-03 ) + 14 ( -3.15432869486022e-01 , 2.14785792588681e-01 , 9.24320922704807e-01 ) ( 2.63086573897204e-03 , -4.29571585177362e-04 , -1.84864184540961e-03 ) + 15 ( -3.14216581896700e-01 , 2.14546290781891e-01 , 9.24790694575203e-01 ) ( 2.62843316379340e-03 , -4.29092581563783e-04 , -1.84958138915041e-03 ) + 16 ( -3.13165103302749e-01 , 2.14209940590278e-01 , 9.25225226323671e-01 ) ( 2.62633020660550e-03 , -4.28419881180556e-04 , -1.85045045264734e-03 ) + 17 ( -3.12299612195620e-01 , 2.13776666349982e-01 , 9.25617895865650e-01 ) ( 2.62459922439124e-03 , -4.27553332699964e-04 , -1.85123579173130e-03 ) + 18 ( -3.11632909053414e-01 , 2.13247200164350e-01 , 9.25964665425724e-01 ) ( 2.62326581810683e-03 , -4.26494400328700e-04 , -1.85192933085145e-03 ) + 19 ( -3.11168697605864e-01 , 2.12622637201006e-01 , 9.26264355235566e-01 ) ( 2.62233739521173e-03 , -4.25245274402012e-04 , -1.85252871047113e-03 ) + 20 ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) ( 2.62180286454399e-03 , -4.23809068324612e-04 , -1.85303725576436e-03 ) diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out index 7b60a6e6d..42c1974d9 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -117,7 +113,6 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,33 +123,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -0.310901 , 0.211905 , 0.926519 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped index 99b9e8168..6b8d538b6 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.08478218972664e-01 , 1.95662054911782e-01 , 9.30890728650335e-01 ) + x ( -3.08478219385086e-01 , 1.95662054939033e-01 , 9.30890728507939e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj index 3c70716e5..0b3f5ab28 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -3.10901432109335e-01 , 2.11904534160048e-01 , 9.26518627937279e-01 ) ( 2.62180286421867e-03 , -4.23809068320096e-04 , -1.85303725587456e-03 ) - 21 ( -3.10816792043180e-01 , 2.11095479023442e-01 , 9.26731687447802e-01 ) ( 2.62163358408636e-03 , -4.22190958046885e-04 , -1.85346337489560e-03 ) - 22 ( -3.10892759556907e-01 , 2.10199933225375e-01 , 9.26909747562911e-01 ) ( 2.62178551911381e-03 , -4.20399866450750e-04 , -1.85381949512582e-03 ) - 23 ( -3.11101193001973e-01 , 2.09225066821485e-01 , 9.27060364337886e-01 ) ( 2.62220238600395e-03 , -4.18450133642970e-04 , -1.85412072867577e-03 ) - 24 ( -3.11409710822334e-01 , 2.08181314892433e-01 , 9.27191745074992e-01 ) ( 2.62281942164467e-03 , -4.16362629784866e-04 , -1.85438349014998e-03 ) - 25 ( -3.11783673220749e-01 , 2.07082466717213e-01 , 9.27312133583558e-01 ) ( 2.62356734644150e-03 , -4.14164933434426e-04 , -1.85462426716712e-03 ) - 26 ( -3.12188067196429e-01 , 2.05945244391887e-01 , 9.27429332624607e-01 ) ( 2.62437613439286e-03 , -4.11890488783774e-04 , -1.85485866524921e-03 ) - 27 ( -3.12589140107981e-01 , 2.04788460679522e-01 , 9.27550384539333e-01 ) ( 2.62517828021596e-03 , -4.09576921359045e-04 , -1.85510076907867e-03 ) - 28 ( -3.12955684858097e-01 , 2.03631959607588e-01 , 9.27681391611028e-01 ) ( 2.62591136971619e-03 , -4.07263919215175e-04 , -1.85536278322206e-03 ) - 29 ( -3.13259948406249e-01 , 2.02495576402221e-01 , 9.27827433449802e-01 ) ( 2.62651989681250e-03 , -4.04991152804443e-04 , -1.85565486689960e-03 ) - 30 ( -3.13478176635625e-01 , 2.01398322556721e-01 , 9.27992536847437e-01 ) ( 2.62695635327125e-03 , -4.02796645113443e-04 , -1.85598507369487e-03 ) - 31 ( -3.13590843690062e-01 , 2.00357900910451e-01 , 9.28179667034628e-01 ) ( 2.62718168738012e-03 , -4.00715801820901e-04 , -1.85635933406926e-03 ) - 32 ( -3.13582620933990e-01 , 1.99390533243234e-01 , 9.28390734066831e-01 ) ( 2.62716524186798e-03 , -3.98781066486467e-04 , -1.85678146813366e-03 ) - 33 ( -3.13442157096821e-01 , 1.98510960961320e-01 , 9.28626627085776e-01 ) ( 2.62688431419364e-03 , -3.97021921922641e-04 , -1.85725325417155e-03 ) - 34 ( -3.13161736228558e-01 , 1.97732440178262e-01 , 9.28887296211691e-01 ) ( 2.62632347245712e-03 , -3.95464880356523e-04 , -1.85777459242338e-03 ) - 35 ( -3.12736895260678e-01 , 1.97066585086681e-01 , 9.29171886889065e-01 ) ( 2.62547379052136e-03 , -3.94133170173362e-04 , -1.85834377377813e-03 ) - 36 ( -3.12166050940956e-01 , 1.96522999337743e-01 , 9.29478922499712e-01 ) ( 2.62433210188191e-03 , -3.93045998675485e-04 , -1.85895784499942e-03 ) - 37 ( -3.11450199233999e-01 , 1.96108732486406e-01 , 9.29806505913826e-01 ) ( 2.62290039846800e-03 , -3.92217464972813e-04 , -1.85961301182765e-03 ) - 38 ( -3.10592727274054e-01 , 1.95827676700691e-01 , 9.30152502981352e-01 ) ( 2.62118545454811e-03 , -3.91655353401382e-04 , -1.86030500596270e-03 ) - 39 ( -3.09599356904062e-01 , 1.95680044103037e-01 , 9.30514674008113e-01 ) ( 2.61919871380812e-03 , -3.91360088206074e-04 , -1.86102934801623e-03 ) - 40 ( -3.08478218972664e-01 , 1.95662054911782e-01 , 9.30890728650335e-01 ) ( 2.61695643794533e-03 , -3.91324109823565e-04 , -1.86178145730067e-03 ) + 20 ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) ( 2.62180286454399e-03 , -4.23809068324612e-04 , -1.85303725576436e-03 ) + 21 ( -3.10816792220306e-01 , 2.11095479027854e-01 , 9.26731687387390e-01 ) ( 2.62163358444061e-03 , -4.22190958055708e-04 , -1.85346337477478e-03 ) + 22 ( -3.10892759748286e-01 , 2.10199933231990e-01 , 9.26909747497221e-01 ) ( 2.62178551949657e-03 , -4.20399866463979e-04 , -1.85381949499444e-03 ) + 23 ( -3.11101193207355e-01 , 2.09225066830326e-01 , 9.27060364266969e-01 ) ( 2.62220238641471e-03 , -4.18450133660652e-04 , -1.85412072853394e-03 ) + 24 ( -3.11409711041452e-01 , 2.08181314903498e-01 , 9.27191744998913e-01 ) ( 2.62281942208290e-03 , -4.16362629806997e-04 , -1.85438348999783e-03 ) + 25 ( -3.11783673453337e-01 , 2.07082466730478e-01 , 9.27312133502395e-01 ) ( 2.62356734690667e-03 , -4.14164933460955e-04 , -1.85462426700479e-03 ) + 26 ( -3.12188067442232e-01 , 2.05945244407307e-01 , 9.27429332538441e-01 ) ( 2.62437613488447e-03 , -4.11890488814613e-04 , -1.85485866507688e-03 ) + 27 ( -3.12589140366756e-01 , 2.04788460697038e-01 , 9.27550384448258e-01 ) ( 2.62517828073351e-03 , -4.09576921394075e-04 , -1.85510076889652e-03 ) + 28 ( -3.12955685129617e-01 , 2.03631959627123e-01 , 9.27681391515142e-01 ) ( 2.62591137025923e-03 , -4.07263919254245e-04 , -1.85536278303028e-03 ) + 29 ( -3.13259948690306e-01 , 2.02495576423685e-01 , 9.27827433349212e-01 ) ( 2.62651989738061e-03 , -4.04991152847370e-04 , -1.85565486669842e-03 ) + 30 ( -3.13478176932022e-01 , 2.01398322580004e-01 , 9.27992536742261e-01 ) ( 2.62695635386404e-03 , -4.02796645160007e-04 , -1.85598507348452e-03 ) + 31 ( -3.13590843998619e-01 , 2.00357900935419e-01 , 9.28179666924991e-01 ) ( 2.62718168799724e-03 , -4.00715801870839e-04 , -1.85635933384998e-03 ) + 32 ( -3.13582621254546e-01 , 1.99390533269725e-01 , 9.28390733952867e-01 ) ( 2.62716524250909e-03 , -3.98781066539451e-04 , -1.85678146790573e-03 ) + 33 ( -3.13442157429236e-01 , 1.98510960989129e-01 , 9.28626626967630e-01 ) ( 2.62688431485847e-03 , -3.97021921978259e-04 , -1.85725325393526e-03 ) + 34 ( -3.13161736572708e-01 , 1.97732440207133e-01 , 9.28887296089519e-01 ) ( 2.62632347314542e-03 , -3.95464880414266e-04 , -1.85777459217904e-03 ) + 35 ( -3.12736895616453e-01 , 1.97066585116309e-01 , 9.29171886763036e-01 ) ( 2.62547379123291e-03 , -3.94133170232619e-04 , -1.85834377352607e-03 ) + 36 ( -3.12166051308255e-01 , 1.96522999367774e-01 , 9.29478922370005e-01 ) ( 2.62433210261651e-03 , -3.93045998735549e-04 , -1.85895784474001e-03 ) + 37 ( -3.11450199612716e-01 , 1.96108732516444e-01 , 9.29806505780634e-01 ) ( 2.62290039922543e-03 , -3.92217465032889e-04 , -1.85961301156127e-03 ) + 38 ( -3.10592727664091e-01 , 1.95827676730295e-01 , 9.30152502844880e-01 ) ( 2.62118545532818e-03 , -3.91655353460590e-04 , -1.86030500568976e-03 ) + 39 ( -3.09599357305329e-01 , 1.95680044131724e-01 , 9.30514673868571e-01 ) ( 2.61919871461066e-03 , -3.91360088263449e-04 , -1.86102934773714e-03 ) + 40 ( -3.08478219385086e-01 , 1.95662054939033e-01 , 9.30890728507939e-01 ) ( 2.61695643877017e-03 , -3.91324109878067e-04 , -1.86178145701588e-03 ) diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out index 74c288689..5b55b80fb 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -120,7 +120,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,27 +131,10 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped index a3cdd7bbc..41cb47258 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.10902612073187e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) + x ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj index 41394b2d9..4806fa83f 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 ( -3.31000066838099e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 2.66200013367620e-03 , -4.30091230223396e-04 , -1.83760097863971e-03 ) 5.32400026735240e-03 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 1 ( -3.30748902386493e-01 , 2.14640582517095e-01 , 9.18985627693302e-01 ) ( 2.65426681755214e-03 , -2.59364533396170e-04 , -1.83797125538660e-03 ) 5.24527031778478e-03 ( 9.96384506389575e-01 , 8.49583158190100e-02 , 0.00000000000000e+00 ) -4.11137793191958e-05 - 2 ( -3.30335278534755e-01 , 2.14351256281980e-01 , 9.19201905288334e-01 ) ( 2.61609431372619e-03 , -8.80022404594749e-06 , -1.83840381057667e-03 ) 5.11187773649830e-03 ( 9.77711878328341e-01 , 2.09951144259006e-01 , 0.00000000000000e+00 ) -1.11474667340389e-04 - 3 ( -3.29748301559332e-01 , 2.14175298816286e-01 , 9.19453641569650e-01 ) ( 2.49361536951405e-03 , 3.69150719454903e-04 , -1.83890728313930e-03 ) 4.86798493036677e-03 ( 9.17059383197694e-01 , 3.98750658543737e-01 , 0.00000000000000e+00 ) -2.40880322518690e-04 - 4 ( -3.28983003639495e-01 , 2.14104951472765e-01 , 9.19744123694835e-01 ) ( 2.15062069976169e-03 , 9.02948227784763e-04 , -1.83948824738967e-03 ) 4.41210095429392e-03 ( 7.46327346241351e-01 , 6.65579065365146e-01 , 0.00000000000000e+00 ) -4.77813021182742e-04 + 2 ( -3.30335278534755e-01 , 2.14351256281980e-01 , 9.19201905288334e-01 ) ( 2.61609431372619e-03 , -8.80022404594755e-06 , -1.83840381057667e-03 ) 5.11187773649830e-03 ( 9.77711878328341e-01 , 2.09951144259006e-01 , 0.00000000000000e+00 ) -1.11474667340389e-04 + 3 ( -3.29748301559333e-01 , 2.14175298816286e-01 , 9.19453641569650e-01 ) ( 2.49361536951405e-03 , 3.69150719454903e-04 , -1.83890728313930e-03 ) 4.86798493036677e-03 ( 9.17059383197694e-01 , 3.98750658543737e-01 , 0.00000000000000e+00 ) -2.40880322518690e-04 + 4 ( -3.28983003639496e-01 , 2.14104951472765e-01 , 9.19744123694835e-01 ) ( 2.15062069976169e-03 , 9.02948227784763e-04 , -1.83948824738967e-03 ) 4.41210095429392e-03 ( 7.46327346241351e-01 , 6.65579065365146e-01 , 0.00000000000000e+00 ) -4.77813021182742e-04 5 ( -3.28041627441930e-01 , 2.14127009680035e-01 , 9.20075167793771e-01 ) ( 1.42145011961404e-03 , 1.41950504566250e-03 , -1.84015033558754e-03 ) 3.71083413738751e-03 ( 3.82683432365090e-01 , 9.23879532511287e-01 , 0.00000000000000e+00 ) -8.12629094252072e-04 - 6 ( -3.26934243989618e-01 , 2.14223123081484e-01 , 9.20446877144005e-01 ) ( 5.39673174025795e-04 , 1.56829094993247e-03 , -1.84089375428801e-03 ) 3.06983672648989e-03 ( -5.70976569767208e-02 , 9.98368598047719e-01 , 0.00000000000000e+00 ) -1.08583725325208e-03 - 7 ( -3.25678716875358e-01 , 2.14370596669932e-01 , 9.20857546343514e-01 ) ( -8.16417941512113e-05 , 1.43209521319758e-03 , -1.84171509268703e-03 ) 2.72473828242342e-03 ( -3.66499613950964e-01 , 9.30418203268721e-01 , 0.00000000000000e+00 ) -1.22624326781898e-03 - 8 ( -3.24300100426940e-01 , 2.14543773657555e-01 , 9.21303649210103e-01 ) ( -4.37177441924497e-04 , 1.25052160675694e-03 , -1.84260729842021e-03 ) 2.57506503044251e-03 ( -5.42888821389189e-01 , 8.39804577036026e-01 , 0.00000000000000e+00 ) -1.28775963537044e-03 - 9 ( -3.22829597532926e-01 , 2.14715908506054e-01 , 9.21779870463197e-01 ) ( -6.43292084741086e-04 , 1.09981786773007e-03 , -1.84355974092639e-03 ) 2.51106828341672e-03 ( -6.44475639903469e-01 , 7.64624842371090e-01 , 0.00000000000000e+00 ) -1.31512027126455e-03 - 10 ( -3.21303195136168e-01 , 2.14861254665660e-01 , 9.22279186601751e-01 ) ( -7.71607172100759e-04 , 9.84491053041776e-04 , -1.84455837320350e-03 ) 2.48349792685589e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 11 ( -3.19760075975256e-01 , 2.14956988805007e-01 , 9.22793035721544e-01 ) ( -7.74693410422583e-04 , 9.84299584763081e-04 , -1.84558607144309e-03 ) 2.48759174991084e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 12 ( -3.18240889009190e-01 , 2.14984610793561e-01 , 9.23311623280343e-01 ) ( -7.77731784354715e-04 , 9.84244340785974e-04 , -1.84662324656069e-03 ) 2.49181053275156e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 13 ( -3.16785934761419e-01 , 2.14930586280875e-01 , 9.23824395985673e-01 ) ( -7.80641692850257e-04 , 9.84352389811345e-04 , -1.84764879197135e-03 ) 2.49607856920830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 6 ( -3.26934243989619e-01 , 2.14223123081484e-01 , 9.20446877144005e-01 ) ( 5.39673174025796e-04 , 1.56829094993247e-03 , -1.84089375428801e-03 ) 3.06983672648989e-03 ( -5.70976569767208e-02 , 9.98368598047719e-01 , 0.00000000000000e+00 ) -1.08583725325208e-03 + 7 ( -3.25678716875359e-01 , 2.14370596669932e-01 , 9.20857546343514e-01 ) ( -8.16417941512103e-05 , 1.43209521319758e-03 , -1.84171509268703e-03 ) 2.72473828242341e-03 ( -3.66499613950964e-01 , 9.30418203268721e-01 , 0.00000000000000e+00 ) -1.22624326781898e-03 + 8 ( -3.24300100426941e-01 , 2.14543773657555e-01 , 9.21303649210103e-01 ) ( -4.37177441924495e-04 , 1.25052160675694e-03 , -1.84260729842021e-03 ) 2.57506503044251e-03 ( -5.42888821389189e-01 , 8.39804577036026e-01 , 0.00000000000000e+00 ) -1.28775963537044e-03 + 9 ( -3.22829597532927e-01 , 2.14715908506054e-01 , 9.21779870463197e-01 ) ( -6.43292084741085e-04 , 1.09981786773007e-03 , -1.84355974092639e-03 ) 2.51106828341672e-03 ( -6.44475639903469e-01 , 7.64624842371090e-01 , 0.00000000000000e+00 ) -1.31512027126455e-03 + 10 ( -3.21303195136169e-01 , 2.14861254665660e-01 , 9.22279186601751e-01 ) ( -7.71607172100758e-04 , 9.84491053041776e-04 , -1.84455837320350e-03 ) 2.48349792685589e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 11 ( -3.19760075975256e-01 , 2.14956988805007e-01 , 9.22793035721544e-01 ) ( -7.74693410422582e-04 , 9.84299584763081e-04 , -1.84558607144309e-03 ) 2.48759174991084e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 12 ( -3.18240889009191e-01 , 2.14984610793561e-01 , 9.23311623280342e-01 ) ( -7.77731784354714e-04 , 9.84244340785974e-04 , -1.84662324656068e-03 ) 2.49181053275155e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 13 ( -3.16785934761420e-01 , 2.14930586280875e-01 , 9.23824395985673e-01 ) ( -7.80641692850256e-04 , 9.84352389811345e-04 , -1.84764879197135e-03 ) 2.49607856920830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 14 ( -3.15433317695425e-01 , 2.14786197242876e-01 , 9.24320675718985e-01 ) ( -7.83346926982245e-04 , 9.84641167887343e-04 , -1.84864135143797e-03 ) 2.50031274187874e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 15 ( -3.14217133435043e-01 , 2.14546757480910e-01 , 9.24790398906851e-01 ) ( -7.85779295503009e-04 , 9.85120047411276e-04 , -1.84958079781370e-03 ) 2.50442986834698e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 16 ( -3.13165766618894e-01 , 2.14210472267861e-01 , 9.25224878712619e-01 ) ( -7.87882029135307e-04 , 9.85792617837373e-04 , -1.85044975742524e-03 ) 2.50835474098607e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 17 ( -3.12300394959219e-01 , 2.13777265827329e-01 , 9.25617493311199e-01 ) ( -7.89612772454658e-04 , 9.86659030718436e-04 , -1.85123498662240e-03 ) 2.51202767450830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 18 ( -3.11633818168871e-01 , 2.13247870196032e-01 , 9.25964205156089e-01 ) ( -7.90945926035354e-04 , 9.87717821981030e-04 , -1.85192841031218e-03 ) 2.51541039534613e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 19 ( -3.11169739281378e-01 , 2.12623380444018e-01 , 9.26263834684329e-01 ) ( -7.91874083810338e-04 , 9.88966801485060e-04 , -1.85252766936866e-03 ) 2.51848933241326e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 20 ( -3.10902612073187e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226722e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 16 ( -3.13165766618895e-01 , 2.14210472267861e-01 , 9.25224878712619e-01 ) ( -7.87882029135306e-04 , 9.85792617837373e-04 , -1.85044975742524e-03 ) 2.50835474098607e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 17 ( -3.12300394959219e-01 , 2.13777265827330e-01 , 9.25617493311199e-01 ) ( -7.89612772454658e-04 , 9.86659030718436e-04 , -1.85123498662240e-03 ) 2.51202767450830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 18 ( -3.11633818168871e-01 , 2.13247870196033e-01 , 9.25964205156089e-01 ) ( -7.90945926035354e-04 , 9.87717821981030e-04 , -1.85192841031218e-03 ) 2.51541039534613e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 19 ( -3.11169739281378e-01 , 2.12623380444018e-01 , 9.26263834684329e-01 ) ( -7.91874083810339e-04 , 9.88966801485059e-04 , -1.85252766936866e-03 ) 2.51848933241326e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 20 ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226723e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out index 28afcc8be..a610a83f9 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,13 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +46,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +59,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -120,7 +120,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,22 +131,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -0.310903 , 0.211905 , 0.926518 ) @@ -157,7 +140,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped index dc793f2a2..e86a2eb4b 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.08482822701286e-01 , 1.95664885198602e-01 , 9.30888608158068e-01 ) + x ( -3.08482822701290e-01 , 1.95664885198602e-01 , 9.30888608158067e-01 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj index 43f39b9f0..d4530bcd2 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 ( -3.10902612073187e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226722e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 21 ( -3.10818115103370e-01 , 2.11096376432417e-01 , 9.26731039288472e-01 ) ( -7.92577332166354e-04 , 9.92020809508262e-04 , -1.85346207857694e-03 ) 2.52380289534206e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 22 ( -3.10894230143356e-01 , 2.10200911472952e-01 , 9.26909032472718e-01 ) ( -7.92425102086383e-04 , 9.93811739427192e-04 , -1.85381806494544e-03 ) 2.52612036687898e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 23 ( -3.11102815077491e-01 , 2.09226128345936e-01 , 9.27059580430638e-01 ) ( -7.92007932218113e-04 , 9.95761305681223e-04 , -1.85411916086128e-03 ) 2.52828750263065e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 24 ( -3.11411487946956e-01 , 2.08182462090056e-01 , 9.27190890622198e-01 ) ( -7.91390586479183e-04 , 9.97848638192983e-04 , -1.85438178124440e-03 ) 2.53036637786130e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 20 ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226723e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 21 ( -3.10818115103370e-01 , 2.11096376432417e-01 , 9.26731039288472e-01 ) ( -7.92577332166356e-04 , 9.92020809508261e-04 , -1.85346207857694e-03 ) 2.52380289534207e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 22 ( -3.10894230143356e-01 , 2.10200911472952e-01 , 9.26909032472718e-01 ) ( -7.92425102086384e-04 , 9.93811739427191e-04 , -1.85381806494544e-03 ) 2.52612036687898e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 23 ( -3.11102815077490e-01 , 2.09226128345936e-01 , 9.27059580430638e-01 ) ( -7.92007932218114e-04 , 9.95761305681222e-04 , -1.85411916086128e-03 ) 2.52828750263065e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 24 ( -3.11411487946955e-01 , 2.08182462090057e-01 , 9.27190890622198e-01 ) ( -7.91390586479184e-04 , 9.97848638192982e-04 , -1.85438178124440e-03 ) 2.53036637786130e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 25 ( -3.11785608613730e-01 , 2.07083701948798e-01 , 9.27311207011189e-01 ) ( -7.90642345145636e-04 , 1.00004615847550e-03 , -1.85462241402238e-03 ) 2.53241596780659e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 26 ( -3.12190163793984e-01 , 2.05946569990115e-01 , 9.27428332508552e-01 ) ( -7.89833234785128e-04 , 1.00232042239287e-03 , -1.85485666501710e-03 ) 2.53448800783766e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 26 ( -3.12190163793984e-01 , 2.05946569990115e-01 , 9.27428332508551e-01 ) ( -7.89833234785128e-04 , 1.00232042239286e-03 , -1.85485666501710e-03 ) 2.53448800783766e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 27 ( -3.12591400614140e-01 , 2.04789878956263e-01 , 9.27549309599856e-01 ) ( -7.89030761144815e-04 , 1.00463380446057e-03 , -1.85509861919971e-03 ) 2.53662475502718e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 28 ( -3.12958111790193e-01 , 2.03633472860108e-01 , 9.27680240705626e-01 ) ( -7.88297338792708e-04 , 1.00694661665288e-03 , -1.85536048141125e-03 ) 2.53885834955947e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 29 ( -3.13262544129310e-01 , 2.02497186917752e-01 , 9.27826205566554e-01 ) ( -7.87688474114474e-04 , 1.00921918853759e-03 , -1.85565241113311e-03 ) 2.54121118685469e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 30 ( -3.13480943392435e-01 , 2.01400032613720e-01 , 9.27991231097030e-01 ) ( -7.87251675588225e-04 , 1.01141349714566e-03 , -1.85598246219406e-03 ) 2.54369668144840e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 31 ( -3.13593783631660e-01 , 2.00359712776967e-01 , 9.28178282639446e-01 ) ( -7.87025995109775e-04 , 1.01349413681916e-03 , -1.85635656527889e-03 ) 2.54631998989970e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 32 ( -3.13585736154326e-01 , 1.99392449174349e-01 , 9.28389270345583e-01 ) ( -7.87042090064442e-04 , 1.01542866402440e-03 , -1.85677854069117e-03 ) 2.54907858621330e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 33 ( -3.13445449674931e-01 , 1.98512983197192e-01 , 9.28625083432615e-01 ) ( -7.87322663023234e-04 , 1.01718759597871e-03 , -1.85725016686523e-03 ) 2.55196288172194e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 34 ( -3.13165208280151e-01 , 1.97734570946912e-01 , 9.28885672069114e-01 ) ( -7.87883145812792e-04 , 1.01874442047927e-03 , -1.85777134413823e-03 ) 2.55495720640733e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 35 ( -3.12740549003456e-01 , 1.97068826614834e-01 , 9.29170181713592e-01 ) ( -7.88732464366183e-04 , 1.02007590914343e-03 , -1.85834036342718e-03 ) 2.55804133355131e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 36 ( -3.12169888759600e-01 , 1.96525353868791e-01 , 9.29477135726622e-01 ) ( -7.89873784853896e-04 , 1.02116285463551e-03 , -1.85895427145324e-03 ) 2.56119257752052e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 37 ( -3.11454223752150e-01 , 1.96111202307429e-01 , 9.29804636919219e-01 ) ( -7.91305114868796e-04 , 1.02199115775824e-03 , -1.85960927383844e-03 ) 2.56438818134973e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 38 ( -3.10596941423872e-01 , 1.95830264173119e-01 , 9.30150551046454e-01 ) ( -7.93019679525352e-04 , 1.02255303402686e-03 , -1.86030110209291e-03 ) 2.56760755498005e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 39 ( -3.09603763986270e-01 , 1.95682751690521e-01 , 9.30512638289433e-01 ) ( -7.95006034400556e-04 , 1.02284805899205e-03 , -1.86102527657887e-03 ) 2.57083391329128e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 40 ( -3.08482822701286e-01 , 1.95664885198602e-01 , 9.30888608158068e-01 ) ( -7.97247916970524e-04 , 1.02288379197589e-03 , -1.86177721631614e-03 ) 2.57405494809734e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 28 ( -3.12958111790194e-01 , 2.03633472860108e-01 , 9.27680240705626e-01 ) ( -7.88297338792708e-04 , 1.00694661665288e-03 , -1.85536048141125e-03 ) 2.53885834955947e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 29 ( -3.13262544129311e-01 , 2.02497186917752e-01 , 9.27826205566553e-01 ) ( -7.87688474114472e-04 , 1.00921918853759e-03 , -1.85565241113311e-03 ) 2.54121118685469e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 30 ( -3.13480943392436e-01 , 2.01400032613720e-01 , 9.27991231097030e-01 ) ( -7.87251675588223e-04 , 1.01141349714565e-03 , -1.85598246219406e-03 ) 2.54369668144840e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 31 ( -3.13593783631662e-01 , 2.00359712776967e-01 , 9.28178282639445e-01 ) ( -7.87025995109772e-04 , 1.01349413681916e-03 , -1.85635656527889e-03 ) 2.54631998989969e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 32 ( -3.13585736154328e-01 , 1.99392449174349e-01 , 9.28389270345582e-01 ) ( -7.87042090064439e-04 , 1.01542866402440e-03 , -1.85677854069116e-03 ) 2.54907858621329e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 33 ( -3.13445449674932e-01 , 1.98512983197192e-01 , 9.28625083432615e-01 ) ( -7.87322663023230e-04 , 1.01718759597871e-03 , -1.85725016686523e-03 ) 2.55196288172193e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 34 ( -3.13165208280154e-01 , 1.97734570946912e-01 , 9.28885672069113e-01 ) ( -7.87883145812788e-04 , 1.01874442047927e-03 , -1.85777134413823e-03 ) 2.55495720640733e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 35 ( -3.12740549003459e-01 , 1.97068826614834e-01 , 9.29170181713591e-01 ) ( -7.88732464366178e-04 , 1.02007590914343e-03 , -1.85834036342718e-03 ) 2.55804133355130e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 36 ( -3.12169888759603e-01 , 1.96525353868791e-01 , 9.29477135726621e-01 ) ( -7.89873784853888e-04 , 1.02116285463551e-03 , -1.85895427145324e-03 ) 2.56119257752050e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 37 ( -3.11454223752153e-01 , 1.96111202307429e-01 , 9.29804636919218e-01 ) ( -7.91305114868789e-04 , 1.02199115775824e-03 , -1.85960927383844e-03 ) 2.56438818134972e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 38 ( -3.10596941423876e-01 , 1.95830264173120e-01 , 9.30150551046453e-01 ) ( -7.93019679525344e-04 , 1.02255303402686e-03 , -1.86030110209291e-03 ) 2.56760755498004e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 39 ( -3.09603763986273e-01 , 1.95682751690521e-01 , 9.30512638289431e-01 ) ( -7.95006034400549e-04 , 1.02284805899205e-03 , -1.86102527657886e-03 ) 2.57083391329127e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 40 ( -3.08482822701290e-01 , 1.95664885198602e-01 , 9.30888608158067e-01 ) ( -7.97247916970515e-04 , 1.02288379197589e-03 , -1.86177721631613e-03 ) 2.57405494809733e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt b/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt index 157cac038..617210efd 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-07-07". +colvars: Using NAMD interface, version "2020-05-04". diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out index 99a22e5fd..2724e6331 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -88,7 +84,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,26 +122,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceInv colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 469850fcd..9745bfb6a 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.42783836136749e+00 + x 2.42783836132997e+00 } restraint { diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj index 9b364a5cf..0f1bd304e 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 2.39061650308305e+00 -9.16246601233221e-03 - 1 2.38234770114191e+00 -9.12939080456763e-03 - 2 2.37511792679912e+00 -9.10047170719648e-03 - 3 2.36945079734406e+00 -9.07780318937623e-03 - 4 2.36577204845768e+00 -9.06308819383071e-03 - 5 2.36436521236120e+00 -9.05746084944482e-03 - 6 2.36534500808037e+00 -9.06138003232147e-03 - 7 2.36864872147381e+00 -9.07459488589523e-03 - 8 2.37404299848291e+00 -9.09617199393162e-03 - 9 2.38114314200753e+00 -9.12457256803010e-03 - 10 2.38944311901955e+00 -9.15777247607821e-03 - 11 2.39835525129330e+00 -9.19342100517319e-03 - 12 2.40725780808025e+00 -9.22903123232098e-03 - 13 2.41554677330587e+00 -9.26218709322349e-03 - 14 2.42268616657072e+00 -9.29074466628286e-03 - 15 2.42825074174393e+00 -9.31300296697570e-03 - 16 2.43195609325616e+00 -9.32782437302463e-03 - 17 2.43367350232427e+00 -9.33469400929707e-03 - 18 2.43342929444717e+00 -9.33371717778869e-03 - 19 2.43139031964034e+00 -9.32556127856135e-03 - 20 2.42783836136749e+00 -9.31135344546996e-03 + 1 2.38234770114368e+00 -9.12939080457472e-03 + 2 2.37511792680581e+00 -9.10047170722326e-03 + 3 2.36945079735818e+00 -9.07780318943272e-03 + 4 2.36577204848084e+00 -9.06308819392336e-03 + 5 2.36436521239393e+00 -9.05746084957573e-03 + 6 2.36534500812203e+00 -9.06138003248811e-03 + 7 2.36864872152266e+00 -9.07459488609063e-03 + 8 2.37404299853629e+00 -9.09617199414514e-03 + 9 2.38114314206215e+00 -9.12457256824860e-03 + 10 2.38944311907187e+00 -9.15777247628748e-03 + 11 2.39835525133988e+00 -9.19342100535952e-03 + 12 2.40725780811812e+00 -9.22903123247246e-03 + 13 2.41554677333277e+00 -9.26218709333110e-03 + 14 2.42268616658529e+00 -9.29074466634115e-03 + 15 2.42825074174577e+00 -9.31300296698308e-03 + 16 2.43195609324583e+00 -9.32782437298332e-03 + 17 2.43367350230322e+00 -9.33469400921286e-03 + 18 2.43342929441762e+00 -9.33371717767048e-03 + 19 2.43139031960514e+00 -9.32556127842056e-03 + 20 2.42783836132997e+00 -9.31135344531990e-03 diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out index fe78368a1..fd5a4f5e9 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -88,7 +84,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -127,31 +122,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceInv colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 2.42784 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index d50294abc..8b74c0b18 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.39535776160792e+00 + x 2.39535776180124e+00 } restraint { diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 8afdaf44b..a892a5839 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.42783836136749e+00 -9.31135344546996e-03 - 21 2.42313713931922e+00 -9.29254855727687e-03 - 22 2.41769617213041e+00 -9.27078468852164e-03 - 23 2.41193587332118e+00 -9.24774349328473e-03 - 24 2.40625738446726e+00 -9.22502953786906e-03 - 25 2.40101869519248e+00 -9.20407478076994e-03 - 26 2.39651622530201e+00 -9.18606490120804e-03 - 27 2.39296966655697e+00 -9.17187866622788e-03 - 28 2.39050847169341e+00 -9.16203388677364e-03 - 29 2.38916060732936e+00 -9.15664242931743e-03 - 30 2.38884732554973e+00 -9.15538930219891e-03 - 31 2.38938907295485e+00 -9.15755629181939e-03 - 32 2.39052656449122e+00 -9.16210625796488e-03 - 33 2.39195711452612e+00 -9.16782845810448e-03 - 34 2.39338167011611e+00 -9.17352668046446e-03 - 35 2.39455393665551e+00 -9.17821574662203e-03 - 36 2.39532170766483e+00 -9.18128683065931e-03 - 37 2.39565155143393e+00 -9.18260620573574e-03 - 38 2.39563139473288e+00 -9.18252557893151e-03 - 39 2.39545006610174e+00 -9.18180026440696e-03 - 40 2.39535776160792e+00 -9.18143104643170e-03 + 20 2.42783836132997e+00 -9.31135344531990e-03 + 21 2.42313713928297e+00 -9.29254855713189e-03 + 22 2.41769617209907e+00 -9.27078468839628e-03 + 23 2.41193587329818e+00 -9.24774349319270e-03 + 24 2.40625738445557e+00 -9.22502953782229e-03 + 25 2.40101869519443e+00 -9.20407478077773e-03 + 26 2.39651622531912e+00 -9.18606490127647e-03 + 27 2.39296966658990e+00 -9.17187866635958e-03 + 28 2.39050847174201e+00 -9.16203388696806e-03 + 29 2.38916060739287e+00 -9.15664242957147e-03 + 30 2.38884732562697e+00 -9.15538930250787e-03 + 31 2.38938907304455e+00 -9.15755629217820e-03 + 32 2.39052656459227e+00 -9.16210625836907e-03 + 33 2.39195711463777e+00 -9.16782845855110e-03 + 34 2.39338167023812e+00 -9.17352668095248e-03 + 35 2.39455393678809e+00 -9.17821574715235e-03 + 36 2.39532170780857e+00 -9.18128683123430e-03 + 37 2.39565155158960e+00 -9.18260620635839e-03 + 38 2.39563139490110e+00 -9.18252557960440e-03 + 39 2.39545006628275e+00 -9.18180026513099e-03 + 40 2.39535776180124e+00 -9.18143104720494e-03 diff --git a/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distanceinv_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out index 18bfc4768..9b43c99fa 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -124,28 +120,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - distancePairs colvar component: -colvars: - histogramRestraint colvar bias implementation: -colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped index 76f57335f..2fdfb6c4c 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.04650863844542e+00 , 4.49435411373106e+00 , 5.18841527687423e+00 , 6.16645837246753e+00 , 2.49717925475228e+00 , 3.86424835988508e+00 , 4.55750848670402e+00 , 5.34080670712767e+00 , 1.36568581550375e+00 , 2.47047097074510e+00 , 3.12336009876006e+00 , 3.85074280234761e+00 , 2.22178524374518e+00 , 2.73185149420872e+00 , 2.91864419945045e+00 , 3.29101397434784e+00 ) + x ( 3.04650863884945e+00 , 4.49435411437724e+00 , 5.18841527762764e+00 , 6.16645837340779e+00 , 2.49717925480425e+00 , 3.86424836018692e+00 , 4.55750848697779e+00 , 5.34080670765490e+00 , 1.36568581546352e+00 , 2.47047097097987e+00 , 3.12336009885461e+00 , 3.85074280281206e+00 , 2.22178524357949e+00 , 2.73185149414085e+00 , 2.91864419906098e+00 , 3.29101397431997e+00 ) } histogramrestraint { diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj index e0a6a3b8e..703c0aa24 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hr 0 ( 2.95543971137580e+00 , 4.40149446295507e+00 , 5.19438956774262e+00 , 6.22241603343745e+00 , 2.46985074910253e+00 , 3.82984200895935e+00 , 4.58947829164686e+00 , 5.41000980054028e+00 , 1.34023744154865e+00 , 2.42537620134385e+00 , 3.12639105039661e+00 , 3.90388793384236e+00 , 2.19602098164167e+00 , 2.66815420835178e+00 , 2.96116058328487e+00 , 3.36815290626777e+00 ) ( -5.92960352862036e-03 , 1.10620242770031e-02 , 1.68173891728727e-02 , 1.87723003472394e-02 , -1.12008206156859e-02 , 4.95828158263673e-03 , 1.27336187454413e-02 , 1.77621382788059e-02 , -1.61490029424512e-02 , -1.16075543291348e-02 , -3.82398122724722e-03 , 5.82475954854570e-03 , -1.34483793610802e-02 , -9.21377746348792e-03 , -5.86053342506391e-03 , -7.62252484367914e-04 ) 3.78092070171140e-01 - 1 ( 2.95875719071828e+00 , 4.40108157301207e+00 , 5.19334777145334e+00 , 6.22377033112801e+00 , 2.46917672947451e+00 , 3.82473616688607e+00 , 4.58659307892583e+00 , 5.40932559983924e+00 , 1.33333768535497e+00 , 2.41676016397270e+00 , 3.12170836496912e+00 , 3.90418294782421e+00 , 2.19936580917941e+00 , 2.66448894985246e+00 , 2.96000465033399e+00 , 3.36551108557249e+00 ) ( -5.86283106865521e-03 , 1.10731958752829e-02 , 1.68140327966110e-02 , 1.87597892711689e-02 , -1.11822547405590e-02 , 4.92033089418465e-03 , 1.27214365048558e-02 , 1.77580366645080e-02 , -1.61363624056552e-02 , -1.16601244086846e-02 , -3.85595598392256e-03 , 5.84982545350766e-03 , -1.34023678457379e-02 , -9.22688145618673e-03 , -5.84776463391588e-03 , -7.69953161976424e-04 ) 3.77945851131380e-01 - 2 ( 2.96294215660827e+00 , 4.40226828651185e+00 , 5.19286012272654e+00 , 6.22443374457976e+00 , 2.46935518847865e+00 , 3.82150874456602e+00 , 4.58422849105882e+00 , 5.40818433918403e+00 , 1.32707626478422e+00 , 2.41052101094634e+00 , 3.11822280908445e+00 , 3.90473321715676e+00 , 2.20349735093127e+00 , 2.66304418493398e+00 , 2.95871521201740e+00 , 3.36219610857201e+00 ) ( -5.79800647502922e-03 , 1.10923908557419e-02 , 1.68129107062924e-02 , 1.87535308678630e-02 , -1.11672628469244e-02 , 4.89409954504780e-03 , 1.27081525944472e-02 , 1.77533370847938e-02 , -1.61279245724598e-02 , -1.17024782043052e-02 , -3.88536413831673e-03 , 5.86771262483623e-03 , -1.33609408182681e-02 , -9.22837266280075e-03 , -5.84907998228004e-03 , -7.98316100680052e-04 ) 3.77862223359593e-01 - 3 ( 2.96775402992694e+00 , 4.40516830459548e+00 , 5.19308580986083e+00 , 6.22426614571086e+00 , 2.47031640871780e+00 , 3.82049095747998e+00 , 4.58271436795677e+00 , 5.40668366046462e+00 , 1.32191637302337e+00 , 2.40699048525175e+00 , 3.11597732152133e+00 , 3.90507762174690e+00 , 2.20806859148285e+00 , 2.66384305029386e+00 , 2.95730260671757e+00 , 3.35823946236147e+00 ) ( -5.73812439859379e-03 , 1.11203452480056e-02 , 1.68145007712454e-02 , 1.87535589647976e-02 , -1.11565343480424e-02 , 4.88326606493625e-03 , 1.26961984974043e-02 , 1.77480942241991e-02 , -1.61238345657143e-02 , -1.17319756039677e-02 , -3.91183713328302e-03 , 5.87286048563701e-03 , -1.33265703304845e-02 , -9.21811206393306e-03 , -5.86446396094804e-03 , -8.47126580670137e-04 ) 3.77840179115355e-01 - 4 ( 2.97293625444857e+00 , 4.40980004758125e+00 , 5.19408774075846e+00 , 6.22316886249381e+00 , 2.47196059702068e+00 , 3.82188498631687e+00 , 4.58227967128769e+00 , 5.40493151507430e+00 , 1.31824010722335e+00 , 2.40633376724167e+00 , 3.11491133209983e+00 , 3.90477299810360e+00 , 2.21271348718989e+00 , 2.66679770357475e+00 , 2.95576116726311e+00 , 3.35371179659075e+00 ) ( -5.68562536211738e-03 , 1.11574404636562e-02 , 1.68189720084544e-02 , 1.87595928078326e-02 , -1.11503656066572e-02 , 4.89069779983769e-03 , 1.26876273223686e-02 , 1.77424383833725e-02 , -1.61240913055969e-02 , -1.17467229287332e-02 , -3.93551745856113e-03 , 5.86059410516952e-03 , -1.33013307602559e-02 , -9.19636281522561e-03 , -5.89333166754952e-03 , -9.14911497713965e-04 ) 3.77876668465000e-01 - 5 ( 2.97824318820620e+00 , 4.41608136345158e+00 , 5.19583111697961e+00 , 6.22109580805119e+00 , 2.47416649816765e+00 , 3.82573442794791e+00 , 4.58302854469209e+00 , 5.40302751449250e+00 , 1.31631479781056e+00 , 2.40854057670679e+00 , 3.11487986891832e+00 , 3.90345112760315e+00 , 2.21707823699791e+00 , 2.67171151319462e+00 , 2.95407669276953e+00 , 3.34871521635490e+00 ) ( -5.64215660564444e-03 , 1.12036160407990e-02 , 1.68261920493138e-02 , 1.87710646714446e-02 , -1.11486629033573e-02 , 4.91802392897703e-03 , 1.26838914739109e-02 , 1.77365452169039e-02 , -1.61285450767192e-02 , -1.17456807872873e-02 , -3.95690439720719e-03 , 5.82769711943081e-03 , -1.32867339927808e-02 , -9.16386239601504e-03 , -5.93452419993883e-03 , -9.99112313017295e-04 ) 3.77966928510290e-01 - 6 ( 2.98346272349810e+00 , 4.42383057898326e+00 , 5.19819070218742e+00 , 6.21805993368695e+00 , 2.47679966397792e+00 , 3.83190740551774e+00 , 4.58492741116317e+00 , 5.40104621783311e+00 , 1.31627480642875e+00 , 2.41343034363858e+00 , 3.11567915001139e+00 , 3.90086651022608e+00 , 2.22085290399274e+00 , 2.67829022321015e+00 , 2.95223463734567e+00 , 3.34337409763593e+00 ) ( -5.60843111665177e-03 , 1.12583138089623e-02 , 1.68357668482585e-02 , 1.87871810209162e-02 , -1.11509975020431e-02 , 4.96532034611288e-03 , 1.26856803073333e-02 , 1.77306125297607e-02 , -1.61369024575768e-02 , -1.17287330746808e-02 , -3.97667165949540e-03 , 5.77284958036822e-03 , -1.32835970604198e-02 , -9.12186140006743e-03 , -5.98634736725953e-03 , -1.09632452077415e-03 ) 3.78105088307123e-01 - 7 ( 2.98843276392426e+00 , 4.43277362477714e+00 , 5.20096598211478e+00 , 6.21413473629710e+00 , 2.47971835572621e+00 , 3.84009332257782e+00 , 4.58780406794513e+00 , 5.39902438389403e+00 , 1.31811662215800e+00 , 2.42066789064899e+00 , 3.11707520828051e+00 , 3.89692854943828e+00 , 2.22379944067799e+00 , 2.68616059178675e+00 , 2.95022670934415e+00 , 3.33782534394336e+00 ) ( -5.58418350468220e-03 , 1.13204634818992e-02 , 1.68471093237251e-02 , 1.88070063172207e-02 , -1.11567058557194e-02 , 5.03094217856181e-03 , 1.26928382677193e-02 , 1.77248424341910e-02 , -1.61487389921320e-02 , -1.16967256678892e-02 , -3.99547330106177e-03 , 5.69688275196239e-03 , -1.32919546974516e-02 , -9.07211334045853e-03 , -6.04665601957078e-03 , -1.20257089414411e-03 ) 3.78284907046422e-01 - 8 ( 2.99305095199572e+00 , 4.44255706227127e+00 , 5.20390279803208e+00 , 6.20945090033049e+00 , 2.48277685514022e+00 , 3.84981382799079e+00 , 4.59135934530626e+00 , 5.39695380930977e+00 , 1.32170353599299e+00 , 2.42978572116422e+00 , 3.11883162759681e+00 , 3.89171382371156e+00 , 2.22577247715835e+00 , 2.69489401029209e+00 , 2.94805450436009e+00 , 3.33220883826211e+00 ) ( -5.56820917282278e-03 , 1.13885155084319e-02 , 1.68595280947096e-02 , 1.88295545639784e-02 , -1.11650126061194e-02 , 5.11152770905446e-03 , 1.27043773431331e-02 , 1.77194261761126e-02 , -1.61635185303969e-02 , -1.16514770997870e-02 , -4.01376337777638e-03 , 5.60281550584254e-03 , -1.33110285193897e-02 , -9.01681060037427e-03 , -6.11297722345335e-03 , -1.31358022351808e-03 ) 3.78500459333923e-01 - 9 ( 2.99727803932683e+00 , 4.45276689003159e+00 , 5.20671940496760e+00 , 6.20418842997876e+00 , 2.48582792210202e+00 , 3.86044838529561e+00 , 4.59519142345580e+00 , 5.39478097747158e+00 , 1.32677703124828e+00 , 2.44021023612503e+00 , 3.12073277454684e+00 , 3.88545705707712e+00 , 2.22673027072218e+00 , 2.70403228030061e+00 , 2.94572999620193e+00 , 3.32665870422601e+00 ) ( -5.55846922909315e-03 , 1.14605208114470e-02 , 1.68723226152897e-02 , 1.88538732088346e-02 , -1.11751436044541e-02 , 5.20218321504213e-03 , 1.27185877234887e-02 , 1.77145300274814e-02 , -1.61806180975511e-02 , -1.15957536333710e-02 , -4.03166013215670e-03 , 5.49565596179502e-03 , -1.33392618858410e-02 , -8.95847435004462e-03 , -6.18265891926579e-03 , -1.42505162862931e-03 ) 3.78746600048281e-01 - 10 ( 3.00113590351193e+00 , 4.46295283628442e+00 , 5.20913451135400e+00 , 6.19856492361509e+00 , 2.48872700417910e+00 , 3.87127405643474e+00 , 4.59883180779499e+00 , 5.39241395041393e+00 , 1.33297408008389e+00 , 2.45129095459194e+00 , 3.12259990733059e+00 , 3.87852252716797e+00 , 2.22673463302703e+00 , 2.71311302779813e+00 , 2.94327377818026e+00 , 3.32129591623069e+00 ) ( -5.55224417164072e-03 , 1.15342512228427e-02 , 1.68848695705750e-02 , 1.88791062752049e-02 , -1.11863975635185e-02 , 5.29683799032226e-03 , 1.27332368515994e-02 , 1.77102817912748e-02 , -1.61993578794913e-02 , -1.15331925419960e-02 , -4.04888243545545e-03 , 5.38197720522603e-03 , -1.33744234726122e-02 , -8.89981537211362e-03 , -6.25302646046828e-03 , -1.53289195785256e-03 ) 3.79019107040781e-01 - 11 ( 3.00470125489972e+00 , 4.47265711210950e+00 , 5.21089460515481e+00 , 6.19282083230316e+00 , 2.49134008903989e+00 , 3.88151734625078e+00 , 4.60179016418336e+00 , 5.38973566924521e+00 , 1.33985118522930e+00 , 2.46233295670471e+00 , 3.12429892040812e+00 , 3.87136030291841e+00 , 2.22594006161918e+00 , 2.72169287077339e+00 , 2.94071248094998e+00 , 3.31622273009373e+00 ) ( -5.54632288013861e-03 , 1.16073489549424e-02 , 1.68966879656824e-02 , 1.89045283476569e-02 , -1.11981583562531e-02 , 5.38873432397986e-03 , 1.27458325723427e-02 , 1.77067581965523e-02 , -1.62190359541145e-02 , -1.14681548206993e-02 , -4.06477383479660e-03 , 5.26930541056336e-03 , -1.34137735934525e-02 , -8.84358548285717e-03 , -6.32152819144142e-03 , -1.63341748115851e-03 ) 3.79314492529018e-01 - 12 ( 3.00809583945475e+00 , 4.48144568605128e+00 , 5.21179795342402e+00 , 6.18720282644011e+00 , 2.49355503432457e+00 , 3.89041360009451e+00 , 4.60360319942864e+00 , 5.38662146956213e+00 , 1.34691612070145e+00 , 2.47263280494077e+00 , 3.12573989585393e+00 , 3.86445347573540e+00 , 2.22457351043668e+00 , 2.72936720512052e+00 , 2.93807666861132e+00 , 3.31151936864297e+00 ) ( -5.53721626795029e-03 , 1.16774905532618e-02 , 1.69074760243028e-02 , 1.89295470420789e-02 , -1.12098518648447e-02 , 5.47099418188079e-03 , 1.27539142271434e-02 , 1.77039734250454e-02 , -1.62389653920810e-02 , -1.14054942040387e-02 , -4.07841190427115e-03 , 5.16538673702184e-03 , -1.34542775132188e-02 , -8.79243550204225e-03 , -6.38585394534860e-03 , -1.72351102574743e-03 ) 3.79629555593815e-01 - 13 ( 3.01147358102753e+00 , 4.48893928194997e+00 , 5.21171292451106e+00 , 6.18194650016787e+00 , 2.49529420874019e+00 , 3.89726774753210e+00 , 4.60388154116292e+00 , 5.38295779117939e+00 , 1.35366684255277e+00 , 2.48151732623380e+00 , 3.12686979147052e+00 , 3.85826315071113e+00 , 2.22290718088401e+00 , 2.73578615464733e+00 , 2.93539988719616e+00 , 3.30724327376658e+00 ) ( -5.52138817482320e-03 , 1.17425495705784e-02 , 1.69171191446419e-02 , 1.89536788062538e-02 , -1.12208703478021e-02 , 5.53719445578204e-03 , 1.27553319589290e-02 , 1.77018696730068e-02 , -1.62585085963099e-02 , -1.13502429741435e-02 , -4.08878426817147e-03 , 5.07741732348955e-03 , -1.34928430954218e-02 , -8.74878890446318e-03 , -6.44401748260910e-03 , -1.80072599449384e-03 ) 3.79960806988138e-01 - 14 ( 3.01500498355936e+00 , 4.49484105603145e+00 , 5.21058888397878e+00 , 6.17725979125500e+00 , 2.49652507990531e+00 , 3.90150978133327e+00 , 4.60234863260006e+00 , 5.37865915135750e+00 , 1.35963468851140e+00 , 2.48838344220267e+00 , 3.12766033460393e+00 , 3.85317752048532e+00 , 2.22122742538576e+00 , 2.74066674507216e+00 , 2.93271867782830e+00 , 3.30343100744147e+00 ) ( -5.49549732867158e-03 , 1.18007441986952e-02 , 1.69256728814974e-02 , 1.89765088186476e-02 , -1.12304979163713e-02 , 5.58188833376368e-03 , 1.27484793036664e-02 , 1.77003118142817e-02 , -1.62771022173966e-02 , -1.13072324040326e-02 , -4.09500221423765e-03 , 5.01132420994778e-03 , -1.35265575664752e-02 , -8.71473341320642e-03 , -6.49440390633471e-03 , -1.86333145708674e-03 ) 3.80303913164440e-01 - 15 ( 3.01885935134200e+00 , 4.49895836101355e+00 , 5.20845880435748e+00 , 6.17330861970770e+00 , 2.49726571448041e+00 , 3.90273958726481e+00 , 4.59886715923434e+00 , 5.37368145631357e+00 , 1.36442685860666e+00 , 2.49273626173455e+00 , 3.12809348126300e+00 , 3.84947011778950e+00 , 2.21980329429498e+00 , 2.74380165828177e+00 , 2.93007263674742e+00 , 3.30010253658084e+00 ) ( -5.45664327434154e-03 , 1.18507598188582e-02 , 1.69333270288283e-02 , 1.89976486937448e-02 , -1.12378675651178e-02 , 5.60103026326155e-03 , 1.27324557193522e-02 , 1.76990895586115e-02 , -1.62942676689069e-02 , -1.12806824591946e-02 , -4.09652022589830e-03 , 4.97117341132816e-03 , -1.35529004612138e-02 , -8.69192881828445e-03 , -6.53579293927686e-03 , -1.91029892067540e-03 ) 3.80653281337756e-01 - 16 ( 3.02318574233431e+00 , 4.50121671715298e+00 , 5.20543347930304e+00 , 6.17020596649946e+00 , 2.49758367078486e+00 , 3.90075791018026e+00 , 4.59345084620333e+00 , 5.36803107326493e+00 , 1.36776218077457e+00 , 2.49422221697351e+00 , 3.12814676409148e+00 , 3.84727076112079e+00 , 2.21885835313521e+00 , 2.74506502298711e+00 , 2.92750329382881e+00 , 3.29726720552320e+00 ) ( -5.40260775227740e-03 , 1.18918393995497e-02 , 1.69403563723388e-02 , 1.90167057123976e-02 , -1.12419666467266e-02 , 5.59228671198299e-03 , 1.27071500736935e-02 , 1.76979317995731e-02 , -1.63096075137775e-02 , -1.12738072092257e-02 , -4.09333242371338e-03 , 4.95876082069397e-03 , -1.35699155635357e-02 , -8.68152857719622e-03 , -6.56737454138995e-03 , -1.94123960773835e-03 ) 3.81001871240511e-01 - 17 ( 3.02809415710879e+00 , 4.50166506104922e+00 , 5.20168811881594e+00 , 6.16800533349194e+00 , 2.49758857964583e+00 , 3.89558236005592e+00 , 4.58626174925325e+00 , 5.36177010617776e+00 , 1.36949463578708e+00 , 2.49265415188493e+00 , 3.12778059652950e+00 , 3.84655116097139e+00 , 2.21854897895857e+00 , 2.74441563397565e+00 , 2.92505081205027e+00 , 3.29493032180216e+00 ) ( -5.33207795486475e-03 , 1.19238375475688e-02 , 1.69470627883182e-02 , 1.90332731864346e-02 , -1.12416911796005e-02 , 5.55523293564110e-03 , 1.26732473366659e-02 , 1.76965367632408e-02 , -1.63227936088094e-02 , -1.12884863427824e-02 , -4.08612201263206e-03 , 4.97341853049439e-03 , -1.35763317145022e-02 , -8.68411432067984e-03 , -6.58877216935854e-03 , -1.95630818933365e-03 ) 3.81341269972205e-01 - 18 ( 3.03363892679024e+00 , 4.50047208564501e+00 , 5.19744285787811e+00 , 6.16669911720665e+00 , 2.49741999764829e+00 , 3.88744865212165e+00 , 4.57759477230416e+00 , 5.35501860432485e+00 , 1.36962096542427e+00 , 2.48802587288390e+00 , 3.12692927006197e+00 , 3.84712592421505e+00 , 2.21895140215167e+00 , 2.74189783528608e+00 , 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3.82208090962526e-01 + 1 ( 2.95875719071982e+00 , 4.40108157301290e+00 , 5.19334777145356e+00 , 6.22377033113224e+00 , 2.46917672947515e+00 , 3.82473616688567e+00 , 4.58659307892474e+00 , 5.40932559984203e+00 , 1.33333768535653e+00 , 2.41676016397346e+00 , 3.12170836496849e+00 , 3.90418294782770e+00 , 2.19936580917918e+00 , 2.66448894985085e+00 , 2.96000465033168e+00 , 3.36551108557328e+00 ) ( -5.86283106863594e-03 , 1.10731958752850e-02 , 1.68140327966034e-02 , 1.87597892711556e-02 , -1.11822547405509e-02 , 4.92033089417690e-03 , 1.27214365048402e-02 , 1.77580366645092e-02 , -1.61363624056526e-02 , -1.16601244086755e-02 , -3.85595598393038e-03 , 5.84982545354479e-03 , -1.34023678457367e-02 , -9.22688145620218e-03 , -5.84776463394309e-03 , -7.69953161967240e-04 ) 3.77945851131251e-01 + 2 ( 2.96294215661432e+00 , 4.40226828651527e+00 , 5.19286012272764e+00 , 6.22443374459694e+00 , 2.46935518848109e+00 , 3.82150874456456e+00 , 4.58422849105476e+00 , 5.40818433919542e+00 , 1.32707626479006e+00 , 2.41052101094915e+00 , 3.11822280908199e+00 , 3.90473321717080e+00 , 2.20349735093029e+00 , 2.66304418492767e+00 , 2.95871521200833e+00 , 3.36219610857531e+00 ) ( -5.79800647495339e-03 , 1.10923908557496e-02 , 1.68129107062616e-02 , 1.87535308678082e-02 , -1.11672628468922e-02 , 4.89409954501751e-03 , 1.27081525943855e-02 , 1.77533370847981e-02 , -1.61279245724480e-02 , -1.17024782042702e-02 , -3.88536413834723e-03 , 5.86771262498385e-03 , -1.33609408182631e-02 , -9.22837266286093e-03 , -5.84907998238668e-03 , -7.98316100642240e-04 ) 3.77862223359046e-01 + 3 ( 2.96775402994024e+00 , 4.40516830460360e+00 , 5.19308580986400e+00 , 6.22426614574961e+00 , 2.47031640872298e+00 , 3.82049095747722e+00 , 4.58271436794834e+00 , 5.40668366049041e+00 , 1.32191637303560e+00 , 2.40699048525786e+00 , 3.11597732151607e+00 , 3.90507762177822e+00 , 2.20806859148045e+00 , 2.66384305028015e+00 , 2.95730260669763e+00 , 3.35823946236896e+00 ) ( -5.73812439842742e-03 , 1.11203452480230e-02 , 1.68145007711762e-02 , 1.87535589646727e-02 , -1.11565343479722e-02 , 4.88326606487158e-03 , 1.26961984972676e-02 , 1.77480942242067e-02 , -1.61238345656856e-02 , -1.17319756038901e-02 , -3.91183713334946e-03 , 5.87286048596288e-03 , -1.33265703304735e-02 , -9.21811206406306e-03 , -5.86446396118304e-03 , -8.47126580585897e-04 ) 3.77840179114077e-01 + 4 ( 2.97293625447158e+00 , 4.40980004759664e+00 , 5.19408774076560e+00 , 6.22316886256237e+00 , 2.47196059702916e+00 , 3.82188498631318e+00 , 4.58227967127418e+00 , 5.40493151511998e+00 , 1.31824010724331e+00 , 2.40633376725236e+00 , 3.11491133209108e+00 , 3.90477299815830e+00 , 2.21271348718521e+00 , 2.66679770355164e+00 , 2.95576116722859e+00 , 3.35371179660392e+00 ) ( -5.68562536183138e-03 , 1.11574404636885e-02 , 1.68189720083336e-02 , 1.87595928076098e-02 , -1.11503656065385e-02 , 4.89069779973133e-03 , 1.26876273221314e-02 , 1.77424383833815e-02 , -1.61240913055418e-02 , -1.17467229285959e-02 , 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5.19819070221187e+00 , 6.21805993383684e+00 , 2.47679966399307e+00 , 3.83190740551612e+00 , 4.58492741114084e+00 , 5.40104621793262e+00 , 1.31627480646442e+00 , 2.41343034366284e+00 , 3.11567914999535e+00 , 3.90086651034176e+00 , 2.22085290398016e+00 , 2.67829022316575e+00 , 2.95223463727300e+00 , 3.34337409766356e+00 ) ( -5.60843111606338e-03 , 1.12583138090471e-02 , 1.68357668480079e-02 , 1.87871810204228e-02 , -1.11509975018142e-02 , 4.96532034592246e-03 , 1.26856803068378e-02 , 1.77306125297571e-02 , -1.61369024574342e-02 , -1.17287330743696e-02 , -3.97667165972031e-03 , 5.77284958152370e-03 , -1.32835970603912e-02 , -9.12186140048792e-03 , -5.98634736812786e-03 , -1.09632452049312e-03 ) 3.78105088301569e-01 + 7 ( 2.98843276398744e+00 , 4.43277362483451e+00 , 5.20096598215456e+00 , 6.21413473649645e+00 , 2.47971835574389e+00 , 3.84009332258054e+00 , 4.58780406792093e+00 , 5.39902438402581e+00 , 1.31811662219982e+00 , 2.42066789068249e+00 , 3.11707520826167e+00 , 3.89692854958901e+00 , 2.22379944065945e+00 , 2.68616059173228e+00 , 2.95022670924909e+00 , 3.33782534397885e+00 ) ( -5.58418350392305e-03 , 1.13204634820250e-02 , 1.68471093234050e-02 , 1.88070063165611e-02 , -1.11567058554382e-02 , 5.03094217833919e-03 , 1.26928382670779e-02 , 1.77248424341677e-02 , -1.61487389919253e-02 , -1.16967256674628e-02 , -3.99547330134301e-03 , 5.69688275344288e-03 , -1.32919546974225e-02 , -9.07211334097645e-03 , -6.04665602071449e-03 , -1.20257089380199e-03 ) 3.78284907038721e-01 + 8 ( 2.99305095207488e+00 , 4.44255706235088e+00 , 5.20390279809292e+00 , 6.20945090058357e+00 , 2.48277685515950e+00 , 3.84981382800082e+00 , 4.59135934528309e+00 , 5.39695380947607e+00 , 1.32170353603877e+00 , 2.42978572120870e+00 , 3.11883162757640e+00 , 3.89171382389852e+00 , 2.22577247713240e+00 , 2.69489401022899e+00 , 2.94805450424125e+00 , 3.33220883830515e+00 ) ( -5.56820917188656e-03 , 1.13885155086110e-02 , 1.68595280943234e-02 , 1.88295545631365e-02 , -1.11650126057927e-02 , 5.11152770881174e-03 , 1.27043773423435e-02 , 1.77194261760565e-02 , -1.61635185301110e-02 , -1.16514770992267e-02 , -4.01376337810813e-03 , 5.60281550764459e-03 , -1.33110285193646e-02 , -9.01681060097791e-03 , -6.11297722489409e-03 , -1.31358022313040e-03 ) 3.78500459323722e-01 + 9 ( 2.99727803942290e+00 , 4.45276689013810e+00 , 5.20671940505602e+00 , 6.20418843028865e+00 , 2.48582792212175e+00 , 3.86044838531630e+00 , 4.59519142343736e+00 , 5.39478097767364e+00 , 1.32677703129530e+00 , 2.44021023618222e+00 , 3.12073277452649e+00 , 3.88545705730016e+00 , 2.22673027068734e+00 , 2.70403228023088e+00 , 2.94572999605854e+00 , 3.32665870427579e+00 ) ( -5.55846922797675e-03 , 1.14605208116932e-02 , 1.68723226148458e-02 , 1.88538732077974e-02 , -1.11751436040917e-02 , 5.20218321479418e-03 , 1.27185877225548e-02 , 1.77145300273766e-02 , -1.61806180971707e-02 , -1.15957536326590e-02 , -4.03166013252892e-03 , 5.49565596389940e-03 , -1.33392618858248e-02 , -8.95847435071736e-03 , -6.18265892101870e-03 , -1.42505162821923e-03 ) 3.78746600035240e-01 + 10 ( 3.00113590362578e+00 , 4.46295283642265e+00 , 5.20913451147704e+00 , 6.19856492398371e+00 , 2.48872700419815e+00 , 3.87127405646959e+00 , 4.59883180778555e+00 , 5.39241395065204e+00 , 1.33297408012915e+00 , 2.45129095466347e+00 , 3.12259990731229e+00 , 3.87852252742574e+00 , 2.22673463298190e+00 , 2.71311302772409e+00 , 2.94327377801210e+00 , 3.32129591628587e+00 ) ( -5.55224417034228e-03 , 1.15342512231714e-02 , 1.68848695700858e-02 , 1.88791062739624e-02 , -1.11863975631308e-02 , 5.29683799008538e-03 , 1.27332368505308e-02 , 1.77102817911029e-02 , -1.61993578790013e-02 , -1.15331925411162e-02 , -4.04888243585471e-03 , 5.38197720759974e-03 , -1.33744234726094e-02 , -8.89981537283595e-03 , -6.25302646254240e-03 , -1.53289195744994e-03 ) 3.79019107024581e-01 + 11 ( 3.00470125503232e+00 , 4.47265711228424e+00 , 5.21089460531976e+00 , 6.19282083273147e+00 , 2.49134008905727e+00 , 3.88151734630328e+00 , 4.60179016418754e+00 , 5.38973566951884e+00 , 1.33985118526983e+00 , 2.46233295679202e+00 , 3.12429892039402e+00 , 3.87136030320866e+00 , 2.22594006156255e+00 , 2.72169287069741e+00 , 2.94071248075728e+00 , 3.31622273015255e+00 ) ( -5.54632287865549e-03 , 1.16073489553701e-02 , 1.68966879651642e-02 , 1.89045283462007e-02 , -1.11981583558499e-02 , 5.38873432377074e-03 , 1.27458325711537e-02 , 1.77067581962933e-02 , -1.62190359535014e-02 , -1.14681548196382e-02 , -4.06477383520721e-03 , 5.26930541316280e-03 , -1.34137735934670e-02 , -8.84358548360923e-03 , -6.32152819384059e-03 , -1.63341748079868e-03 ) 3.79314492509373e-01 + 12 ( 3.00809583960727e+00 , 4.48144568626711e+00 , 5.21179795363804e+00 , 6.18720282692826e+00 , 2.49355503433962e+00 , 3.89041360016790e+00 , 4.60360319945111e+00 , 5.38662146987011e+00 , 1.34691612073454e+00 , 2.47263280504502e+00 , 3.12573989584620e+00 , 3.86445347605522e+00 , 2.22457351036754e+00 , 2.72936720504478e+00 , 2.93807666839465e+00 , 3.31151936870328e+00 ) ( -5.53721626627702e-03 , 1.16774905538055e-02 , 1.69074760237742e-02 , 1.89295470404025e-02 , -1.12098518644332e-02 , 5.47099418171554e-03 , 1.27539142258515e-02 , 1.77039734246792e-02 , -1.62389653913332e-02 , -1.14054942027861e-02 , -4.07841190467654e-03 , 5.16538673979658e-03 , -1.34542775132534e-02 , -8.79243550280625e-03 , -6.38585394807292e-03 , -1.72351102546992e-03 ) 3.79629555570475e-01 + 13 ( 3.01147358120148e+00 , 4.48893928221114e+00 , 5.21171292478083e+00 , 6.18194650071545e+00 , 2.49529420875273e+00 , 3.89726774762925e+00 , 4.60388154120812e+00 , 5.38295779152011e+00 , 1.35366684257626e+00 , 2.48151732635576e+00 , 3.12686979147126e+00 , 3.85826315105735e+00 , 2.22290718080169e+00 , 2.73578615457354e+00 , 2.93539988695624e+00 , 3.30724327382593e+00 ) ( -5.52138817294984e-03 , 1.17425495712558e-02 , 1.69171191441226e-02 , 1.89536788043514e-02 , -1.12208703473856e-02 , 5.53719445567561e-03 , 1.27553319575538e-02 , 1.77018696725139e-02 , -1.62585085954183e-02 , -1.13502429726935e-02 , -4.08878426855555e-03 , 5.07741732638636e-03 , -1.34928430954787e-02 , -8.74878890522558e-03 , -6.44401748565672e-03 , -1.80072599434109e-03 ) 3.79960806960900e-01 + 14 ( 3.01500498375669e+00 , 4.49484105634166e+00 , 5.21058888431015e+00 , 6.17725979186124e+00 , 2.49652507991581e+00 , 3.90150978145652e+00 , 4.60234863267193e+00 , 5.37865915172911e+00 , 1.35963468852382e+00 , 2.48838344234272e+00 , 3.12766033461501e+00 , 3.85317752085478e+00 , 2.22122742528990e+00 , 2.74066674500144e+00 , 2.93271867756587e+00 , 3.30343100749719e+00 ) ( -5.49549732658235e-03 , 1.18007441995238e-02 , 1.69256728810072e-02 , 1.89765088165145e-02 , -1.12304979159479e-02 , 5.58188833372983e-03 , 1.27484793022279e-02 , 1.77003118136450e-02 , -1.62771022163553e-02 , -1.13072324023837e-02 , -4.09500221458595e-03 , 5.01132421291456e-03 , -1.35265575665557e-02 , -8.71473341395976e-03 , -6.49440390970358e-03 , -1.86333145710300e-03 ) 3.80303913133154e-01 + 15 ( 3.01885935156514e+00 , 4.49895836137591e+00 , 5.20845880475518e+00 , 6.17330862037168e+00 , 2.49726571449010e+00 , 3.90273958741594e+00 , 4.59886715933612e+00 , 5.37368145671421e+00 , 1.36442685860736e+00 , 2.49273626189266e+00 , 3.12809348128601e+00 , 3.84947011817928e+00 , 2.21980329418561e+00 , 2.74380165821453e+00 , 2.93007263646310e+00 , 3.30010253663009e+00 ) ( -5.45664327201426e-03 , 1.18507598198550e-02 , 1.69333270283853e-02 , 1.89976486913772e-02 , -1.12378675646792e-02 , 5.60103026331286e-03 , 1.27324557178694e-02 , 1.76990895578171e-02 , -1.62942676677129e-02 , -1.12806824573500e-02 , -4.09652022619895e-03 , 4.97117341431712e-03 , -1.35529004613194e-02 , -8.69192881902856e-03 , -6.53579294296637e-03 , -1.91029892090598e-03 ) 3.80653281302327e-01 + 16 ( 3.02318574258621e+00 , 4.50121671756992e+00 , 5.20543347977050e+00 , 6.17020596722025e+00 , 2.49758367079577e+00 , 3.90075791036053e+00 , 4.59345084633747e+00 , 5.36803107369289e+00 , 1.36776218076375e+00 , 2.49422221714921e+00 , 3.12814676412765e+00 , 3.84727076152845e+00 , 2.21885835301271e+00 , 2.74506502292299e+00 , 2.92750329352306e+00 , 3.29726720556305e+00 ) ( -5.40260774968335e-03 , 1.18918394007310e-02 , 1.69403563719583e-02 , 1.90167057097929e-02 , -1.12419666462581e-02 , 5.59228671213132e-03 , 1.27071500721839e-02 , 1.76979317986111e-02 , -1.63096075124309e-02 , -1.12738072071936e-02 , -4.09333242395765e-03 , 4.95876082366399e-03 , -1.35699155636684e-02 , -8.68152857793866e-03 , -6.56737454540186e-03 , -1.94123960822893e-03 ) 3.81001871200905e-01 + 17 ( 3.02809415739285e+00 , 4.50166506152248e+00 , 5.20168811935516e+00 , 6.16800533426867e+00 , 2.49758857966083e+00 , 3.89558236026613e+00 , 4.58626174942138e+00 , 5.36177010663164e+00 , 1.36949463576574e+00 , 2.49265415207740e+00 , 3.12778059657973e+00 , 3.84655116139501e+00 , 2.21854897882363e+00 , 2.74441563391359e+00 , 2.92505081172337e+00 , 3.29493032182962e+00 ) ( -5.33207795196924e-03 , 1.19238375489492e-02 , 1.69470627880117e-02 , 1.90332731835913e-02 , -1.12416911790806e-02 , 5.55523293589804e-03 , 1.26732473351448e-02 , 1.76965367621060e-02 , -1.63227936073129e-02 , -1.12884863405751e-02 , -4.08612201281463e-03 , 4.97341853341229e-03 , -1.35763317146644e-02 , -8.68411432143570e-03 , -6.58877217369707e-03 , -1.95630819012991e-03 ) 3.81341269928444e-01 + 18 ( 3.03363892711023e+00 , 4.50047208617566e+00 , 5.19744285848972e+00 , 6.16669911803858e+00 , 2.49741999767105e+00 , 3.88744865236222e+00 , 4.57759477250720e+00 , 5.35501860480364e+00 , 1.36962096539415e+00 , 2.48802587309199e+00 , 3.12692927012681e+00 , 3.84712592465320e+00 , 2.21895140200526e+00 , 2.74189783522437e+00 , 2.92274822912038e+00 , 3.29309909620042e+00 ) ( -5.24483234153983e-03 , 1.19472351653105e-02 , 1.69537131712506e-02 , 1.90469452579835e-02 , -1.12359373167835e-02 , 5.49144095261838e-03 , 1.26321668651098e-02 , 1.76946183373094e-02 , -1.63335559224151e-02 , -1.13250482243768e-02 , -4.07634438292505e-03 , 5.01204954472087e-03 , -1.35716288071488e-02 , -8.69964479575904e-03 , -6.60008084859376e-03 , -1.95609218183908e-03 ) 3.81662024495540e-01 + 19 ( 3.03980638930293e+00 , 4.49791396578241e+00 , 5.19293926757803e+00 , 6.16622192484240e+00 , 2.49723246067585e+00 , 3.87679761700838e+00 , 4.56785187541893e+00 , 5.34795393898199e+00 , 1.36827142971955e+00 , 2.48051460702728e+00 , 3.12549701705262e+00 , 3.84866874600845e+00 , 2.22005841855173e+00 , 2.73764013697229e+00 , 2.92061396044736e+00 , 3.29178674652055e+00 ) ( -5.14186564988213e-03 , 1.19631117675662e-02 , 1.69604787021299e-02 , 1.90573528714360e-02 , -1.12237144451809e-02 , 5.40445708266560e-03 , 1.25859420474585e-02 , 1.76919640583354e-02 , -1.63416796379246e-02 , -1.13821966907384e-02 , -4.06622804413393e-03 , 5.06938813592078e-03 , -1.35560499548848e-02 , -8.72742264831989e-03 , -6.60191447726332e-03 , -1.94150498787041e-03 ) 3.81954197395723e-01 + 20 ( 3.04650863884945e+00 , 4.49435411437724e+00 , 5.18841527762764e+00 , 6.16645837340779e+00 , 2.49717925480425e+00 , 3.86424836018692e+00 , 4.55750848697779e+00 , 5.34080670765490e+00 , 1.36568581546352e+00 , 2.47047097097987e+00 , 3.12336009885461e+00 , 3.85074280281206e+00 , 2.22178524357949e+00 , 2.73185149414085e+00 , 2.91864419906098e+00 , 3.29101397431997e+00 ) ( -5.02542974750439e-03 , 1.19730728164444e-02 , 1.69673824742426e-02 , 1.90642123537368e-02 , -1.12042672914772e-02 , 5.29965572263668e-03 , 1.25370495916030e-02 , 1.76884949726336e-02 , -1.63470133927038e-02 , -1.14570941759426e-02 , -4.05868153495143e-03 , 5.13846947912402e-03 , -1.35305636185385e-02 , -8.76608365877139e-03 , -6.59544443572543e-03 , -1.91369494935530e-03 ) 3.82208090906906e-01 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat index 03221b542..1a12c5a95 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.hr.hist.dat @@ -1,10 +1,10 @@ # one p(one ) - 2.00000000000000 0.09030392972369 - 4.00000000000000 0.19798865120683 - 6.00000000000000 0.14853769410307 - 8.00000000000000 0.04657771648442 - 10.00000000000000 0.00481731601539 - 12.00000000000000 0.00011856440761 + 2.00000000000000 0.09030392971801 + 4.00000000000000 0.19798865118667 + 6.00000000000000 0.14853769410362 + 8.00000000000000 0.04657771650417 + 10.00000000000000 0.00481731602070 + 12.00000000000000 0.00011856440783 14.00000000000000 0.00000057948069 16.00000000000000 0.00000000051553 18.00000000000000 0.00000000000008 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out index 852f8a3ae..c7b2aef1d 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -124,33 +120,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - distancePairs colvar component: -colvars: - histogramRestraint colvar bias implementation: -colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 3.04651 , 4.49435 , 5.18842 , 6.16646 , 2.49718 , 3.86425 , 4.55751 , 5.34081 , 1.36569 , 2.47047 , 3.12336 , 3.85074 , 2.22179 , 2.73185 , 2.91864 , 3.29101 ) colvars: Restarting histogramrestraint bias "hr" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped index 7bec45097..0ecc9386e 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.03953158571266e+00 , 4.51209497787138e+00 , 5.09894673253801e+00 , 6.16578599788259e+00 , 2.46957015768712e+00 , 3.86055335003907e+00 , 4.47595360314062e+00 , 5.36499714872809e+00 , 1.33944926913138e+00 , 2.47813660022930e+00 , 3.01476283614106e+00 , 3.86080601681174e+00 , 2.22155937137345e+00 , 2.76529935955117e+00 , 2.86078736612033e+00 , 3.36901381742548e+00 ) + x ( 3.03953158726547e+00 , 4.51209497961311e+00 , 5.09894673434180e+00 , 6.16578599928733e+00 , 2.46957015850689e+00 , 3.86055335115988e+00 , 4.47595360418285e+00 , 5.36499714940424e+00 , 1.33944926924420e+00 , 2.47813660080028e+00 , 3.01476283660714e+00 , 3.86080601707240e+00 , 2.22155937101033e+00 , 2.76529935945446e+00 , 2.86078736535835e+00 , 3.36901381632414e+00 ) } histogramrestraint { diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj index c3e1e1b2e..2c3a7993e 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hr - 20 ( 3.04650863844542e+00 , 4.49435411373106e+00 , 5.18841527687423e+00 , 6.16645837246753e+00 , 2.49717925475228e+00 , 3.86424835988508e+00 , 4.55750848670402e+00 , 5.34080670712767e+00 , 1.36568581550375e+00 , 2.47047097074510e+00 , 3.12336009876006e+00 , 3.85074280234761e+00 , 2.22178524374518e+00 , 2.73185149420872e+00 , 2.91864419945045e+00 , 3.29101397434784e+00 ) ( -5.02542975155399e-03 , 1.19730728144022e-02 , 1.69673824743050e-02 , 1.90642123572900e-02 , -1.12042672923401e-02 , 5.29965572198335e-03 , 1.25370495930876e-02 , 1.76884949742769e-02 , -1.63470133946114e-02 , -1.14570941785658e-02 , -4.05868153495528e-03 , 5.13846947648582e-03 , -1.35305636182661e-02 , -8.76608365782640e-03 , -6.59544443037070e-03 , -1.91369494736973e-03 ) 3.82208090962526e-01 - 21 ( 3.05358451385306e+00 , 4.49021607823814e+00 , 5.18408103497026e+00 , 6.16725452583661e+00 , 2.49739586880410e+00 , 3.85055803143711e+00 , 4.54707448734276e+00 , 5.33385181822192e+00 , 1.36217943433076e+00 , 2.45839729703337e+00 , 3.12037538151779e+00 , 3.85284349899673e+00 , 2.22398282808873e+00 , 2.72481510491786e+00 , 2.91680739909571e+00 , 3.29080759711060e+00 ) ( -4.89897222682100e-03 , 1.19791313892808e-02 , 1.69742633770304e-02 , 1.90673755298261e-02 , -1.11771991099852e-02 , 5.18394936419736e-03 , 1.24881958022913e-02 , 1.76843138080640e-02 , -1.63494863620738e-02 , -1.15455916073648e-02 , -4.05710100270291e-03 , 5.21127645896876e-03 , -1.34967807331177e-02 , -8.81361359377299e-03 , -6.58240414263767e-03 , -1.87397588595395e-03 ) 3.82415073675832e-01 - 22 ( 3.06080810157937e+00 , 4.48595132736801e+00 , 5.18009807716127e+00 , 6.16843183886407e+00 , 2.49798391776076e+00 , 3.83656952216095e+00 , 4.53705219467757e+00 , 5.32739339712202e+00 , 1.35810535034214e+00 , 2.44491630836693e+00 , 3.11639519244157e+00 , 3.85445062126223e+00 , 2.22645629784030e+00 , 2.71687952046412e+00 , 2.91504287509639e+00 , 3.29119674282126e+00 ) ( -4.76696535704344e-03 , 1.19835479428934e-02 , 1.69807629788419e-02 , 1.90668703443345e-02 , -1.11425894939780e-02 , 5.06534159075236e-03 , 1.24420691537260e-02 , 1.76797272308617e-02 , -1.63491285200756e-02 , -1.16425743101174e-02 , -4.06508397900589e-03 , 5.27951326523871e-03 , -1.34568327359927e-02 , -8.86739837013206e-03 , -6.56503633186065e-03 , -1.82377839047625e-03 ) 3.82568429560664e-01 - 23 ( 3.06790413948872e+00 , 4.48200450053951e+00 , 5.17656382698377e+00 , 6.16980236968489e+00 , 2.49899682551938e+00 , 3.82315020141056e+00 , 4.52789434427541e+00 , 5.32174323321216e+00 , 1.35381897118564e+00 , 2.43073302835376e+00 , 3.11128737624436e+00 , 3.85508563435849e+00 , 2.22898609581243e+00 , 2.70844682608125e+00 , 2.91326470584562e+00 , 3.29220745968855e+00 ) ( -4.63463283787862e-03 , 1.19886381009935e-02 , 1.69863384513460e-02 , 1.90629238582122e-02 , -1.11010960470692e-02 , 4.95233310116970e-03 , 1.24010752264571e-02 , 1.76752321496742e-02 , -1.63460880185607e-02 , -1.17423776658788e-02 , -4.08607045622158e-03 , 5.33543540458643e-03 , -1.34132176175144e-02 , -8.92431330337852e-03 , -6.54597178283978e-03 , -1.76461824947690e-03 ) 3.82664136179363e-01 - 24 ( 3.07456896189780e+00 , 4.47877932702159e+00 , 5.17350292321320e+00 , 6.17118403121453e+00 , 2.50042929754554e+00 , 3.81112677805404e+00 , 4.51996576437108e+00 , 5.31719422066849e+00 , 1.34964937408689e+00 , 2.41659320666385e+00 , 3.10495847659781e+00 , 3.85436853999778e+00 , 2.23134971001298e+00 , 2.69995765874844e+00 , 2.91137078731589e+00 , 3.29385683034138e+00 ) ( -4.50759628033739e-03 , 1.19965650752233e-02 , 1.69902999511294e-02 , 1.90559636503187e-02 , -1.10540221258452e-02 , 4.85322332152704e-03 , 1.23670789601672e-02 , 1.76714640602726e-02 , -1.63406409728297e-02 , -1.18392197142181e-02 , -4.12294937353427e-03 , 5.37265037296092e-03 , -1.33686231651157e-02 , -8.98085589401957e-03 , -6.52804678895842e-03 , -1.69807764903222e-03 ) 3.82701469869588e-01 - 25 ( 3.08049503044240e+00 , 4.47660862577235e+00 , 5.17086621112506e+00 , 6.17241473688239e+00 , 2.50221287162265e+00 , 3.80122270018355e+00 , 4.51351282021268e+00 , 5.31399204853792e+00 , 1.34587887726960e+00 , 2.40324136970565e+00 , 3.09737705582823e+00 , 3.85206778233211e+00 , 2.23334232029070e+00 , 2.69187293457495e+00 , 2.90925556253781e+00 , 3.29614768342963e+00 ) ( -4.39147561366562e-03 , 1.20091384936196e-02 , 1.69918666389837e-02 , 1.90465983751812e-02 , -1.10033293365613e-02 , 4.77538069587196e-03 , 1.23411865325813e-02 , 1.76691155106009e-02 , -1.63331907134106e-02 , 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4.47627640260616e+00 , 5.16634667844742e+00 , 6.17394349813873e+00 , 2.50627068458191e+00 , 3.78984102049283e+00 , 4.50532543258662e+00 , 5.31222723639859e+00 , 1.34035363315651e+00 , 2.38163676655146e+00 , 3.07875275662228e+00 , 3.84272979858715e+00 , 2.23558983282953e+00 , 2.67873088564368e+00 , 2.90400432206480e+00 , 3.30257333791634e+00 ) ( -4.21205605492461e-03 , 1.20527080280103e-02 , 1.69846407370455e-02 , 1.90237651466753e-02 , -1.09017840062163e-02 , 4.70442293946673e-03 , 1.23135748682848e-02 , 1.76711728222598e-02 , -1.63144400090597e-02 , -1.20603163406075e-02 , -4.34220656326890e-03 , 5.34122227042115e-03 , -1.32547619860300e-02 , -9.11150666597606e-03 , -6.50795643020656e-03 , -1.47076879228184e-03 ) 3.82510078913831e-01 - 28 ( 3.09123422921692e+00 , 4.47825901442763e+00 , 5.16409003425862e+00 , 6.17410853348936e+00 , 2.50815760679602e+00 , 3.78888026398353e+00 , 4.50338659978164e+00 , 5.31372412141838e+00 , 1.33882620806712e+00 , 2.37452389462613e+00 , 3.06809741606238e+00 , 3.83619894758952e+00 , 2.23566954506562e+00 , 2.67449273825598e+00 , 2.90075730703912e+00 , 3.30661925645080e+00 ) ( -4.15653937678158e-03 , 1.20842556425878e-02 , 1.69744443916726e-02 , 1.90120465148651e-02 , -1.08572245330596e-02 , 4.71610016144383e-03 , 1.23094771136140e-02 , 1.76764515744409e-02 , -1.63044061247141e-02 , -1.20976332906350e-02 , -4.44916678162194e-03 , 5.28592246110960e-03 , -1.32304641404146e-02 , -9.13080845840673e-03 , -6.51952625382809e-03 , -1.39145151027727e-03 ) 3.82377079925851e-01 - 29 ( 3.09190509421309e+00 , 4.48157956404059e+00 , 5.16155211354150e+00 , 6.17386201037197e+00 , 2.50965699766396e+00 , 3.79104075049304e+00 , 4.50254293446649e+00 , 5.31667718768969e+00 , 1.33813889021320e+00 , 2.37041835800957e+00 , 3.05696001570915e+00 , 3.82906376008603e+00 , 2.23504287481449e+00 , 2.67224775269306e+00 , 2.89708163089409e+00 , 3.31113228156639e+00 ) ( -4.12697760466075e-03 , 1.21214889662362e-02 , 1.69591787208369e-02 , 1.90013176269185e-02 , -1.08211850017392e-02 , 4.75819485382931e-03 , 1.23089551817022e-02 , 1.76848031284823e-02 , -1.62948248999482e-02 , -1.21127058785823e-02 , -4.56838460845013e-03 , 5.21600003410379e-03 , -1.32152197145269e-02 , -9.13363621823788e-03 , -6.54228804046270e-03 , -1.31315219908283e-03 ) 3.82231264856908e-01 - 30 ( 3.09104253687721e+00 , 4.48603307826026e+00 , 5.15853060452976e+00 , 6.17324867828692e+00 , 2.51055204362215e+00 , 3.79602095739377e+00 , 4.50242469586112e+00 , 5.32087138875897e+00 , 1.33819822704847e+00 , 2.36953676664519e+00 , 3.04574554871881e+00 , 3.82196513028943e+00 , 2.23378273956030e+00 , 2.67220981860937e+00 , 2.89301507576693e+00 , 3.31603007026754e+00 ) ( -4.12399775228976e-03 , 1.21629569237827e-02 , 1.69386135407473e-02 , 1.89924164921859e-02 , -1.07967128795658e-02 , 4.82686270427262e-03 , 1.23091825422540e-02 , 1.76961399144551e-02 , -1.62863384458131e-02 , -1.21047856641569e-02 , -4.69525042105293e-03 , 5.13908728020596e-03 , -1.32094206825129e-02 , -9.11853167377214e-03 , -6.57644050305645e-03 , -1.23738605053167e-03 ) 3.82087235611880e-01 - 31 ( 3.08872930034045e+00 , 4.49132288916588e+00 , 5.15485959375857e+00 , 6.17234728763030e+00 , 2.51064912969521e+00 , 3.80332415543735e+00 , 4.50261440796340e+00 , 5.32601736250928e+00 , 1.33883231975609e+00 , 2.37192384271979e+00 , 3.03490626617957e+00 , 3.81560419549194e+00 , 2.23201834770136e+00 , 2.67448174873522e+00 , 2.88863286961083e+00 , 3.32122334543885e+00 ) ( -4.14681389844940e-03 , 1.22066593920410e-02 , 1.69127991486588e-02 , 1.89860855706422e-02 , -1.07863857447177e-02 , 4.91617372007565e-03 , 1.23071555309342e-02 , 1.77101930919321e-02 , -1.62795237560133e-02 , -1.20742429299629e-02 , -4.82436126980393e-03 , 5.06384588223362e-03 , -1.32128196421779e-02 , -9.08495906809948e-03 , -6.62146792223792e-03 , -1.16545021409847e-03 ) 3.81959230272477e-01 - 32 ( 3.08512587407585e+00 , 4.49707969992627e+00 , 5.15042982483635e+00 , 6.17125913901907e+00 , 2.50979233827432e+00 , 3.81229855394099e+00 , 4.50268874982513e+00 , 5.33177568452012e+00 , 1.33980944632461e+00 , 2.37745103512446e+00 , 3.02491187404977e+00 , 3.81067490080305e+00 , 2.22992148435915e+00 , 2.67904816565005e+00 , 2.88404450587321e+00 , 3.32662115516356e+00 ) ( -4.19334740738677e-03 , 1.22501856597967e-02 , 1.68820961190666e-02 , 1.89829372788785e-02 , -1.07921188400013e-02 , 5.01864637029710e-03 , 1.23000120215299e-02 , 1.77265599742085e-02 , -1.62748657233307e-02 , -1.20225135633812e-02 , -4.94989687037609e-03 , 4.99914062134037e-03 , -1.32246045788317e-02 , -9.03332860324969e-03 , -6.67616648316557e-03 , -1.09835120335049e-03 ) 3.81860258406506e-01 - 33 ( 3.08045463612035e+00 , 4.50288519574339e+00 , 5.14520389945312e+00 , 6.17009473437244e+00 , 2.50787564665153e+00 , 3.82219055462722e+00 , 4.50226213985759e+00 , 5.33778558315697e+00 , 1.34086920751867e+00 , 2.38582693260688e+00 , 3.01621801871649e+00 , 3.80779720585457e+00 , 2.22768857418667e+00 , 2.68577746739276e+00 , 2.87938997999308e+00 , 3.33213575320596e+00 ) ( -4.26045165351063e-03 , 1.22908700845057e-02 , 1.68471856050619e-02 , 1.89834261058958e-02 , -1.08150192814251e-02 , 5.12591079306563e-03 , 1.22853421660068e-02 , 1.77447558708082e-02 , -1.62727379942027e-02 , -1.19520165190434e-02 , -5.06601412276133e-03 , 4.95319659434038e-03 , -1.32435252222438e-02 , -8.96495734999776e-03 , -6.73869467996829e-03 , -1.03675678531612e-03 ) 3.81801393250440e-01 - 34 ( 3.07497912028674e+00 , 4.50829914380588e+00 , 5.13922512638278e+00 , 6.16896017294668e+00 , 2.50485309322197e+00 , 3.83220702719942e+00 , 4.50102851686806e+00 , 5.34369562943610e+00 , 1.34176277954839e+00 , 2.39661859710098e+00 , 3.00923587723178e+00 , 3.80745750891794e+00 , 2.22552073001822e+00 , 2.69443239824280e+00 , 2.87483587690196e+00 , 3.33768680861078e+00 ) ( -4.34421640334799e-03 , 1.23259510194731e-02 , 1.68090579813687e-02 , 1.89878261610829e-02 , -1.08552901312531e-02 , 5.22942992226076e-03 , 1.22614658996729e-02 , 1.77642609680764e-02 , -1.62733896680575e-02 , -1.18660435429885e-02 , -5.16722789914439e-03 , 4.93281774262076e-03 , -1.32680512200940e-02 , -8.88197829739069e-03 , -6.80664460048118e-03 , -9.80979854271153e-04 ) 3.81791215770808e-01 - 35 ( 3.06898072833861e+00 , 4.51288823770881e+00 , 5.13261897921919e+00 , 6.16794500499526e+00 , 2.50074653237299e+00 , 3.84158061480535e+00 , 4.49879685463616e+00 , 5.34919353390091e+00 , 1.34229502305346e+00 , 2.40928100895182e+00 , 3.00430451680425e+00 , 3.80996140411077e+00 , 2.22360417042348e+00 , 2.70468750491233e+00 , 2.87057086954244e+00 , 3.34320509110129e+00 ) ( -4.44031491071235e-03 , 1.23527234681521e-02 , 1.67689785292895e-02 , 1.89962130882339e-02 , -1.09121854118585e-02 , 5.32120212173631e-03 , 1.22276539257989e-02 , 1.77845576873594e-02 , -1.62769366926278e-02 , -1.17686217470126e-02 , -5.24875745576491e-03 , 4.94273803932348e-03 , -1.32965365848290e-02 , -8.78720894171396e-03 , -6.87713385744937e-03 , -9.30987598810157e-04 ) 3.81835385504166e-01 - 36 ( 3.06273532842122e+00 , 4.51625453668437e+00 , 5.12558687876965e+00 , 6.16711285462378e+00 , 2.49564989962145e+00 , 3.84963128763360e+00 , 4.49551609079525e+00 , 5.35403199606795e+00 , 1.34235952057393e+00 , 2.42319130947787e+00 , 3.00166756440291e+00 , 3.81540250051618e+00 , 2.22209336160822e+00 , 2.71615108200234e+00 , 2.86679976404971e+00 , 3.34863558090078e+00 ) ( -4.54435368066141e-03 , 1.23686804950677e-02 , 1.67284311224198e-02 , 1.90084516119658e-02 , -1.09840196310911e-02 , 5.39437685684171e-03 , 1.21842739531386e-02 , 1.78051583090107e-02 , -1.62833596534709e-02 , -1.16643470067951e-02 , -5.30682059345081e-03 , 4.98516473295461e-03 , -1.33273660427321e-02 , -8.68399148739366e-03 , -6.94692018851069e-03 , -8.86427786439946e-04 ) 3.81936327036083e-01 - 37 ( 3.05649192132167e+00 , 4.51806131059166e+00 , 5.11839243202510e+00 , 6.16649586507377e+00 , 2.48972865327600e+00 , 3.85581806466917e+00 , 4.49128596625538e+00 , 5.35804830483488e+00 , 1.34195825281763e+00 , 2.43768478118170e+00 , 3.00145507450914e+00 , 3.82364960560225e+00 , 2.22109872744306e+00 , 2.72838935969239e+00 , 2.86373525953246e+00 , 3.35394019899047e+00 ) ( -4.65218982014911e-03 , 1.23716418558672e-02 , 1.66890397155335e-02 , 1.90241913089743e-02 , -1.10682357362770e-02 , 5.44373642248271e-03 , 1.21328465988092e-02 , 1.78256268057558e-02 , -1.62925100639911e-02 , -1.15581857866223e-02 , -5.33886828047797e-03 , 5.05955490104775e-03 , -1.33590658100595e-02 , -8.57601333848149e-03 , -7.01254065783080e-03 , -8.46660146239399e-04 ) 3.82093031722223e-01 - 38 ( 3.05045519889590e+00 , 4.51805473611829e+00 , 5.11134114887472e+00 , 6.16609340466301e+00 , 2.48321341701307e+00 , 3.85977678463866e+00 , 4.48635217324219e+00 , 5.36117618444632e+00 , 1.34120085885188e+00 , 2.45209075172033e+00 , 3.00367159434843e+00 , 3.83435311397414e+00 , 2.22068007522442e+00 , 2.74095124971729e+00 , 2.86158715760799e+00 , 3.35910007198241e+00 ) ( -4.76019163320950e-03 , 1.23598714041820e-02 , 1.66524680402616e-02 , 1.90428744709146e-02 , -1.11615338118528e-02 , 5.46602270063782e-03 , 1.20759997181952e-02 , 1.78455990056507e-02 , -1.63041248954833e-02 , -1.14552422088381e-02 , -5.34375549496949e-03 , 5.16264172534908e-03 , -1.33903719338111e-02 , -8.46711508398639e-03 , -7.07047588479804e-03 , -8.10789012685766e-04 ) 3.82300990443223e-01 - 39 ( 3.04477330521684e+00 , 4.51608052262827e+00 , 5.10475536253321e+00 , 6.16587487663191e+00 , 2.47638766200614e+00 , 3.86134206537838e+00 , 4.48108638301749e+00 , 5.36344937417303e+00 , 1.34028312443992e+00 , 2.46576763054109e+00 , 3.00819152091531e+00 , 3.84697007374176e+00 , 2.22084607834437e+00 , 2.75339260865446e+00 , 2.86054956607522e+00 , 3.36411702305049e+00 ) ( -4.86543044142400e-03 , 1.23321843370416e-02 , 1.66202988292410e-02 , 1.90637594104161e-02 , -1.12600574805245e-02 , 5.46010858659612e-03 , 1.20173150916460e-02 , 1.78648032651105e-02 , -1.63178447979581e-02 , -1.13604904210382e-02 , -5.32184447669693e-03 , 5.28870221435157e-03 , -1.34202591847899e-02 , -8.36109247803980e-03 , -7.11733590781375e-03 , -7.77701446405796e-04 ) 3.82552280895823e-01 - 40 ( 3.03953158571266e+00 , 4.51209497787138e+00 , 5.09894673253801e+00 , 6.16578599788259e+00 , 2.46957015768712e+00 , 3.86055335003907e+00 , 4.47595360314062e+00 , 5.36499714872809e+00 , 1.33944926913138e+00 , 2.47813660022930e+00 , 3.01476283614106e+00 , 3.86080601681174e+00 , 2.22155937137345e+00 , 2.76529935955117e+00 , 2.86078736612033e+00 , 3.36901381742548e+00 ) ( -4.96580059531963e-03 , 1.22880424119538e-02 , 1.65938976533907e-02 , 1.90859603276296e-02 , -1.13596279919568e-02 , 5.42702340653616e-03 , 1.19610688381882e-02 , 1.78830800540778e-02 , -1.63332290150278e-02 , -1.12784800774510e-02 , -5.27503313674526e-03 , 5.43003604266082e-03 , -1.34479399632883e-02 , -8.26149951627528e-03 , -7.15005910784782e-03 , -7.46119889758067e-04 ) 3.82835834419373e-01 + 20 ( 3.04650863884945e+00 , 4.49435411437724e+00 , 5.18841527762764e+00 , 6.16645837340779e+00 , 2.49717925480425e+00 , 3.86424836018692e+00 , 4.55750848697779e+00 , 5.34080670765490e+00 , 1.36568581546352e+00 , 2.47047097097987e+00 , 3.12336009885461e+00 , 3.85074280281206e+00 , 2.22178524357949e+00 , 2.73185149414085e+00 , 2.91864419906098e+00 , 3.29101397431997e+00 ) ( -5.02542974750439e-03 , 1.19730728164444e-02 , 1.69673824742426e-02 , 1.90642123537368e-02 , -1.12042672914772e-02 , 5.29965572263668e-03 , 1.25370495916030e-02 , 1.76884949726336e-02 , -1.63470133927038e-02 , -1.14570941759426e-02 , -4.05868153495143e-03 , 5.13846947912402e-03 , -1.35305636185385e-02 , -8.76608365877139e-03 , -6.59544443572543e-03 , -1.91369494935530e-03 ) 3.82208090906906e-01 + 21 ( 3.05358451430521e+00 , 4.49021607894136e+00 , 5.18408103579128e+00 , 6.16725452682985e+00 , 2.49739586887847e+00 , 3.85055803176977e+00 , 4.54707448765203e+00 , 5.33385181877346e+00 , 1.36217943428986e+00 , 2.45839729727885e+00 , 3.12037538162696e+00 , 3.85284349947326e+00 , 2.22398282791541e+00 , 2.72481510484303e+00 , 2.91680739868595e+00 , 3.29080759705819e+00 ) ( -4.89897222229807e-03 , 1.19791313915530e-02 , 1.69742633770421e-02 , 1.90673755260435e-02 , -1.11771991089292e-02 , 5.18394936500707e-03 , 1.24881958008396e-02 , 1.76843138062651e-02 , -1.63494863600467e-02 , -1.15455916046476e-02 , -4.05710100264393e-03 , 5.21127646149069e-03 , -1.34967807334349e-02 , -8.81361359484131e-03 , -6.58240414833905e-03 , -1.87397588842609e-03 ) 3.82415073616570e-01 + 22 ( 3.06080810208345e+00 , 4.48595132812722e+00 , 5.18009807804700e+00 , 6.16843183990917e+00 , 2.49798391786306e+00 , 3.83656952252473e+00 , 4.53705219502262e+00 , 5.32739339769826e+00 , 1.35810535030362e+00 , 2.44491630862121e+00 , 3.11639519256500e+00 , 3.85445062174997e+00 , 2.22645629766064e+00 , 2.71687952037979e+00 , 2.91504287466697e+00 , 3.29119674274122e+00 ) ( -4.76696535200487e-03 , 1.19835479453930e-02 , 1.69807629789190e-02 , 1.90668703403292e-02 , -1.11425894926847e-02 , 5.06534159173061e-03 , 1.24420691523186e-02 , 1.76797272289167e-02 , -1.63491285179391e-02 , -1.16425743073302e-02 , -4.06508397889694e-03 , 5.27951326763638e-03 , -1.34568327363580e-02 , -8.86739837135399e-03 , -6.56503633790696e-03 , -1.82377839347999e-03 ) 3.82568429497945e-01 + 23 ( 3.06790414004814e+00 , 4.48200450135334e+00 , 5.17656382793119e+00 , 6.16980237078029e+00 , 2.49899682565506e+00 , 3.82315020180593e+00 , 4.52789434465689e+00 , 5.32174323381354e+00 , 1.35381897115236e+00 , 2.43073302861496e+00 , 3.11128737638165e+00 , 3.85508563485620e+00 , 2.22898609562760e+00 , 2.70844682598514e+00 , 2.91326470539741e+00 , 3.29220745957774e+00 ) ( -4.63463283228587e-03 , 1.19886381037132e-02 , 1.69863384514790e-02 , 1.90629238539922e-02 , -1.11010960454939e-02 , 4.95233310232833e-03 , 1.24010752251076e-02 , 1.76752321475924e-02 , -1.63460880163246e-02 , -1.17423776630453e-02 , -4.08607045606707e-03 , 5.33543540685033e-03 , -1.34132176179305e-02 , -8.92431330478125e-03 , -6.54597178922480e-03 , -1.76461825305729e-03 ) 3.82664136113375e-01 + 24 ( 3.07456896251547e+00 , 4.47877932788847e+00 , 5.17350292421948e+00 , 6.17118403235812e+00 , 2.50042929771976e+00 , 3.81112677848175e+00 , 4.51996576479011e+00 , 5.31719422129534e+00 , 1.34964937406132e+00 , 2.41659320693017e+00 , 3.10495847674859e+00 , 3.85436854050369e+00 , 2.23134970982392e+00 , 2.69995765863871e+00 , 2.91137078684994e+00 , 3.29385683019661e+00 ) ( -4.50759627415720e-03 , 1.19965650781519e-02 , 1.69902999513099e-02 , 1.90559636458943e-02 , -1.10540221239449e-02 , 4.85322332287748e-03 , 1.23670789588916e-02 , 1.76714640580619e-02 , -1.63406409705032e-02 , -1.18392197113602e-02 , -4.12294937333665e-03 , 5.37265037507770e-03 , -1.33686231655847e-02 , -8.98085589562544e-03 , -6.52804679567177e-03 , -1.69807765323451e-03 ) 3.82701469800512e-01 + 25 ( 3.08049503112063e+00 , 4.47660862669065e+00 , 5.17086621218778e+00 , 6.17241473807144e+00 , 2.50221287184003e+00 , 3.80122270064462e+00 , 4.51351282067087e+00 , 5.31399204919024e+00 , 1.34587887725366e+00 , 2.40324136997555e+00 , 3.09737705599232e+00 , 3.85206778284383e+00 , 2.23334232009805e+00 , 2.69187293445037e+00 , 2.90925556205525e+00 , 3.29614768324761e+00 ) ( -4.39147560687099e-03 , 1.20091384967429e-02 , 1.69918666392056e-02 , 1.90465983705643e-02 , -1.10033293342962e-02 , 4.77538069742523e-03 , 1.23411865313985e-02 , 1.76691155082667e-02 , -1.63331907110018e-02 , -1.19276016500482e-02 , -4.17768182170728e-03 , 5.38679797880718e-03 , -1.33257388623057e-02 , -9.03332249848839e-03 , -6.51408373611267e-03 , -1.62579454590789e-03 ) 3.82683339776474e-01 + 26 ( 3.08539660358762e+00 , 4.47573108499616e+00 , 5.16853739700106e+00 , 6.17336434836052e+00 , 2.50421915077741e+00 , 3.79400439259247e+00 , 4.50864423698743e+00 , 5.31230947973394e+00 , 1.34272952084209e+00 , 2.39138079579576e+00 , 3.08859350101493e+00 , 3.84813653919452e+00 , 2.23479506256020e+00 , 2.68465243778064e+00 , 2.90682401269869e+00 , 3.29906482208583e+00 ) ( -4.29148411013601e-03 , 1.20276418302263e-02 , 1.69902333323270e-02 , 1.90355816605932e-02 , -1.09515770435773e-02 , 4.72457054302800e-03 , 1.23236006618263e-02 , 1.76688416325359e-02 , -1.63242548543774e-02 , -1.20026405094288e-02 , -4.25099682919303e-03 , 5.37602868959405e-03 , -1.32870692584683e-02 , -9.07802146377075e-03 , -6.50666849324502e-03 , -1.54945341877789e-03 ) 3.82616280373843e-01 + 27 ( 3.08903403490314e+00 , 4.47627640362272e+00 , 5.16634667961830e+00 , 6.17394349940788e+00 , 2.50627068489644e+00 , 3.78984102102476e+00 , 4.50532543312949e+00 , 5.31222723709983e+00 , 1.34035363316288e+00 , 2.38163676682551e+00 , 3.07875275681351e+00 , 3.84272979910075e+00 , 2.23558983263006e+00 , 2.67873088548860e+00 , 2.90400432155214e+00 , 3.30257333764965e+00 ) ( -4.21205604684754e-03 , 1.20527080314771e-02 , 1.69846407373501e-02 , 1.90237651417156e-02 , -1.09017840031264e-02 , 4.70442294145814e-03 , 1.23135748673525e-02 , 1.76711728196835e-02 , -1.63144400065064e-02 , -1.20603163377734e-02 , -4.34220656291962e-03 , 5.34122227195625e-03 , -1.32547619866681e-02 , -9.11150666826031e-03 , -6.50795643781969e-03 , -1.47076879862291e-03 ) 3.82510078836494e-01 + 28 ( 3.09123423008446e+00 , 4.47825901549156e+00 , 5.16409003548264e+00 , 6.17410853479198e+00 , 2.50815760716265e+00 , 3.78888026455344e+00 , 4.50338660037037e+00 , 5.31372412214171e+00 , 1.33882620808478e+00 , 2.37452389490195e+00 , 3.06809741626824e+00 , 3.83619894809814e+00 , 2.23566954486208e+00 , 2.67449273808684e+00 , 2.90075730651259e+00 , 3.30661925613651e+00 ) ( -4.15653936805056e-03 , 1.20842556462065e-02 , 1.69744443920294e-02 , 1.90120465097577e-02 , -1.08572245295259e-02 , 4.71610016367071e-03 , 1.23094771128419e-02 , 1.76764515717399e-02 , -1.63044061220960e-02 , -1.20976332878248e-02 , -4.44916678119855e-03 , 5.28592246238156e-03 , -1.32304641411155e-02 , -9.13080846091652e-03 , -6.51952626171290e-03 , -1.39145151742301e-03 ) 3.82377079846062e-01 + 29 ( 3.09190509514426e+00 , 4.48157956515127e+00 , 5.16155211481890e+00 , 6.17386201170314e+00 , 2.50965699808364e+00 , 3.79104075110282e+00 , 4.50254293510334e+00 , 5.31667718843253e+00 , 1.33813889024149e+00 , 2.37041835828804e+00 , 3.05696001593096e+00 , 3.82906376058536e+00 , 2.23504287460586e+00 , 2.67224775251169e+00 , 2.89708163035411e+00 , 3.31113228120092e+00 ) ( -4.12697759527618e-03 , 1.21214889699991e-02 , 1.69591787212609e-02 , 1.90013176216806e-02 , -1.08211849977542e-02 , 4.75819485630298e-03 , 1.23089551811130e-02 , 1.76848031256508e-02 , -1.62948248972696e-02 , -1.21127058757935e-02 , -4.56838460793265e-03 , 5.21600003506868e-03 , -1.32152197152968e-02 , -9.13363622096200e-03 , -6.54228804860898e-03 , -1.31315220707965e-03 ) 3.82231264774811e-01 + 30 ( 3.09104253787141e+00 , 4.48603307941766e+00 , 5.15853060586121e+00 , 6.17324867964149e+00 , 2.51055204409471e+00 , 3.79602095804537e+00 , 4.50242469654790e+00 , 5.32087138951799e+00 , 1.33819822708635e+00 , 2.36953676692819e+00 , 3.04574554895833e+00 , 3.82196513077521e+00 , 2.23378273934522e+00 , 2.67220981841834e+00 , 2.89301507521361e+00 , 3.31603006984730e+00 ) ( -4.12399774225813e-03 , 1.21629569276891e-02 , 1.69386135412590e-02 , 1.89924164868352e-02 , -1.07967128751336e-02 , 4.82686270700478e-03 , 1.23091825418685e-02 , 1.76961399114859e-02 , -1.62863384430780e-02 , -1.21047856613801e-02 , -4.69525042041774e-03 , 5.13908728081744e-03 , -1.32094206833609e-02 , -9.11853167669410e-03 , -6.57644051145824e-03 , -1.23738605942613e-03 ) 3.82087235527624e-01 + 31 ( 3.08872930139670e+00 , 4.49132289037063e+00 , 5.15485959514491e+00 , 6.17234728900319e+00 , 2.51064913021942e+00 , 3.80332415613268e+00 , 4.50261440870123e+00 , 5.32601736328046e+00 , 1.33883231980242e+00 , 2.37192384301024e+00 , 3.03490626643892e+00 , 3.81560419596028e+00 , 2.23201834747819e+00 , 2.67448174853771e+00 , 2.88863286904395e+00 , 3.32122334496031e+00 ) ( -4.14681388778250e-03 , 1.22066593960987e-02 , 1.69127991492826e-02 , 1.89860855651968e-02 , -1.07863857398542e-02 , 4.91617372307837e-03 , 1.23071555307691e-02 , 1.77101930888175e-02 , -1.62795237532260e-02 , -1.20742429271807e-02 , -4.82436126902551e-03 , 5.06384588244620e-03 , -1.32128196431162e-02 , -9.08495907119860e-03 , -6.62146793089459e-03 , -1.16545022393692e-03 ) 3.81959230186222e-01 + 32 ( 3.08512587519288e+00 , 4.49707970117971e+00 , 5.15042982627826e+00 , 6.17125914040548e+00 , 2.50979233884791e+00 , 3.81229855468180e+00 , 4.50268875061413e+00 , 5.33177568529891e+00 , 1.33980944637834e+00 , 2.37745103542636e+00 , 3.02491187433124e+00 , 3.81067490125072e+00 , 2.22992148412604e+00 , 2.67904816544973e+00 , 2.88404450529218e+00 , 3.32662115462332e+00 ) ( -4.19334739610082e-03 , 1.22501856640234e-02 , 1.68820961198294e-02 , 1.89829372733566e-02 , -1.07921188347344e-02 , 5.01864637358304e-03 , 1.23000120215964e-02 , 1.77265599709417e-02 , -1.62748657204962e-02 , -1.20225135605685e-02 , -4.94989686942951e-03 , 4.99914062111286e-03 , -1.32246045798754e-02 , -9.03332860650218e-03 , -6.67616649208281e-03 , -1.09835121417817e-03 ) 3.81860258318432e-01 + 33 ( 3.08045463729672e+00 , 4.50288519704754e+00 , 5.14520390095076e+00 , 6.17009473576804e+00 , 2.50787564727135e+00 , 3.82219055541500e+00 , 4.50226214069664e+00 , 5.33778558393846e+00 , 1.34086920757905e+00 , 2.38582693292515e+00 , 3.01621801902235e+00 , 3.80779720627924e+00 , 2.22768857394173e+00 , 2.68577746719359e+00 , 2.87938997939690e+00 , 3.33213575260088e+00 ) ( -4.26045164162495e-03 , 1.22908700889301e-02 , 1.68471856059909e-02 , 1.89834261003156e-02 , -1.08150192757933e-02 , 5.12591079664833e-03 , 1.22853421663085e-02 , 1.77447558673838e-02 , -1.62727379913271e-02 , -1.19520165161674e-02 , -5.06601412162525e-03 , 4.95319659363923e-03 , -1.32435252234106e-02 , -8.96495735337770e-03 , -6.73869468915883e-03 , -1.03675679717580e-03 ) 3.81801393160747e-01 + 34 ( 3.07497912152090e+00 , 4.50829914516339e+00 , 5.13922512793544e+00 , 6.16896017434785e+00 , 2.50485309388411e+00 , 3.83220702803533e+00 , 4.50102851775461e+00 , 5.34369563021521e+00 , 1.34176277961509e+00 , 2.39661859744123e+00 , 3.00923587756392e+00 , 3.80745750931824e+00 , 2.22552072975963e+00 , 2.69443239804884e+00 , 2.87483587628920e+00 , 3.33768680793807e+00 ) ( -4.34421639088351e-03 , 1.23259510241342e-02 , 1.68090579824887e-02 , 1.89878261554619e-02 , -1.08552901253035e-02 , 5.22942992615502e-03 , 1.22614659002049e-02 , 1.77642609644918e-02 , -1.62733896651479e-02 , -1.18660435400099e-02 , -5.16722789780436e-03 , 4.93281774142251e-03 , -1.32680512214032e-02 , -8.88197830087080e-03 , -6.80664460996510e-03 , -9.80979867201091e-04 ) 3.81791215679719e-01 + 35 ( 3.06898072962898e+00 , 4.51288823912276e+00 , 5.13261898082506e+00 , 6.16794500639919e+00 , 2.50074653307297e+00 , 3.84158061569010e+00 , 4.49879685556613e+00 , 5.34919353467269e+00 , 1.34229502312659e+00 , 2.40928100931996e+00 , 3.00430451716382e+00 , 3.80996140448631e+00 , 2.22360417014956e+00 , 2.70468750472754e+00 , 2.87057086891121e+00 , 3.34320509035869e+00 ) ( -4.44031489768969e-03 , 1.23527234730989e-02 , 1.67689785306207e-02 , 1.89962130825891e-02 , -1.09121854056437e-02 , 5.32120212595859e-03 , 1.22276539265459e-02 , 1.77845576836149e-02 , -1.62769366896918e-02 , -1.17686217438871e-02 , -5.24875745421665e-03 , 4.94273803761624e-03 , -1.32965365863000e-02 , -8.78720894526610e-03 , -6.87713386725385e-03 , -9.30987612841641e-04 ) 3.81835385411921e-01 + 36 ( 3.06273532976632e+00 , 4.51625453815810e+00 , 5.12558688042565e+00 , 6.16711285602853e+00 , 2.49564990035453e+00 , 3.84963128856745e+00 , 4.49551609176305e+00 , 5.35403199682776e+00 , 1.34235952065396e+00 , 2.42319130987960e+00 , 3.00166756478992e+00 , 3.81540250086734e+00 , 2.22209336131761e+00 , 2.71615108183038e+00 , 2.86679976339768e+00 , 3.34863558008665e+00 ) ( -4.54435366709869e-03 , 1.23686805003577e-02 , 1.67284311239753e-02 , 1.90084516063127e-02 , -1.09840196246657e-02 , 5.39437686141032e-03 , 1.21842739540751e-02 , 1.78051583051095e-02 , -1.62833596505170e-02 , -1.16643470034764e-02 , -5.30682059170320e-03 , 4.98516473073789e-03 , -1.33273660443829e-02 , -8.68399149098933e-03 , -6.94692019866868e-03 , -8.86427801594670e-04 ) 3.81936326942932e-01 + 37 ( 3.05649192272016e+00 , 4.51806131212852e+00 , 5.11839243372688e+00 , 6.16649586647833e+00 , 2.48972865403734e+00 , 3.85581806565182e+00 , 4.49128596725413e+00 , 5.35804830557854e+00 , 1.34195825290523e+00 , 2.43768478162201e+00 , 3.00145507492219e+00 , 3.82364960592987e+00 , 2.22109872713473e+00 , 2.72838935953640e+00 , 2.86373525885699e+00 , 3.35394019810392e+00 ) ( -4.65218980605975e-03 , 1.23716418615644e-02 , 1.66890397173181e-02 , 1.90241913033266e-02 , -1.10682357296936e-02 , 5.44373642741758e-03 , 1.21328465998996e-02 , 1.78256268017041e-02 , -1.62925100610275e-02 , -1.15581857830655e-02 , -5.33886827855517e-03 , 5.05955489833097e-03 , -1.33590658119049e-02 , -8.57601334209215e-03 , -7.01254066837880e-03 , -8.46660162526817e-04 ) 3.82093031628418e-01 + 38 ( 3.05045520034663e+00 , 4.51805473772131e+00 , 5.11134115061683e+00 , 6.16609340606711e+00 , 2.48321341779800e+00 , 3.85977678566920e+00 , 4.48635217426398e+00 , 5.36117618517027e+00 , 1.34120085894772e+00 , 2.45209075220292e+00 , 3.00367159478445e+00 , 3.83435311427914e+00 , 2.22068007489778e+00 , 2.74095124957973e+00 , 2.86158715690625e+00 , 3.35910007102331e+00 ) ( -4.76019161860031e-03 , 1.23598714103535e-02 , 1.66524680422709e-02 , 1.90428744652835e-02 , -1.11615338051583e-02 , 5.46602270595950e-03 , 1.20759997193952e-02 , 1.78455990014566e-02 , -1.63041248925182e-02 , -1.14552422050043e-02 , -5.34375549291192e-03 , 5.16264172214884e-03 , -1.33903719358613e-02 , -8.46711508758403e-03 , -7.07047589577285e-03 , -8.10789030101033e-04 ) 3.82300990349005e-01 + 39 ( 3.04477330671893e+00 , 4.51608052429989e+00 , 5.10475536430945e+00 , 6.16587487803593e+00 , 2.47638766281039e+00 , 3.86134206645524e+00 , 4.48108638405379e+00 , 5.36344937487428e+00 , 1.34028312454434e+00 , 2.46576763106795e+00 , 3.00819152136954e+00 , 3.84697007402470e+00 , 2.22084607799930e+00 , 2.75339260853697e+00 , 2.86054956534452e+00 , 3.36411702201955e+00 ) ( -4.86543042629372e-03 , 1.23321843437552e-02 , 1.66202988314624e-02 , 1.90637594048100e-02 , -1.12600574737574e-02 , 5.46010859232420e-03 , 1.20173150929056e-02 , 1.78648032607835e-02 , -1.63178447949989e-02 , -1.13604904168987e-02 , -5.32184447456055e-03 , 5.28870221068816e-03 , -1.34202591870486e-02 , -8.36109248159763e-03 , -7.11733591924846e-03 , -7.77701464928409e-04 ) 3.82552280801419e-01 + 40 ( 3.03953158726547e+00 , 4.51209497961311e+00 , 5.09894673434180e+00 , 6.16578599928733e+00 , 2.46957015850689e+00 , 3.86055335115988e+00 , 4.47595360418285e+00 , 5.36499714940424e+00 , 1.33944926924420e+00 , 2.47813660080028e+00 , 3.01476283660714e+00 , 3.86080601707240e+00 , 2.22155937101033e+00 , 2.76529935945446e+00 , 2.86078736535835e+00 , 3.36901381632414e+00 ) ( -4.96580057965820e-03 , 1.22880424192736e-02 , 1.65938976558053e-02 , 1.90859603220539e-02 , -1.13596279851453e-02 , 5.42702341268680e-03 , 1.19610688394556e-02 , 1.78830800496280e-02 , -1.63332290120811e-02 , -1.12784800729915e-02 , -5.27503313459921e-03 , 5.43003603855418e-03 , -1.34479399657521e-02 , -8.26149951976874e-03 , -7.15005911976767e-03 , -7.46119909351650e-04 ) 3.82835834324984e-01 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat index 83bec1298..ead9fed19 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/AutoDiff/test.restart.hr.hist.dat @@ -1,10 +1,10 @@ # one p(one ) - 2.00000000000000 0.09106555930578 - 4.00000000000000 0.19841141658836 - 6.00000000000000 0.14791554501384 - 8.00000000000000 0.04585062002305 - 10.00000000000000 0.00473153262406 - 12.00000000000000 0.00011711012676 + 2.00000000000000 0.09106555928620 + 4.00000000000000 0.19841141655022 + 6.00000000000000 0.14791554502557 + 8.00000000000000 0.04585062006277 + 10.00000000000000 0.00473153263289 + 12.00000000000000 0.00011711012711 14.00000000000000 0.00000057531671 16.00000000000000 0.00000000051315 18.00000000000000 0.00000000000008 diff --git a/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt b/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt index 157cac038..655c0f78c 100644 --- a/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt +++ b/namd/tests/library/000_distancepairs_histogramrestraint-dp/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2019-04-11". +colvars: Using NAMD interface, version "2019-02-12". diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out index 3c82fd483..43bcebeb7 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -113,7 +109,6 @@ colvars: # centers = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 colvars: # targetCenters = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -124,28 +119,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - distancePairs colvar component: -colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped index f4aa065ec..416f80c08 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.04629582292620e+00 , 4.49408974875934e+00 , 5.18802765002996e+00 , 6.16600456423064e+00 , 2.49712681741192e+00 , 3.86413458721172e+00 , 4.55726429580482e+00 , 5.34046966370213e+00 , 1.36572415582545e+00 , 2.47043282429680e+00 , 3.12318599145701e+00 , 3.85046871322657e+00 , 2.22191835525029e+00 , 2.73196623733898e+00 , 2.91861957044130e+00 , 3.29084860719824e+00 ) + x ( 3.04629582333038e+00 , 4.49408974940565e+00 , 5.18802765078345e+00 , 6.16600456517094e+00 , 2.49712681746392e+00 , 3.86413458751360e+00 , 4.55726429607857e+00 , 5.34046966422931e+00 , 1.36572415578523e+00 , 2.47043282453162e+00 , 3.12318599155152e+00 , 3.85046871369096e+00 , 2.22191835508463e+00 , 2.73196623727117e+00 , 2.91861957005182e+00 , 3.29084860717030e+00 ) } restraint { diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj index 6323d1e0e..a7fca080e 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 ( 2.95543971137580e+00 , 4.40149446295507e+00 , 5.19438956774262e+00 , 6.22241603343745e+00 , 2.46985074910253e+00 , 3.82984200895935e+00 , 4.58947829164686e+00 , 5.41000980054028e+00 , 1.34023744154865e+00 , 2.42537620134385e+00 , 3.12639105039661e+00 , 3.90388793384236e+00 , 2.19602098164167e+00 , 2.66815420835178e+00 , 2.96116058328487e+00 , 3.36815290626777e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 1 ( 2.95875682371162e+00 , 4.40108078803336e+00 , 5.19334659297185e+00 , 6.22376901215503e+00 , 2.46917670614475e+00 , 3.82473558076916e+00 , 4.58659203732382e+00 , 5.40932438791137e+00 , 1.33333853625533e+00 , 2.41676042305281e+00 , 3.12170808828270e+00 , 3.90418242702239e+00 , 2.19936646916507e+00 , 2.66448925154634e+00 , 2.96000447713555e+00 , 3.36551061362995e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 2 ( 2.96294067406152e+00 , 4.40226515811672e+00 , 5.19285541585537e+00 , 6.22442847367682e+00 , 2.46935508867047e+00 , 3.82150643041244e+00 , 4.58422435395019e+00 , 5.40817951631011e+00 , 1.32707961473676e+00 , 2.41052202222919e+00 , 3.11822168290825e+00 , 3.90473111479922e+00 , 2.20349997298880e+00 , 2.66304540103662e+00 , 2.95871452980397e+00 , 3.36219422430421e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 3 ( 2.96775064184085e+00 , 4.40516130339314e+00 , 5.19307524760769e+00 , 6.22425430968166e+00 , 2.47031615575903e+00 , 3.82048584858974e+00 , 4.58270515959952e+00 , 5.40667289707967e+00 , 1.32192370925505e+00 , 2.40699266423868e+00 , 3.11597471298471e+00 , 3.90507282356790e+00 , 2.20807442665232e+00 , 2.66384581355879e+00 , 2.95730110419459e+00 , 3.35823523823449e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 4 ( 2.97293010489448e+00 , 4.40978768834604e+00 , 5.19406903504745e+00 , 6.22314788319532e+00 , 2.47196007303898e+00 , 3.82187612852118e+00 , 4.58226353677337e+00 , 5.40491259095799e+00 , 1.31825265737252e+00 , 2.40633740937283e+00 , 3.11490651576023e+00 , 3.90476431055031e+00 , 2.21272370240332e+00 , 2.66680267302744e+00 , 2.95575856583674e+00 , 3.35370432605342e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 5 ( 2.97823333783396e+00 , 4.41606221701169e+00 , 5.19580203466429e+00 , 6.22106315761185e+00 , 2.47416553030952e+00 , 3.82572100741359e+00 , 4.58300378562911e+00 , 5.40299835185958e+00 , 1.31633344994455e+00 , 2.40854582463045e+00 , 3.11487200509147e+00 , 3.90343726008758e+00 , 2.21709388501265e+00 , 2.67171937535336e+00 , 2.95407275180430e+00 , 3.34870361989151e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , 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-2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 7 ( 2.98841232078424e+00 , 4.43273687426315e+00 , 5.20090974397531e+00 , 6.21407143163464e+00 , 2.47971573108845e+00 , 3.84006896947682e+00 , 4.58775771850319e+00 , 5.39896919272286e+00 , 1.31814854769203e+00 , 2.42067606925974e+00 , 3.11705824330467e+00 , 3.89690002594713e+00 , 2.22382854108974e+00 , 2.68617638138061e+00 , 2.95021953228176e+00 , 3.33780297993749e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 8 ( 2.99302343356408e+00 , 4.44250962515450e+00 , 5.20382996327586e+00 , 6.20936877721994e+00 , 2.48277289806301e+00 , 3.84978342368457e+00 , 4.59130044217903e+00 , 5.39688319381903e+00 , 1.32174181291561e+00 , 2.42979485534901e+00 , 3.11880839063538e+00 , 3.89167562021842e+00 , 2.22580927850425e+00 , 2.69491484659868e+00 , 2.94804551633442e+00 , 3.33217989345794e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 9 ( 2.99724215297088e+00 , 4.45270758695142e+00 , 5.20662810065605e+00 , 6.20408528397123e+00 , 2.48582223191489e+00 , 3.86041172949691e+00 , 4.59511907153488e+00 , 5.39469356936545e+00 , 1.32682097132025e+00 , 2.44021975217169e+00 , 3.12070201377177e+00 , 3.88540749241064e+00 , 2.22677520657858e+00 , 2.70405886573605e+00 , 2.94571912723301e+00 , 3.32662241630005e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 10 ( 3.00109029649387e+00 , 4.46288053096414e+00 , 5.20902297741288e+00 , 6.19843864704866e+00 , 2.48871914762448e+00 , 3.87123105742002e+00 , 4.59874530583182e+00 , 5.39230854017706e+00 , 1.33302269914505e+00 , 2.45130012843502e+00 , 3.12256033871251e+00 , 3.87845986454653e+00 , 2.22678798490271e+00 , 2.71314602610314e+00 , 2.94326100418863e+00 , 3.32125154369191e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 11 ( 3.00464453588942e+00 , 4.47257069558543e+00 , 5.21076119638848e+00 , 6.19266941370346e+00 , 2.49132961385451e+00 , 3.88146798331951e+00 , 4.60168898224801e+00 , 5.38961117979994e+00 , 1.33990328901335e+00 , 2.46234094539705e+00 , 3.12424927277303e+00 , 3.87128278227091e+00 , 2.22600197549542e+00 , 2.72173288748063e+00 , 2.94069782584860e+00 , 3.31616954666578e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 12 ( 3.00802660466872e+00 , 4.48134406067423e+00 , 5.21164113891315e+00 , 6.18702434833565e+00 , 2.49354148220516e+00 , 3.89035788116353e+00 , 4.60348694964941e+00 , 5.38647692484132e+00 , 1.34697040085023e+00 , 2.47263868606845e+00 , 3.12567895935487e+00 , 3.86435935223959e+00 , 2.22464401788052e+00 , 2.72941476960870e+00 , 2.93806020605167e+00 , 3.31145665762186e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 13 ( 3.01139044165349e+00 , 4.48882134512637e+00 , 5.21153128241426e+00 , 6.18173913371892e+00 , 2.49527712738787e+00 , 3.89720566631697e+00 , 4.60374994484304e+00 , 5.38279228320668e+00 , 1.35372197426113e+00 , 2.48152014333316e+00 , 3.12679646629641e+00 , 3.85815073776481e+00 , 2.22298622217618e+00 , 2.73584170506168e+00 , 2.93538174058148e+00 , 3.30717032254531e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 14 ( 3.01490659498393e+00 , 4.49470568819819e+00 , 5.21038109514539e+00 , 6.17702179178737e+00 , 2.49650403390072e+00 , 3.90144127859289e+00 , 4.60220148662660e+00 , 5.37847180935563e+00 , 1.35968942213934e+00 , 2.48838225386361e+00 , 3.12757367670257e+00 , 3.85304523490686e+00 , 2.22131487194857e+00 , 2.74073061696419e+00 , 2.93269901676913e+00 , 3.30334710226797e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 15 ( 3.01874444119857e+00 , 4.49880441908766e+00 , 5.20822364477587e+00 , 6.17303832367595e+00 , 2.49724029422419e+00 , 3.90266451985451e+00 , 4.59870430385402e+00 , 5.37347142047251e+00 , 1.36448009941900e+00 , 2.49273019193462e+00 , 3.12799274187020e+00 , 3.84931652446014e+00 , 2.21989896798406e+00 , 2.74387407746985e+00 , 2.93005166803435e+00 , 3.30000695737880e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 16 ( 3.02305313447408e+00 , 4.50104303470608e+00 , 5.20516981193190e+00 , 6.16990179071024e+00 , 2.49755349805131e+00 , 3.90067603040690e+00 , 4.59327213529618e+00 , 5.36779747466957e+00 , 1.36781305325599e+00 , 2.49421050420414e+00 , 3.12803142014580e+00 , 3.84709461387514e+00 , 2.21896204065284e+00 , 2.74514610274893e+00 , 2.92748124535385e+00 , 3.29715922041988e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 17 ( 3.02794278893498e+00 , 4.50147045589817e+00 , 5.20139488515695e+00 , 6.16766577694110e+00 , 2.49755330822387e+00 , 3.89549330657652e+00 , 4.58606702348901e+00 , 5.36151205347158e+00 , 1.36954253121641e+00 , 2.49263619481708e+00 , 3.12765036949056e+00 , 3.84635143644652e+00 , 2.21866044064897e+00 , 2.74450537655344e+00 , 2.92502790904681e+00 , 3.29480918130467e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 18 ( 3.03346785795678e+00 , 4.50025537469709e+00 , 5.19711906941881e+00 , 6.16632276542483e+00 , 2.49737930806754e+00 , 3.88735195260522e+00 , 4.57738383543644e+00 , 5.35473517728416e+00 , 1.36966557262771e+00 , 2.48800127032887e+00 , 3.12678413131530e+00 , 3.84690184564267e+00 , 2.21907037548788e+00 , 2.74199613753820e+00 , 2.92272466370839e+00 , 3.29296402717016e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 19 ( 3.03961480062799e+00 , 4.49767398572291e+00 , 5.19258399657282e+00 , 6.16580745526214e+00 , 2.49718604910831e+00 , 3.87669270182968e+00 , 4.56762447403876e+00 , 5.34764418843780e+00 , 1.36831274917687e+00 , 2.48048318980352e+00 , 3.12533717889256e+00 , 3.84841979399148e+00 , 2.22018461761734e+00 , 2.73774680015523e+00 , 2.92058985495922e+00 , 3.29163694657683e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 20 ( 3.04629582333038e+00 , 4.49408974940565e+00 , 5.18802765078345e+00 , 6.16600456517094e+00 , 2.49712681746392e+00 , 3.86413458751360e+00 , 4.55726429607857e+00 , 5.34046966422931e+00 , 1.36572415578523e+00 , 2.47043282453162e+00 , 3.12318599155152e+00 , 3.85046871369096e+00 , 2.22191835508463e+00 , 2.73196623727117e+00 , 2.91861957005182e+00 , 3.29084860717030e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out index ffd401600..a84b20ece 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,27 +55,27 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -113,7 +109,6 @@ colvars: # centers = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 colvars: # targetCenters = { ( 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 , 0.1 , 0.2 , 0.3 , -0.2 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.002 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -124,33 +119,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - distancePairs colvar component: -colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 3.0463 , 4.49409 , 5.18803 , 6.166 , 2.49713 , 3.86413 , 4.55726 , 5.34047 , 1.36572 , 2.47043 , 3.12319 , 3.85047 , 2.22192 , 2.73197 , 2.91862 , 3.29085 ) colvars: Restarting linear bias "linear1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped index aebc65c59..0d4ecbc07 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 3.03877998802839e+00 , 4.51126454702547e+00 , 5.09780825674884e+00 , 6.16443491397830e+00 , 2.46931564760306e+00 , 3.86026518189025e+00 , 4.47534635751221e+00 , 5.36404748288555e+00 , 1.33947834845631e+00 , 2.47810087575991e+00 , 3.01439850051918e+00 , 3.86006418847475e+00 , 2.22172886244241e+00 , 2.76552022649790e+00 , 2.86065452181562e+00 , 3.36835466836590e+00 ) + x ( 3.03877998958173e+00 , 4.51126454876777e+00 , 5.09780825855294e+00 , 6.16443491538328e+00 , 2.46931564842291e+00 , 3.86026518301130e+00 , 4.47534635855439e+00 , 5.36404748356174e+00 , 1.33947834856915e+00 , 2.47810087633114e+00 , 3.01439850098518e+00 , 3.86006418873543e+00 , 2.22172886207939e+00 , 2.76552022640159e+00 , 2.86065452105383e+00 , 3.36835466726488e+00 ) } restraint { diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj index fd76bbf8c..305b720d8 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( 3.04629582292620e+00 , 4.49408974875934e+00 , 5.18802765002996e+00 , 6.16600456423064e+00 , 2.49712681741192e+00 , 3.86413458721172e+00 , 4.55726429580482e+00 , 5.34046966370213e+00 , 1.36572415582545e+00 , 2.47043282429680e+00 , 3.12318599145701e+00 , 3.85046871322657e+00 , 2.22191835525029e+00 , 2.73196623733898e+00 , 2.91861957044130e+00 , 3.29084860719824e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 21 ( 3.05334985718046e+00 , 4.48992628670576e+00 , 5.18366022382011e+00 , 6.16676026418638e+00 , 2.49733708339840e+00 , 3.85043471960129e+00 , 4.54681310121844e+00 , 5.33348650495467e+00 , 1.36221538959227e+00 , 2.45835277038889e+00 , 3.12018761704542e+00 , 3.85254424598379e+00 , 2.22412250678503e+00 , 2.72493758209268e+00 , 2.91678212339134e+00 , 3.29062579006844e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 22 ( 3.06055105810745e+00 , 4.48563517046779e+00 , 5.17964329258940e+00 , 6.16789612191897e+00 , 2.49791842471156e+00 , 3.83643598957093e+00 , 4.53677312706362e+00 , 5.32699885023723e+00 , 1.35813975612152e+00 , 2.44486600970885e+00 , 3.11619451803498e+00 , 3.85412638365591e+00 , 2.22660216073093e+00 , 2.71700934103147e+00 , 2.91501666461826e+00 , 3.29099758720831e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 23 ( 3.06762420481496e+00 , 4.48166116738223e+00 , 5.17607431570745e+00 , 6.16922431262149e+00 , 2.49892421159898e+00 , 3.82300581028315e+00 , 4.52759703894498e+00 , 5.32131852844794e+00 , 1.35385283880720e+00 , 2.43067780472622e+00 , 3.11107462093897e+00 , 3.85473675493696e+00 , 2.22913771659230e+00 , 2.70858357698744e+00 , 2.91323709555557e+00 , 3.29199001472266e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 24 ( 3.07426564475834e+00 , 4.47840815394115e+00 , 5.17297796752752e+00 , 6.17056286761805e+00 , 2.50034908316076e+00 , 3.81097097826291e+00 , 4.51964961664415e+00 , 5.31673850301500e+00 , 1.34968380481030e+00 , 2.41653410780135e+00 , 3.10473449529925e+00 , 3.85399547441392e+00 , 2.23150661412188e+00 , 2.70010092754582e+00 , 2.91134113983847e+00 , 3.29362013061070e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 25 ( 3.08016782736078e+00 , 4.47620910758893e+00 , 5.17030513268353e+00 , 6.17174981694759e+00 , 2.50212450409709e+00 , 3.80105506960300e+00 , 4.51317720954952e+00 , 5.31350456313651e+00 , 1.34591496239228e+00 , 2.40317959728505e+00 , 3.09714267643763e+00 , 3.85167104521135e+00 , 2.23350398143146e+00 , 2.69202233139669e+00 , 2.90922309147424e+00 , 3.29589074948067e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 26 ( 3.08504497817861e+00 , 4.47530287579147e+00 , 5.16793956182435e+00 , 6.17265513248033e+00 , 2.50412200519066e+00 , 3.79382467008278e+00 , 4.50828856695274e+00 , 5.31178960054300e+00 , 1.34276823546416e+00 , 2.39131763866671e+00 , 3.08834947577683e+00 , 3.84771664952257e+00 , 2.23496090215041e+00 , 2.68480761443058e+00 , 2.90678782288796e+00 , 3.29878667345143e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 27 ( 3.08865740711938e+00 , 4.47581931105760e+00 , 5.16571150996081e+00 , 6.17318955294432e+00 , 2.50616407527288e+00 , 3.78964913201902e+00 , 4.50494917964554e+00 , 5.31167449396980e+00 , 1.34039573489298e+00 , 2.38157352804933e+00 , 3.07849972498533e+00 , 3.84228723277161e+00 , 2.23575922249565e+00 , 2.67889154901620e+00 , 2.90396346178722e+00 , 3.30227300577226e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 28 ( 3.09083196919183e+00 , 4.47777297896991e+00 , 5.16341701569090e+00 , 6.17330951202142e+00 , 2.50804080733283e+00 , 3.78867633326440e+00 , 4.50298935955436e+00 , 5.31313821781415e+00 , 1.33887215231506e+00 , 2.37446181201830e+00 , 3.06783587774327e+00 , 3.83573409487052e+00 , 2.23584181663426e+00 , 2.67465865897245e+00 , 2.90071083416943e+00 , 3.30629579777209e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 29 ( 3.09147652487028e+00 , 4.48106462931359e+00 , 5.16084080078625e+00 , 6.17301764230806e+00 , 2.50952927510470e+00 , 3.79082510368283e+00 , 4.50212447064938e+00 , 5.31605801097917e+00 , 1.33818877022267e+00 , 2.37035852457148e+00 , 3.05669031820349e+00 , 3.82857689384771e+00 , 2.23521733474407e+00 , 2.67241876523844e+00 , 2.89702867596283e+00 , 3.31078478908618e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 30 ( 3.09058694977931e+00 , 4.48548936034949e+00 , 5.15778063240666e+00 , 6.17235875247401e+00 , 2.51041270196689e+00 , 3.79579411480670e+00 , 4.50198498078247e+00 , 5.32021901611626e+00 , 1.33825174758459e+00 , 2.36948006067847e+00 , 3.04546788921847e+00 , 3.82145639023017e+00 , 2.23395869069158e+00 , 2.67238581517616e+00 , 2.89295490314345e+00 , 3.31565768022867e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 31 ( 3.08824597625239e+00 , 4.49075053845246e+00 , 5.15407068114639e+00 , 6.17141163619470e+00 , 2.51049756105646e+00 , 3.80308681405192e+00 , 4.50215365271137e+00 , 5.32533205627038e+00 , 1.33888880659581e+00 , 2.37187086964207e+00 , 3.03462070382300e+00 , 3.81507358119468e+00 , 2.23219511591932e+00 , 2.67466266655001e+00 , 2.88856492653725e+00 , 3.32082524147622e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 32 ( 3.08461411097271e+00 , 4.49647886423009e+00 , 5.14960177736290e+00 , 6.17027762362695e+00 , 2.50962807667604e+00 , 3.81205156126135e+00 , 4.50220741948503e+00 , 5.33105788079286e+00 , 1.33986789053847e+00 , 2.37740208949063e+00 , 3.02461835056944e+00 , 3.81012227680463e+00 , 2.23009844809748e+00 , 2.67923396951857e+00 , 2.88396845444278e+00 , 3.32619656883699e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 33 ( 3.07991378221424e+00 , 4.50225598774368e+00 , 5.14433661074996e+00 , 6.16906723638448e+00 , 2.50769841868323e+00 , 3.82193487530121e+00 , 4.50176095190848e+00 , 5.33703587344653e+00 , 1.34092834047650e+00 , 2.38578198626423e+00 , 3.01591638646605e+00 , 3.80722231814434e+00 , 2.22786519374588e+00 , 2.68596812945528e+00 , 2.87930570927184e+00 , 3.33168396197019e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 34 ( 3.07440860931254e+00 , 4.50764161547249e+00 , 5.13831857639857e+00 , 6.16788658820268e+00 , 2.50466285985335e+00 , 3.83194370405047e+00 , 4.50050842022841e+00 , 5.34291473611270e+00 , 1.34182117051647e+00 , 2.39657731482946e+00 , 3.00892592878546e+00 , 3.80686000972107e+00 , 2.22569657351854e+00 , 2.69462787716750e+00 , 2.87474349267268e+00 , 3.33720713274434e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 35 ( 3.06838011503852e+00 , 4.51220236445887e+00 , 5.13167322979288e+00 , 6.16682524216936e+00 , 2.50054351728456e+00 , 3.84131072638630e+00 , 4.49825898981490e+00 , 5.34838227913630e+00 , 1.34235119113145e+00 , 2.40924279123168e+00 , 3.00398601326731e+00 , 3.80934088105348e+00 , 2.22377893326655e+00 , 2.70488772649367e+00 , 2.87047066148171e+00 , 3.34269688957208e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) - 36 ( 3.06210432223467e+00 , 4.51554021275385e+00 , 5.12460206898545e+00 , 6.16594684094431e+00 , 2.49543460132950e+00 , 3.84935590471168e+00 , 4.49496173590441e+00 , 5.35319126883816e+00 , 1.34241205405189e+00 , 2.42315536036212e+00 , 3.00134026458716e+00 , 3.81475851235681e+00 , 2.22226687749169e+00 , 2.71635592301934e+00 , 2.86669215483321e+00 , 3.34809824928536e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , 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-2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 37 ( 3.05583041579255e+00 , 4.51731835619197e+00 , 5.11736877060765e+00 , 6.16528355530079e+00 , 2.48950184007420e+00 , 3.85553820919296e+00 , 4.49071647008138e+00 , 5.35717902530618e+00 , 1.34200592550321e+00 , 2.43765019178148e+00 , 3.00111875581802e+00 , 3.82298171446182e+00 , 2.22127096949007e+00 , 2.72859863684456e+00 , 2.86362073623295e+00 , 3.35337316792672e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 38 ( 3.04976328673567e+00 , 4.51728290748607e+00 , 5.11027889780887e+00 , 6.16483478581600e+00 , 2.48297610118552e+00 , 3.85949338940809e+00 , 4.48576887839106e+00 , 5.36027926465160e+00 , 1.34124273659856e+00 , 2.45205659120844e+00 , 3.00332606707948e+00 , 3.83366091194011e+00 , 2.22085114879278e+00 , 2.74116471578633e+00 , 2.86146619671611e+00 , 3.35850281090275e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 39 ( 3.04405129241968e+00 , 4.51527953922953e+00 , 5.10365482996787e+00 , 6.16456998222725e+00 , 2.47614106272950e+00 , 3.86105594621195e+00 , 4.48049055445589e+00 , 5.36252568437131e+00 , 1.34031865526981e+00 , 2.46573303996854e+00 , 3.00783663914838e+00 , 3.84625320482145e+00 , 2.22101620382144e+00 , 2.75360995497976e+00 , 2.86042255254939e+00 , 3.36348904078277e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) + 40 ( 3.03877998958173e+00 , 4.51126454876777e+00 , 5.09780825855294e+00 , 6.16443491538328e+00 , 2.46931564842291e+00 , 3.86026518301130e+00 , 4.47534635855439e+00 , 5.36404748356174e+00 , 1.33947834856915e+00 , 2.47810087633114e+00 , 3.01439850098518e+00 , 3.86006418873543e+00 , 2.22172886207939e+00 , 2.76552022640159e+00 , 2.86065452105383e+00 , 3.36835466726488e+00 ) ( -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 , -2.00000000000000e-03 ) diff --git a/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt b/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt index 157cac038..afda7aab6 100644 --- a/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt +++ b/namd/tests/library/000_distancepairs_linear-distancepairs/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-09-12. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out index 8f7a57a73..aecf18686 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -152,7 +148,6 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -163,28 +158,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped index 13ed1c8c9..572603c28 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -1.02062769534156e+00 , -6.08213499811239e-03 , 3.05064351584125e+00 ) + x ( -1.02062769591997e+00 , -6.08213500496868e-03 , 3.05064351583999e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj index 193c60552..8bd23f911 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -1.08926570435186e+00 , 2.48645332384574e-02 , 3.01469929653834e+00 ) ( 4.35706281740742e-03 , -9.94581329538296e-05 , -1.20587971861533e-02 ) - 1 ( -1.08757103024838e+00 , 2.23275217750993e-02 , 3.01408140364127e+00 ) ( 4.35028412099354e-03 , -8.93100871003973e-05 , -1.20563256145651e-02 ) - 2 ( -1.08562847072074e+00 , 2.01398180220937e-02 , 3.01423212069547e+00 ) ( 4.34251388288294e-03 , -8.05592720883750e-05 , -1.20569284827819e-02 ) - 3 ( -1.08340349189933e+00 , 1.83171614296354e-02 , 3.01517854062312e+00 ) ( 4.33361396759732e-03 , -7.32686457185414e-05 , -1.20607141624925e-02 ) - 4 ( -1.08086495647312e+00 , 1.68568842988528e-02 , 3.01690562336607e+00 ) ( 4.32345982589247e-03 , -6.74275371954112e-05 , -1.20676224934643e-02 ) - 5 ( -1.07799014209397e+00 , 1.57362299347954e-02 , 3.01935667906812e+00 ) ( 4.31196056837589e-03 , -6.29449197391816e-05 , -1.20774267162725e-02 ) - 6 ( -1.07476840344796e+00 , 1.49116811703516e-02 , 3.02243644259714e+00 ) ( 4.29907361379183e-03 , -5.96467246814063e-05 , -1.20897457703886e-02 ) - 7 ( -1.07120346036405e+00 , 1.43200030870987e-02 , 3.02601615447875e+00 ) ( 4.28481384145619e-03 , -5.72800123483947e-05 , -1.21040646179150e-02 ) - 8 ( -1.06731460018291e+00 , 1.38814843649557e-02 , 3.02994023634960e+00 ) ( 4.26925840073163e-03 , -5.55259374598229e-05 , -1.21197609453984e-02 ) - 9 ( -1.06313721621703e+00 , 1.35053849628509e-02 , 3.03403440483742e+00 ) ( 4.25254886486811e-03 , -5.40215398514037e-05 , -1.21361376193497e-02 ) - 10 ( -1.05872297659907e+00 , 1.30969846845709e-02 , 3.03811518636264e+00 ) ( 4.23489190639626e-03 , -5.23879387382835e-05 , -1.21524607454506e-02 ) - 11 ( -1.05413959104298e+00 , 1.25651406036256e-02 , 3.04200058103587e+00 ) ( 4.21655836417193e-03 , -5.02605624145023e-05 , -1.21680023241435e-02 ) - 12 ( -1.04946980433283e+00 , 1.18290706904701e-02 , 3.04552119753946e+00 ) ( 4.19787921733132e-03 , -4.73162827618805e-05 , -1.21820847901579e-02 ) - 13 ( -1.04480903884802e+00 , 1.08232102376193e-02 , 3.04853081094912e+00 ) ( 4.17923615539206e-03 , -4.32928409504774e-05 , -1.21941232437965e-02 ) - 14 ( -1.04026127373743e+00 , 9.49942103360235e-03 , 3.05091517276253e+00 ) ( 4.16104509494973e-03 , -3.79976841344094e-05 , -1.22036606910501e-02 ) - 15 ( -1.03593320366363e+00 , 7.82645303080387e-03 , 3.05259815153299e+00 ) ( 4.14373281465451e-03 , -3.13058121232155e-05 , -1.22103926061320e-02 ) - 16 ( -1.03192718274189e+00 , 5.78719768553504e-03 , 3.05354476802529e+00 ) ( 4.12770873096756e-03 , -2.31487907421402e-05 , -1.22141790721012e-02 ) - 17 ( -1.02833380767736e+00 , 3.37481068352563e-03 , 3.05376123022586e+00 ) ( 4.11333523070946e-03 , -1.34992427341025e-05 , -1.22150449209035e-02 ) - 18 ( -1.02522512504349e+00 , 5.89042613610813e-04 , 3.05329243257632e+00 ) ( 4.10090050017395e-03 , -2.35617045444325e-06 , -1.22131697303053e-02 ) - 19 ( -1.02264934622731e+00 , -2.56602061946254e-03 , 3.05221745998716e+00 ) ( 4.09059738490925e-03 , 1.02640824778502e-05 , -1.22088698399486e-02 ) - 20 ( -1.02062769534156e+00 , -6.08213499811239e-03 , 3.05064351584125e+00 ) ( 4.08251078136622e-03 , 2.43285399924496e-05 , -1.22025740633650e-02 ) + 0 ( -1.08926570435185e+00 , 2.48645332384094e-02 , 3.01469929653834e+00 ) ( 4.35706281740739e-03 , -9.94581329536377e-05 , -1.20587971861534e-02 ) + 1 ( -1.08757103024997e+00 , 2.23275217747934e-02 , 3.01408140364135e+00 ) ( 4.35028412099990e-03 , -8.93100870991734e-05 , -1.20563256145654e-02 ) + 2 ( -1.08562847089983e+00 , 2.01398180516252e-02 , 3.01423212068838e+00 ) ( 4.34251388359932e-03 , -8.05592722065010e-05 , -1.20569284827535e-02 ) + 3 ( -1.08340349194734e+00 , 1.83171614284610e-02 , 3.01517854061388e+00 ) ( 4.33361396778937e-03 , -7.32686457138438e-05 , -1.20607141624555e-02 ) + 4 ( -1.08086495662244e+00 , 1.68568843161550e-02 , 3.01690562336324e+00 ) ( 4.32345982648975e-03 , -6.74275372646198e-05 , -1.20676224934530e-02 ) + 5 ( -1.07799014212969e+00 , 1.57362299159951e-02 , 3.01935667906087e+00 ) ( 4.31196056851875e-03 , -6.29449196639804e-05 , -1.20774267162435e-02 ) + 6 ( -1.07476840349588e+00 , 1.49116811517320e-02 , 3.02243644260053e+00 ) ( 4.29907361398352e-03 , -5.96467246069281e-05 , -1.20897457704021e-02 ) + 7 ( -1.07120346043007e+00 , 1.43200030669788e-02 , 3.02601615449288e+00 ) ( 4.28481384172026e-03 , -5.72800122679151e-05 , -1.21040646179715e-02 ) + 8 ( -1.06731460026733e+00 , 1.38814843394630e-02 , 3.02994023637554e+00 ) ( 4.26925840106931e-03 , -5.55259373578521e-05 , -1.21197609455021e-02 ) + 9 ( -1.06313721632696e+00 , 1.35053849341971e-02 , 3.03403440487335e+00 ) ( 4.25254886530783e-03 , -5.40215397367883e-05 , -1.21361376194934e-02 ) + 10 ( -1.05872297673822e+00 , 1.30969846539595e-02 , 3.03811518640717e+00 ) ( 4.23489190695288e-03 , -5.23879386158379e-05 , -1.21524607456287e-02 ) + 11 ( -1.05413959121528e+00 , 1.25651405718566e-02 , 3.04200058108683e+00 ) ( 4.21655836486113e-03 , -5.02605622874266e-05 , -1.21680023243473e-02 ) + 12 ( -1.04946980454194e+00 , 1.18290706584114e-02 , 3.04552119759417e+00 ) ( 4.19787921816777e-03 , -4.73162826336457e-05 , -1.21820847903767e-02 ) + 13 ( -1.04480903909869e+00 , 1.08232101954363e-02 , 3.04853081100414e+00 ) ( 4.17923615639474e-03 , -4.32928407817452e-05 , -1.21941232440166e-02 ) + 14 ( -1.04026127402952e+00 , 9.49942100347867e-03 , 3.05091517281576e+00 ) ( 4.16104509611809e-03 , -3.79976840139147e-05 , -1.22036606912630e-02 ) + 15 ( -1.03593320400088e+00 , 7.82645299533791e-03 , 3.05259815158109e+00 ) ( 4.14373281600352e-03 , -3.13058119813516e-05 , -1.22103926063244e-02 ) + 16 ( -1.03192718312749e+00 , 5.78719766133096e-03 , 3.05354476806524e+00 ) ( 4.12770873250994e-03 , -2.31487906453238e-05 , -1.22141790722609e-02 ) + 17 ( -1.02833380809396e+00 , 3.37481068267376e-03 , 3.05376123026148e+00 ) ( 4.11333523237583e-03 , -1.34992427306950e-05 , -1.22150449210459e-02 ) + 18 ( -1.02522512552484e+00 , 5.89042585372512e-04 , 3.05329243259600e+00 ) ( 4.10090050209936e-03 , -2.35617034149005e-06 , -1.22131697303840e-02 ) + 19 ( -1.02264934677565e+00 , -2.56602063071965e-03 , 3.05221745999499e+00 ) ( 4.09059738710258e-03 , 1.02640825228786e-05 , -1.22088698399800e-02 ) + 20 ( -1.02062769591997e+00 , -6.08213500496868e-03 , 3.05064351583999e+00 ) ( 4.08251078367986e-03 , 2.43285400198747e-05 , -1.22025740633599e-02 ) diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out index cfa942a30..39d87c2b9 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -152,7 +148,6 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -163,33 +158,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -1.02063 , -0.00608213 , 3.05064 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped index fa080941c..57ad6cdde 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -1.00146957910752e+00 , -7.86134846594192e-02 , 3.05294498810129e+00 ) + x ( -1.00146958058144e+00 , -7.86134845943720e-02 , 3.05294498811922e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj index a8901e5cb..411da6154 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -1.02062769534156e+00 , -6.08213499811239e-03 , 3.05064351584125e+00 ) ( 4.08251078136622e-03 , 2.43285399924496e-05 , -1.22025740633650e-02 ) - 21 ( -1.01915362990077e+00 , -9.94509781004160e-03 , 3.04869855746548e+00 ) ( 4.07661451960309e-03 , 3.97803912401664e-05 , -1.21947942298619e-02 ) - 22 ( -1.01819426467457e+00 , -1.41317848486685e-02 , 3.04652291624334e+00 ) ( 4.07277705869829e-03 , 5.65271393946740e-05 , -1.21860916649734e-02 ) - 23 ( -1.01769353572269e+00 , -1.86072293092575e-02 , 3.04426035191247e+00 ) ( 4.07077414289074e-03 , 7.44289172370300e-05 , -1.21770414076499e-02 ) - 24 ( -1.01757652300947e+00 , -2.33228912331954e-02 , 3.04204924926634e+00 ) ( 4.07030609203789e-03 , 9.32915649327817e-05 , -1.21681969970653e-02 ) - 25 ( -1.01775441423944e+00 , -2.82168582658865e-02 , 3.04001482319277e+00 ) ( 4.07101765695776e-03 , 1.12867433063546e-04 , -1.21600592927711e-02 ) - 26 ( -1.01812972547680e+00 , -3.32161441751850e-02 , 3.03826306323336e+00 ) ( 4.07251890190722e-03 , 1.32864576700740e-04 , -1.21530522529335e-02 ) - 27 ( -1.01860146079953e+00 , -3.82407265723690e-02 , 3.03687681895852e+00 ) ( 4.07440584319812e-03 , 1.52962906289476e-04 , -1.21475072758341e-02 ) - 28 ( -1.01906990926088e+00 , -4.32085185509670e-02 , 3.03591402640151e+00 ) ( 4.07627963704352e-03 , 1.72834074203868e-04 , -1.21436561056061e-02 ) - 29 ( -1.01944079088857e+00 , -4.80403043559997e-02 , 3.03540770557330e+00 ) ( 4.07776316355427e-03 , 1.92161217423999e-04 , -1.21416308222932e-02 ) - 30 ( -1.01962854699229e+00 , -5.26637607211525e-02 , 3.03536739031026e+00 ) ( 4.07851418796916e-03 , 2.10655042884610e-04 , -1.21414695612410e-02 ) - 31 ( -1.01955869904214e+00 , -5.70160615819230e-02 , 3.03578166763320e+00 ) ( 4.07823479616858e-03 , 2.28064246327692e-04 , -1.21431266705328e-02 ) - 32 ( -1.01916934949446e+00 , -6.10450112992021e-02 , 3.03662168653196e+00 ) ( 4.07667739797783e-03 , 2.44180045196809e-04 , -1.21464867461279e-02 ) - 33 ( -1.01841199592886e+00 , -6.47090594473295e-02 , 3.03784542784121e+00 ) ( 4.07364798371542e-03 , 2.58836237789318e-04 , -1.21513817113648e-02 ) - 34 ( -1.01725180900141e+00 , -6.79766894059315e-02 , 3.03940247260780e+00 ) ( 4.06900723600566e-03 , 2.71906757623726e-04 , -1.21576098904312e-02 ) - 35 ( -1.01566747325464e+00 , -7.08256323783010e-02 , 3.04123879381492e+00 ) ( 4.06266989301856e-03 , 2.83302529513204e-04 , -1.21649551752597e-02 ) - 36 ( -1.01365053401866e+00 , -7.32422529508256e-02 , 3.04330111209864e+00 ) ( 4.05460213607464e-03 , 2.92969011803303e-04 , -1.21732044483946e-02 ) - 37 ( -1.01120429036970e+00 , -7.52213164514461e-02 , 3.04554044991178e+00 ) ( 4.04481716147881e-03 , 3.00885265805785e-04 , -1.21821617996471e-02 ) - 38 ( -1.00834237984516e+00 , -7.67661955129212e-02 , 3.04791477756569e+00 ) ( 4.03336951938062e-03 , 3.07064782051685e-04 , -1.21916591102628e-02 ) - 39 ( -1.00508734834212e+00 , -7.78894402311651e-02 , 3.05039080321297e+00 ) ( 4.02034939336848e-03 , 3.11557760924660e-04 , -1.22015632128519e-02 ) - 40 ( -1.00146957910752e+00 , -7.86134846594192e-02 , 3.05294498810129e+00 ) ( 4.00587831643010e-03 , 3.14453938637677e-04 , -1.22117799524052e-02 ) + 20 ( -1.02062769591997e+00 , -6.08213500496868e-03 , 3.05064351583999e+00 ) ( 4.08251078367986e-03 , 2.43285400198747e-05 , -1.22025740633599e-02 ) + 21 ( -1.01915363052765e+00 , -9.94509780830111e-03 , 3.04869855745494e+00 ) ( 4.07661452211062e-03 , 3.97803912332044e-05 , -1.21947942298198e-02 ) + 22 ( -1.01819426535002e+00 , -1.41317848404291e-02 , 3.04652291622540e+00 ) ( 4.07277706140009e-03 , 5.65271393617164e-05 , -1.21860916649016e-02 ) + 23 ( -1.01769353644663e+00 , -1.86072292938941e-02 , 3.04426035188961e+00 ) ( 4.07077414578651e-03 , 7.44289171755765e-05 , -1.21770414075584e-02 ) + 24 ( -1.01757652378195e+00 , -2.33228912103368e-02 , 3.04204924924129e+00 ) ( 4.07030609512782e-03 , 9.32915648413473e-05 , -1.21681969969652e-02 ) + 25 ( -1.01775441505923e+00 , -2.82168582418595e-02 , 3.04001482316877e+00 ) ( 4.07101766023693e-03 , 1.12867432967438e-04 , -1.21600592926751e-02 ) + 26 ( -1.01812972634717e+00 , -3.32161441348876e-02 , 3.03826306321224e+00 ) ( 4.07251890538870e-03 , 1.32864576539550e-04 , -1.21530522528490e-02 ) + 27 ( -1.01860146171764e+00 , -3.82407265273962e-02 , 3.03687681894353e+00 ) ( 4.07440584687057e-03 , 1.52962906109585e-04 , -1.21475072757741e-02 ) + 28 ( -1.01906991022665e+00 , -4.32085185057993e-02 , 3.03591402639455e+00 ) ( 4.07627964090659e-03 , 1.72834074023197e-04 , -1.21436561055782e-02 ) + 29 ( -1.01944079190354e+00 , -4.80403042958217e-02 , 3.03540770557534e+00 ) ( 4.07776316761414e-03 , 1.92161217183287e-04 , -1.21416308223013e-02 ) + 30 ( -1.01962854805362e+00 , -5.26637606618744e-02 , 3.03536739032252e+00 ) ( 4.07851419221450e-03 , 2.10655042647498e-04 , -1.21414695612901e-02 ) + 31 ( -1.01955870015183e+00 , -5.70160615084173e-02 , 3.03578166765498e+00 ) ( 4.07823480060733e-03 , 2.28064246033669e-04 , -1.21431266706199e-02 ) + 32 ( -1.01916935065016e+00 , -6.10450112208311e-02 , 3.03662168656281e+00 ) ( 4.07667740260063e-03 , 2.44180044883324e-04 , -1.21464867462512e-02 ) + 33 ( -1.01841199712945e+00 , -6.47090593651689e-02 , 3.03784542787964e+00 ) ( 4.07364798851779e-03 , 2.58836237460676e-04 , -1.21513817115186e-02 ) + 34 ( -1.01725181024562e+00 , -6.79766893212266e-02 , 3.03940247265176e+00 ) ( 4.06900724098247e-03 , 2.71906757284906e-04 , -1.21576098906070e-02 ) + 35 ( -1.01566747454107e+00 , -7.08256322924462e-02 , 3.04123879386186e+00 ) ( 4.06266989816427e-03 , 2.83302529169785e-04 , -1.21649551754474e-02 ) + 36 ( -1.01365053534415e+00 , -7.32422528716987e-02 , 3.04330111214608e+00 ) ( 4.05460214137660e-03 , 2.92969011486795e-04 , -1.21732044485843e-02 ) + 37 ( -1.01120429173592e+00 , -7.52213163683270e-02 , 3.04554044995591e+00 ) ( 4.04481716694370e-03 , 3.00885265473308e-04 , -1.21821617998237e-02 ) + 38 ( -1.00834238124957e+00 , -7.67661954318190e-02 , 3.04791477760370e+00 ) ( 4.03336952499827e-03 , 3.07064781727276e-04 , -1.21916591104148e-02 ) + 39 ( -1.00508734978189e+00 , -7.78894401522693e-02 , 3.05039080324243e+00 ) ( 4.02034939912757e-03 , 3.11557760609077e-04 , -1.22015632129697e-02 ) + 40 ( -1.00146958058144e+00 , -7.86134845943720e-02 , 3.05294498811922e+00 ) ( 4.00587832232574e-03 , 3.14453938377488e-04 , -1.22117799524769e-02 ) diff --git a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt +++ b/namd/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out index d5a9ba71d..049f980a2 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -117,7 +113,6 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,28 +123,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped index 9da6963c4..4798692a9 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -1.00012595304074e+00 , 6.81665091817865e-01 , 2.98047387612439e+00 ) + x ( -1.00012595362068e+00 , 6.81665091863780e-01 , 2.98047387611607e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj index 0460e926b..2c4dc1d5b 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -1.06103618343284e+00 , 6.89338769329275e-01 , 2.94525790836472e+00 ) ( 4.24414473373135e-03 , -2.75735507731710e-03 , -1.17810316334589e-02 ) - 1 ( -1.05984233192313e+00 , 6.87788139043843e-01 , 2.94477124393299e+00 ) ( 4.23936932769251e-03 , -2.75115255617537e-03 , -1.17790849757320e-02 ) - 2 ( -1.05834139767053e+00 , 6.86747097207406e-01 , 2.94497571748830e+00 ) ( 4.23336559068213e-03 , -2.74698838882962e-03 , -1.17799028699532e-02 ) - 3 ( -1.05650257668221e+00 , 6.86210421251529e-01 , 2.94589847749821e+00 ) ( 4.22601030672886e-03 , -2.74484168500611e-03 , -1.17835939099928e-02 ) - 4 ( -1.05430079770892e+00 , 6.86147780863856e-01 , 2.94752842221134e+00 ) ( 4.21720319083568e-03 , -2.74459112345542e-03 , -1.17901136888454e-02 ) - 5 ( -1.05172167277253e+00 , 6.86504075704956e-01 , 2.94981674140592e+00 ) ( 4.20688669109011e-03 , -2.74601630281983e-03 , -1.17992669656237e-02 ) - 6 ( -1.04876508122907e+00 , 6.87201123721589e-01 , 2.95267979110080e+00 ) ( 4.19506032491627e-03 , -2.74880449488636e-03 , -1.18107191644032e-02 ) - 7 ( -1.04544721826884e+00 , 6.88141185039855e-01 , 2.95600363775429e+00 ) ( 4.18178887307535e-03 , -2.75256474015942e-03 , -1.18240145510172e-02 ) - 8 ( -1.04180123376858e+00 , 6.89212570640885e-01 , 2.95964984567615e+00 ) ( 4.16720493507430e-03 , -2.75685028256354e-03 , -1.18385993827046e-02 ) - 9 ( -1.03787678373610e+00 , 6.90297113537972e-01 , 2.96346243142858e+00 ) ( 4.15150713494440e-03 , -2.76118845415189e-03 , -1.18538497257143e-02 ) - 10 ( -1.03373882399961e+00 , 6.91278691950712e-01 , 2.96727611987909e+00 ) ( 4.13495529599842e-03 , -2.76511476780285e-03 , -1.18691044795164e-02 ) - 11 ( -1.02946582281404e+00 , 6.92051560786413e-01 , 2.97092585771778e+00 ) ( 4.11786329125617e-03 , -2.76820624314565e-03 , -1.18837034308711e-02 ) - 12 ( -1.02514737799452e+00 , 6.92527153631102e-01 , 2.97425707642372e+00 ) ( 4.10058951197807e-03 , -2.77010861452441e-03 , -1.18970283056949e-02 ) - 13 ( -1.02088104335244e+00 , 6.92638311699283e-01 , 2.97713574419012e+00 ) ( 4.08352417340977e-03 , -2.77055324679713e-03 , -1.19085429767605e-02 ) - 14 ( -1.01676819341134e+00 , 6.92340498830537e-01 , 2.97945703485996e+00 ) ( 4.06707277364537e-03 , -2.76936199532215e-03 , -1.19178281394398e-02 ) - 15 ( -1.01290896014230e+00 , 6.91610275878003e-01 , 2.98115162233085e+00 ) ( 4.05163584056920e-03 , -2.76644110351201e-03 , -1.19246064893234e-02 ) - 16 ( -1.00939651098372e+00 , 6.90441852787200e-01 , 2.98218905906499e+00 ) ( 4.03758604393490e-03 , -2.76176741114880e-03 , -1.19287562362600e-02 ) - 17 ( -1.00631118523086e+00 , 6.88842837382683e-01 , 2.98257821430650e+00 ) ( 4.02524474092344e-03 , -2.75537134953073e-03 , -1.19303128572260e-02 ) - 18 ( -1.00371516461503e+00 , 6.86830298535374e-01 , 2.98236510041194e+00 ) ( 4.01486065846013e-03 , -2.74732119414150e-03 , -1.19294604016477e-02 ) - 19 ( -1.00164834841389e+00 , 6.84427986279444e-01 , 2.98162851652728e+00 ) ( 4.00659339365556e-03 , -2.73771194511777e-03 , -1.19265140661091e-02 ) - 20 ( -1.00012595304074e+00 , 6.81665091817865e-01 , 2.98047387612439e+00 ) ( 4.00050381216295e-03 , -2.72666036727146e-03 , -1.19218955044975e-02 ) + 0 ( -1.06103618343284e+00 , 6.89338769329276e-01 , 2.94525790836472e+00 ) ( 4.24414473373135e-03 , -2.75735507731710e-03 , -1.17810316334589e-02 ) + 1 ( -1.05984233192469e+00 , 6.87788139043584e-01 , 2.94477124393315e+00 ) ( 4.23936932769878e-03 , -2.75115255617434e-03 , -1.17790849757326e-02 ) + 2 ( -1.05834139784456e+00 , 6.86747097242960e-01 , 2.94497571747643e+00 ) ( 4.23336559137826e-03 , -2.74698838897184e-03 , -1.17799028699057e-02 ) + 3 ( -1.05650257672870e+00 , 6.86210421249889e-01 , 2.94589847749012e+00 ) ( 4.22601030691479e-03 , -2.74484168499956e-03 , -1.17835939099605e-02 ) + 4 ( -1.05430079785211e+00 , 6.86147780883707e-01 , 2.94752842220746e+00 ) ( 4.21720319140842e-03 , -2.74459112353483e-03 , -1.17901136888298e-02 ) + 5 ( -1.05172167280505e+00 , 6.86504075687213e-01 , 2.94981674140398e+00 ) ( 4.20688669122020e-03 , -2.74601630274885e-03 , -1.17992669656159e-02 ) + 6 ( -1.04876508127498e+00 , 6.87201123703198e-01 , 2.95267979110959e+00 ) ( 4.19506032509991e-03 , -2.74880449481279e-03 , -1.18107191644384e-02 ) + 7 ( -1.04544721833213e+00 , 6.88141185021492e-01 , 2.95600363777447e+00 ) ( 4.18178887332851e-03 , -2.75256474008597e-03 , -1.18240145510979e-02 ) + 8 ( -1.04180123385309e+00 , 6.89212570623204e-01 , 2.95964984570740e+00 ) ( 4.16720493541237e-03 , -2.75685028249282e-03 , -1.18385993828296e-02 ) + 9 ( -1.03787678384604e+00 , 6.90297113521857e-01 , 2.96346243146993e+00 ) ( 4.15150713538415e-03 , -2.76118845408743e-03 , -1.18538497258797e-02 ) + 10 ( -1.03373882413909e+00 , 6.91278691937061e-01 , 2.96727611992879e+00 ) ( 4.13495529655637e-03 , -2.76511476774824e-03 , -1.18691044797152e-02 ) + 11 ( -1.02946582298704e+00 , 6.92051560776091e-01 , 2.97092585777341e+00 ) ( 4.11786329194816e-03 , -2.76820624310436e-03 , -1.18837034310937e-02 ) + 12 ( -1.02514737820470e+00 , 6.92527153624911e-01 , 2.97425707648239e+00 ) ( 4.10058951281881e-03 , -2.77010861449964e-03 , -1.18970283059295e-02 ) + 13 ( -1.02088104360310e+00 , 6.92638311697926e-01 , 2.97713574424865e+00 ) ( 4.08352417441239e-03 , -2.77055324679170e-03 , -1.19085429769946e-02 ) + 14 ( -1.01676819370524e+00 , 6.92340498834602e-01 , 2.97945703491512e+00 ) ( 4.06707277482098e-03 , -2.76936199533841e-03 , -1.19178281396605e-02 ) + 15 ( -1.01290896048165e+00 , 6.91610275887974e-01 , 2.98115162237959e+00 ) ( 4.05163584192661e-03 , -2.76644110355190e-03 , -1.19246064895184e-02 ) + 16 ( -1.00939651136992e+00 , 6.90441852803797e-01 , 2.98218905910471e+00 ) ( 4.03758604547969e-03 , -2.76176741121519e-03 , -1.19287562364189e-02 ) + 17 ( -1.00631118564907e+00 , 6.88842837429205e-01 , 2.98257821433475e+00 ) ( 4.02524474259627e-03 , -2.75537134971682e-03 , -1.19303128573390e-02 ) + 18 ( -1.00371516509773e+00 , 6.86830298565906e-01 , 2.98236510042806e+00 ) ( 4.01486066039091e-03 , -2.74732119426362e-03 , -1.19294604017122e-02 ) + 19 ( -1.00164834896320e+00 , 6.84427986320491e-01 , 2.98162851652942e+00 ) ( 4.00659339585280e-03 , -2.73771194528196e-03 , -1.19265140661177e-02 ) + 20 ( -1.00012595362068e+00 , 6.81665091863780e-01 , 2.98047387611607e+00 ) ( 4.00050381448271e-03 , -2.72666036745512e-03 , -1.19218955044643e-02 ) diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out index 0678a53ba..33501e601 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -117,7 +113,6 @@ colvars: # centers = { ( 0 , 0 , 0 ) } colvars: # targetCenters = { ( 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -128,33 +123,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -1.00013 , 0.681665 , 2.98047 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped index 91a4697ed..a98e88769 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -9.91441714242838e-01 , 6.28848618783027e-01 , 2.99185347905522e+00 ) + x ( -9.91441715714853e-01 , 6.28848618963486e-01 , 2.99185347903944e+00 ) } restraint { diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj index 620786d60..03b7dd3c1 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -1.00012595304074e+00 , 6.81665091817865e-01 , 2.98047387612439e+00 ) ( 4.00050381216295e-03 , -2.72666036727146e-03 , -1.19218955044975e-02 ) - 21 ( -9.99138074265429e-01 , 6.78576393035151e-01 , 2.97902552992938e+00 ) ( 3.99655229706172e-03 , -2.71430557214061e-03 , -1.19161021197175e-02 ) - 22 ( -9.98651127330001e-01 , 6.75203199213713e-01 , 2.97741796071850e+00 ) ( 3.99460450932001e-03 , -2.70081279685485e-03 , -1.19096718428740e-02 ) - 23 ( -9.98610824984928e-01 , 6.71594275046680e-01 , 2.97578645097527e+00 ) ( 3.99444329993971e-03 , -2.68637710018672e-03 , -1.19031458039011e-02 ) - 24 ( -9.98946203875902e-01 , 6.67806005224566e-01 , 2.97425809128013e+00 ) ( 3.99578481550361e-03 , -2.67122402089826e-03 , -1.18970323651205e-02 ) - 25 ( -9.99574198422540e-01 , 6.63901368074702e-01 , 2.97294412314502e+00 ) ( 3.99829679369016e-03 , -2.65560547229881e-03 , -1.18917764925801e-02 ) - 26 ( -1.00040433097533e+00 , 6.59947725499445e-01 , 2.97193439794950e+00 ) ( 4.00161732390132e-03 , -2.63979090199778e-03 , -1.18877375917980e-02 ) - 27 ( -1.00134314895068e+00 , 6.56013782494476e-01 , 2.97129431693768e+00 ) ( 4.00537259580271e-03 , -2.62405512997790e-03 , -1.18851772677507e-02 ) - 28 ( -1.00229811929707e+00 , 6.52166332519549e-01 , 2.97106411686442e+00 ) ( 4.00919247718828e-03 , -2.60866533007820e-03 , -1.18842564674577e-02 ) - 29 ( -1.00318079719258e+00 , 6.48467421337220e-01 , 2.97125993942505e+00 ) ( 4.01272318877031e-03 , -2.59386968534888e-03 , -1.18850397577002e-02 ) - 30 ( -1.00390921995519e+00 , 6.44972467377165e-01 , 2.97187614716835e+00 ) ( 4.01563687982076e-03 , -2.57988986950866e-03 , -1.18875045886734e-02 ) - 31 ( -1.00440958895174e+00 , 6.41729568214161e-01 , 2.97288843458850e+00 ) ( 4.01763835580695e-03 , -2.56691827285664e-03 , -1.18915537383540e-02 ) - 32 ( -1.00461737929322e+00 , 6.38779886442533e-01 , 2.97425757145681e+00 ) ( 4.01846951717287e-03 , -2.55511954577013e-03 , -1.18970302858273e-02 ) - 33 ( -1.00447804965225e+00 , 6.36158624483086e-01 , 2.97593366047442e+00 ) ( 4.01791219860901e-03 , -2.54463449793234e-03 , -1.19037346418977e-02 ) - 34 ( -1.00394748506057e+00 , 6.33895972784570e-01 , 2.97786077690709e+00 ) ( 4.01578994024229e-03 , -2.53558389113828e-03 , -1.19114431076284e-02 ) - 35 ( -1.00299228402442e+00 , 6.32017486363480e-01 , 2.97998162117694e+00 ) ( 4.01196913609766e-03 , -2.52806994545392e-03 , -1.19199264847078e-02 ) - 36 ( -1.00158988930755e+00 , 6.30543620030167e-01 , 2.98224176225043e+00 ) ( 4.00635955723021e-03 , -2.52217448012067e-03 , -1.19289670490017e-02 ) - 37 ( -9.99728646517214e-01 , 6.29488492386688e-01 , 2.98459308225513e+00 ) ( 3.99891458606886e-03 , -2.51795396954675e-03 , -1.19383723290205e-02 ) - 38 ( -9.97407894168705e-01 , 6.28858255557523e-01 , 2.98699626416501e+00 ) ( 3.98963157667482e-03 , -2.51543302223009e-03 , -1.19479850566600e-02 ) - 39 ( -9.94638187594213e-01 , 6.28649565173414e-01 , 2.98942235139329e+00 ) ( 3.97855275037685e-03 , -2.51459826069366e-03 , -1.19576894055732e-02 ) - 40 ( -9.91441714242838e-01 , 6.28848618783027e-01 , 2.99185347905522e+00 ) ( 3.96576685697135e-03 , -2.51539447513211e-03 , -1.19674139162209e-02 ) + 20 ( -1.00012595362068e+00 , 6.81665091863780e-01 , 2.98047387611607e+00 ) ( 4.00050381448271e-03 , -2.72666036745512e-03 , -1.19218955044643e-02 ) + 21 ( -9.99138074893485e-01 , 6.78576393089195e-01 , 2.97902552991010e+00 ) ( 3.99655229957394e-03 , -2.71430557235678e-03 , -1.19161021196404e-02 ) + 22 ( -9.98651128006031e-01 , 6.75203199276404e-01 , 2.97741796069013e+00 ) ( 3.99460451202413e-03 , -2.70081279710561e-03 , -1.19096718427605e-02 ) + 23 ( -9.98610825708839e-01 , 6.71594275118549e-01 , 2.97578645094022e+00 ) ( 3.99444330283536e-03 , -2.68637710047419e-03 , -1.19031458037609e-02 ) + 24 ( -9.98946204647680e-01 , 6.67806005306121e-01 , 2.97425809124110e+00 ) ( 3.99578481859072e-03 , -2.67122402122448e-03 , -1.18970323649644e-02 ) + 25 ( -9.99574199242226e-01 , 6.63901368166392e-01 , 2.97294412310483e+00 ) ( 3.99829679696891e-03 , -2.65560547266557e-03 , -1.18917764924193e-02 ) + 26 ( -1.00040433184298e+00 , 6.59947725601624e-01 , 2.97193439791086e+00 ) ( 4.00161732737193e-03 , -2.63979090240649e-03 , -1.18877375916435e-02 ) + 27 ( -1.00134314986632e+00 , 6.56013782607379e-01 , 2.97129431690302e+00 ) ( 4.00537259946528e-03 , -2.62405513042951e-03 , -1.18851772676121e-02 ) + 28 ( -1.00229812026062e+00 , 6.52166332643251e-01 , 2.97106411683570e+00 ) ( 4.00919248104249e-03 , -2.60866533057301e-03 , -1.18842564673428e-02 ) + 29 ( -1.00318079820382e+00 , 6.48467421471618e-01 , 2.97125993940365e+00 ) ( 4.01272319281527e-03 , -2.59386968588647e-03 , -1.18850397576146e-02 ) + 30 ( -1.00390922101371e+00 , 6.44972467521952e-01 , 2.97187614715496e+00 ) ( 4.01563688405484e-03 , -2.57988987008781e-03 , -1.18875045886199e-02 ) + 31 ( -1.00440959005691e+00 , 6.41729568368808e-01 , 2.97288843458314e+00 ) ( 4.01763836022764e-03 , -2.56691827347523e-03 , -1.18915537383326e-02 ) + 32 ( -1.00461738044422e+00 , 6.38779886606265e-01 , 2.97425757145878e+00 ) ( 4.01846952177690e-03 , -2.55511954642506e-03 , -1.18970302858351e-02 ) + 33 ( -1.00447805084808e+00 , 6.36158624654867e-01 , 2.97593366048238e+00 ) ( 4.01791220339232e-03 , -2.54463449861947e-03 , -1.19037346419295e-02 ) + 34 ( -1.00394748630005e+00 , 6.33895972963095e-01 , 2.97786077691918e+00 ) ( 4.01578994520019e-03 , -2.53558389185238e-03 , -1.19114431076767e-02 ) + 35 ( -1.00299228530624e+00 , 6.32017486547197e-01 , 2.97998162119086e+00 ) ( 4.01196914122495e-03 , -2.52806994618879e-03 , -1.19199264847635e-02 ) + 36 ( -1.00158989063031e+00 , 6.30543620217316e-01 , 2.98224176226361e+00 ) ( 4.00635956252122e-03 , -2.52217448086926e-03 , -1.19289670490544e-02 ) + 37 ( -9.99728647879413e-01 , 6.29488492575348e-01 , 2.98459308226489e+00 ) ( 3.99891459151765e-03 , -2.51795397030139e-03 , -1.19383723290595e-02 ) + 38 ( -9.97407895568871e-01 , 6.28858255745633e-01 , 2.98699626416867e+00 ) ( 3.98963158227548e-03 , -2.51543302298253e-03 , -1.19479850566747e-02 ) + 39 ( -9.94638189030939e-01 , 6.28649565358814e-01 , 2.98942235138835e+00 ) ( 3.97855275612376e-03 , -2.51459826143525e-03 , -1.19576894055534e-02 ) + 40 ( -9.91441715714853e-01 , 6.28848618963486e-01 , 2.99185347903944e+00 ) ( 3.96576686285941e-03 , -2.51539447585394e-03 , -1.19674139161578e-02 ) diff --git a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt +++ b/namd/tests/library/000_distancevec_harmonic-dvec-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out index c28a9ea83..402d5433b 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: Reading legacy options lowerWall and lowerWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). colvars: # lowerWall = 0.1 colvars: Reading legacy options upperWall and upperWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). @@ -117,7 +113,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -131,7 +126,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -147,27 +141,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped index c116ac47b..e53a1f4de 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491521323e+00 + x 3.21685491539556e+00 } restraint { diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj index d5d525eb6..222aa6880 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095402e+00 -1.20174855638161e-02 - 2 3.20383991841948e+00 -1.20153596736779e-02 - 3 3.20396638982490e+00 -1.20158655592996e-02 - 4 3.20472672277551e+00 -1.20189068911021e-02 - 5 3.20606083670179e+00 -1.20242433468072e-02 - 6 3.20787669543948e+00 -1.20315067817579e-02 - 7 3.21005568755800e+00 -1.20402227502320e-02 - 8 3.21245908142754e+00 -1.20498363257101e-02 - 9 3.21493559049101e+00 -1.20597423619640e-02 - 10 3.21733015640955e+00 -1.20693206256382e-02 - 11 3.21949374123820e+00 -1.20779749649528e-02 - 12 3.22129339461899e+00 -1.20851735784760e-02 - 13 3.22262143319445e+00 -1.20904857327778e-02 - 14 3.22340249773966e+00 -1.20936099909586e-02 - 15 3.22359762729192e+00 -1.20943905091677e-02 - 16 3.22320508654863e+00 -1.20928203461945e-02 - 17 3.22225829334495e+00 -1.20890331733798e-02 - 18 3.22082156074746e+00 -1.20832862429898e-02 - 19 3.21898439787187e+00 -1.20759375914875e-02 - 20 3.21685491521323e+00 -1.20674196608529e-02 +# step one fa_one + 0 3.20554673468334e+00 -1.20221869387334e-02 + 1 3.20437139095464e+00 -1.20174855638185e-02 + 2 3.20383991847368e+00 -1.20153596738947e-02 + 3 3.20396638983244e+00 -1.20158655593298e-02 + 4 3.20472672282330e+00 -1.20189068912932e-02 + 5 3.20606083670688e+00 -1.20242433468275e-02 + 6 3.20787669545864e+00 -1.20315067818346e-02 + 7 3.21005568759325e+00 -1.20402227503730e-02 + 8 3.21245908147994e+00 -1.20498363259198e-02 + 9 3.21493559056115e+00 -1.20597423622446e-02 + 10 3.21733015649727e+00 -1.20693206259891e-02 + 11 3.21949374134263e+00 -1.20779749653705e-02 + 12 3.22129339473872e+00 -1.20851735789549e-02 + 13 3.22262143332763e+00 -1.20904857333105e-02 + 14 3.22340249788422e+00 -1.20936099915369e-02 + 15 3.22359762744577e+00 -1.20943905097831e-02 + 16 3.22320508670988e+00 -1.20928203468395e-02 + 17 3.22225829351165e+00 -1.20890331740466e-02 + 18 3.22082156091933e+00 -1.20832862436773e-02 + 19 3.21898439805351e+00 -1.20759375922140e-02 + 20 3.21685491539556e+00 -1.20674196615823e-02 diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out index 2607e31b0..2340e1d34 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: Reading legacy options lowerWall and lowerWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). colvars: # lowerWall = 0.1 colvars: Reading legacy options upperWall and upperWallConstant: consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2). @@ -117,7 +113,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -131,7 +126,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -147,32 +141,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "onew" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped index 1b9898933..c542b2a71 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397364200070e+00 + x 3.21397364247543e+00 } restraint { diff --git a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj index 8b5e494a7..1b5a859eb 100644 --- a/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancewalls-compatible/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 20 3.21685491521323e+00 -1.20674196608529e-02 - 21 3.21455264073267e+00 -1.20582105629307e-02 - 22 3.21220094103318e+00 -1.20488037641327e-02 - 23 3.20991934284523e+00 -1.20396773713809e-02 - 24 3.20781628562398e+00 -1.20312651424959e-02 - 25 3.20598302292944e+00 -1.20239320917178e-02 - 26 3.20448930614687e+00 -1.20179572245875e-02 - 27 3.20338117886792e+00 -1.20135247154717e-02 - 28 3.20268080933861e+00 -1.20107232373544e-02 - 29 3.20238791142161e+00 -1.20095516456865e-02 - 30 3.20248233467135e+00 -1.20099293386854e-02 - 31 3.20292744714189e+00 -1.20117097885676e-02 - 32 3.20367415705454e+00 -1.20146966282182e-02 - 33 3.20466539988114e+00 -1.20186615995246e-02 - 34 3.20584087581816e+00 -1.20233635032726e-02 - 35 3.20714161837695e+00 -1.20285664735078e-02 - 36 3.20851394921166e+00 -1.20340557968466e-02 - 37 3.20991249801338e+00 -1.20396499920535e-02 - 38 3.21130224431234e+00 -1.20452089772494e-02 - 39 3.21265973069097e+00 -1.20506389227639e-02 - 40 3.21397364200070e+00 -1.20558945680028e-02 +# step one fa_one + 20 3.21685491539556e+00 -1.20674196615823e-02 + 21 3.21455264092142e+00 -1.20582105636857e-02 + 22 3.21220094123025e+00 -1.20488037649210e-02 + 23 3.20991934305299e+00 -1.20396773722120e-02 + 24 3.20781628584511e+00 -1.20312651433804e-02 + 25 3.20598302316673e+00 -1.20239320926669e-02 + 26 3.20448930640296e+00 -1.20179572256119e-02 + 27 3.20338117914512e+00 -1.20135247165805e-02 + 28 3.20268080963872e+00 -1.20107232385549e-02 + 29 3.20238791174576e+00 -1.20095516469830e-02 + 30 3.20248233501992e+00 -1.20099293400797e-02 + 31 3.20292744751448e+00 -1.20117097900579e-02 + 32 3.20367415744996e+00 -1.20146966297998e-02 + 33 3.20466540029747e+00 -1.20186616011899e-02 + 34 3.20584087625286e+00 -1.20233635050114e-02 + 35 3.20714161882697e+00 -1.20285664753079e-02 + 36 3.20851394967362e+00 -1.20340557986945e-02 + 37 3.20991249848372e+00 -1.20396499939349e-02 + 38 3.21130224478748e+00 -1.20452089791499e-02 + 39 3.21265973116748e+00 -1.20506389246699e-02 + 40 3.21397364247543e+00 -1.20558945699017e-02 diff --git a/namd/tests/library/000_distancewalls-compatible/namd-version.txt b/namd/tests/library/000_distancewalls-compatible/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancewalls-compatible/namd-version.txt +++ b/namd/tests/library/000_distancewalls-compatible/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out index 5da428bfa..104a466ca 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -132,27 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped index a0bbaca3d..ed4ff587f 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685491521323e+00 + x 3.21685491541898e+00 } restraint { diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj index d5d525eb6..222aa6880 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 0 3.20554673468334e+00 -1.20221869387334e-02 - 1 3.20437139095402e+00 -1.20174855638161e-02 - 2 3.20383991841948e+00 -1.20153596736779e-02 - 3 3.20396638982490e+00 -1.20158655592996e-02 - 4 3.20472672277551e+00 -1.20189068911021e-02 - 5 3.20606083670179e+00 -1.20242433468072e-02 - 6 3.20787669543948e+00 -1.20315067817579e-02 - 7 3.21005568755800e+00 -1.20402227502320e-02 - 8 3.21245908142754e+00 -1.20498363257101e-02 - 9 3.21493559049101e+00 -1.20597423619640e-02 - 10 3.21733015640955e+00 -1.20693206256382e-02 - 11 3.21949374123820e+00 -1.20779749649528e-02 - 12 3.22129339461899e+00 -1.20851735784760e-02 - 13 3.22262143319445e+00 -1.20904857327778e-02 - 14 3.22340249773966e+00 -1.20936099909586e-02 - 15 3.22359762729192e+00 -1.20943905091677e-02 - 16 3.22320508654863e+00 -1.20928203461945e-02 - 17 3.22225829334495e+00 -1.20890331733798e-02 - 18 3.22082156074746e+00 -1.20832862429898e-02 - 19 3.21898439787187e+00 -1.20759375914875e-02 - 20 3.21685491521323e+00 -1.20674196608529e-02 +# step one fa_one + 0 3.20554673468334e+00 -1.20221869387334e-02 + 1 3.20437139095464e+00 -1.20174855638185e-02 + 2 3.20383991847368e+00 -1.20153596738947e-02 + 3 3.20396638983244e+00 -1.20158655593298e-02 + 4 3.20472672282330e+00 -1.20189068912932e-02 + 5 3.20606083670688e+00 -1.20242433468275e-02 + 6 3.20787669545864e+00 -1.20315067818346e-02 + 7 3.21005568759325e+00 -1.20402227503730e-02 + 8 3.21245908147994e+00 -1.20498363259198e-02 + 9 3.21493559056115e+00 -1.20597423622446e-02 + 10 3.21733015649727e+00 -1.20693206259891e-02 + 11 3.21949374134263e+00 -1.20779749653705e-02 + 12 3.22129339473872e+00 -1.20851735789549e-02 + 13 3.22262143332763e+00 -1.20904857333105e-02 + 14 3.22340249788422e+00 -1.20936099915369e-02 + 15 3.22359762744577e+00 -1.20943905097831e-02 + 16 3.22320508670988e+00 -1.20928203468395e-02 + 17 3.22225829351165e+00 -1.20890331740466e-02 + 18 3.22082156091933e+00 -1.20832862436773e-02 + 19 3.21898439805351e+00 -1.20759375922140e-02 + 20 3.21685491539556e+00 -1.20674196615823e-02 diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out index abfe2c323..442f83cc6 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -116,7 +112,6 @@ colvars: # timeStepFactor = 1 [default] colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } colvars: # upperWalls = { 0.2 } @@ -132,32 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonicwalls bias "harmonicwalls1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped index 24da413b3..6869425e6 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.state.stripped @@ -5,6 +5,6 @@ configuration { colvar { name one - x 3.21397364200070e+00 + x 3.21397364247543e+00 } diff --git a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj index 8b5e494a7..744ca6324 100644 --- a/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancewalls/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 20 3.21685491521323e+00 -1.20674196608529e-02 - 21 3.21455264073267e+00 -1.20582105629307e-02 - 22 3.21220094103318e+00 -1.20488037641327e-02 - 23 3.20991934284523e+00 -1.20396773713809e-02 - 24 3.20781628562398e+00 -1.20312651424959e-02 - 25 3.20598302292944e+00 -1.20239320917178e-02 - 26 3.20448930614687e+00 -1.20179572245875e-02 - 27 3.20338117886792e+00 -1.20135247154717e-02 - 28 3.20268080933861e+00 -1.20107232373544e-02 - 29 3.20238791142161e+00 -1.20095516456865e-02 - 30 3.20248233467135e+00 -1.20099293386854e-02 - 31 3.20292744714189e+00 -1.20117097885676e-02 - 32 3.20367415705454e+00 -1.20146966282182e-02 - 33 3.20466539988114e+00 -1.20186615995246e-02 - 34 3.20584087581816e+00 -1.20233635032726e-02 - 35 3.20714161837695e+00 -1.20285664735078e-02 - 36 3.20851394921166e+00 -1.20340557968466e-02 - 37 3.20991249801338e+00 -1.20396499920535e-02 - 38 3.21130224431234e+00 -1.20452089772494e-02 - 39 3.21265973069097e+00 -1.20506389227639e-02 - 40 3.21397364200070e+00 -1.20558945680028e-02 +# step one fa_one + 20 3.21685491539556e+00 -1.20674196615823e-02 + 21 3.21455264092142e+00 -1.20582105636857e-02 + 22 3.21220094123025e+00 -1.20488037649210e-02 + 23 3.20991934305299e+00 -1.20396773722120e-02 + 24 3.20781628584511e+00 -1.20312651433804e-02 + 25 3.20598302316673e+00 -1.20239320926669e-02 + 26 3.20448930640296e+00 -1.20179572256119e-02 + 27 3.20338117914513e+00 -1.20135247165805e-02 + 28 3.20268080963872e+00 -1.20107232385549e-02 + 29 3.20238791174576e+00 -1.20095516469830e-02 + 30 3.20248233501992e+00 -1.20099293400797e-02 + 31 3.20292744751448e+00 -1.20117097900579e-02 + 32 3.20367415744996e+00 -1.20146966297998e-02 + 33 3.20466540029747e+00 -1.20186616011899e-02 + 34 3.20584087625286e+00 -1.20233635050114e-02 + 35 3.20714161882697e+00 -1.20285664753079e-02 + 36 3.20851394967362e+00 -1.20340557986945e-02 + 37 3.20991249848372e+00 -1.20396499939349e-02 + 38 3.21130224478748e+00 -1.20452089791499e-02 + 39 3.21265973116748e+00 -1.20506389246699e-02 + 40 3.21397364247543e+00 -1.20558945699017e-02 diff --git a/namd/tests/library/000_distancewalls/namd-version.txt b/namd/tests/library/000_distancewalls/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancewalls/namd-version.txt +++ b/namd/tests/library/000_distancewalls/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out index 77591e0dc..6050e7b8b 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -93,7 +89,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,28 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceXY colvar component (derived from distanceZ): -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped index c8670d81f..e4b21622a 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.10714243532007e+00 + x 6.10714243551413e+00 } restraint { diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj index 53d38880d..f720fa8df 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 6.28105056411478e+00 -2.47242022564591e-02 - 1 6.27348215345428e+00 -2.46939286138171e-02 - 2 6.26560937402036e+00 -2.46624374960814e-02 - 3 6.25746867772245e+00 -2.46298747108898e-02 - 4 6.24910164328359e+00 -2.45964065731343e-02 - 5 6.24055013191846e+00 -2.45622005276738e-02 - 6 6.23185200432364e+00 -2.45274080172946e-02 - 7 6.22303839583394e+00 -2.44921535833358e-02 - 8 6.21413319108828e+00 -2.44565327643531e-02 - 9 6.20515473551492e+00 -2.44206189420597e-02 - 10 6.19611912777932e+00 -2.43844765111173e-02 - 11 6.18704379217786e+00 -2.43481751687115e-02 - 12 6.17794986550634e+00 -2.43117994620254e-02 - 13 6.16886233368985e+00 -2.42754493347594e-02 - 14 6.15980779734801e+00 -2.42392311893920e-02 - 15 6.15081082211236e+00 -2.42032432884494e-02 - 16 6.14189045972150e+00 -2.41675618388860e-02 - 17 6.13305851983281e+00 -2.41322340793312e-02 - 18 6.12432058994875e+00 -2.40972823597950e-02 - 19 6.11567981072365e+00 -2.40627192428946e-02 - 20 6.10714243532007e+00 -2.40285697412803e-02 + 1 6.27348215345519e+00 -2.46939286138208e-02 + 2 6.26560937402416e+00 -2.46624374960966e-02 + 3 6.25746867772978e+00 -2.46298747109191e-02 + 4 6.24910164339331e+00 -2.45964065735732e-02 + 5 6.24055013199026e+00 -2.45622005279610e-02 + 6 6.23185200440414e+00 -2.45274080176166e-02 + 7 6.22303839597047e+00 -2.44921535838819e-02 + 8 6.21413319113433e+00 -2.44565327645373e-02 + 9 6.20515473557225e+00 -2.44206189422890e-02 + 10 6.19611912784920e+00 -2.43844765113968e-02 + 11 6.18704379226119e+00 -2.43481751690448e-02 + 12 6.17794986560366e+00 -2.43117994624146e-02 + 13 6.16886233380139e+00 -2.42754493352055e-02 + 14 6.15980779747392e+00 -2.42392311898957e-02 + 15 6.15081082225229e+00 -2.42032432890092e-02 + 16 6.14189045993828e+00 -2.41675618397531e-02 + 17 6.13305851999790e+00 -2.41322340799916e-02 + 18 6.12432059012462e+00 -2.40972823604985e-02 + 19 6.11567981090937e+00 -2.40627192436375e-02 + 20 6.10714243551413e+00 -2.40285697420565e-02 diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out index 075f0e20f..41e804f09 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -93,7 +89,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,33 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceXY colvar component (derived from distanceZ): -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 6.10714 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 4c3a90cc1..7dee8d34e 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.98331278916950e+00 + x 5.98331278931269e+00 } restraint { diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 911bdd5e5..32bba6125 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 6.10714243532007e+00 -2.40285697412803e-02 - 21 6.09872341342112e+00 -2.39948936536845e-02 - 22 6.09045001143359e+00 -2.39618000457344e-02 - 23 6.08236193472670e+00 -2.39294477389068e-02 - 24 6.07450749039471e+00 -2.38980299615788e-02 - 25 6.06693661268103e+00 -2.38677464507241e-02 - 26 6.05969250620041e+00 -2.38387700248016e-02 - 27 6.05280395335489e+00 -2.38112158134196e-02 - 28 6.04628004883300e+00 -2.37851201953320e-02 - 29 6.04010849181403e+00 -2.37604339672561e-02 - 30 6.03425782309445e+00 -2.37370312923778e-02 - 31 6.02868299608911e+00 -2.37147319843564e-02 - 32 6.02333268352863e+00 -2.36933307341145e-02 - 33 6.01815611215759e+00 -2.36726244486304e-02 - 34 6.01310736859049e+00 -2.36524294743619e-02 - 35 6.00814619516367e+00 -2.36325847806547e-02 - 36 6.00323573477869e+00 -2.36129429391148e-02 - 37 5.99833888974827e+00 -2.35933555589931e-02 - 38 5.99341543880525e+00 -2.35736617552210e-02 - 39 5.98842160564732e+00 -2.35536864225893e-02 - 40 5.98331278916950e+00 -2.35332511566780e-02 + 20 6.10714243551413e+00 -2.40285697420565e-02 + 21 6.09872341362206e+00 -2.39948936544883e-02 + 22 6.09045001163983e+00 -2.39618000465593e-02 + 23 6.08236193493661e+00 -2.39294477397464e-02 + 24 6.07450749060677e+00 -2.38980299624271e-02 + 25 6.06693661289397e+00 -2.38677464515759e-02 + 26 6.05969250641318e+00 -2.38387700256527e-02 + 27 6.05280395356655e+00 -2.38112158142662e-02 + 28 6.04628004904281e+00 -2.37851201961713e-02 + 29 6.04010849202162e+00 -2.37604339680865e-02 + 30 6.03425782329929e+00 -2.37370312931972e-02 + 31 6.02868299629071e+00 -2.37147319851628e-02 + 32 6.02333268372630e+00 -2.36933307349052e-02 + 33 6.01815611235053e+00 -2.36726244494021e-02 + 34 6.01310736877805e+00 -2.36524294751122e-02 + 35 6.00814619534536e+00 -2.36325847813815e-02 + 36 6.00323573491681e+00 -2.36129429396672e-02 + 37 5.99833888991827e+00 -2.35933555596731e-02 + 38 5.99341543896732e+00 -2.35736617558693e-02 + 39 5.98842160580047e+00 -2.35536864232019e-02 + 40 5.98331278931269e+00 -2.35332511572508e-02 diff --git a/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancexy-axis_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 2c3cfb574..47628ecd0 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -128,7 +124,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -156,7 +152,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -167,27 +162,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 72f369787..176efa019 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -8.59990180563031e-01 + x -8.59990198173114e-01 } restraint { diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 4c2bf9e40..70fa4a67c 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 -8.26433309912956e-01 3.70573323965182e-03 - 1 -8.30798422481479e-01 3.72319368992592e-03 - 2 -8.34843463278505e-01 3.73937385311402e-03 - 3 -8.38485394485613e-01 3.75394157794245e-03 - 4 -8.41661116098088e-01 3.76664446439235e-03 - 5 -8.44330033670842e-01 3.77732013468337e-03 - 6 -8.46475937017231e-01 3.78590374806892e-03 - 7 -8.48108706693449e-01 3.79243482677379e-03 - 8 -8.49265839004939e-01 3.79706335601975e-03 - 9 -8.50013078434704e-01 3.80005231373882e-03 - 10 -8.50442876788669e-01 3.80177150715468e-03 - 11 -8.50669506981126e-01 3.80267802792450e-03 - 12 -8.50820419731476e-01 3.80328167892590e-03 - 13 -8.51024556129912e-01 3.80409822451965e-03 - 14 -8.51399343953497e-01 3.80559737581399e-03 - 15 -8.52038548534679e-01 3.80815419413872e-03 - 16 -8.53002864518614e-01 3.81201145807446e-03 - 17 -8.54314489576230e-01 3.81725795830492e-03 - 18 -8.55956217377252e-01 3.82382486950901e-03 - 19 -8.57875090444802e-01 3.83150036177921e-03 - 20 -8.59990180563031e-01 3.83996072225212e-03 + 0 -8.26433309912938e-01 3.70573323965175e-03 + 1 -8.30798422653703e-01 3.72319369061481e-03 + 2 -8.34843463959367e-01 3.73937385583747e-03 + 3 -8.38485395966467e-01 3.75394158386587e-03 + 4 -8.41661118716793e-01 3.76664447486717e-03 + 5 -8.44330037532375e-01 3.77732015012950e-03 + 6 -8.46475942328684e-01 3.78590376931474e-03 + 7 -8.48108713604438e-01 3.79243485441775e-03 + 8 -8.49265847455379e-01 3.79706338982152e-03 + 9 -8.50013088506371e-01 3.80005235402549e-03 + 10 -8.50442888427590e-01 3.80177155371036e-03 + 11 -8.50669520082139e-01 3.80267808032856e-03 + 12 -8.50820434143500e-01 3.80328173657400e-03 + 13 -8.51024571667568e-01 3.80409828667027e-03 + 14 -8.51399360397394e-01 3.80559744158957e-03 + 15 -8.52038565660105e-01 3.80815426264042e-03 + 16 -8.53002882142410e-01 3.81201152856964e-03 + 17 -8.54314507410905e-01 3.81725802964362e-03 + 18 -8.55956235278788e-01 3.82382494111515e-03 + 19 -8.57875108259331e-01 3.83150043303732e-03 + 20 -8.59990198173114e-01 3.83996079269246e-03 diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index c538704bb..f5cc9bea4 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -128,7 +124,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -156,7 +152,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -167,32 +162,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -0.85999 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index e14a8519c..45102536d 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -8.73679341988515e-01 + x -8.73679344015558e-01 } restraint { diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 196573273..3deea24fd 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -8.59990180563031e-01 3.83996072225212e-03 - 21 -8.62203454907955e-01 3.84881381963182e-03 - 22 -8.64411966660376e-01 3.85764786664150e-03 - 23 -8.66519183472681e-01 3.86607673389073e-03 - 24 -8.68443525944736e-01 3.87377410377894e-03 - 25 -8.70123145503911e-01 3.88049258201564e-03 - 26 -8.71517297801704e-01 3.88606919120682e-03 - 27 -8.72605590311192e-01 3.89042236124477e-03 - 28 -8.73386584894720e-01 3.89354633957888e-03 - 29 -8.73876656083864e-01 3.89550662433546e-03 - 30 -8.74108973746083e-01 3.89643589498433e-03 - 31 -8.74131737353112e-01 3.89652694941245e-03 - 32 -8.74004671163881e-01 3.89601868465552e-03 - 33 -8.73793440724393e-01 3.89517376289757e-03 - 34 -8.73562583048199e-01 3.89425033219280e-03 - 35 -8.73368244828915e-01 3.89347297931566e-03 - 36 -8.73251943874718e-01 3.89300777549887e-03 - 37 -8.73236008871937e-01 3.89294403548775e-03 - 38 -8.73320778720346e-01 3.89328311488138e-03 - 39 -8.73483517910175e-01 3.89393407164070e-03 - 40 -8.73679341988515e-01 3.89471736795406e-03 + 20 -8.59990198173114e-01 3.83996079269246e-03 + 21 -8.62203472237901e-01 3.84881388895160e-03 + 22 -8.64411983661211e-01 3.85764793464484e-03 + 23 -8.66519200121738e-01 3.86607680048695e-03 + 24 -8.68443542236674e-01 3.87377416894670e-03 + 25 -8.70123161439966e-01 3.88049264575987e-03 + 26 -8.71517313394698e-01 3.88606925357879e-03 + 27 -8.72605605560332e-01 3.89042242224133e-03 + 28 -8.73386599791250e-01 3.89354639916500e-03 + 29 -8.73876670619764e-01 3.89550668247906e-03 + 30 -8.74108987877203e-01 3.89643595150881e-03 + 31 -8.74131751029475e-01 3.89652700411790e-03 + 32 -8.74004684295612e-01 3.89601873718245e-03 + 33 -8.73793453194366e-01 3.89517381277746e-03 + 34 -8.73562594705087e-01 3.89425037882035e-03 + 35 -8.73368255487214e-01 3.89347302194886e-03 + 36 -8.73251953225498e-01 3.89300781290199e-03 + 37 -8.73236016855329e-01 3.89294406742132e-03 + 38 -8.73320784989416e-01 3.89328313995766e-03 + 39 -8.73483522192930e-01 3.89393408877172e-03 + 40 -8.73679344015558e-01 3.89471737606223e-03 diff --git a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out index 2e51c81a1..f979e078c 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -93,7 +89,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,27 +127,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 743d82299..315e08bfa 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.36084906819583e+00 + x -1.36084906835146e+00 } restraint { diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj index 04f28cf76..5a45e7f71 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 -1.30811322832419e+00 5.63245291329675e-03 - 1 -1.31312967389517e+00 5.65251869558068e-03 - 2 -1.31783653970327e+00 5.67134615881307e-03 - 3 -1.32215424605829e+00 5.68861698423318e-03 - 4 -1.32602357036953e+00 5.70409428147812e-03 - 5 -1.32940837597080e+00 5.71763350388318e-03 - 6 -1.33229787218032e+00 5.72919148872128e-03 - 7 -1.33470872947835e+00 5.73883491791339e-03 - 8 -1.33668672329647e+00 5.74674689318588e-03 - 9 -1.33830687027260e+00 5.75322748109041e-03 - 10 -1.33967061044650e+00 5.75868244178601e-03 - 11 -1.34089899817730e+00 5.76359599270922e-03 - 12 -1.34212195003997e+00 5.76848780015989e-03 - 13 -1.34346488791768e+00 5.77385955167074e-03 - 14 -1.34503502472400e+00 5.78014009889602e-03 - 15 -1.34690966827500e+00 5.78763867309998e-03 - 16 -1.34912827121975e+00 5.79651308487899e-03 - 17 -1.35168908892136e+00 5.80675635568542e-03 - 18 -1.35455056705533e+00 5.81820226822131e-03 - 19 -1.35763717560197e+00 5.83054870240789e-03 - 20 -1.36084906819583e+00 5.84339627278333e-03 + 1 -1.31312967389554e+00 5.65251869558218e-03 + 2 -1.31783653970528e+00 5.67134615882111e-03 + 3 -1.32215424606121e+00 5.68861698424484e-03 + 4 -1.32602357044897e+00 5.70409428179589e-03 + 5 -1.32940837601300e+00 5.71763350405199e-03 + 6 -1.33229787222417e+00 5.72919148889668e-03 + 7 -1.33470872956429e+00 5.73883491825714e-03 + 8 -1.33668672330288e+00 5.74674689321152e-03 + 9 -1.33830687028298e+00 5.75322748113191e-03 + 10 -1.33967061046305e+00 5.75868244185221e-03 + 11 -1.34089899820229e+00 5.76359599280915e-03 + 12 -1.34212195007558e+00 5.76848780030233e-03 + 13 -1.34346488796592e+00 5.77385955186369e-03 + 14 -1.34503502478640e+00 5.78014009914560e-03 + 15 -1.34690966835284e+00 5.78763867341137e-03 + 16 -1.34912827135129e+00 5.79651308540518e-03 + 17 -1.35168908903116e+00 5.80675635612465e-03 + 18 -1.35455056718115e+00 5.81820226872460e-03 + 19 -1.35763717574320e+00 5.83054870297280e-03 + 20 -1.36084906835146e+00 5.84339627340585e-03 diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out index a23ca29bd..485b39b01 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "main". colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "ref". colvars: # printAtomIDs = off [default] @@ -93,7 +89,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -121,7 +117,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -132,32 +127,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -1.36085 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 136c16382..412aeb991 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.39034316039439e+00 + x -1.39034316080283e+00 } restraint { diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj index a4c9b3a4c..befbe002b 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -1.36084906819583e+00 5.84339627278333e-03 - 21 -1.36407445392026e+00 5.85629781568104e-03 - 22 -1.36720290808304e+00 5.86881163233218e-03 - 23 -1.37013738742009e+00 5.88054954968036e-03 - 24 -1.37280289903525e+00 5.89121159614099e-03 - 25 -1.37515071153241e+00 5.90060284612964e-03 - 26 -1.37715842575073e+00 5.90863370300290e-03 - 27 -1.37882731750845e+00 5.91530927003381e-03 - 28 -1.38017874358088e+00 5.92071497432353e-03 - 29 -1.38125089771898e+00 5.92500359087591e-03 - 30 -1.38209611844487e+00 5.92838447377948e-03 - 31 -1.38277799970331e+00 5.93111199881324e-03 - 32 -1.38336718471100e+00 5.93346873884401e-03 - 33 -1.38393522958249e+00 5.93574091832994e-03 - 34 -1.38454693837034e+00 5.93818775348136e-03 - 35 -1.38525254040143e+00 5.94101016160571e-03 - 36 -1.38608129795618e+00 5.94432519182472e-03 - 37 -1.38703765719641e+00 5.94815062878565e-03 - 38 -1.38810029482091e+00 5.95240117928366e-03 - 39 -1.38922386299017e+00 5.95689545196067e-03 - 40 -1.39034316039439e+00 5.96137264157755e-03 + 20 -1.36084906835146e+00 5.84339627340585e-03 + 21 -1.36407445408937e+00 5.85629781635750e-03 + 22 -1.36720290826447e+00 5.86881163305788e-03 + 23 -1.37013738761253e+00 5.88054955045011e-03 + 24 -1.37280289923745e+00 5.89121159694979e-03 + 25 -1.37515071174335e+00 5.90060284697339e-03 + 26 -1.37715842596968e+00 5.90863370387872e-03 + 27 -1.37882731773524e+00 5.91530927094096e-03 + 28 -1.38017874381549e+00 5.92071497526196e-03 + 29 -1.38125089796176e+00 5.92500359184703e-03 + 30 -1.38209611869660e+00 5.92838447478640e-03 + 31 -1.38277799996508e+00 5.93111199986032e-03 + 32 -1.38336718498411e+00 5.93346873993646e-03 + 33 -1.38393522986837e+00 5.93574091947349e-03 + 34 -1.38454693867054e+00 5.93818775468217e-03 + 35 -1.38525254071746e+00 5.94101016286982e-03 + 36 -1.38608129820739e+00 5.94432519282957e-03 + 37 -1.38703765754614e+00 5.94815063018456e-03 + 38 -1.38810029519008e+00 5.95240118076033e-03 + 39 -1.38922386337907e+00 5.95689545351630e-03 + 40 -1.39034316080283e+00 5.96137264321130e-03 diff --git a/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancez-axis_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index c0a1e5523..6a560e3a5 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -122,25 +118,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "ref" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "ref2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -158,7 +154,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -186,7 +182,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -197,27 +192,16 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index d5eed6ce9..2e49c4c9e 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.08397176151429e+00 + x -1.08397176799240e+00 } restraint { diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index f93b97049..65f7e07c6 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 -9.80249904624397e-01 4.32099961849759e-03 - 1 -9.84212417024538e-01 4.33684966809815e-03 - 2 -9.88661109713663e-01 4.35464443885465e-03 - 3 -9.93533514317858e-01 4.37413405727143e-03 - 4 -9.98748276916619e-01 4.39499310766648e-03 - 5 -1.00421405294110e+00 4.41685621176441e-03 - 6 -1.00983863113832e+00 4.43935452455326e-03 - 7 -1.01553670456534e+00 4.46214681826137e-03 - 8 -1.02123525373971e+00 4.48494101495885e-03 - 9 -1.02687633616795e+00 4.50750534467179e-03 - 10 -1.03241787163978e+00 4.52967148655913e-03 - 11 -1.03783351061600e+00 4.55133404246400e-03 - 12 -1.04311256849593e+00 4.57245027398371e-03 - 13 -1.04826043601893e+00 4.59304174407571e-03 - 14 -1.05329903171149e+00 4.61319612684598e-03 - 15 -1.05826630299168e+00 4.63306521196671e-03 - 16 -1.06321375752698e+00 4.65285503010794e-03 - 17 -1.06820149508569e+00 4.67280598034278e-03 - 18 -1.07329085286143e+00 4.69316341144574e-03 - 19 -1.07853543510507e+00 4.71414174042029e-03 - 20 -1.08397176151429e+00 4.73588704605716e-03 + 1 -9.84212417045979e-01 4.33684966818392e-03 + 2 -9.88661109800629e-01 4.35464443920252e-03 + 3 -9.93533514516252e-01 4.37413405806501e-03 + 4 -9.98748277164812e-01 4.39499310865925e-03 + 5 -1.00421405344078e+00 4.41685621376314e-03 + 6 -1.00983863188372e+00 4.43935452753490e-03 + 7 -1.01553670554762e+00 4.46214682219049e-03 + 8 -1.02123525515648e+00 4.48494102062594e-03 + 9 -1.02687633794460e+00 4.50750535177839e-03 + 10 -1.03241787380232e+00 4.52967149520928e-03 + 11 -1.03783351318359e+00 4.55133405273438e-03 + 12 -1.04311257148085e+00 4.57245028592339e-03 + 13 -1.04826043942746e+00 4.59304175770984e-03 + 14 -1.05329903554539e+00 4.61319614218156e-03 + 15 -1.05826630725091e+00 4.63306522900363e-03 + 16 -1.06321376214922e+00 4.65285504859689e-03 + 17 -1.06820150020073e+00 4.67280600080292e-03 + 18 -1.07329085842513e+00 4.69316343370051e-03 + 19 -1.07853544110981e+00 4.71414176443922e-03 + 20 -1.08397176799240e+00 4.73588707196959e-03 diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index 061d003d9..ba5525f63 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "main". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "main": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -91,25 +87,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "main" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "ref". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -122,25 +118,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "ref" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "ref2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "ref2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -158,7 +154,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -186,7 +182,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -197,32 +192,21 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - distanceZ colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -1.08397 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index fe4b2733e..d4af65402 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.16407036445456e+00 + x -1.16407038814966e+00 } restraint { diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index e130970be..6b3544c2b 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -1.08397176151429e+00 4.73588704605716e-03 - 21 -1.08961113878614e+00 4.75844455514457e-03 - 22 -1.09543448080392e+00 4.78173792321566e-03 - 23 -1.10139152374815e+00 4.80556609499262e-03 - 24 -1.10740502102334e+00 4.82962008409337e-03 - 25 -1.11337932023318e+00 4.85351728093272e-03 - 26 -1.11921161432554e+00 4.87684645730215e-03 - 27 -1.12480356375684e+00 4.89921425502736e-03 - 28 -1.13007105240499e+00 4.92028420961995e-03 - 29 -1.13495045141868e+00 4.93980180567474e-03 - 30 -1.13940077305703e+00 4.95760309222813e-03 - 31 -1.14340231104241e+00 4.97360924416963e-03 - 32 -1.14695342368223e+00 4.98781369472891e-03 - 33 -1.15006758434473e+00 5.00027033737893e-03 - 34 -1.15277234867027e+00 5.01108939468107e-03 - 35 -1.15511060843172e+00 5.02044243372689e-03 - 36 -1.15714306128669e+00 5.02857224514677e-03 - 37 -1.15894998077622e+00 5.03579992310487e-03 - 38 -1.16063037878806e+00 5.04252151515225e-03 - 39 -1.16229745749708e+00 5.04918982998831e-03 - 40 -1.16407036445456e+00 5.05628145781825e-03 + 20 -1.08397176799240e+00 4.73588707196959e-03 + 21 -1.08961114576828e+00 4.75844458307313e-03 + 22 -1.09543448832272e+00 4.78173795329088e-03 + 23 -1.10139153184823e+00 4.80556612739293e-03 + 24 -1.10740502975272e+00 4.82962011901087e-03 + 25 -1.11337932964347e+00 4.85351731857390e-03 + 26 -1.11921162447008e+00 4.87684649788032e-03 + 27 -1.12480357468871e+00 4.89921429875483e-03 + 28 -1.13007106417501e+00 4.92028425670005e-03 + 29 -1.13495046407338e+00 4.93980185629353e-03 + 30 -1.13940078663755e+00 4.95760314655019e-03 + 31 -1.14340232558319e+00 4.97360930233275e-03 + 32 -1.14695343921062e+00 4.98781375684249e-03 + 33 -1.15006760088067e+00 5.00027040352269e-03 + 34 -1.15277236622642e+00 5.01108946490570e-03 + 35 -1.15511062701432e+00 5.02044250805728e-03 + 36 -1.15714308092986e+00 5.02857232371945e-03 + 37 -1.15895000141084e+00 5.03580000564338e-03 + 38 -1.16063040046971e+00 5.04252160187884e-03 + 39 -1.16229748017487e+00 5.04918992069947e-03 + 40 -1.16407038814966e+00 5.05628155259863e-03 diff --git a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_distancez-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out index 39a4e5160..d0a584bcb 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,123 +1,104 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). colvars: # smp = on [default] +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 +colvars: # colvarsTrajAppend = off [default] colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] +colvars: # scriptingAfterBiases = on [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" colvars: Initializing a new "eigenvector" component. -colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. +colvars: Atom group "atoms" defined, 10 atoms initialized: total mass = 120.11, total charge = 0.53. colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_refpos2.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( -0.0422 , 0.1463 , 0.0241 ) colvars: # differenceVector = on -colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = x_vec - x_ref. -colvars: # normalizeVector = off [default] -colvars: Normalizing the vector so that the norm of the projection |v ⋅ (x_vec - x_ref)| = 1. +colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = v - x0. +colvars: "differenceVector" is on: normalizing the vector. colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerWallConstant = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] +colvars: # timeStepFactor = 1 [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = on colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] -colvars: # outputFreq = 10 [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] +colvars: # forceConstant = 0.001 colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] +colvars: # targetForceConstant = 0 [default] colvars: # outputCenters = off [default] -colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] -colvars: # targetForceConstant = -1 [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -126,32 +107,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - eigenvector colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group one:0/0. 10 atoms: total mass = 120.11. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Writing to colvar trajectory file "test.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Writing the state file "test.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.tmp.colvars.state". -colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Writing the state file "test.tmp.colvars.state". colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 394993cd3..76e206e36 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -3.60947829036805e-02 + x -3.60947829208825e-02 } restraint { diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj index 9598d462c..4a835eab3 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 -3.63490056109624e-02 5.45396022443850e-04 - 1 -3.61854039791530e-02 5.44741615916612e-04 - 2 -3.60399977705685e-02 5.44159991082274e-04 - 3 -3.59299659182762e-02 5.43719863673105e-04 - 4 -3.58694335566139e-02 5.43477734226456e-04 - 5 -3.58677543994292e-02 5.43471017597717e-04 - 6 -3.59283042400466e-02 5.43713216960186e-04 - 7 -3.60479478822797e-02 5.44191791529119e-04 - 8 -3.62172258806581e-02 5.44868903522632e-04 - 9 -3.64212097862254e-02 5.45684839144902e-04 - 10 -3.66409048748858e-02 5.46563619499543e-04 - 11 -3.68550253056277e-02 5.47420101222511e-04 - 12 -3.70419376830354e-02 5.48167750732142e-04 - 13 -3.71815653192522e-02 5.48726261277009e-04 - 14 -3.72570812792000e-02 5.49028325116800e-04 - 15 -3.72562760818578e-02 5.49025104327431e-04 - 16 -3.71725450680349e-02 5.48690180272139e-04 - 17 -3.70054820445949e-02 5.48021928178380e-04 - 18 -3.67610840776074e-02 5.47044336310430e-04 - 19 -3.64515682403436e-02 5.45806272961374e-04 - 20 -3.60947829036805e-02 5.44379131614722e-04 + 0 -3.63490056109622e-02 5.45396022443849e-04 + 1 -3.61854039791939e-02 5.44741615916776e-04 + 2 -3.60399977707408e-02 5.44159991082963e-04 + 3 -3.59299659186929e-02 5.43719863674771e-04 + 4 -3.58694335574107e-02 5.43477734229643e-04 + 5 -3.58677544007612e-02 5.43471017603045e-04 + 6 -3.59283042420775e-02 5.43713216968310e-04 + 7 -3.60479478851721e-02 5.44191791540688e-04 + 8 -3.62172258845634e-02 5.44868903538253e-04 + 9 -3.64212097912740e-02 5.45684839165096e-04 + 10 -3.66409048811813e-02 5.46563619524725e-04 + 11 -3.68550253132438e-02 5.47420101252975e-04 + 12 -3.70419376920114e-02 5.48167750768046e-04 + 13 -3.71815653295922e-02 5.48726261318369e-04 + 14 -3.72570812908718e-02 5.49028325163487e-04 + 15 -3.72562760947929e-02 5.49025104379172e-04 + 16 -3.71725450821299e-02 5.48690180328520e-04 + 17 -3.70054820597152e-02 5.48021928238861e-04 + 18 -3.67610840935948e-02 5.47044336374379e-04 + 19 -3.64515682570253e-02 5.45806273028101e-04 + 20 -3.60947829208825e-02 5.44379131683530e-04 diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out index dbec86827..2ea9819fd 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,123 +1,104 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": -colvars: # units = "" [default] colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). colvars: # smp = on [default] +colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 +colvars: # colvarsTrajAppend = off [default] colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] +colvars: # scriptingAfterBiases = on [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" colvars: Initializing a new "eigenvector" component. -colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". -colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] -colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. +colvars: Atom group "atoms" defined, 10 atoms initialized: total mass = 120.11, total charge = 0.53. colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_refpos2.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( -0.0422 , 0.1463 , 0.0241 ) colvars: # differenceVector = on -colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = x_vec - x_ref. -colvars: # normalizeVector = off [default] -colvars: Normalizing the vector so that the norm of the projection |v ⋅ (x_vec - x_ref)| = 1. +colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = v - x0. +colvars: "differenceVector" is on: normalizing the vector. colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] -colvars: # hardLowerBoundary = off [default] -colvars: # hardUpperBoundary = off [default] +colvars: # lowerWallConstant = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] +colvars: # timeStepFactor = 1 [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = on colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] -colvars: # outputFreq = 10 [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] +colvars: # forceConstant = 0.001 colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] +colvars: # targetForceConstant = 0 [default] colvars: # outputCenters = off [default] -colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] -colvars: # targetForceConstant = -1 [default] -colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -126,37 +107,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - eigenvector colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -0.0360948 -colvars: Restarting harmonic bias "harmonic1" from step number 20. +colvars: Restarting restraint bias "harmonic1". colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). -colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group one:0/0. 10 atoms: total mass = 120.11. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Writing to colvar trajectory file "test.restart.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Writing the state file "test.restart.tmp.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Saving collective variables state to "test.restart.tmp.colvars.state". -colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Saving collective variables state to "test.restart.tmp.colvars.state". +colvars: Writing the state file "test.restart.tmp.colvars.state". colvars: Saving collective variables state to "test.restart.colvars.state". diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 4076dc85b..1fe5f317a 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -3.91331067677280e-02 + x -3.91331067913926e-02 } restraint { diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 4d83b139d..4abf779ac 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -3.60947829036805e-02 5.44379131614722e-04 - 21 -3.57131824132596e-02 5.42852729653038e-04 - 22 -3.53323468161238e-02 5.41329387264495e-04 - 23 -3.49790898711468e-02 5.39916359484587e-04 - 24 -3.46792960881774e-02 5.38717184352710e-04 - 25 -3.44557301955042e-02 5.37822920782017e-04 - 26 -3.43261260186189e-02 5.37304504074476e-04 - 27 -3.43018371648415e-02 5.37207348659366e-04 - 28 -3.43872193023786e-02 5.37548877209514e-04 - 29 -3.45797526537476e-02 5.38319010614990e-04 - 30 -3.48707654110141e-02 5.39483061644056e-04 - 31 -3.52465332512768e-02 5.40986133005107e-04 - 32 -3.56895209286986e-02 5.42758083714794e-04 - 33 -3.61795835030006e-02 5.44718334012002e-04 - 34 -3.66950290848698e-02 5.46780116339479e-04 - 35 -3.72135323147184e-02 5.48854129258874e-04 - 36 -3.77129610291621e-02 5.50851844116648e-04 - 37 -3.81722113079504e-02 5.52688845231802e-04 - 38 -3.85721257419771e-02 5.54288502967908e-04 - 39 -3.88965020615558e-02 5.55586008246223e-04 - 40 -3.91331067677280e-02 5.56532427070912e-04 + 20 -3.60947829208825e-02 5.44379131683530e-04 + 21 -3.57131824308181e-02 5.42852729723272e-04 + 22 -3.53323468338979e-02 5.41329387335592e-04 + 23 -3.49790898890280e-02 5.39916359556112e-04 + 24 -3.46792961060943e-02 5.38717184424377e-04 + 25 -3.44557302134239e-02 5.37822920853696e-04 + 26 -3.43261260365440e-02 5.37304504146176e-04 + 27 -3.43018371828071e-02 5.37207348731229e-04 + 28 -3.43872193204467e-02 5.37548877281787e-04 + 29 -3.45797526720018e-02 5.38319010688007e-04 + 30 -3.48707654295545e-02 5.39483061718218e-04 + 31 -3.52465332702127e-02 5.40986133080851e-04 + 32 -3.56895209481391e-02 5.42758083792556e-04 + 33 -3.61795835230441e-02 5.44718334092176e-04 + 34 -3.66950291055903e-02 5.46780116422361e-04 + 35 -3.72135323361536e-02 5.48854129344615e-04 + 36 -3.77129610513006e-02 5.50851844205202e-04 + 37 -3.81722113307229e-02 5.52688845322892e-04 + 38 -3.85721257652529e-02 5.54288503061011e-04 + 39 -3.88965020851454e-02 5.55586008340582e-04 + 40 -3.91331067913926e-02 5.56532427165571e-04 diff --git a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt index 157cac038..fc4f9e327 100644 --- a/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_eigenvector-difference_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. +colvars: Using NAMD interface, version 2016-11-23. diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out index 49596f239..4e6b96f89 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -115,7 +116,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -140,12 +140,10 @@ colvars: colvars: - NAMD engine: colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 496bf49f0..b33e34fce 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.24500295778074e-01 + x 4.24500295670889e-01 } restraint { diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj index 70125860e..7342a9653 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 3.02535061282782e-01 -8.10140245131129e-04 - 1 3.02349470333834e-01 -8.09397881335335e-04 - 2 3.02228609121183e-01 -8.08914436484731e-04 - 3 3.02455495419550e-01 -8.09821981678201e-04 - 4 3.03339070528187e-01 -8.13356282112746e-04 - 5 3.05186413718739e-01 -8.20745654874956e-04 - 6 3.08272259775151e-01 -8.33089039100606e-04 - 7 3.12808407688626e-01 -8.51233630754504e-04 - 8 3.18915879048982e-01 -8.75663516195929e-04 - 9 3.26602899382103e-01 -9.06411597528411e-04 - 10 3.35751830583773e-01 -9.43007322335093e-04 - 11 3.46117928882162e-01 -9.84471715528649e-04 - 12 3.57341831565545e-01 -1.02936732626218e-03 - 13 3.68975854299315e-01 -1.07590341719726e-03 - 14 3.80521732691115e-01 -1.12208693076446e-03 - 15 3.91475201717795e-01 -1.16590080687118e-03 - 16 4.01371580289910e-01 -1.20548632115964e-03 - 17 4.09826708750263e-01 -1.23930683500105e-03 - 18 4.16568902011881e-01 -1.26627560804752e-03 - 19 4.21459383117517e-01 -1.28583753247007e-03 - 20 4.24500295778074e-01 -1.29800118311230e-03 + 0 3.02535061282783e-01 -8.10140245131131e-04 + 1 3.02349470333696e-01 -8.09397881334783e-04 + 2 3.02228609120613e-01 -8.08914436482450e-04 + 3 3.02455495418290e-01 -8.09821981673159e-04 + 4 3.03339070526050e-01 -8.13356282104201e-04 + 5 3.05186413715613e-01 -8.20745654862452e-04 + 6 3.08272259770955e-01 -8.33089039083821e-04 + 7 3.12808407683237e-01 -8.51233630732947e-04 + 8 3.18915879042108e-01 -8.75663516168431e-04 + 9 3.26602899373167e-01 -9.06411597492667e-04 + 10 3.35751830571806e-01 -9.43007322287224e-04 + 11 3.46117928865759e-01 -9.84471715463035e-04 + 12 3.57341831542918e-01 -1.02936732617167e-03 + 13 3.68975854268464e-01 -1.07590341707386e-03 + 14 3.80521732650089e-01 -1.12208693060036e-03 + 15 3.91475201665008e-01 -1.16590080666003e-03 + 16 4.01371580224434e-01 -1.20548632089774e-03 + 17 4.09826708672045e-01 -1.23930683468818e-03 + 18 4.16568901921835e-01 -1.26627560768734e-03 + 19 4.21459383017533e-01 -1.28583753207013e-03 + 20 4.24500295670889e-01 -1.29800118268356e-03 diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out index 61612ef51..db684e80d 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -7,6 +7,7 @@ colvars: This version was built with the C++11 standard or higher. colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -115,7 +116,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -140,7 +140,6 @@ colvars: colvars: - NAMD engine: colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.4245 @@ -150,7 +149,6 @@ colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index f4f671fdc..d9441d73e 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.37434841876234e-01 + x 4.37434841805229e-01 } restraint { diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 2f8530fb3..6dd2653f7 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 4.24500295778074e-01 -1.29800118311230e-03 - 21 4.25830516124699e-01 -1.30332206449880e-03 - 22 4.25710168991809e-01 -1.30284067596723e-03 - 23 4.24495296936454e-01 -1.29798118774582e-03 - 24 4.22604814614221e-01 -1.29041925845688e-03 - 25 4.20482665167116e-01 -1.28193066066846e-03 - 26 4.18558612471422e-01 -1.27423444988569e-03 - 27 4.17211123890820e-01 -1.26884449556328e-03 - 28 4.16735269467297e-01 -1.26694107786919e-03 - 29 4.17317729261698e-01 -1.26927091704679e-03 - 30 4.19020232680582e-01 -1.27608093072233e-03 - 31 4.21772286278215e-01 -1.28708914511286e-03 - 32 4.25373865453946e-01 -1.30149546181578e-03 - 33 4.29508654225993e-01 -1.31803461690397e-03 - 34 4.33768111234715e-01 -1.33507244493886e-03 - 35 4.37685869084879e-01 -1.35074347633952e-03 - 36 4.40780679735902e-01 -1.36312271894361e-03 - 37 4.42604459084554e-01 -1.37041783633822e-03 - 38 4.42790500312300e-01 -1.37116200124920e-03 - 39 4.41096173922242e-01 -1.36438469568897e-03 - 40 4.37434841876234e-01 -1.34973936750494e-03 + 20 4.24500295670889e-01 -1.29800118268356e-03 + 21 4.25830516013726e-01 -1.30332206405490e-03 + 22 4.25710168880892e-01 -1.30284067552357e-03 + 23 4.24495296829610e-01 -1.29798118731844e-03 + 24 4.22604814515337e-01 -1.29041925806135e-03 + 25 4.20482665079664e-01 -1.28193066031866e-03 + 26 4.18558612398180e-01 -1.27423444959272e-03 + 27 4.17211123833643e-01 -1.26884449533457e-03 + 28 4.16735269426941e-01 -1.26694107770777e-03 + 29 4.17317729237757e-01 -1.26927091695103e-03 + 30 4.19020232671458e-01 -1.27608093068583e-03 + 31 4.21772286281203e-01 -1.28708914512481e-03 + 32 4.25373865465361e-01 -1.30149546186144e-03 + 33 4.29508654241388e-01 -1.31803461696555e-03 + 34 4.33768111249166e-01 -1.33507244499666e-03 + 35 4.37685869093343e-01 -1.35074347637337e-03 + 36 4.40780679733648e-01 -1.36312271893459e-03 + 37 4.42604459067608e-01 -1.37041783627043e-03 + 38 4.42790500277900e-01 -1.37116200111160e-03 + 39 4.41096173869207e-01 -1.36438469547683e-03 + 40 4.37434841805229e-01 -1.34973936722092e-03 diff --git a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt index 157cac038..017b69b3a 100644 --- a/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_eigenvector-normalized_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +colvars: Initializing the collective variables module, version 2022-04-14. +colvars: Using NAMD interface, version "2022-04-06". diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out index 479a448a6..99840490b 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,20 +70,19 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_random.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( 2.23122 , -1.11745 , -1.91143 ) colvars: # differenceVector = off [default] colvars: Centering the provided vector to zero. -colvars: # normalizeVector = off [default] -colvars: The norm of the vector is |v| = 23.5625. +colvars: The norm of the vector is |v| = 0.00180118. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,7 +110,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -126,26 +120,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - eigenvector colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 98d60150c..81e913df1 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.96593083265021e+00 + x 9.96593083012934e+00 } restraint { diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj index 4010095ee..57c3f5382 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 7.12848384426395e+00 -2.81139353770558e-02 - 1 7.12389036856740e+00 -2.80955614742696e-02 - 2 7.12039004727828e+00 -2.80815601891131e-02 - 3 7.12467766714325e+00 -2.80987106685730e-02 - 4 7.14407407731135e+00 -2.81762963092454e-02 - 5 7.18586833886829e+00 -2.83434733554732e-02 - 6 7.25659559563629e+00 -2.86263823825451e-02 - 7 7.36131202502140e+00 -2.90452481000856e-02 - 8 7.50293456624851e+00 -2.96117382649940e-02 - 9 7.68171812033882e+00 -3.03268724813553e-02 - 10 7.89494414916322e+00 -3.11797765966529e-02 - 11 8.13688859836978e+00 -3.21475543934791e-02 - 12 8.39911418370808e+00 -3.31964567348323e-02 - 13 8.67108915525047e+00 -3.42843566210019e-02 - 14 8.94107690223794e+00 -3.53643076089518e-02 - 15 9.19718784397990e+00 -3.63887513759196e-02 - 16 9.42845597136909e+00 -3.73138238854764e-02 - 17 9.62580650887713e+00 -3.81032260355085e-02 - 18 9.78281209829472e+00 -3.87312483931789e-02 - 19 9.89617742737599e+00 -3.91847097095039e-02 - 20 9.96593083265021e+00 -3.94637233306008e-02 + 0 7.12848384426398e+00 -2.81139353770559e-02 + 1 7.12389036856418e+00 -2.80955614742567e-02 + 2 7.12039004726484e+00 -2.80815601890594e-02 + 3 7.12467766711354e+00 -2.80987106684541e-02 + 4 7.14407407726102e+00 -2.81762963090441e-02 + 5 7.18586833879461e+00 -2.83434733551784e-02 + 6 7.25659559553746e+00 -2.86263823821498e-02 + 7 7.36131202489437e+00 -2.90452480995775e-02 + 8 7.50293456608652e+00 -2.96117382643461e-02 + 9 7.68171812012824e+00 -3.03268724805129e-02 + 10 7.89494414888129e+00 -3.11797765955252e-02 + 11 8.13688859798339e+00 -3.21475543919336e-02 + 12 8.39911418317517e+00 -3.31964567327007e-02 + 13 8.67108915452401e+00 -3.42843566180960e-02 + 14 8.94107690127196e+00 -3.53643076050878e-02 + 15 9.19718784273722e+00 -3.63887513709489e-02 + 16 9.42845596982786e+00 -3.73138238793115e-02 + 17 9.62580650703617e+00 -3.81032260281447e-02 + 18 9.78281209617585e+00 -3.87312483847034e-02 + 19 9.89617742502377e+00 -3.91847097000951e-02 + 20 9.96593083012934e+00 -3.94637233205174e-02 diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out index ea096f39d..f758c6696 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,20 +70,19 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "rmsd_atoms_random.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( 2.23122 , -1.11745 , -1.91143 ) colvars: # differenceVector = off [default] colvars: Centering the provided vector to zero. -colvars: # normalizeVector = off [default] -colvars: The norm of the vector is |v| = 23.5625. +colvars: The norm of the vector is |v| = 0.00180118. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -115,7 +110,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -126,31 +120,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - eigenvector colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 9.96593 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index d228f8399..5b5148d25 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.02340499670145e+01 + x 1.02340499653749e+01 } restraint { diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 977dc1547..eb7bf1ecb 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.96593083265021e+00 -3.94637233306008e-02 - 21 9.99532793321660e+00 -3.95813117328664e-02 - 22 9.99048850273347e+00 -3.95619540109339e-02 - 23 9.95980058803785e+00 -3.94392023521514e-02 - 24 9.91314195361405e+00 -3.92525678144562e-02 - 25 9.86098750735006e+00 -3.90439500294002e-02 - 26 9.81348370507768e+00 -3.88539348203107e-02 - 27 9.77957161075872e+00 -3.87182864430349e-02 - 28 9.76622794926487e+00 -3.86649117970595e-02 - 29 9.77787383954832e+00 -3.87114953581933e-02 - 30 9.81598266583797e+00 -3.88639306633519e-02 - 31 9.87890737157304e+00 -3.91156294862921e-02 - 32 9.96194305255191e+00 -3.94477722102076e-02 - 33 1.00576385222471e+01 -3.98305540889885e-02 - 34 1.01563633552530e+01 -4.02254534210120e-02 - 35 1.02471188262364e+01 -4.05884753049457e-02 - 36 1.03185507061932e+01 -4.08742028247726e-02 - 37 1.03600827317051e+01 -4.10403309268204e-02 - 38 1.03630544983541e+01 -4.10522179934165e-02 - 39 1.03217296680099e+01 -4.08869186720396e-02 - 40 1.02340499670145e+01 -4.05361998680579e-02 + 20 9.96593083012934e+00 -3.94637233205174e-02 + 21 9.99532793060757e+00 -3.95813117224303e-02 + 22 9.99048850012704e+00 -3.95619540005082e-02 + 23 9.95980058552870e+00 -3.94392023421148e-02 + 24 9.91314195129389e+00 -3.92525678051756e-02 + 25 9.86098750530072e+00 -3.90439500212029e-02 + 26 9.81348370336466e+00 -3.88539348134586e-02 + 27 9.77957160942564e+00 -3.87182864377026e-02 + 28 9.76622794832969e+00 -3.86649117933188e-02 + 29 9.77787383900133e+00 -3.87114953560053e-02 + 30 9.81598266564158e+00 -3.88639306625663e-02 + 31 9.87890737166341e+00 -3.91156294866536e-02 + 32 9.96194305284228e+00 -3.94477722113691e-02 + 33 1.00576385226328e+01 -3.98305540905312e-02 + 34 1.01563633556180e+01 -4.02254534224719e-02 + 35 1.02471188264620e+01 -4.05884753058479e-02 + 36 1.03185507061678e+01 -4.08742028246714e-02 + 37 1.03600827313353e+01 -4.10403309253412e-02 + 38 1.03630544975746e+01 -4.10522179902983e-02 + 39 1.03217296667927e+01 -4.08869186671706e-02 + 40 1.02340499653749e+01 -4.05361998614995e-02 diff --git a/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt b/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt index 157cac038..fc4f9e327 100644 --- a/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_eigenvector_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. +colvars: Using NAMD interface, version 2016-11-23. diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out index ac4d45dde..cabed47f2 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "eulerTheta" @@ -59,9 +55,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -74,15 +69,15 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -105,9 +100,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -119,15 +113,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -150,9 +144,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -164,15 +157,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -198,7 +191,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPsi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -215,7 +207,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPhi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -232,7 +223,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerTheta" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -244,30 +234,17 @@ colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - eulerPhi colvar component (derived from orientation): -colvars: - eulerPsi colvar component (derived from orientation): -colvars: - eulerTheta colvar component (derived from orientation): -colvars: Fu2017 https://doi.org/10.1021/acs.jctc.7b00791 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped index 9750dbd1a..9fed64568 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name eulerTheta - x 7.42926968363036e-01 + x 7.42926968363034e-01 } colvar { @@ -15,7 +15,7 @@ colvar { colvar { name eulerPsi - x -4.93710444441009e+00 + x -4.93710444441010e+00 } restraint { diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj index 1109293ce..d0984ff5d 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step eulerTheta fa_eulerTheta eulerPhi fa_eulerPhi eulerPsi fa_eulerPsi E_harmonic1 E_harmonic2 E_harmonic3 - 0 1.12335897633008e+00 -1.12335897633008e-01 -9.19929987926339e+00 9.19929987926340e-01 -5.23950348243898e+00 5.23950348243898e-01 1.37261983712451e+00 4.23135591343078e+00 6.30967694850688e-02 - 1 1.10359290098423e+00 -1.10359290098423e-01 -9.22565834570168e+00 9.22565834570168e-01 -5.25149538780149e+00 5.25149538780149e-01 1.37891019040501e+00 4.25563859558075e+00 6.08958645551400e-02 - 2 1.08440461653865e+00 -1.08440461653865e-01 -9.25678498979173e+00 9.25678498979173e-01 -5.25779637281106e+00 5.25779637281106e-01 1.38222113489726e+00 4.28440341736168e+00 5.87966686185170e-02 - 3 1.06529304335568e+00 -1.06529304335568e-01 -9.29208424764168e+00 9.29208424764168e-01 -5.25763403749821e+00 5.25763403749821e-01 1.38213578361299e+00 4.31714148326353e+00 5.67424634111001e-02 - 4 1.04571544240957e+00 -1.04571544240957e-01 -9.33104631969662e+00 9.33104631969662e-01 -5.25046695843815e+00 5.25046695843815e-01 1.37837016408254e+00 4.35342127101619e+00 5.46760393246926e-02 + 0 1.12335897633009e+00 -1.12335897633009e-01 -9.19929987926340e+00 9.19929987926340e-01 -5.23950348243898e+00 5.23950348243898e-01 1.37261983712451e+00 4.23135591343078e+00 6.30967694850690e-02 + 1 1.10359290098423e+00 -1.10359290098423e-01 -9.22565834570168e+00 9.22565834570168e-01 -5.25149538780149e+00 5.25149538780149e-01 1.37891019040502e+00 4.25563859558075e+00 6.08958645551397e-02 + 2 1.08440461653865e+00 -1.08440461653865e-01 -9.25678498979173e+00 9.25678498979173e-01 -5.25779637281105e+00 5.25779637281106e-01 1.38222113489725e+00 4.28440341736168e+00 5.87966686185170e-02 + 3 1.06529304335568e+00 -1.06529304335568e-01 -9.29208424764168e+00 9.29208424764168e-01 -5.25763403749821e+00 5.25763403749821e-01 1.38213578361299e+00 4.31714148326353e+00 5.67424634110999e-02 + 4 1.04571544240957e+00 -1.04571544240957e-01 -9.33104631969663e+00 9.33104631969663e-01 -5.25046695843814e+00 5.25046695843814e-01 1.37837016408253e+00 4.35342127101620e+00 5.46760393246926e-02 5 1.02517685434404e+00 -1.02517685434404e-01 -9.37327661318995e+00 9.37327661318995e-01 -5.23607026451037e+00 5.23607026451037e-01 1.37082159074448e+00 4.39291572336868e+00 5.25493791341371e-02 6 1.00330582597764e+00 -1.00330582597764e-01 -9.41848339102013e+00 9.41848339102013e-01 -5.21460973558002e+00 5.21460973558002e-01 1.35960773472030e+00 4.43539146934610e+00 5.03311290220341e-02 - 7 9.79907540363570e-01 -9.79907540363570e-02 -9.46643852313838e+00 9.46643852313838e-01 -5.18668671653799e+00 5.18668671653799e-01 1.34508595477558e+00 4.48067291561792e+00 4.80109393830691e-02 - 8 9.54992420449578e-01 -9.54992420449578e-02 -9.51692832794413e+00 9.51692832794413e-01 -5.15334195139500e+00 5.15334195139500e-01 1.32784666340038e+00 4.52859623996127e+00 4.56005261558072e-02 - 9 9.28783692054886e-01 -9.28783692054886e-02 -9.56970831738818e+00 9.56970831738818e-01 -5.11601429466745e+00 5.11601429466745e-01 1.30868011316208e+00 4.57896586399443e+00 4.31319573313553e-02 - 10 9.01709043906521e-01 -9.01709043906521e-02 -9.62447028619222e+00 9.62447028619222e-01 -5.07645787560575e+00 5.07645787560575e-01 1.28852122813998e+00 4.63152141448985e+00 4.06539599931406e-02 - 11 8.74379467191584e-01 -8.74379467191584e-02 -9.68082504780323e+00 9.68082504780323e-01 -5.03662790099944e+00 5.03662790099944e-01 1.26838103065630e+00 4.68591868030872e+00 3.82269726323119e-02 + 7 9.79907540363569e-01 -9.79907540363569e-02 -9.46643852313838e+00 9.46643852313838e-01 -5.18668671653799e+00 5.18668671653799e-01 1.34508595477558e+00 4.48067291561792e+00 4.80109393830689e-02 + 8 9.54992420449583e-01 -9.54992420449583e-02 -9.51692832794413e+00 9.51692832794413e-01 -5.15334195139500e+00 5.15334195139500e-01 1.32784666340038e+00 4.52859623996127e+00 4.56005261558077e-02 + 9 9.28783692054884e-01 -9.28783692054884e-02 -9.56970831738819e+00 9.56970831738819e-01 -5.11601429466744e+00 5.11601429466744e-01 1.30868011316208e+00 4.57896586399444e+00 4.31319573313551e-02 + 10 9.01709043906520e-01 -9.01709043906520e-02 -9.62447028619222e+00 9.62447028619222e-01 -5.07645787560575e+00 5.07645787560575e-01 1.28852122813998e+00 4.63152141448985e+00 4.06539599931406e-02 + 11 8.74379467191583e-01 -8.74379467191583e-02 -9.68082504780323e+00 9.68082504780323e-01 -5.03662790099944e+00 5.03662790099944e-01 1.26838103065630e+00 4.68591868030872e+00 3.82269726323119e-02 12 8.47554676237916e-01 -8.47554676237916e-02 -9.73829978053727e+00 9.73829978053727e-01 -4.99855008771719e+00 4.99855008771719e-01 1.24927514897088e+00 4.74172413078062e+00 3.59174464606379e-02 - 13 8.22093180764617e-01 -8.22093180764617e-02 -9.79634420282249e+00 9.79634420282249e-01 -4.96419034641283e+00 4.96419034641283e-01 1.23215928977092e+00 4.79841798700869e+00 3.37918598929842e-02 + 13 8.22093180764618e-01 -8.22093180764618e-02 -9.79634420282249e+00 9.79634420282249e-01 -4.96419034641283e+00 4.96419034641283e-01 1.23215928977092e+00 4.79841798700869e+00 3.37918598929844e-02 14 7.98887326318826e-01 -7.98887326318826e-02 -9.85433604587600e+00 9.85433604587600e-01 -4.93533870265480e+00 4.93533870265480e-01 1.21787840549612e+00 4.85539694525255e+00 3.19110480076421e-02 - 15 7.78788129749853e-01 -7.78788129749853e-02 -9.91157703203216e+00 9.91157703203216e-01 -4.91351570715390e+00 4.91351570715390e-01 1.20713183022241e+00 4.91196796309537e+00 3.03255475519637e-02 - 16 7.62528356252244e-01 -7.62528356252244e-02 -9.96727776858339e+00 9.96727776858339e-01 -4.89990324848287e+00 4.89990324848287e-01 1.20045259222465e+00 4.96733130580484e+00 2.90724747044375e-02 - 17 7.50652833132862e-01 -7.50652833132862e-02 -1.00205407738012e+01 1.00205407738012e+00 -4.89529691190416e+00 4.89529691190416e-01 1.19819659278492e+00 5.02056186997061e+00 2.81739837945196e-02 + 15 7.78788129749855e-01 -7.78788129749855e-02 -9.91157703203216e+00 9.91157703203216e-01 -4.91351570715390e+00 4.91351570715390e-01 1.20713183022241e+00 4.91196796309537e+00 3.03255475519638e-02 + 16 7.62528356252240e-01 -7.62528356252240e-02 -9.96727776858340e+00 9.96727776858340e-01 -4.89990324848287e+00 4.89990324848287e-01 1.20045259222465e+00 4.96733130580484e+00 2.90724747044372e-02 + 17 7.50652833132860e-01 -7.50652833132860e-02 -1.00205407738012e+01 1.00205407738012e+00 -4.89529691190416e+00 4.89529691190416e-01 1.19819659278492e+00 5.02056186997061e+00 2.81739837945194e-02 18 7.43463015261251e-01 -7.43463015261251e-02 -1.00703584090617e+01 1.00703584090617e+00 -4.90007484689111e+00 4.90007484689111e-01 1.20053667525675e+00 5.07060592434798e+00 2.76368627530676e-02 - 19 7.40979904753968e-01 -7.40979904753968e-02 -1.01156425246949e+01 1.01156425246949e+00 -4.91417861741104e+00 4.91417861741104e-01 1.20745757419099e+00 5.11631118437074e+00 2.74525609624600e-02 - 20 7.42926968363036e-01 -7.42926968363036e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441009e+00 4.93710444441009e-01 1.21875001475069e+00 5.15650108652104e+00 2.75970240160545e-02 + 19 7.40979904753968e-01 -7.40979904753968e-02 -1.01156425246949e+01 1.01156425246949e+00 -4.91417861741104e+00 4.91417861741104e-01 1.20745757419099e+00 5.11631118437075e+00 2.74525609624599e-02 + 20 7.42926968363034e-01 -7.42926968363034e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441010e+00 4.93710444441010e-01 1.21875001475070e+00 5.15650108652104e+00 2.75970240160544e-02 diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out index 7ec5027d5..17479fe12 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "eulerTheta" @@ -59,9 +55,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -74,15 +69,15 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -105,9 +100,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -119,15 +113,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -150,9 +144,8 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] @@ -164,15 +157,15 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -198,7 +191,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPsi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -215,7 +207,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerPhi" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -232,7 +223,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eulerTheta" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -244,25 +234,9 @@ colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - eulerPhi colvar component (derived from orientation): -colvars: - eulerPsi colvar component (derived from orientation): -colvars: - eulerTheta colvar component (derived from orientation): -colvars: Fu2017 https://doi.org/10.1021/acs.jctc.7b00791 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "eulerTheta" from value: 0.742927 @@ -272,11 +246,14 @@ colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: Restarting harmonic bias "harmonic2" from step number 20. colvars: Restarting harmonic bias "harmonic3" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "eulerTheta":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPhi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "eulerPsi":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped index 2c39b1548..0abbdad76 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name eulerTheta - x 4.92888911241030e-01 + x 4.92888911241022e-01 } colvar { @@ -15,7 +15,7 @@ colvar { colvar { name eulerPsi - x -5.16556439137703e+00 + x -5.16556439137704e+00 } restraint { diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj index 3f2d8e1ad..b66de304b 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step eulerTheta fa_eulerTheta eulerPhi fa_eulerPhi eulerPsi fa_eulerPsi E_harmonic1 E_harmonic2 E_harmonic3 - 20 7.42926968363036e-01 -7.42926968363036e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441009e+00 4.93710444441009e-01 1.21875001475069e+00 5.15650108652104e+00 2.75970240160545e-02 - 21 7.48733320101761e-01 -7.48733320101761e-02 -1.01883183460673e+01 1.01883183460673e+00 -4.96790750263877e+00 4.96790750263877e-01 1.23400524773873e+00 5.19009153604058e+00 2.80300792315303e-02 - 22 7.57557122198821e-01 -7.57557122198821e-02 -1.02139454102856e+01 1.02139454102856e+00 -5.00522572559092e+00 5.00522572559092e-01 1.25261422820586e+00 5.21623404221472e+00 2.86946396697080e-02 - 23 7.68329051637894e-01 -7.68329051637894e-02 -1.02317713436666e+01 1.02317713436666e+00 -5.04733083960333e+00 5.04733083960333e-01 1.27377743022054e+00 5.23445724145382e+00 2.95164765795393e-02 - 24 7.79814875676107e-01 -7.79814875676107e-02 -1.02418490445600e+01 1.02418490445600e+00 -5.09221216535160e+00 5.09221216535160e-01 1.29653123684774e+00 5.24477359257776e+00 3.04055620162871e-02 - 25 7.90694011146757e-01 -7.90694011146757e-02 -1.02447281510328e+01 1.02447281510328e+00 -5.13769297452897e+00 5.13769297452897e-01 1.31979445502622e+00 5.24772274442816e+00 3.12598509631674e-02 - 26 7.99647836011620e-01 -7.99647836011620e-02 -1.02414229458545e+01 1.02414229458545e+00 -5.18157169207901e+00 5.18157169207901e-01 1.34243426000773e+00 5.24433719779371e+00 3.19718330819034e-02 - 27 8.05448995815155e-01 -8.05448995815155e-02 -1.02333134884667e+01 1.02333134884667e+00 -5.22177344695617e+00 5.22177344695617e-01 1.36334589656683e+00 5.23603524766171e+00 3.24374042429820e-02 - 28 8.07042333855102e-01 -8.07042333855102e-02 -1.02219996119654e+01 1.02219996119654e+00 -5.25649361343075e+00 5.25649361343075e-01 1.38153625540191e+00 5.22446380335108e+00 3.25658664317145e-02 - 29 8.03610000016903e-01 -8.03610000016903e-02 -1.02091368712812e+01 1.02091368712812e+00 -5.28431542925356e+00 5.28431542925356e-01 1.39619947779236e+00 5.21132378282767e+00 3.22894516063584e-02 - 30 7.94616975119391e-01 -7.94616975119391e-02 -1.01962849681356e+01 1.01962849681356e+00 -5.30428814909504e+00 5.30428814909504e-01 1.40677363843150e+00 5.19821135757143e+00 3.15708068573945e-02 - 31 7.79837159581488e-01 -7.79837159581488e-02 -1.01847936556627e+01 1.01847936556627e+00 -5.31595928178051e+00 5.31595928178051e-01 1.41297115427742e+00 5.18650109042138e+00 3.04072997732061e-02 - 32 7.59362971789403e-01 -7.59362971789403e-02 -1.01757407630825e+01 1.01757407630825e+00 -5.31936241154539e+00 5.31936241154539e-01 1.41478082326810e+00 5.17728500387294e+00 2.88316061462417e-02 - 33 7.33602066496011e-01 -7.33602066496011e-02 -1.01699237742566e+01 1.01699237742566e+00 -5.31496943853745e+00 5.31496943853745e-01 1.41244500662936e+00 5.17136747870943e+00 2.69085995983609e-02 - 34 7.03263342872247e-01 -7.03263342872247e-02 -1.01678925721792e+01 1.01678925721792e+00 -5.30362109991434e+00 5.30362109991434e-01 1.40641983857283e+00 5.16930196796881e+00 2.47289664713924e-02 - 35 6.69331542581692e-01 -6.69331542581692e-02 -1.01700001127699e+01 1.01700001127699e+00 -5.28645108127907e+00 5.28645108127907e-01 1.39732825173783e+00 5.17144511468704e+00 2.24002356947393e-02 - 36 6.33027051643078e-01 -6.33027051643078e-02 -1.01764433502072e+01 1.01764433502072e+00 -5.26481622337318e+00 5.26481622337318e-01 1.38591449329467e+00 5.17799996299881e+00 2.00361624055964e-02 - 37 5.95746809302786e-01 -5.95746809302786e-02 -1.01872719611055e+01 1.01872719611055e+00 -5.24023891452942e+00 5.24023891452942e-01 1.37300519406742e+00 5.18902550047631e+00 1.77457130397225e-02 - 38 5.58984709726032e-01 -5.58984709726032e-02 -1.02023564051939e+01 1.02023564051939e+00 -5.21435969588687e+00 5.21435969588687e-01 1.35947735190447e+00 5.20440381093002e+00 1.56231952853748e-02 - 39 5.24235101803498e-01 -5.24235101803498e-02 -1.02213251856666e+01 1.02213251856666e+00 -5.18889149341549e+00 5.18889149341549e-01 1.34622974652198e+00 5.22377442755710e+00 1.37411220981462e-02 - 40 4.92888911241030e-01 -4.92888911241030e-02 -1.02434969074251e+01 1.02434969074251e+00 -5.16556439137703e+00 5.16556439137703e-01 1.33415277407312e+00 5.24646144462135e+00 1.21469739412184e-02 + 20 7.42926968363034e-01 -7.42926968363034e-02 -1.01552952556989e+01 1.01552952556989e+00 -4.93710444441010e+00 4.93710444441010e-01 1.21875001475070e+00 5.15650108652104e+00 2.75970240160544e-02 + 21 7.48733320101764e-01 -7.48733320101764e-02 -1.01883183460673e+01 1.01883183460673e+00 -4.96790750263877e+00 4.96790750263877e-01 1.23400524773873e+00 5.19009153604059e+00 2.80300792315305e-02 + 22 7.57557122198820e-01 -7.57557122198820e-02 -1.02139454102856e+01 1.02139454102856e+00 -5.00522572559092e+00 5.00522572559092e-01 1.25261422820586e+00 5.21623404221472e+00 2.86946396697079e-02 + 23 7.68329051637896e-01 -7.68329051637896e-02 -1.02317713436666e+01 1.02317713436666e+00 -5.04733083960333e+00 5.04733083960333e-01 1.27377743022054e+00 5.23445724145384e+00 2.95164765795395e-02 + 24 7.79814875676108e-01 -7.79814875676108e-02 -1.02418490445600e+01 1.02418490445600e+00 -5.09221216535160e+00 5.09221216535160e-01 1.29653123684774e+00 5.24477359257777e+00 3.04055620162872e-02 + 25 7.90694011146758e-01 -7.90694011146758e-02 -1.02447281510328e+01 1.02447281510328e+00 -5.13769297452897e+00 5.13769297452897e-01 1.31979445502622e+00 5.24772274442817e+00 3.12598509631674e-02 + 26 7.99647836011618e-01 -7.99647836011618e-02 -1.02414229458545e+01 1.02414229458545e+00 -5.18157169207901e+00 5.18157169207901e-01 1.34243426000773e+00 5.24433719779373e+00 3.19718330819032e-02 + 27 8.05448995815154e-01 -8.05448995815154e-02 -1.02333134884667e+01 1.02333134884667e+00 -5.22177344695617e+00 5.22177344695617e-01 1.36334589656682e+00 5.23603524766172e+00 3.24374042429820e-02 + 28 8.07042333855100e-01 -8.07042333855101e-02 -1.02219996119655e+01 1.02219996119655e+00 -5.25649361343075e+00 5.25649361343075e-01 1.38153625540191e+00 5.22446380335109e+00 3.25658664317144e-02 + 29 8.03610000016902e-01 -8.03610000016902e-02 -1.02091368712812e+01 1.02091368712812e+00 -5.28431542925356e+00 5.28431542925356e-01 1.39619947779236e+00 5.21132378282767e+00 3.22894516063583e-02 + 30 7.94616975119385e-01 -7.94616975119385e-02 -1.01962849681356e+01 1.01962849681356e+00 -5.30428814909504e+00 5.30428814909504e-01 1.40677363843151e+00 5.19821135757144e+00 3.15708068573941e-02 + 31 7.79837159581490e-01 -7.79837159581490e-02 -1.01847936556627e+01 1.01847936556627e+00 -5.31595928178051e+00 5.31595928178051e-01 1.41297115427742e+00 5.18650109042140e+00 3.04072997732063e-02 + 32 7.59362971789398e-01 -7.59362971789398e-02 -1.01757407630825e+01 1.01757407630825e+00 -5.31936241154539e+00 5.31936241154539e-01 1.41478082326810e+00 5.17728500387295e+00 2.88316061462413e-02 + 33 7.33602066496012e-01 -7.33602066496012e-02 -1.01699237742566e+01 1.01699237742566e+00 -5.31496943853745e+00 5.31496943853745e-01 1.41244500662935e+00 5.17136747870945e+00 2.69085995983609e-02 + 34 7.03263342872243e-01 -7.03263342872243e-02 -1.01678925721792e+01 1.01678925721792e+00 -5.30362109991434e+00 5.30362109991434e-01 1.40641983857283e+00 5.16930196796882e+00 2.47289664713921e-02 + 35 6.69331542581688e-01 -6.69331542581688e-02 -1.01700001127700e+01 1.01700001127700e+00 -5.28645108127908e+00 5.28645108127908e-01 1.39732825173784e+00 5.17144511468705e+00 2.24002356947391e-02 + 36 6.33027051643073e-01 -6.33027051643073e-02 -1.01764433502072e+01 1.01764433502072e+00 -5.26481622337318e+00 5.26481622337318e-01 1.38591449329467e+00 5.17799996299882e+00 2.00361624055961e-02 + 37 5.95746809302784e-01 -5.95746809302784e-02 -1.01872719611055e+01 1.01872719611055e+00 -5.24023891452942e+00 5.24023891452942e-01 1.37300519406743e+00 5.18902550047632e+00 1.77457130397224e-02 + 38 5.58984709726027e-01 -5.58984709726027e-02 -1.02023564051939e+01 1.02023564051939e+00 -5.21435969588688e+00 5.21435969588688e-01 1.35947735190448e+00 5.20440381093004e+00 1.56231952853745e-02 + 39 5.24235101803488e-01 -5.24235101803488e-02 -1.02213251856666e+01 1.02213251856666e+00 -5.18889149341550e+00 5.18889149341550e-01 1.34622974652199e+00 5.22377442755711e+00 1.37411220981457e-02 + 40 4.92888911241022e-01 -4.92888911241022e-02 -1.02434969074251e+01 1.02434969074251e+00 -5.16556439137704e+00 5.16556439137704e-01 1.33415277407312e+00 5.24646144462136e+00 1.21469739412180e-02 diff --git a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt index 157cac038..3226d7191 100644 --- a/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt +++ b/namd/tests/library/000_eulerangles_harmonic-fixed-euler/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.15alpha1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-11-09". +colvars: Using NAMD interface, version "2020-10-26". diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out index 346415abf..92061cd24 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,28 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - groupCoord colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped index f285fde00..bb2a2b55a 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.19072319981190e-06 + x 3.19072319783456e-06 } restraint { diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj index 3bfd80daf..194c5d94f 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.17405979638661e-06 3.99987303760814e-04 - 1 3.18134448326459e-06 3.99987274622067e-04 - 2 3.18580682150308e-06 3.99987256772714e-04 - 3 3.18739100900219e-06 3.99987250435964e-04 - 4 3.18623907585806e-06 3.99987255043697e-04 - 5 3.18267103066260e-06 3.99987269315877e-04 - 6 3.17715514861791e-06 3.99987291379406e-04 - 7 3.17027321053934e-06 3.99987318907158e-04 - 8 3.16268340733906e-06 3.99987349266371e-04 - 9 3.15508117715307e-06 3.99987379675291e-04 - 10 3.14815708828368e-06 3.99987407371647e-04 - 11 3.14255208141271e-06 3.99987429791674e-04 - 12 3.13881288855239e-06 3.99987444748446e-04 - 13 3.13735264456987e-06 3.99987450589422e-04 - 14 3.13842207883868e-06 3.99987446311685e-04 - 15 3.14209486005973e-06 3.99987431620560e-04 - 16 3.14826794572284e-06 3.99987406928217e-04 - 17 3.15667508008936e-06 3.99987373299680e-04 - 18 3.16691009231148e-06 3.99987332359631e-04 - 19 3.17845677325003e-06 3.99987286172907e-04 - 20 3.19072319981190e-06 3.99987237107201e-04 + 1 3.18134448325853e-06 3.99987274622067e-04 + 2 3.18580682147849e-06 3.99987256772714e-04 + 3 3.18739100894646e-06 3.99987250435964e-04 + 4 3.18623907575867e-06 3.99987255043697e-04 + 5 3.18267103050743e-06 3.99987269315878e-04 + 6 3.17715514839544e-06 3.99987291379406e-04 + 7 3.17027321023885e-06 3.99987318907159e-04 + 8 3.16268340695069e-06 3.99987349266372e-04 + 9 3.15508117666781e-06 3.99987379675293e-04 + 10 3.14815708769336e-06 3.99987407371649e-04 + 11 3.14255208070990e-06 3.99987429791677e-04 + 12 3.13881288773027e-06 3.99987444748449e-04 + 13 3.13735264362211e-06 3.99987450589426e-04 + 14 3.13842207775938e-06 3.99987446311689e-04 + 15 3.14209485884323e-06 3.99987431620565e-04 + 16 3.14826794436374e-06 3.99987406928223e-04 + 17 3.15667507858251e-06 3.99987373299686e-04 + 18 3.16691009065201e-06 3.99987332359637e-04 + 19 3.17845677143355e-06 3.99987286172914e-04 + 20 3.19072319783456e-06 3.99987237107209e-04 diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out index da182042c..d73e8c3c6 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,33 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - groupCoord colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.19072e-06 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 6e6309f87..2617a40e7 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.18473698183816e-06 + x 3.18473697725417e-06 } restraint { diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj index d3a79e359..e995df08f 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.19072319981190e-06 3.99987237107201e-04 - 21 3.20307950136251e-06 3.99987187681995e-04 - 22 3.21489838209560e-06 3.99987140406472e-04 - 23 3.22559675174575e-06 3.99987097612993e-04 - 24 3.23467513046995e-06 3.99987061299478e-04 - 25 3.24175015008330e-06 3.99987032999400e-04 - 26 3.24657591479334e-06 3.99987013696341e-04 - 27 3.24905200103034e-06 3.99987003791996e-04 - 28 3.24921865907333e-06 3.99987003125364e-04 - 29 3.24724234522045e-06 3.99987011030619e-04 - 30 3.24339473356695e-06 3.99987026421066e-04 - 31 3.23802801454050e-06 3.99987047887942e-04 - 32 3.23154776620721e-06 3.99987073808935e-04 - 33 3.22438446230774e-06 3.99987102462151e-04 - 34 3.21696475248629e-06 3.99987132140990e-04 - 35 3.20968467122739e-06 3.99987161261315e-04 - 36 3.20288713565953e-06 3.99987188451457e-04 - 37 3.19684522920946e-06 3.99987212619083e-04 - 38 3.19175121091107e-06 3.99987232995156e-04 - 39 3.18771015284195e-06 3.99987249159389e-04 - 40 3.18473698183816e-06 3.99987261052073e-04 + 20 3.19072319783456e-06 3.99987237107209e-04 + 21 3.20307949922131e-06 3.99987187682003e-04 + 22 3.21489837978856e-06 3.99987140406481e-04 + 23 3.22559674927215e-06 3.99987097613003e-04 + 24 3.23467512783040e-06 3.99987061299489e-04 + 25 3.24175014727985e-06 3.99987032999411e-04 + 26 3.24657591182937e-06 3.99987013696353e-04 + 27 3.24905199791042e-06 3.99987003792008e-04 + 28 3.24921865580300e-06 3.99987003125377e-04 + 29 3.24724234180586e-06 3.99987011030633e-04 + 30 3.24339473001463e-06 3.99987026421080e-04 + 31 3.23802801085701e-06 3.99987047887957e-04 + 32 3.23154776239895e-06 3.99987073808950e-04 + 33 3.22438445838087e-06 3.99987102462166e-04 + 34 3.21696474844672e-06 3.99987132141006e-04 + 35 3.20968466708086e-06 3.99987161261332e-04 + 36 3.20288713141188e-06 3.99987188451474e-04 + 37 3.19684522486685e-06 3.99987212619101e-04 + 38 3.19175120648019e-06 3.99987232995174e-04 + 39 3.18771014833031e-06 3.99987249159407e-04 + 40 3.18473697725417e-06 3.99987261052091e-04 diff --git a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_groupcoord-aniso_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out index 346415abf..92061cd24 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,28 +128,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - groupCoord colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped index a61c41a68..79a79deb8 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 7.87058667467717e-01 + x 7.87058667403396e-01 } restraint { diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj index 5a74dc300..9c2fb8adc 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 7.90587472610727e-01 -2.76234989044291e-03 - 1 7.90951498267255e-01 -2.76380599306902e-03 - 2 7.91115918558132e-01 -2.76446367423253e-03 - 3 7.91076626157176e-01 -2.76430650462870e-03 - 4 7.90841020777686e-01 -2.76336408311074e-03 - 5 7.90427382732787e-01 -2.76170953093115e-03 - 6 7.89863736340070e-01 -2.75945494536028e-03 - 7 7.89186342108997e-01 -2.75674536843599e-03 - 8 7.88437860267658e-01 -2.75375144107063e-03 - 9 7.87665135265936e-01 -2.75066054106374e-03 - 10 7.86916534938388e-01 -2.74766613975355e-03 - 11 7.86238889949708e-01 -2.74495555979883e-03 - 12 7.85674262880010e-01 -2.74269705152004e-03 - 13 7.85256932814059e-01 -2.74102773125624e-03 - 14 7.85011021491553e-01 -2.74004408596621e-03 - 15 7.84949075541991e-01 -2.73979630216797e-03 - 16 7.85071723408572e-01 -2.74028689363429e-03 - 17 7.85368315181469e-01 -2.74147326072588e-03 - 18 7.85818317068877e-01 -2.74327326827551e-03 - 19 7.86393206518082e-01 -2.74557282607233e-03 - 20 7.87058667467717e-01 -2.74823466987087e-03 + 1 7.90951498267062e-01 -2.76380599306825e-03 + 2 7.91115918557351e-01 -2.76446367422940e-03 + 3 7.91076626155406e-01 -2.76430650462163e-03 + 4 7.90841020774526e-01 -2.76336408309811e-03 + 5 7.90427382727841e-01 -2.76170953091136e-03 + 6 7.89863736332951e-01 -2.75945494533180e-03 + 7 7.89186342099336e-01 -2.75674536839735e-03 + 8 7.88437860255107e-01 -2.75375144102043e-03 + 9 7.87665135250171e-01 -2.75066054100068e-03 + 10 7.86916534919116e-01 -2.74766613967646e-03 + 11 7.86238889926666e-01 -2.74495555970666e-03 + 12 7.85674262852968e-01 -2.74269705141187e-03 + 13 7.85256932782819e-01 -2.74102773113128e-03 + 14 7.85011021455946e-01 -2.74004408582379e-03 + 15 7.84949075501872e-01 -2.73979630200749e-03 + 16 7.85071723363813e-01 -2.74028689345525e-03 + 17 7.85368315131961e-01 -2.74147326052785e-03 + 18 7.85818317014519e-01 -2.74327326805808e-03 + 19 7.86393206458784e-01 -2.74557282583514e-03 + 20 7.87058667403396e-01 -2.74823466961359e-03 diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out index 1fe205c90..0cd0f727b 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -122,7 +118,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -133,33 +128,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - groupCoord colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.787059 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index e43a36e68..5187120c9 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 7.87942474885153e-01 + x 7.87942474735044e-01 } restraint { diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj index ec60b338f..93a7f33a7 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 7.87058667467717e-01 -2.74823466987087e-03 - 21 7.87776958977482e-01 -2.75110783590993e-03 - 22 7.88509370083721e-01 -2.75403748033489e-03 - 23 7.89218651458299e-01 -2.75687460583319e-03 - 24 7.89871253752910e-01 -2.75948501501164e-03 - 25 7.90439158435954e-01 -2.76175663374382e-03 - 26 7.90901124501041e-01 -2.76360449800416e-03 - 27 7.91243274323407e-01 -2.76497309729363e-03 - 28 7.91459063648406e-01 -2.76583625459362e-03 - 29 7.91548789417463e-01 -2.76619515766985e-03 - 30 7.91518769927385e-01 -2.76607507970954e-03 - 31 7.91380310221072e-01 -2.76552124088429e-03 - 32 7.91148491294645e-01 -2.76459396517858e-03 - 33 7.90840825111090e-01 -2.76336330044436e-03 - 34 7.90475830319600e-01 -2.76190332127840e-03 - 35 7.90071649332906e-01 -2.76028659733162e-03 - 36 7.89644839916602e-01 -2.75857935966641e-03 - 37 7.89209440664736e-01 -2.75683776265894e-03 - 38 7.88776327332720e-01 -2.75510530933088e-03 - 39 7.88352818509478e-01 -2.75341127403791e-03 - 40 7.87942474885153e-01 -2.75176989954061e-03 + 20 7.87058667403396e-01 -2.74823466961359e-03 + 21 7.87776958908072e-01 -2.75110783563229e-03 + 22 7.88509370009168e-01 -2.75403748003667e-03 + 23 7.89218651378568e-01 -2.75687460551427e-03 + 24 7.89871253667991e-01 -2.75948501467196e-03 + 25 7.90439158345860e-01 -2.76175663338344e-03 + 26 7.90901124405813e-01 -2.76360449762325e-03 + 27 7.91243274223110e-01 -2.76497309689244e-03 + 28 7.91459063543128e-01 -2.76583625417251e-03 + 29 7.91548789307309e-01 -2.76619515722924e-03 + 30 7.91518769812477e-01 -2.76607507924991e-03 + 31 7.91380310101543e-01 -2.76552124040617e-03 + 32 7.91148491170643e-01 -2.76459396468257e-03 + 33 7.90840824982783e-01 -2.76336329993113e-03 + 34 7.90475830187182e-01 -2.76190332074873e-03 + 35 7.90071649196610e-01 -2.76028659678644e-03 + 36 7.89644839776708e-01 -2.75857935910683e-03 + 37 7.89209440521591e-01 -2.75683776208636e-03 + 38 7.88776327186739e-01 -2.75510530874696e-03 + 39 7.88352818361151e-01 -2.75341127344460e-03 + 40 7.87942474735044e-01 -2.75176989894018e-03 diff --git a/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt b/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_groupcoord_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out index 74de50e14..722ed98b3 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -102,7 +98,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -113,26 +108,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 36d404925..390d537cf 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.00485448890467e+00 + x 5.00485448897596e+00 } restraint { diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj index 023e68dee..cbea421ce 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 5.03768855197227e+00 -1.97507542078891e-02 - 1 5.03744876419417e+00 -1.97497950567767e-02 - 2 5.03694642879576e+00 -1.97477857151830e-02 - 3 5.03620505705731e+00 -1.97448202282292e-02 - 4 5.03525398207188e+00 -1.97410159282875e-02 - 5 5.03412335571070e+00 -1.97364934228428e-02 - 6 5.03284080256979e+00 -1.97313632102792e-02 - 7 5.03142972215272e+00 -1.97257188886109e-02 - 8 5.02990878553163e+00 -1.97196351421265e-02 - 9 5.02829203784451e+00 -1.97131681513781e-02 - 10 5.02658916662064e+00 -1.97063566664825e-02 - 11 5.02480574439595e+00 -1.96992229775838e-02 - 12 5.02294349117820e+00 -1.96917739647128e-02 - 13 5.02100072378728e+00 -1.96840028951491e-02 - 14 5.01897316903736e+00 -1.96758926761494e-02 - 15 5.01685523476086e+00 -1.96674209390434e-02 - 16 5.01464172185107e+00 -1.96585668874043e-02 - 17 5.01232984699556e+00 -1.96493193879822e-02 - 18 5.00992134539975e+00 -1.96396853815990e-02 - 19 5.00742432915842e+00 -1.96296973166337e-02 - 20 5.00485448890467e+00 -1.96194179556187e-02 + 0 5.03768855197214e+00 -1.97507542078886e-02 + 1 5.03744876419419e+00 -1.97497950567768e-02 + 2 5.03694642879595e+00 -1.97477857151838e-02 + 3 5.03620505705716e+00 -1.97448202282286e-02 + 4 5.03525398207157e+00 -1.97410159282863e-02 + 5 5.03412335568541e+00 -1.97364934227416e-02 + 6 5.03284080257023e+00 -1.97313632102809e-02 + 7 5.03142972215521e+00 -1.97257188886209e-02 + 8 5.02990878553720e+00 -1.97196351421488e-02 + 9 5.02829203785433e+00 -1.97131681514173e-02 + 10 5.02658916663561e+00 -1.97063566665424e-02 + 11 5.02480574441698e+00 -1.96992229776679e-02 + 12 5.02294349120610e+00 -1.96917739648244e-02 + 13 5.02100072380662e+00 -1.96840028952265e-02 + 14 5.01897316908046e+00 -1.96758926763219e-02 + 15 5.01685523480251e+00 -1.96674209392100e-02 + 16 5.01464172191010e+00 -1.96585668876404e-02 + 17 5.01232984706209e+00 -1.96493193882483e-02 + 18 5.00992134545152e+00 -1.96396853818061e-02 + 19 5.00742432922767e+00 -1.96296973169107e-02 + 20 5.00485448897596e+00 -1.96194179559038e-02 diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out index 42156fb61..c40533751 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -102,7 +98,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -113,31 +108,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 5.00485 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index ab515bb61..9d22ab655 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 4.96897275206382e+00 + x 4.96897275199397e+00 } restraint { diff --git a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj index a61b26a78..12760b2af 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_gyration_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.00485448890467e+00 -1.96194179556187e-02 - 21 5.00223519406431e+00 -1.96089407762573e-02 - 22 4.99959613490376e+00 -1.95983845396151e-02 - 23 4.99697045871106e+00 -1.95878818348442e-02 - 24 4.99439079635605e+00 -1.95775631854242e-02 - 25 4.99188501582648e+00 -1.95675400633059e-02 - 26 4.98947279561833e+00 -1.95578911824733e-02 - 27 4.98716399834632e+00 -1.95486559933853e-02 - 28 4.98495936495158e+00 -1.95398374598063e-02 - 29 4.98285340667393e+00 -1.95314136266957e-02 - 30 4.98083878791299e+00 -1.95233551516520e-02 - 31 4.97891115941913e+00 -1.95156446376765e-02 - 32 4.97707338948989e+00 -1.95082935579595e-02 - 33 4.97533838450258e+00 -1.95013535380103e-02 - 34 4.97373007483673e+00 -1.94949202993469e-02 - 35 4.97228253708149e+00 -1.94891301483260e-02 - 36 4.97103753059614e+00 -1.94841501223846e-02 - 37 4.97004091948501e+00 -1.94801636779400e-02 - 38 4.96933848311783e+00 -1.94773539324713e-02 - 39 4.96897154887735e+00 -1.94758861955094e-02 - 40 4.96897275206382e+00 -1.94758910082553e-02 + 20 5.00485448897596e+00 -1.96194179559038e-02 + 21 5.00223519413610e+00 -1.96089407765444e-02 + 22 4.99959613497035e+00 -1.95983845398814e-02 + 23 4.99697045876934e+00 -1.95878818350774e-02 + 24 4.99439079640308e+00 -1.95775631856123e-02 + 25 4.99188501584048e+00 -1.95675400633619e-02 + 26 4.98947279563574e+00 -1.95578911825430e-02 + 27 4.98716399834319e+00 -1.95486559933728e-02 + 28 4.98495936493070e+00 -1.95398374597228e-02 + 29 4.98285340663966e+00 -1.95314136265587e-02 + 30 4.98083878784580e+00 -1.95233551513832e-02 + 31 4.97891115935444e+00 -1.95156446374178e-02 + 32 4.97707338941302e+00 -1.95082935576521e-02 + 33 4.97533838441641e+00 -1.95013535376657e-02 + 34 4.97373007474449e+00 -1.94949202989780e-02 + 35 4.97228253698659e+00 -1.94891301479464e-02 + 36 4.97103753049164e+00 -1.94841501219666e-02 + 37 4.97004091939466e+00 -1.94801636775786e-02 + 38 4.96933848303369e+00 -1.94773539321348e-02 + 39 4.96897154880133e+00 -1.94758861952053e-02 + 40 4.96897275199397e+00 -1.94758910079759e-02 diff --git a/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt b/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_gyration_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out index 62fe7a40c..2331c1a41 100644 --- a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -94,7 +90,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -105,26 +100,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - hBond colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out index 293e9d354..07423f3dd 100644 --- a/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_hbond_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -94,7 +90,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -105,31 +100,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - hBond colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.999923 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (2 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 2 atoms: total mass = 15.015, total charge = -0.31. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt b/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt index 157cac038..9e5d53306 100644 --- a/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_hbond_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-21. +colvars: Using NAMD interface, version 2018-12-20. diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out index 9b7934c0b..1c304f72b 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -102,7 +98,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -113,27 +108,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: - inertia colvar component (derived from gyration): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped index b526c1a3b..d529f420f 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.47943794570369e+02 + x 2.47943794577146e+02 } restraint { diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj index 54b38db6c..9c2662344 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 2.53783059466725e+02 -1.01473223786690e+00 + 0 2.53783059466712e+02 -1.01473223786685e+00 1 2.53741340236853e+02 -1.01456536094741e+00 - 2 2.53638721286741e+02 -1.01415488514697e+00 - 3 2.53479585453035e+02 -1.01351834181214e+00 - 4 2.53270136271682e+02 -1.01268054508673e+00 - 5 2.53017700005431e+02 -1.01167080002172e+00 - 6 2.52730128240016e+02 -1.01052051296007e+00 - 7 2.52415319838942e+02 -1.00926127935577e+00 - 8 2.52080840138270e+02 -1.00792336055308e+00 - 9 2.51733604628119e+02 -1.00653441851248e+00 - 10 2.51379609094601e+02 -1.00511843637841e+00 - 11 2.51023709838303e+02 -1.00369483935321e+00 - 12 2.50669473380297e+02 -1.00227789352119e+00 - 13 2.50319117864268e+02 -1.00087647145707e+00 - 14 2.49973559958431e+02 -9.99494239833723e-01 - 15 2.49632568521358e+02 -9.98130274085430e-01 - 16 2.49295012996826e+02 -9.96780051987302e-01 - 17 2.48959183654063e+02 -9.95436734616253e-01 - 18 2.48623152206619e+02 -9.94092608826476e-01 - 19 2.48285132610319e+02 -9.92740530441276e-01 - 20 2.47943794570369e+02 -9.91375178281476e-01 + 2 2.53638721286758e+02 -1.01415488514703e+00 + 3 2.53479585453019e+02 -1.01351834181208e+00 + 4 2.53270136271656e+02 -1.01268054508662e+00 + 5 2.53017700001829e+02 -1.01167080000732e+00 + 6 2.52730128240095e+02 -1.01052051296038e+00 + 7 2.52415319839252e+02 -1.00926127935701e+00 + 8 2.52080840138888e+02 -1.00792336055555e+00 + 9 2.51733604629136e+02 -1.00653441851654e+00 + 10 2.51379609096128e+02 -1.00511843638451e+00 + 11 2.51023709840432e+02 -1.00369483936173e+00 + 12 2.50669473383116e+02 -1.00227789353246e+00 + 13 2.50319117866126e+02 -1.00087647146451e+00 + 14 2.49973559962786e+02 -9.99494239851145e-01 + 15 2.49632568526903e+02 -9.98130274107611e-01 + 16 2.49295013002611e+02 -9.96780052010444e-01 + 17 2.48959183660263e+02 -9.95436734641053e-01 + 18 2.48623152213820e+02 -9.94092608855281e-01 + 19 2.48285132616888e+02 -9.92740530467554e-01 + 20 2.47943794577146e+02 -9.91375178308586e-01 diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out index c94891992..33f101cd0 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -102,7 +98,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -113,32 +108,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: - inertia colvar component (derived from gyration): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 247.944 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 9096628e7..1d4d73e13 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.41656580638813e+02 + x 2.41656580632151e+02 } restraint { diff --git a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 270b72c1a..72dbacfd9 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_inertia_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.47943794570369e+02 -9.91375178281476e-01 - 21 2.47598477040393e+02 -9.89993908161571e-01 - 22 2.47249255867815e+02 -9.88597023471262e-01 - 23 2.46896846069752e+02 -9.87187384279007e-01 - 24 2.46542363780136e+02 -9.85769455120543e-01 - 25 2.46187019170014e+02 -9.84348076680055e-01 - 26 2.45831840553059e+02 -9.82927362212236e-01 - 27 2.45477524529067e+02 -9.81510098116269e-01 - 28 2.45124466798686e+02 -9.80097867194745e-01 - 29 2.44772967366842e+02 -9.78691869467368e-01 - 30 2.44423548281158e+02 -9.77294193124631e-01 - 31 2.44077290782282e+02 -9.75909163129130e-01 - 32 2.43736099728340e+02 -9.74544398913360e-01 - 33 2.43402829973457e+02 -9.73211319893828e-01 - 34 2.43081248681633e+02 -9.71924994726533e-01 - 35 2.42775844782379e+02 -9.70703379129517e-01 - 36 2.42491523393473e+02 -9.69566093573892e-01 - 37 2.42233234222450e+02 -9.68532936889801e-01 - 38 2.42005579220911e+02 -9.67622316883644e-01 - 39 2.41812431256466e+02 -9.66849725025865e-01 - 40 2.41656580638813e+02 -9.66226322555252e-01 + 20 2.47943794577146e+02 -9.91375178308586e-01 + 21 2.47598477046097e+02 -9.89993908184388e-01 + 22 2.47249255874236e+02 -9.88597023496945e-01 + 23 2.46896846075395e+02 -9.87187384301580e-01 + 24 2.46542363784743e+02 -9.85769455138973e-01 + 25 2.46187019172168e+02 -9.84348076688674e-01 + 26 2.45831840554944e+02 -9.82927362219775e-01 + 27 2.45477524529089e+02 -9.81510098116355e-01 + 28 2.45124466797313e+02 -9.80097867189253e-01 + 29 2.44772967363848e+02 -9.78691869455392e-01 + 30 2.44423548274181e+02 -9.77294193096724e-01 + 31 2.44077290776696e+02 -9.75909163106782e-01 + 32 2.43736099721675e+02 -9.74544398886700e-01 + 33 2.43402829965980e+02 -9.73211319863919e-01 + 34 2.43081248673642e+02 -9.71924994694569e-01 + 35 2.42775844774184e+02 -9.70703379096737e-01 + 36 2.42491523384140e+02 -9.69566093536562e-01 + 37 2.42233234214778e+02 -9.68532936859112e-01 + 38 2.42005579213859e+02 -9.67622316855437e-01 + 39 2.41812431250163e+02 -9.66849725000653e-01 + 40 2.41656580632151e+02 -9.66226322528602e-01 diff --git a/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt b/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_inertia_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out index 71d0dcbba..bb024e575 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -76,7 +72,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -104,7 +100,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -115,28 +110,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: - inertia colvar component (derived from gyration): -colvars: - inertiaZ colvar component (derived from inertia): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 179a7851f..3f0ca8ee3 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.75096078961602e+01 + x 2.75096079010709e+01 } restraint { diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj index bdcc58815..208c352c5 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 2.74164641878496e+01 -1.09265856751398e-01 - 1 2.74002934369676e+01 -1.09201173747870e-01 - 2 2.73891905422880e+01 -1.09156762169152e-01 - 3 2.73840806710794e+01 -1.09136322684318e-01 - 4 2.73853106962415e+01 -1.09141242784966e-01 - 5 2.73926707772583e+01 -1.09170683109033e-01 - 6 2.74054700019287e+01 -1.09221880007715e-01 - 7 2.74226468646496e+01 -1.09290587458598e-01 - 8 2.74428938157855e+01 -1.09371575263142e-01 - 9 2.74647792825400e+01 -1.09459117130160e-01 - 10 2.74868564347115e+01 -1.09547425738846e-01 - 11 2.75077518051641e+01 -1.09631007220656e-01 - 12 2.75262294370741e+01 -1.09704917748296e-01 - 13 2.75412308249068e+01 -1.09764923299627e-01 - 14 2.75518987119582e+01 -1.09807594847833e-01 - 15 2.75575987144433e+01 -1.09830394857773e-01 - 16 2.75579511788616e+01 -1.09831804715446e-01 - 17 2.75528755131993e+01 -1.09811502052797e-01 - 18 2.75426367029528e+01 -1.09770546811811e-01 - 19 2.75278759428108e+01 -1.09711503771243e-01 - 20 2.75096078961602e+01 -1.09638431584641e-01 + 0 2.74164641878528e+01 -1.09265856751411e-01 + 1 2.74002934369697e+01 -1.09201173747879e-01 + 2 2.73891905423028e+01 -1.09156762169211e-01 + 3 2.73840806711159e+01 -1.09136322684464e-01 + 4 2.73853106963141e+01 -1.09141242785257e-01 + 5 2.73926707769495e+01 -1.09170683107798e-01 + 6 2.74054700020936e+01 -1.09221880008374e-01 + 7 2.74226468649512e+01 -1.09290587459805e-01 + 8 2.74428938162688e+01 -1.09371575265075e-01 + 9 2.74647792832602e+01 -1.09459117133041e-01 + 10 2.74868564357227e+01 -1.09547425742891e-01 + 11 2.75077518065206e+01 -1.09631007226083e-01 + 12 2.75262294388280e+01 -1.09704917755312e-01 + 13 2.75412308252314e+01 -1.09764923300926e-01 + 14 2.75518987145933e+01 -1.09807594858373e-01 + 15 2.75575987160543e+01 -1.09830394864217e-01 + 16 2.75579511825093e+01 -1.09831804730037e-01 + 17 2.75528755165223e+01 -1.09811502066089e-01 + 18 2.75426367051080e+01 -1.09770546820432e-01 + 19 2.75278759473936e+01 -1.09711503789574e-01 + 20 2.75096079010709e+01 -1.09638431604284e-01 diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out index 938486ff2..297ae52c8 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -76,7 +72,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -104,7 +100,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -115,33 +110,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - gyration colvar component: -colvars: - inertia colvar component (derived from gyration): -colvars: - inertiaZ colvar component (derived from inertia): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 27.5096 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index f8c9a41c7..8f94c73f0 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.83560354842176e+01 + x 2.83560354929576e+01 } restraint { diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 060386c56..88f514f27 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.75096078961602e+01 -1.09638431584641e-01 - 21 2.74891754878350e+01 -1.09556701951340e-01 - 22 2.74681653014033e+01 -1.09472661205613e-01 - 23 2.74482979809375e+01 -1.09393191923750e-01 - 24 2.74313142837939e+01 -1.09325257135176e-01 - 25 2.74188770303968e+01 -1.09275508121587e-01 - 26 2.74125030723945e+01 -1.09250012289578e-01 - 27 2.74135300949930e+01 -1.09254120379972e-01 - 28 2.74231135180919e+01 -1.09292454072368e-01 - 29 2.74422414944483e+01 -1.09368965977793e-01 - 30 2.74717522224079e+01 -1.09487008889632e-01 - 31 2.75123380776605e+01 -1.09649352310642e-01 - 32 2.75645249027809e+01 -1.09858099611124e-01 - 33 2.76286215047991e+01 -1.10114486019196e-01 - 34 2.77046429906839e+01 -1.10418571962736e-01 - 35 2.77922201138172e+01 -1.10768880455269e-01 - 36 2.78905144303044e+01 -1.11162057721218e-01 - 37 2.79981624989707e+01 -1.11592649995883e-01 - 38 2.81132700839839e+01 -1.12053080335936e-01 - 39 2.82334689354104e+01 -1.12533875741642e-01 - 40 2.83560354842176e+01 -1.13024141936871e-01 + 20 2.75096079010709e+01 -1.09638431604284e-01 + 21 2.74891754936655e+01 -1.09556701974662e-01 + 22 2.74681653074554e+01 -1.09472661229822e-01 + 23 2.74482979871198e+01 -1.09393191948479e-01 + 24 2.74313142900221e+01 -1.09325257160089e-01 + 25 2.74188770369929e+01 -1.09275508147972e-01 + 26 2.74125030784876e+01 -1.09250012313950e-01 + 27 2.74135301010474e+01 -1.09254120404190e-01 + 28 2.74231135227322e+01 -1.09292454090929e-01 + 29 2.74422414999913e+01 -1.09368965999965e-01 + 30 2.74717522279309e+01 -1.09487008911723e-01 + 31 2.75123380832048e+01 -1.09649352332819e-01 + 32 2.75645249083534e+01 -1.09858099633413e-01 + 33 2.76286215104829e+01 -1.10114486041931e-01 + 34 2.77046429965729e+01 -1.10418571986291e-01 + 35 2.77922201200098e+01 -1.10768880480039e-01 + 36 2.78905144368573e+01 -1.11162057747429e-01 + 37 2.79981625060488e+01 -1.11592650024195e-01 + 38 2.81132700916190e+01 -1.12053080366476e-01 + 39 2.82334689436511e+01 -1.12533875774604e-01 + 40 2.83560354929576e+01 -1.13024141971830e-01 diff --git a/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt b/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_inertiaz_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out index 6906658ec..7a60e0951 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -124,7 +120,6 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -135,27 +130,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped index fc86e531f..1fc7844e2 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99760693961232e-01 , 1.39216433781234e-02 , 1.19362778059823e-02 , -1.19276119968650e-02 ) + x ( 9.99760693961651e-01 , 1.39216433541339e-02 , 1.19362778078050e-02 , -1.19276119878887e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj index 6b248bf72..0b4deda96 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ) ( 3.40696724956404e-06 , -8.24547608834386e-05 , -5.71707735043921e-05 , 5.95895265542447e-05 ) - 1 ( 9.99574091957316e-01 , 2.05772012681827e-02 , 1.42218162872608e-02 , -1.50317469765464e-02 ) ( 3.40702245731717e-06 , -8.22854314314116e-05 , -5.68711105890293e-05 , 6.01099133459647e-05 ) - 2 ( 9.99576136464269e-01 , 2.04824081529267e-02 , 1.41395609289210e-02 , -1.51026879779696e-02 ) ( 3.39066871847757e-06 , -8.19064783448245e-05 , -5.65422596983307e-05 , 6.03936791309106e-05 ) - 3 ( 9.99580389456459e-01 , 2.03360832362100e-02 , 1.40447201598598e-02 , -1.51074342068980e-02 ) ( 3.35664956461634e-06 , -8.13215747866998e-05 , -5.61631631603791e-05 , 6.04128300627651e-05 ) - 4 ( 9.99586941288893e-01 , 2.01392187843744e-02 , 1.39321349532439e-02 , -1.50417514643494e-02 ) ( 3.30424218006268e-06 , -8.05346892421722e-05 , -5.57131918051387e-05 , 6.01504354667054e-05 ) - 5 ( 9.99595790783329e-01 , 1.98928875288094e-02 , 1.37976726200861e-02 , -1.49047745466495e-02 ) ( 3.23345586896751e-06 , -7.95501051453821e-05 , -5.51758162860883e-05 , 5.96030305121391e-05 ) - 6 ( 9.99606822686916e-01 , 1.95985462816866e-02 , 1.36390185716578e-02 , -1.46994623648640e-02 ) ( 3.14521237059840e-06 , -7.83736341592375e-05 , -5.45417724591643e-05 , 5.87824356543135e-05 ) - 7 ( 9.99619795207092e-01 , 1.92585009913588e-02 , 1.34562172678871e-02 , -1.44327885918466e-02 ) ( 3.04144558769446e-06 , -7.70144759396220e-05 , -5.38112245330522e-05 , 5.77165195903442e-05 ) - 8 ( 9.99634343041458e-01 , 1.88763707874475e-02 , 1.32519032638778e-02 , -1.41155905952574e-02 ) ( 2.92507738195028e-06 , -7.54870750602017e-05 , -5.29946899027906e-05 , 5.64485969671590e-05 ) - 9 ( 9.99649997284953e-01 , 1.84574075512748e-02 , 1.30312276083930e-02 , -1.37620544141233e-02 ) ( 2.79985837307062e-06 , -7.38124013486557e-05 , -5.21127465828725e-05 , 5.50353716238521e-05 ) - 10 ( 9.99666219499820e-01 , 1.80085725925678e-02 , 1.28015269417140e-02 , -1.33888689618389e-02 ) ( 2.67009544562864e-06 , -7.20182596706942e-05 , -5.11947122255672e-05 , 5.35435574715432e-05 ) - 11 ( 9.99682444082188e-01 , 1.75383327410858e-02 , 1.25717990443000e-02 , -1.30141364413955e-02 ) ( 2.54031287827201e-06 , -7.01384778123604e-05 , -5.02765491650432e-05 , 5.20455241394477e-05 ) - 12 ( 9.99698121444835e-01 , 1.70562079173577e-02 , 1.23520473368371e-02 , -1.26561715276433e-02 ) ( 2.41490692643697e-06 , -6.82111000167390e-05 , -4.93982449315156e-05 , 5.06144968497088e-05 ) - 13 ( 9.99712754470273e-01 , 1.65721860651408e-02 , 1.21525545409691e-02 , -1.23323402730933e-02 ) ( 2.29785421817066e-06 , -6.62760490695734e-05 , -4.86009086497119e-05 , 4.93199138526125e-05 ) - 14 ( 9.99725922506310e-01 , 1.60961851478372e-02 , 1.19831437077868e-02 , -1.20580661581261e-02 ) ( 2.19251978606965e-06 , -6.43729753517290e-05 , -4.79238159509638e-05 , 4.82234509889984e-05 ) - 15 ( 9.99737290704466e-01 , 1.56377365616588e-02 , 1.18524811131054e-02 , -1.18460736780739e-02 ) ( 2.10158233787459e-06 , -6.25399902397942e-05 , -4.74016204460428e-05 , 4.73759951950515e-05 ) - 16 ( 9.99746606872211e-01 , 1.52059608592562e-02 , 1.17674662824491e-02 , -1.17058762653601e-02 ) ( 2.02705940720648e-06 , -6.08135677599179e-05 , -4.70619130717184e-05 , 4.68155946238250e-05 ) - 17 ( 9.99753691558999e-01 , 1.48097478384659e-02 , 1.17327398910912e-02 , -1.16434701770315e-02 ) ( 1.97038663356000e-06 , -5.92292632592778e-05 , -4.69232526672145e-05 , 4.65662324496665e-05 ) - 18 ( 9.99758428359742e-01 , 1.44579282356846e-02 , 1.17503257360525e-02 , -1.16611783232732e-02 ) ( 1.93249530916090e-06 , -5.78223985998645e-05 , -4.69937329410254e-05 , 4.66372007220352e-05 ) - 19 ( 9.99760760149601e-01 , 1.41591986489713e-02 , 1.18194125264703e-02 , -1.17575952575529e-02 ) ( 1.91384248526716e-06 , -5.66277607619860e-05 , -4.72701090993454e-05 , 4.70228794642514e-05 ) - 20 ( 9.99760693961232e-01 , 1.39216433781234e-02 , 1.19362778059823e-02 , -1.19276119968650e-02 ) ( 1.91437194998574e-06 , -5.56776887857508e-05 , -4.77374935480734e-05 , 4.77028358420824e-05 ) + 0 ( 9.99574098859266e-01 , 2.06195455609807e-02 , 1.42967532305094e-02 , -1.49016132553015e-02 ) ( 3.40696724955871e-06 , -8.24547608833287e-05 , -5.71707735043578e-05 , 5.95895265542064e-05 ) + 1 ( 9.99574091957315e-01 , 2.05772012682538e-02 , 1.42218162872588e-02 , -1.50317469765650e-02 ) ( 3.40702245733137e-06 , -8.22854314316960e-05 , -5.68711105890215e-05 , 6.01099133460393e-05 ) + 2 ( 9.99576136464277e-01 , 2.04824081529012e-02 , 1.41395609284123e-02 , -1.51026879779233e-02 ) ( 3.39066871841008e-06 , -8.19064783447229e-05 , -5.65422596962969e-05 , 6.03936791307258e-05 ) + 3 ( 9.99580389456449e-01 , 2.03360832367537e-02 , 1.40447201596166e-02 , -1.51074342070060e-02 ) ( 3.35664956469004e-06 , -8.13215747888733e-05 , -5.61631631594061e-05 , 6.04128300631967e-05 ) + 4 ( 9.99586941288897e-01 , 2.01392187847421e-02 , 1.39321349524241e-02 , -1.50417514643484e-02 ) ( 3.30424218003071e-06 , -8.05346892436429e-05 , -5.57131918018609e-05 , 6.01504354667014e-05 ) + 5 ( 9.99595790783300e-01 , 1.98928875282193e-02 , 1.37976726208478e-02 , -1.49047745486655e-02 ) ( 3.23345586919841e-06 , -7.95501051430208e-05 , -5.51758162891334e-05 , 5.96030305201998e-05 ) + 6 ( 9.99606822686883e-01 , 1.95985462834746e-02 , 1.36390185710864e-02 , -1.46994623652575e-02 ) ( 3.14521237086393e-06 , -7.83736341663858e-05 , -5.45417724568780e-05 , 5.87824356558856e-05 ) + 7 ( 9.99619795207068e-01 , 1.92585009929308e-02 , 1.34562172673074e-02 , -1.44327885919656e-02 ) ( 3.04144558788717e-06 , -7.70144759459075e-05 , -5.38112245307334e-05 , 5.77165195908192e-05 ) + 8 ( 9.99634343041421e-01 , 1.88763707892861e-02 , 1.32519032639492e-02 , -1.41155905953322e-02 ) ( 2.92507738224423e-06 , -7.54870750675527e-05 , -5.29946899030751e-05 , 5.64485969674567e-05 ) + 9 ( 9.99649997284929e-01 , 1.84574075526462e-02 , 1.30312276086889e-02 , -1.37620544137684e-02 ) ( 2.79985837326511e-06 , -7.38124013541386e-05 , -5.21127465840553e-05 , 5.50353716224322e-05 ) + 10 ( 9.99666219499819e-01 , 1.80085725929327e-02 , 1.28015269423414e-02 , -1.33888689608095e-02 ) ( 2.67009544563575e-06 , -7.20182596721535e-05 , -5.11947122280763e-05 , 5.35435574674263e-05 ) + 11 ( 9.99682444082219e-01 , 1.75383327400058e-02 , 1.25717990452909e-02 , -1.30141364395225e-02 ) ( 2.54031287802513e-06 , -7.01384778080426e-05 , -5.02765491690069e-05 , 5.20455241319585e-05 ) + 12 ( 9.99698121444904e-01 , 1.70562079144180e-02 , 1.23520473382012e-02 , -1.26561715247952e-02 ) ( 2.41490692588102e-06 , -6.82111000049856e-05 , -4.93982449369732e-05 , 5.06144968383214e-05 ) + 13 ( 9.99712754470511e-01 , 1.65721860535352e-02 , 1.21525545431810e-02 , -1.23323402672332e-02 ) ( 2.29785421626925e-06 , -6.62760490231703e-05 , -4.86009086585655e-05 , 4.93199138291843e-05 ) + 14 ( 9.99725922506467e-01 , 1.60961851402786e-02 , 1.19831437097085e-02 , -1.20580661532487e-02 ) ( 2.19251978481122e-06 , -6.43729753215068e-05 , -4.79238159586543e-05 , 4.82234509694974e-05 ) + 15 ( 9.99737290704757e-01 , 1.56377365465832e-02 , 1.18524811149563e-02 , -1.18460736715164e-02 ) ( 2.10158233554066e-06 , -6.25399901795148e-05 , -4.74016204534546e-05 , 4.73759951688351e-05 ) + 16 ( 9.99746606872466e-01 , 1.52059608462364e-02 , 1.17674662844455e-02 , -1.17058762584516e-02 ) ( 2.02705940516384e-06 , -6.08135677078579e-05 , -4.70619130797105e-05 , 4.68155945962039e-05 ) + 17 ( 9.99753691559363e-01 , 1.48097478197070e-02 , 1.17327398928793e-02 , -1.16434701678110e-02 ) ( 1.97038663064612e-06 , -5.92292631842689e-05 , -4.69232526743774e-05 , 4.65662324128018e-05 ) + 18 ( 9.99758428360226e-01 , 1.44579282082185e-02 , 1.17503257388760e-02 , -1.16611783129527e-02 ) ( 1.93249530528609e-06 , -5.78223984900366e-05 , -4.69937329523329e-05 , 4.66372006807749e-05 ) + 19 ( 9.99760760149993e-01 , 1.41591986268333e-02 , 1.18194125288315e-02 , -1.17575952484608e-02 ) ( 1.91384248212681e-06 , -5.66277606734629e-05 , -4.72701091088012e-05 , 4.70228794279011e-05 ) + 20 ( 9.99760693961651e-01 , 1.39216433541339e-02 , 1.19362778078050e-02 , -1.19276119878887e-02 ) ( 1.91437194663135e-06 , -5.56776886898237e-05 , -4.77374935553765e-05 , 4.77028358061962e-05 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out index 69fbc3cc3..d4c3e96c6 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -124,7 +120,6 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -135,32 +130,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.999761 , 0.0139216 , 0.0119363 , -0.0119276 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped index ad9c0da83..a1d021f26 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99742652479780e-01 , 1.40902379967357e-02 , 1.15309598522144e-02 , -1.35325892118309e-02 ) + x ( 9.99742652480851e-01 , 1.40902379472968e-02 , 1.15309598520170e-02 , -1.35325891843641e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj index 326f48b81..7507a9c22 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( 9.99760693961232e-01 , 1.39216433781234e-02 , 1.19362778059823e-02 , -1.19276119968650e-02 ) ( 1.91437194998574e-06 , -5.56776887857508e-05 , -4.77374935480734e-05 , 4.77028358420824e-05 ) - 21 ( 9.99758313633365e-01 , 1.37518501939863e-02 , 1.20943629910000e-02 , -1.21625376074929e-02 ) ( 1.93341304624615e-06 , -5.49985371073767e-05 , -4.83696566183854e-05 , 4.86423111428367e-05 ) - 22 ( 9.99753796261908e-01 , 1.36537811906101e-02 , 1.22845204605505e-02 , -1.24503685149034e-02 ) ( 1.96954907904872e-06 , -5.46061598016831e-05 , -4.91300159268110e-05 , 4.97932992497502e-05 ) - 23 ( 9.99747426627959e-01 , 1.36276729311783e-02 , 1.24954569253732e-02 , -1.27762685273114e-02 ) ( 2.02050191429012e-06 , -5.45015123963486e-05 , -4.99734110112214e-05 , 5.10964682698865e-05 ) - 24 ( 9.99739603282054e-01 , 1.36692734966396e-02 , 1.27143797755336e-02 , -1.31233051644571e-02 ) ( 2.08308333026075e-06 , -5.46676014211123e-05 , -5.08486896583343e-05 , 5.24841072376327e-05 ) - 25 ( 9.99730831051212e-01 , 1.37696613473913e-02 , 1.29278128060350e-02 , -1.34734378717380e-02 ) ( 2.15325498254029e-06 , -5.50687609506525e-05 , -5.17019710993255e-05 , 5.38840796896415e-05 ) - 26 ( 9.99721697040658e-01 , 1.39157628774382e-02 , 1.31225011979706e-02 , -1.38086919002263e-02 ) ( 2.22632039893925e-06 , -5.56527231861050e-05 , -5.24802652295864e-05 , 5.52245187456788e-05 ) - 27 ( 9.99712830629082e-01 , 1.40915177790539e-02 , 1.32862957768867e-02 , -1.41123969189936e-02 ) ( 2.29724500602795e-06 , -5.63552791136652e-05 , -5.31350077850472e-05 , 5.64387796831146e-05 ) - 28 ( 9.99704851767406e-01 , 1.42794879664030e-02 , 1.34089105192784e-02 , -1.43703408036104e-02 ) ( 2.36106970392215e-06 , -5.71067120286679e-05 , -5.36250874992332e-05 , 5.74700518643537e-05 ) - 29 ( 9.99698315096535e-01 , 1.44626114353530e-02 , 1.34824838999583e-02 , -1.45716948741664e-02 ) ( 2.41335786868624e-06 , -5.78388096174942e-05 , -5.39190880531035e-05 , 5.82750556079333e-05 ) - 30 ( 9.99693659068928e-01 , 1.46257879779070e-02 , 1.35019242353861e-02 , -1.47096018078657e-02 ) ( 2.45060231455666e-06 , -5.84912028734389e-05 , -5.39966660823142e-05 , 5.88263897186958e-05 ) - 31 ( 9.99691168692138e-01 , 1.47570433407831e-02 , 1.34650605673288e-02 , -1.47813752642869e-02 ) ( 2.47052328600467e-06 , -5.90160190716963e-05 , -5.38491520890833e-05 , 5.91133267252955e-05 ) - 32 ( 9.99690957800930e-01 , 1.48481228383961e-02 , 1.33726419051513e-02 , -1.47883260618358e-02 ) ( 2.47221024191153e-06 , -5.93802536948794e-05 , -5.34795460369745e-05 , 5.91411158724805e-05 ) - 33 ( 9.99692972559779e-01 , 1.48944891632750e-02 , 1.32282283630868e-02 , -1.47352903443807e-02 ) ( 2.45609382625367e-06 , -5.95657608180521e-05 , -5.29020819770730e-05 , 5.89290958968973e-05 ) - 34 ( 9.99697013269497e-01 , 1.48948261575969e-02 , 1.30380054972646e-02 , -1.46299769799956e-02 ) ( 2.42377143532588e-06 , -5.95672690438967e-05 , -5.21414867843392e-05 , 5.85080863417083e-05 ) - 35 ( 9.99702767875048e-01 , 1.48502581713688e-02 , 1.28105336093448e-02 , -1.44822637683003e-02 ) ( 2.37773919669474e-06 , -5.93892610389970e-05 , -5.12319796595224e-05 , 5.79175751320903e-05 ) - 36 ( 9.99709848841837e-01 , 1.47635626794789e-02 , 1.25564244174860e-02 , -1.43035503105882e-02 ) ( 2.32109700852655e-06 , -5.90428266173175e-05 , -5.02159814612746e-05 , 5.72031331010642e-05 ) - 37 ( 9.99717826025458e-01 , 1.46386367865957e-02 , 1.22879235275554e-02 , -1.41062247019792e-02 ) ( 2.25728562747236e-06 , -5.85435311676375e-05 , -4.91424471081696e-05 , 5.64142834839795e-05 ) - 38 ( 9.99726251232708e-01 , 1.44803731708344e-02 , 1.20183761975352e-02 , -1.39032378460851e-02 ) ( 2.18989021501695e-06 , -5.79109211903237e-05 , -4.80647306944381e-05 , 5.56028012328199e-05 ) - 39 ( 9.99734674139844e-01 , 1.42949333703084e-02 , 1.17615680015969e-02 , -1.37077248507170e-02 ) ( 2.12251301251851e-06 , -5.71696185014405e-05 , -4.70379496155383e-05 , 5.48211999270969e-05 ) - 40 ( 9.99742652479780e-01 , 1.40902379967357e-02 , 1.15309598522144e-02 , -1.35325892118309e-02 ) ( 2.05869185355315e-06 , -5.63512816728506e-05 , -4.61159255607322e-05 , 5.41210692548650e-05 ) + 20 ( 9.99760693961651e-01 , 1.39216433541339e-02 , 1.19362778078050e-02 , -1.19276119878887e-02 ) ( 1.91437194663135e-06 , -5.56776886898237e-05 , -4.77374935553765e-05 , 4.77028358061962e-05 ) + 21 ( 9.99758313633772e-01 , 1.37518501706272e-02 , 1.20943629928691e-02 , -1.21625375985983e-02 ) ( 1.93341304299124e-06 , -5.49985370139702e-05 , -4.83696566258740e-05 , 4.86423111072771e-05 ) + 22 ( 9.99753796262334e-01 , 1.36537811661746e-02 , 1.22845204621472e-02 , -1.24503685059100e-02 ) ( 1.96954907564106e-06 , -5.46061597039727e-05 , -4.91300159332110e-05 , 4.97932992137969e-05 ) + 23 ( 9.99747426628399e-01 , 1.36276729060903e-02 , 1.24954569267165e-02 , -1.27762685182456e-02 ) ( 2.02050191076346e-06 , -5.45015122960296e-05 , -4.99734110166082e-05 , 5.10964682336444e-05 ) + 24 ( 9.99739603282506e-01 , 1.36692734713397e-02 , 1.27143797766633e-02 , -1.31233051552796e-02 ) ( 2.08308332664440e-06 , -5.46676013199467e-05 , -5.08486896628677e-05 , 5.24841072009449e-05 ) + 25 ( 9.99730831051754e-01 , 1.37696613185747e-02 , 1.29278128058886e-02 , -1.34734378611172e-02 ) ( 2.15325497820459e-06 , -5.50687608354267e-05 , -5.17019710987588e-05 , 5.38840796471852e-05 ) + 26 ( 9.99721697041131e-01 , 1.39157628525684e-02 , 1.31225011988153e-02 , -1.38086918902498e-02 ) ( 2.22632039515597e-06 , -5.56527230866618e-05 , -5.24802652329812e-05 , 5.52245187057974e-05 ) + 27 ( 9.99712830629568e-01 , 1.40915177545030e-02 , 1.32862957776279e-02 , -1.41123969084309e-02 ) ( 2.29724500214521e-06 , -5.63552790154987e-05 , -5.31350077880288e-05 , 5.64387796408899e-05 ) + 28 ( 9.99704851767985e-01 , 1.42794879373133e-02 , 1.34089105192648e-02 , -1.43703407922426e-02 ) ( 2.36106969928898e-06 , -5.71067119123539e-05 , -5.36250874991995e-05 , 5.74700518189137e-05 ) + 29 ( 9.99698315097026e-01 , 1.44626114126131e-02 , 1.34824839010541e-02 , -1.45716948620744e-02 ) ( 2.41335786476355e-06 , -5.78388095265717e-05 , -5.39190880575035e-05 , 5.82750555595938e-05 ) + 30 ( 9.99693659069529e-01 , 1.46257879511962e-02 , 1.35019242354909e-02 , -1.47096017934521e-02 ) ( 2.45060230974677e-06 , -5.84912027666410e-05 , -5.39966660827548e-05 , 5.88263896610770e-05 ) + 31 ( 9.99691168692650e-01 , 1.47570433195187e-02 , 1.34650605688713e-02 , -1.47813752494873e-02 ) ( 2.47052328190881e-06 , -5.90160189866762e-05 , -5.38491520952702e-05 , 5.91133266661292e-05 ) + 32 ( 9.99690957801472e-01 , 1.48481228167761e-02 , 1.33726419068354e-02 , -1.47883260454137e-02 ) ( 2.47221023758033e-06 , -5.93802536084388e-05 , -5.34795460437290e-05 , 5.91411158068268e-05 ) + 33 ( 9.99692972560360e-01 , 1.48944891406353e-02 , 1.32282283648437e-02 , -1.47352903262270e-02 ) ( 2.45609382160275e-06 , -5.95657607275349e-05 , -5.29020819841198e-05 , 5.89290958243205e-05 ) + 34 ( 9.99697013270129e-01 , 1.48948261332085e-02 , 1.30380054990091e-02 , -1.46299769600688e-02 ) ( 2.42377143026910e-06 , -5.95672689463881e-05 , -5.21414867913377e-05 , 5.85080862620418e-05 ) + 35 ( 9.99702767875741e-01 , 1.48502581444742e-02 , 1.28105336109831e-02 , -1.44822637466295e-02 ) ( 2.37773919115572e-06 , -5.93892609314672e-05 , -5.12319796660980e-05 , 5.79175750454513e-05 ) + 36 ( 9.99709848842744e-01 , 1.47635626439325e-02 , 1.25564244173485e-02 , -1.43035502840116e-02 ) ( 2.32109700127172e-06 , -5.90428264751950e-05 , -5.02159814607548e-05 , 5.72031329948130e-05 ) + 37 ( 9.99717826026293e-01 , 1.46386367524169e-02 , 1.22879235287665e-02 , -1.41062246772189e-02 ) ( 2.25728562079388e-06 , -5.85435310309807e-05 , -4.91424471130407e-05 , 5.64142833849880e-05 ) + 38 ( 9.99726251233621e-01 , 1.44803731319332e-02 , 1.20183761983179e-02 , -1.39032378202861e-02 ) ( 2.18989020771502e-06 , -5.79109210347829e-05 , -4.80647306975977e-05 , 5.56028011296765e-05 ) + 39 ( 9.99734674140845e-01 , 1.42949333257481e-02 , 1.17615680020998e-02 , -1.37077248236990e-02 ) ( 2.12251300450785e-06 , -5.71696183232687e-05 , -4.70379496175808e-05 , 5.48211998190806e-05 ) + 40 ( 9.99742652480851e-01 , 1.40902379472968e-02 , 1.15309598520170e-02 , -1.35325891843641e-02 ) ( 2.05869184498829e-06 , -5.63512814751691e-05 , -4.61159255599756e-05 , 5.41210691450550e-05 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out index ec40acc6d..9a2c9b63c 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -127,7 +123,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -138,27 +133,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped index 279228b77..01d155e7c 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99760693817830e-01 , 1.39216455125237e-02 , 1.19362887805905e-02 , -1.19276105428297e-02 ) + x ( 9.99760693818246e-01 , 1.39216454886428e-02 , 1.19362887828950e-02 , -1.19276105335207e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.27813232055650e-03 + accumulatedWork 2.27813232055700e-03 } } diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj index b339c9cfb..7b97e03f8 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 0 ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ) ( 3.40696724956404e-06 , -8.24547608834386e-05 , -5.71707735043921e-05 , 5.95895265542447e-05 ) 1.70372550452894e-06 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 - 1 ( 9.99574091957316e-01 , 2.05772012681827e-02 , 1.42218162872608e-02 , -1.50317469765464e-02 ) ( -2.89857105413568e-06 , -8.20357344749931e-05 , 3.85760678003605e-04 , 5.99275084882400e-05 ) 1.98926088015520e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.24615390673096e-05 - 2 ( 9.99576136464117e-01 , 2.04824081526900e-02 , 1.41395609423227e-02 , -1.51026879758038e-02 ) ( -1.05168657309248e-05 , -8.04517476314451e-05 , 9.23378079065106e-04 , 5.93210345447713e-05 ) 1.07841143774898e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.63130419745432e-04 - 3 ( 9.99580389455824e-01 , 2.03360832354197e-02 , 1.40447202158084e-02 , -1.51074341979379e-02 ) ( -1.95312689952873e-05 , -7.71426868980550e-05 , 1.56340858862322e-03 , 5.73083839534375e-05 ) 3.06732891307828e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.94155785846739e-04 - 4 ( 9.99586941287241e-01 , 2.01392187829879e-02 , 1.39321350986197e-02 , -1.50417514413077e-02 ) ( -2.97615745192475e-05 , -7.14911802640544e-05 , 2.29629026903105e-03 , 5.33959422838193e-05 ) 6.60224608309061e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.47035553394974e-04 - 5 ( 9.99595790779906e-01 , 1.98928875276492e-02 , 1.37976729205755e-02 , -1.49047744995720e-02 ) ( -4.06413192373749e-05 , -6.31016250631435e-05 , 3.08637898561543e-03 , 4.72789830443403e-05 ) 1.19170050962515e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.18350423122506e-03 - 6 ( 9.99606822680751e-01 , 1.95985462832515e-02 , 1.36390191111118e-02 , -1.46994622814130e-02 ) ( -5.12953295469620e-05 , -5.21496651296818e-05 , 3.87653754434035e-03 , 3.91137191750376e-05 ) 1.87930300176431e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.61639198938578e-03 - 7 ( 9.99619795197032e-01 , 1.92585010007719e-02 , 1.34562181453815e-02 , -1.44327884579218e-02 ) ( -6.08644895994507e-05 , -3.94609367964904e-05 , 4.60962560797712e-03 , 2.95729845802817e-05 ) 2.65684805734531e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.95913218474063e-03 - 8 ( 9.99634343026221e-01 , 1.88763708133848e-02 , 1.32519045886273e-02 , -1.41155903958815e-02 ) ( -6.88272478670076e-05 , -2.61706583210457e-05 , 5.24998743936081e-03 , 1.95701968827877e-05 ) 3.44602164993228e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.17342875845415e-03 - 9 ( 9.99649997263207e-01 , 1.84574076067301e-02 , 1.30312294934032e-02 , -1.37620541344282e-02 ) ( -7.50701457814478e-05 , -1.32797169768971e-05 , 5.78803752266657e-03 , 9.90150880448157e-06 ) 4.18841103516792e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.26930643841353e-03 - 10 ( 9.99666219470249e-01 , 1.80085726953522e-02 , 1.28015294972442e-02 , -1.33888685880002e-02 ) ( -7.97587545516019e-05 , -1.43682091227853e-06 , 6.23146712392729e-03 , 1.06823603982523e-06 ) 4.85469339763710e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 11 ( 9.99682444043555e-01 , 1.75383329140093e-02 , 1.25718023719501e-02 , -1.30141359614126e-02 ) ( -7.83400542234201e-05 , -1.37439039732904e-06 , 6.23240419814605e-03 , 1.01985197695800e-06 ) 4.85612527277641e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 12 ( 9.99698121396159e-01 , 1.70562081867899e-02 , 1.23520515136698e-02 , -1.26561709329443e-02 ) ( -7.69825486892822e-05 , -1.31342687266466e-06 , 6.23330027301218e-03 , 9.74598505501407e-07 ) 4.85749516015860e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 13 ( 9.99712754410809e-01 , 1.65721864606089e-02 , 1.21525596183800e-02 , -1.23323395586735e-02 ) ( -7.57498609725947e-05 , -1.25570151512460e-06 , 6.23411347952713e-03 , 9.34441421212952e-07 ) 4.85873892087829e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 14 ( 9.99725922435513e-01 , 1.60961857012553e-02 , 1.19831497116778e-02 , -1.20580653224807e-02 ) ( -7.47028381344618e-05 , -1.20276040466548e-06 , 6.23480386682432e-03 , 9.01018650997467e-07 ) 4.85979525378250e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 15 ( 9.99737290621952e-01 , 1.56377373062154e-02 , 1.18524880452973e-02 , -1.18460727229225e-02 ) ( -7.38952136243442e-05 , -1.15585759347365e-06 , 6.23533622413239e-03 , 8.75598102302748e-07 ) 4.86061005415662e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 16 ( 9.99746606777718e-01 , 1.52059618280014e-02 , 1.17674741231820e-02 , -1.17058751951783e-02 ) ( -7.33697991663691e-05 , -1.11594113737261e-06 , 6.23568254122528e-03 , 8.59075396019594e-07 ) 4.86114023321333e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 17 ( 9.99753691452358e-01 , 1.48097490626708e-02 , 1.17327486023943e-02 , -1.16434689984246e-02 ) ( -7.31554048026095e-05 , -1.08368010737810e-06 , 6.23582398802628e-03 , 8.51992540931742e-07 ) 4.86135680289371e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 18 ( 9.99758428240858e-01 , 1.44579297430799e-02 , 1.17503352657271e-02 , -1.16611770442436e-02 ) ( -7.32645959690450e-05 , -1.05951032894958e-06 , 6.23575235353917e-03 , 8.54557861715953e-07 ) 4.86124712106538e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 19 ( 9.99760760018442e-01 , 1.41592004620220e-02 , 1.18194228124135e-02 , -1.17575938867382e-02 ) ( -7.36923301249498e-05 , -1.04367416334025e-06 , 6.23547092568478e-03 , 8.66651827943935e-07 ) 4.86081625811507e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 20 ( 9.99760693817830e-01 , 1.39216455125237e-02 , 1.19362887805905e-02 , -1.19276105428297e-02 ) ( -7.44154910767136e-05 , -1.03623406462822e-06 , 6.23499480535782e-03 , 8.87811454686164e-07 ) 4.86008746876767e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 1 ( 9.99574091957314e-01 , 2.05772012682737e-02 , 1.42218162872633e-02 , -1.50317469765766e-02 ) ( -2.89857105411844e-06 , -8.20357344753561e-05 , 3.85760678003595e-04 , 5.99275084883605e-05 ) 1.98926088015600e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.24615390673084e-05 + 2 ( 9.99576136464107e-01 , 2.04824081530443e-02 , 1.41395609423345e-02 , -1.51026879759213e-02 ) ( -1.05168657308638e-05 , -8.04517476328365e-05 , 9.23378079065062e-04 , 5.93210345452325e-05 ) 1.07841143774923e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.63130419745423e-04 + 3 ( 9.99580389455804e-01 , 2.03360832361746e-02 , 1.40447202158361e-02 , -1.51074341981852e-02 ) ( -1.95312689951841e-05 , -7.71426869009185e-05 , 1.56340858862312e-03 , 5.73083839543752e-05 ) 3.06732891307857e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.94155785846709e-04 + 4 ( 9.99586941287210e-01 , 2.01392187842197e-02 , 1.39321350986691e-02 , -1.50417514416994e-02 ) ( -2.97615745191412e-05 , -7.14911802684271e-05 , 2.29629026903087e-03 , 5.33959422852095e-05 ) 6.60224608309056e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.47035553394905e-04 + 5 ( 9.99595790779864e-01 , 1.98928875293495e-02 , 1.37976729206519e-02 , -1.49047745000832e-02 ) ( -4.06413192373453e-05 , -6.31016250685387e-05 , 3.08637898561516e-03 , 4.72789830459629e-05 ) 1.19170050962504e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.18350423122495e-03 + 6 ( 9.99606822680701e-01 , 1.95985462853154e-02 , 1.36390191112217e-02 , -1.46994622819746e-02 ) ( -5.12953295471253e-05 , -5.21496651351779e-05 , 3.87653754433995e-03 , 3.91137191765353e-05 ) 1.87930300176401e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.61639198938565e-03 + 7 ( 9.99619795196980e-01 , 1.92585010029931e-02 , 1.34562181455343e-02 , -1.44327884584219e-02 ) ( -6.08644895999444e-05 , -3.94609368010510e-05 , 4.60962560797654e-03 , 2.95729845813135e-05 ) 2.65684805734470e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.95913218474054e-03 + 8 ( 9.99634343026175e-01 , 1.88763708154653e-02 , 1.32519045888371e-02 , -1.41155903961733e-02 ) ( -6.88272478679810e-05 , -2.61706583239472e-05 , 5.24998743935999e-03 , 1.95701968832050e-05 ) 3.44602164993124e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.17342875845418e-03 + 9 ( 9.99649997263176e-01 , 1.84574076082982e-02 , 1.30312294936897e-02 , -1.37620541343428e-02 ) ( -7.50701457830531e-05 , -1.32797169780534e-05 , 5.78803752266541e-03 , 9.90150880444109e-06 ) 4.18841103516628e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.26930643841376e-03 + 10 ( 9.99666219470242e-01 , 1.80085726959886e-02 , 1.28015294976327e-02 , -1.33888685873615e-02 ) ( -7.97587545540024e-05 , -1.43682091237256e-06 , 6.23146712392570e-03 , 1.06823603980643e-06 ) 4.85469339763468e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 11 ( 9.99682444043579e-01 , 1.75383329132778e-02 , 1.25718023724709e-02 , -1.30141359600538e-02 ) ( -7.83400542266416e-05 , -1.37439039732819e-06 , 6.23240419814393e-03 , 1.01985197689343e-06 ) 4.85612527277317e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 12 ( 9.99698121396221e-01 , 1.70562081842655e-02 , 1.23520515143566e-02 , -1.26561709307220e-02 ) ( -7.69825486935338e-05 , -1.31342687254272e-06 , 6.23330027300938e-03 , 9.74598505384046e-07 ) 4.85749516015432e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 13 ( 9.99712754410915e-01 , 1.65721864559041e-02 , 1.21525596192655e-02 , -1.23323395554808e-02 ) ( -7.57498609780799e-05 , -1.25570151485890e-06 , 6.23411347952353e-03 , 9.34441421038598e-07 ) 4.85873892087277e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 14 ( 9.99725922435667e-01 , 1.60961856940404e-02 , 1.19831497127895e-02 , -1.20580653182552e-02 ) ( -7.47028381413507e-05 , -1.20276040423710e-06 , 6.23480386681979e-03 , 9.01018650764673e-07 ) 4.85979525377557e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 15 ( 9.99737290622154e-01 , 1.56377372962370e-02 , 1.18524880466519e-02 , -1.18460727176508e-02 ) ( -7.38952136327416e-05 , -1.15585759286722e-06 , 6.23533622412687e-03 , 8.75598102012420e-07 ) 4.86061005414818e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 16 ( 9.99746606777969e-01 , 1.52059618150989e-02 , 1.17674741247817e-02 , -1.17058751888952e-02 ) ( -7.33697991762876e-05 , -1.11594113657630e-06 , 6.23568254121877e-03 , 8.59075395674407e-07 ) 4.86114023320336e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 17 ( 9.99753691452656e-01 , 1.48097490467918e-02 , 1.17327486042245e-02 , -1.16434689912063e-02 ) ( -7.31554048139585e-05 , -1.08368010638398e-06 , 6.23582398801883e-03 , 8.51992540535477e-07 ) 4.86135680288230e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 18 ( 9.99758428241199e-01 , 1.44579297242938e-02 , 1.17503352677578e-02 , -1.16611770361988e-02 ) ( -7.32645959816383e-05 , -1.05951032775465e-06 , 6.23575235353089e-03 , 8.54557861273005e-07 ) 4.86124712105271e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 19 ( 9.99760760018823e-01 , 1.41592004405267e-02 , 1.18194228146038e-02 , -1.17575938779946e-02 ) ( -7.36923301385327e-05 , -1.04367416194781e-06 , 6.23547092567585e-03 , 8.66651827458857e-07 ) 4.86081625810141e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 20 ( 9.99760693818246e-01 , 1.39216454886428e-02 , 1.19362887828950e-02 , -1.19276105335207e-02 ) ( -7.44154910910036e-05 , -1.03623406304924e-06 , 6.23499480534843e-03 , 8.87811454163381e-07 ) 4.86008746875330e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out index 124c00f20..f89ad9c5b 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -127,7 +123,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -138,32 +133,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.999761 , 0.0139216 , 0.0119363 , -0.0119276 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped index 938849f24..cc10dd18f 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.99742652208198e-01 , 1.40902436380753e-02 , 1.15309792258764e-02 , -1.35325868934950e-02 ) + x ( 9.99742652209286e-01 , 1.40902435879328e-02 , 1.15309792246189e-02 , -1.35325868663831e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.27813232055650e-03 + accumulatedWork 2.27813232055700e-03 } } diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj index f4c99c252..789205d92 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 ( 9.99760693817830e-01 , 1.39216455125237e-02 , 1.19362887805905e-02 , -1.19276105428297e-02 ) ( -7.44154910767136e-05 , -1.03623406462822e-06 , 6.23499480535782e-03 , 8.87811454686164e-07 ) 4.86008746876767e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 21 ( 9.99758313477823e-01 , 1.37518526575684e-02 , 1.20943745854034e-02 , -1.21625360781649e-02 ) ( -7.53933764513610e-05 , -1.03704924514109e-06 , 6.23435061795974e-03 , 9.17196335136740e-07 ) 4.85910171319849e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 22 ( 9.99753796094403e-01 , 1.36537839828244e-02 , 1.22845326084587e-02 , -1.24503669172219e-02 ) ( -7.65692635123717e-05 , -1.04571764348986e-06 , 6.23357553387972e-03 , 9.53550193092197e-07 ) 4.85791609893525e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 23 ( 9.99747426448760e-01 , 1.36276760432249e-02 , 1.24954695663346e-02 , -1.27762668671144e-02 ) ( -7.78731950221508e-05 , -1.06149878072943e-06 , 6.23271549316725e-03 , 9.95180077564155e-07 ) 4.85660109630414e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 24 ( 9.99739603091531e-01 , 1.36692769122303e-02 , 1.27143928574664e-02 , -1.31233034465857e-02 ) ( -7.92260158415096e-05 , -1.08324442268912e-06 , 6.23182259924548e-03 , 1.03997785377014e-06 ) 4.85523649062815e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 25 ( 9.99730830849845e-01 , 1.37696650440250e-02 , 1.29278262869396e-02 , -1.34734361002817e-02 ) ( -8.05444416081335e-05 , -1.10936858990258e-06 , 6.23095181082655e-03 , 1.08550257104459e-06 ) 4.85390628561639e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 26 ( 9.99721696829043e-01 , 1.39157668280219e-02 , 1.31225150468116e-02 , -1.38086900788067e-02 ) ( -8.17466563396149e-05 , -1.13788408534165e-06 , 6.23015725332975e-03 , 1.12912848240953e-06 ) 4.85269306084392e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 27 ( 9.99712830407931e-01 , 1.40915219536903e-02 , 1.32863099736998e-02 , -1.41123950509825e-02 ) ( -8.27577572384685e-05 , -1.16651774138799e-06 , 6.22948859731456e-03 , 1.16824564830883e-06 ) 4.85167246950209e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 28 ( 9.99704851537533e-01 , 1.42794923342033e-02 , 1.34089250546046e-02 , -1.43703388922140e-02 ) ( -8.35143962951262e-05 , -1.19289526289459e-06 , 6.22898794028392e-03 , 1.20048449829351e-06 ) 4.85090853484415e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 29 ( 9.99698314858842e-01 , 1.44626159661916e-02 , 1.34824987737283e-02 , -1.45716929223678e-02 ) ( -8.39681998992706e-05 , -1.21476630545989e-06 , 6.22868748240922e-03 , 1.22392806508725e-06 ) 4.85045017322160e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 30 ( 9.99693658824374e-01 , 1.46257926440631e-02 , 1.35019394553724e-02 , -1.47095998182711e-02 ) ( -8.40878559098745e-05 , -1.23022841404033e-06 , 6.22860808562373e-03 , 1.23727773912788e-06 ) 4.85032906201587e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 31 ( 9.99691168441709e-01 , 1.47570481184252e-02 , 1.34650761472677e-02 , -1.47813732389598e-02 ) ( -8.38600119204497e-05 , -1.23790853634409e-06 , 6.22875863536561e-03 , 1.23994907142371e-06 ) 4.85055871364153e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 32 ( 9.99690957545599e-01 , 1.48481277088428e-02 , 1.33726578626311e-02 , -1.47883240021993e-02 ) ( -8.32892561524428e-05 , -1.23707181983747e-06 , 6.22913603471590e-03 , 1.23208927377770e-06 ) 4.85113448594715e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 33 ( 9.99692972300467e-01 , 1.48944941139382e-02 , 1.32282447172976e-02 , -1.47352882512418e-02 ) ( -8.23974522780850e-05 , -1.22764528906839e-06 , 6.22972565465496e-03 , 1.21452310271978e-06 ) 4.85203425682343e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 34 ( 9.99697013007040e-01 , 1.48948311824960e-02 , 1.30380222667125e-02 , -1.46299748536945e-02 ) ( -8.12226196239937e-05 , -1.21016387141186e-06 , 6.23050211131550e-03 , 1.18864502663254e-06 ) 4.85321956880239e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 35 ( 9.99702767610164e-01 , 1.48502632711203e-02 , 1.28105508096523e-02 , -1.44822616089398e-02 ) ( -7.98174260852071e-05 , -1.18566220820019e-06 , 6.23143031865720e-03 , 1.15628052954330e-06 ) 4.85463717257082e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 36 ( 9.99709848575105e-01 , 1.47635678606929e-02 , 1.25564420594164e-02 , -1.43035481182791e-02 ) ( -7.82472390280891e-05 , -1.15554370595586e-06 , 6.23246684237661e-03 , 1.11953798410207e-06 ) 4.85622102004825e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 37 ( 9.99717825757301e-01 , 1.46386420606817e-02 , 1.22879416154002e-02 , -1.41062224770323e-02 ) ( -7.65875917958683e-05 , -1.12145478824491e-06 , 6.23356163672657e-03 , 1.08066654511663e-06 ) 4.85789484544842e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 38 ( 9.99726250963382e-01 , 1.44803785522926e-02 , 1.20183947280021e-02 , -1.39032355891063e-02 ) ( -7.49209174022956e-05 , -1.08518031253540e-06 , 6.23466024929070e-03 , 1.04192839208965e-06 ) 4.85957547889764e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 39 ( 9.99734673869434e-01 , 1.42949388746288e-02 , 1.17615869633091e-02 , -1.37077225625754e-02 ) ( -7.33324894813423e-05 , -1.04856166546951e-06 , 6.23570652180672e-03 , 1.00548820292743e-06 ) 4.86117694882555e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 - 40 ( 9.99742652208198e-01 , 1.40902436380753e-02 , 1.15309792258764e-02 , -1.35325868934950e-02 ) ( -7.19056858067241e-05 , -1.01342943580709e-06 , 6.23664570366618e-03 , 9.73320423177462e-07 ) 4.86261525438764e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055650e-03 + 20 ( 9.99760693818246e-01 , 1.39216454886428e-02 , 1.19362887828950e-02 , -1.19276105335207e-02 ) ( -7.44154910910036e-05 , -1.03623406304924e-06 , 6.23499480534843e-03 , 8.87811454163381e-07 ) 4.86008746875330e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 21 ( 9.99758313478268e-01 , 1.37518526317376e-02 , 1.20943745877787e-02 , -1.21625360684149e-02 ) ( -7.53933764660893e-05 , -1.03704924339528e-06 , 6.23435061795005e-03 , 9.17196334580247e-07 ) 4.85910171318368e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 22 ( 9.99753796094871e-01 , 1.36537839555646e-02 , 1.22845326108695e-02 , -1.24503669071325e-02 ) ( -7.65692635273181e-05 , -1.04571764160572e-06 , 6.23357553386989e-03 , 9.53550192505157e-07 ) 4.85791609892022e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 23 ( 9.99747426449245e-01 , 1.36276760151045e-02 , 1.24954695687563e-02 , -1.27762668567522e-02 ) ( -7.78731950371622e-05 , -1.06149877874316e-06 , 6.23271549315738e-03 , 9.95180076948371e-07 ) 4.85660109628904e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 24 ( 9.99739603092028e-01 , 1.36692768838184e-02 , 1.27143928598848e-02 , -1.31233034359725e-02 ) ( -7.92260158564982e-05 , -1.08324442064198e-06 , 6.23182259923561e-03 , 1.03997785312531e-06 ) 4.85523649061308e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 25 ( 9.99730830850349e-01 , 1.37696650158448e-02 , 1.29278262893479e-02 , -1.34734360893895e-02 ) ( -8.05444416230567e-05 , -1.10936858783720e-06 , 6.23095181081672e-03 , 1.08550257036763e-06 ) 4.85390628560139e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 26 ( 9.99721696829550e-01 , 1.39157668005032e-02 , 1.31225150492047e-02 , -1.38086900675579e-02 ) ( -8.17466563544410e-05 , -1.13788408329726e-06 , 6.23015725331999e-03 , 1.12912848169394e-06 ) 4.85269306082901e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 27 ( 9.99712830408440e-01 , 1.40915219271310e-02 , 1.32863099760682e-02 , -1.41123950392548e-02 ) ( -8.27577572531398e-05 , -1.16651773939557e-06 , 6.22948859730489e-03 , 1.16824564754451e-06 ) 4.85167246948734e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 28 ( 9.99704851538043e-01 , 1.42794923087412e-02 , 1.34089250569295e-02 , -1.43703388798510e-02 ) ( -8.35143963095269e-05 , -1.19289526097260e-06 , 6.22898794027442e-03 , 1.20048449746711e-06 ) 4.85090853482966e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 29 ( 9.99698314859356e-01 , 1.44626159417893e-02 , 1.34824987759774e-02 , -1.45716929091923e-02 ) ( -8.39681999132023e-05 , -1.21476630361119e-06 , 6.22868748240004e-03 , 1.22392806418303e-06 ) 4.85045017320758e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 30 ( 9.99693658824898e-01 , 1.46257926205038e-02 , 1.35019394575005e-02 , -1.47095998041003e-02 ) ( -8.40878559230599e-05 , -1.23022841225092e-06 , 6.22860808561504e-03 , 1.23727773812928e-06 ) 4.85032906200261e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 31 ( 9.99691168442251e-01 , 1.47570480953222e-02 , 1.34650761492187e-02 , -1.47813732236213e-02 ) ( -8.38600119325431e-05 , -1.23790853458392e-06 , 6.22875863535765e-03 , 1.23994907031517e-06 ) 4.85055871362938e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 32 ( 9.99690957546167e-01 , 1.48481276856586e-02 , 1.33726578643432e-02 , -1.47883239855450e-02 ) ( -8.32892561630635e-05 , -1.23707181806292e-06 , 6.22913603470891e-03 , 1.23208927254656e-06 ) 4.85113448593648e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 33 ( 9.99692972301071e-01 , 1.48944940900112e-02 , 1.32282447187099e-02 , -1.47352882331596e-02 ) ( -8.23974522868586e-05 , -1.22764528722624e-06 , 6.22972565464919e-03 , 1.21452310135798e-06 ) 4.85203425681462e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 34 ( 9.99697013007692e-01 , 1.48948311570748e-02 , 1.30380222677718e-02 , -1.46299748341174e-02 ) ( -8.12226196305917e-05 , -1.21016386944397e-06 , 6.23050211131118e-03 , 1.18864502513774e-06 ) 4.85321956879579e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 35 ( 9.99702767610873e-01 , 1.48502632434009e-02 , 1.28105508103196e-02 , -1.44822615878513e-02 ) ( -7.98174260893882e-05 , -1.18566220604831e-06 , 6.23143031865448e-03 , 1.15628052791932e-06 ) 4.85463717256666e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 36 ( 9.99709848575880e-01 , 1.47635678298615e-02 , 1.25564420596702e-02 , -1.43035480957163e-02 ) ( -7.82472390297188e-05 , -1.15554370356586e-06 , 6.23246684237558e-03 , 1.11953798235853e-06 ) 4.85622102004666e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 37 ( 9.99717825758149e-01 , 1.46386420259571e-02 , 1.22879416152389e-02 , -1.41062224530848e-02 ) ( -7.65875917949357e-05 , -1.12145478557008e-06 , 6.23356163672723e-03 , 1.08066654326796e-06 ) 4.85789484544943e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 38 ( 9.99726250964308e-01 , 1.44803785129685e-02 , 1.20183947274420e-02 , -1.39032355639129e-02 ) ( -7.49209173989000e-05 , -1.08518030953821e-06 , 6.23466024929299e-03 , 1.04192839015343e-06 ) 4.85957547890113e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 39 ( 9.99734673870441e-01 , 1.42949388301149e-02 , 1.17615869623806e-02 , -1.37077225363170e-02 ) ( -7.33324894756701e-05 , -1.04856166212217e-06 , 6.23570652181050e-03 , 1.00548820092254e-06 ) 4.86117694883134e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 + 40 ( 9.99742652209286e-01 , 1.40902435879328e-02 , 1.15309792246189e-02 , -1.35325868663831e-02 ) ( -7.19056857990176e-05 , -1.01342943209091e-06 , 6.23664570367131e-03 , 9.73320421122090e-07 ) 4.86261525439548e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.27813232055700e-03 diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-moving/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out index ab5aa163d..116aff668 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -106,7 +102,6 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -117,26 +112,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped index 869052fe0..1f5d27b1f 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.95047582249982e-01 , -8.94218407198434e-02 , 1.03501830123263e-02 , -4.21534953752505e-02 ) + x ( 9.95047582247901e-01 , -8.94218407474711e-02 , 1.03501830154734e-02 , -4.21534953649891e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj index 479a43598..883efbc35 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( 9.95725692918276e-01 , -7.96585470771598e-02 , 1.34264420545571e-02 , -4.47726589977838e-02 ) ( 3.41700762028735e-05 , 3.17725061894150e-04 , -5.35525350301741e-05 , 1.78579654954758e-04 ) - 1 ( 9.95703202497434e-01 , -7.99005029585730e-02 , 1.32741369737813e-02 , -4.48869630396400e-02 ) ( 3.43497422149501e-05 , 3.18685319686495e-04 , -5.29442547720273e-05 , 1.79032867583579e-04 ) - 2 ( 9.95678521556875e-01 , -8.01968009437818e-02 , 1.31263198798365e-02 , -4.49494666832817e-02 ) ( 3.45469057626449e-05 , 3.19861820323622e-04 , -5.23538161311184e-05 , 1.79279199004076e-04 ) - 3 ( 9.95652403679467e-01 , -8.05419873410536e-02 , 1.29777382161078e-02 , -4.49539501406355e-02 ) ( 3.47555464982458e-05 , 3.21232958651731e-04 , -5.17602977204288e-05 , 1.79293941998351e-04 ) - 4 ( 9.95625468036827e-01 , -8.09309980554691e-02 , 1.28228853926643e-02 , -4.48962644370436e-02 ) ( 3.49707179806798e-05 , 3.22778657195090e-04 , -5.11417606091293e-05 , 1.79060635556877e-04 ) - 5 ( 9.95598135270229e-01 , -8.13594233176651e-02 , 1.26568594199537e-02 , -4.47750063482282e-02 ) ( 3.51890598474303e-05 , 3.24481408186395e-04 , -5.04786710663926e-05 , 1.78573747440431e-04 ) - 6 ( 9.95570599010826e-01 , -8.18234325659399e-02 , 1.24760860076073e-02 , -4.45921018374740e-02 ) ( 3.54090252523799e-05 , 3.26325967036996e-04 , -4.97567836449325e-05 , 1.77840996130284e-04 ) - 7 ( 9.95542831967203e-01 , -8.23194900206118e-02 , 1.22788215872927e-02 , -4.43531489512843e-02 ) ( 3.56308321570564e-05 , 3.28298218081753e-04 , -4.89691474794440e-05 , 1.76884717864206e-04 ) - 8 ( 9.95514620285900e-01 , -8.28440052668668e-02 , 1.20654160973878e-02 , -4.40674179270895e-02 ) ( 3.58561887764231e-05 , 3.30383787230043e-04 , -4.81171552717718e-05 , 1.75741870293466e-04 ) - 9 ( 9.95485617186302e-01 , -8.33930320021245e-02 , 1.18383657119753e-02 , -4.37474717666082e-02 ) ( 3.60878650745618e-05 , 3.32566851194540e-04 , -4.72107550666910e-05 , 1.74462525031735e-04 ) - 10 ( 9.95455406148209e-01 , -8.39620802385744e-02 , 1.16022024359213e-02 , -4.34084364029869e-02 ) ( 3.63291879744745e-05 , 3.34829401794161e-04 , -4.62680115842287e-05 , 1.73106963909578e-04 ) - 11 ( 9.95423564349720e-01 , -8.45460630928600e-02 , 1.13632516811963e-02 , -4.30670089979245e-02 ) ( 3.65835345916786e-05 , 3.37151047680939e-04 , -4.53141408272277e-05 , 1.71741730755538e-04 ) - 12 ( 9.95389718654174e-01 , -8.51393630184037e-02 , 1.11292589640790e-02 , -4.27403375898543e-02 ) ( 3.68538850093158e-05 , 3.39509291391604e-04 , -4.43800222441335e-05 , 1.70435169051391e-04 ) - 13 ( 9.95353590494649e-01 , -8.57359613149864e-02 , 1.09088757881713e-02 , -4.24449202596133e-02 ) ( 3.71424637623492e-05 , 3.41880056834273e-04 , -4.35001487970268e-05 , 1.69253036043655e-04 ) - 14 ( 9.95315031423055e-01 , -8.63295419632000e-02 , 1.07110129745439e-02 , -4.21956467992482e-02 ) ( 3.74504559166966e-05 , 3.44238112758864e-04 , -4.27100481277245e-05 , 1.68254684207691e-04 ) - 15 ( 9.95274054252229e-01 , -8.69134880395287e-02 , 1.05441067567461e-02 , -4.20050513847555e-02 ) ( 3.77777583793028e-05 , 3.46557067272315e-04 , -4.20433559514056e-05 , 1.67490084069610e-04 ) - 16 ( 9.95230862600358e-01 , -8.74807544192303e-02 , 1.04153736849348e-02 , -4.18827855448026e-02 ) ( 3.81227440029491e-05 , 3.48808869035314e-04 , -4.15288452842110e-05 , 1.66997726013206e-04 ) - 17 ( 9.95185875295753e-01 , -8.80236982613176e-02 , 1.03301362013300e-02 , -4.18352774854899e-02 ) ( 3.84820667784462e-05 , 3.50963139203125e-04 , -4.11877380890261e-05 , 1.66803265549611e-04 ) - 18 ( 9.95139736354077e-01 , -8.85340180775604e-02 , 1.02912848947750e-02 , -4.18655255239391e-02 ) ( 3.88505822918751e-05 , 3.52986932995553e-04 , -4.10315624487717e-05 , 1.66918702819926e-04 ) - 19 ( 9.95093299817054e-01 , -8.90029543523046e-02 , 1.02989187503535e-02 , -4.19729799792916e-02 ) ( 3.92214689751451e-05 , 3.54845537784723e-04 , -4.10607197161619e-05 , 1.67341913103511e-04 ) - 20 ( 9.95047582249982e-01 , -8.94218407198434e-02 , 1.03501830123263e-02 , -4.21534953752505e-02 ) ( 3.95866076414231e-05 , 3.56504660172752e-04 , -4.12638394360000e-05 , 1.68056454920554e-04 ) + 0 ( 9.95725692918273e-01 , -7.96585470771966e-02 , 1.34264420545491e-02 , -4.47726589977706e-02 ) ( 3.41700762028921e-05 , 3.17725061894297e-04 , -5.35525350301423e-05 , 1.78579654954705e-04 ) + 1 ( 9.95703202497440e-01 , -7.99005029584874e-02 , 1.32741369737811e-02 , -4.48869630396686e-02 ) ( 3.43497422149066e-05 , 3.18685319686154e-04 , -5.29442547720266e-05 , 1.79032867583693e-04 ) + 2 ( 9.95678521556900e-01 , -8.01968009433796e-02 , 1.31263198798460e-02 , -4.49494666834364e-02 ) ( 3.45469057624427e-05 , 3.19861820322023e-04 , -5.23538161311571e-05 , 1.79279199004696e-04 ) + 3 ( 9.95652403679522e-01 , -8.05419873402017e-02 , 1.29777382160836e-02 , -4.49539501409555e-02 ) ( 3.47555464978077e-05 , 3.21232958648346e-04 , -5.17602977203342e-05 , 1.79293941999634e-04 ) + 4 ( 9.95625468036919e-01 , -8.09309980540691e-02 , 1.28228853926206e-02 , -4.48962644375516e-02 ) ( 3.49707179799499e-05 , 3.22778657189527e-04 , -5.11417606089582e-05 , 1.79060635558914e-04 ) + 5 ( 9.95598135270061e-01 , -8.13594233179634e-02 , 1.26568594211301e-02 , -4.47750063510777e-02 ) ( 3.51890598487685e-05 , 3.24481408187548e-04 , -5.04786710710785e-05 , 1.78573747451775e-04 ) + 6 ( 9.95570599011000e-01 , -8.18234325633647e-02 , 1.24760860073947e-02 , -4.45921018383624e-02 ) ( 3.54090252509857e-05 , 3.26325967026764e-04 , -4.97567836440902e-05 , 1.77840996133848e-04 ) + 7 ( 9.95542831967394e-01 , -8.23194900179106e-02 , 1.22788215872136e-02 , -4.43531489520439e-02 ) ( 3.56308321555336e-05 , 3.28298218071023e-04 , -4.89691474791349e-05 , 1.76884717867258e-04 ) + 8 ( 9.95514620286082e-01 , -8.28440052644148e-02 , 1.20654160975387e-02 , -4.40674179275458e-02 ) ( 3.58561887749678e-05 , 3.30383787220305e-04 , -4.81171552723796e-05 , 1.75741870295307e-04 ) + 9 ( 9.95485617186446e-01 , -8.33930320003749e-02 , 1.18383657124410e-02 , -4.37474717665303e-02 ) ( 3.60878650734080e-05 , 3.32566851187595e-04 , -4.72107550685531e-05 , 1.74462525031441e-04 ) + 10 ( 9.95455406148282e-01 , -8.39620802380189e-02 , 1.16022024367708e-02 , -4.34084364021512e-02 ) ( 3.63291879738892e-05 , 3.34829401791962e-04 , -4.62680115876186e-05 , 1.73106963906254e-04 ) + 11 ( 9.95423564349686e-01 , -8.45460630939964e-02 , 1.13632516824820e-02 , -4.30670089961288e-02 ) ( 3.65835345919473e-05 , 3.37151047685463e-04 , -4.53141408323535e-05 , 1.71741730748373e-04 ) + 12 ( 9.95389718653998e-01 , -8.51393630217013e-02 , 1.11292589658322e-02 , -4.27403375869374e-02 ) ( 3.68538850107258e-05 , 3.39509291404714e-04 , -4.43800222511196e-05 , 1.70435169039739e-04 ) + 13 ( 9.95353590493668e-01 , -8.57359613292896e-02 , 1.09088757916328e-02 , -4.24449202528342e-02 ) ( 3.71424637701849e-05 , 3.41880056891084e-04 , -4.35001488108009e-05 , 1.69253036016511e-04 ) + 14 ( 9.95315031422500e-01 , -8.63295419718748e-02 , 1.07110129770663e-02 , -4.21956467939341e-02 ) ( 3.74504559211243e-05 , 3.44238112793326e-04 , -4.27100481377666e-05 , 1.68254684186438e-04 ) + 15 ( 9.95274054250948e-01 , -8.69134880574461e-02 , 1.05441067595788e-02 , -4.20050513773208e-02 ) ( 3.77777583895344e-05 , 3.46557067343460e-04 , -4.20433559626645e-05 , 1.67490084039822e-04 ) + 16 ( 9.95230862599338e-01 , -8.74807544340958e-02 , 1.04153736880360e-02 , -4.18827855372420e-02 ) ( 3.81227440111029e-05 , 3.48808869094348e-04 , -4.15288452965480e-05 , 1.66997725982946e-04 ) + 17 ( 9.95185875294234e-01 , -8.80236982832042e-02 , 1.03301362042927e-02 , -4.18352774748477e-02 ) ( 3.84820667905813e-05 , 3.50963139290033e-04 , -4.11877381007968e-05 , 1.66803265507009e-04 ) + 18 ( 9.95139736351655e-01 , -8.85340181100190e-02 , 1.02912848994442e-02 , -4.18655255117140e-02 ) ( 3.88505823112175e-05 , 3.52986933124393e-04 , -4.10315624673211e-05 , 1.66918702770913e-04 ) + 19 ( 9.95093299815157e-01 , -8.90029543780060e-02 , 1.02989187541513e-02 , -4.19729799688224e-02 ) ( 3.92214689902938e-05 , 3.54845537886740e-04 , -4.10607197312513e-05 , 1.67341913061558e-04 ) + 20 ( 9.95047582247901e-01 , -8.94218407474711e-02 , 1.03501830154734e-02 , -4.21534953649891e-02 ) ( 3.95866076580436e-05 , 3.56504660282400e-04 , -4.12638394484893e-05 , 1.68056454879410e-04 ) diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out index 90fb86396..5914612e6 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -106,7 +102,6 @@ colvars: # centers = { ( 1 , 0 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -117,31 +112,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.995048 , -0.0894218 , 0.0103502 , -0.0421535 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped index dfd0bab71..ed7e25462 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.94724148740762e-01 , -9.22283983670171e-02 , 8.57198031977685e-03 , -4.40943488444842e-02 ) + x ( 9.94724148736992e-01 , -9.22283984220502e-02 , 8.57198032337350e-03 , -4.40943488137254e-02 ) } restraint { diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj index 726901e4a..c0667eff6 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( 9.95047582249982e-01 , -8.94218407198434e-02 , 1.03501830123263e-02 , -4.21534953752505e-02 ) ( 3.95866076414231e-05 , 3.56504660172752e-04 , -4.12638394360000e-05 , 1.68056454920554e-04 ) - 21 ( 9.95003682841854e-01 , -8.97829884973678e-02 , 1.04393119593296e-02 , -4.23993735029785e-02 ) ( 3.99372197110201e-05 , 3.57933932791603e-04 , -4.16179506583343e-05 , 1.69031737078635e-04 ) - 22 ( 9.94962679616141e-01 , -9.00807729420692e-02 , 1.05578791054915e-02 , -4.26995515904153e-02 ) ( 4.02646961408769e-05 , 3.59111217737913e-04 , -4.20894792359408e-05 , 1.70223761050075e-04 ) - 23 ( 9.94925517924194e-01 , -9.03126986506125e-02 , 1.06952529194415e-02 , -4.30400024478075e-02 ) ( 4.05614878861151e-05 , 3.60026823408699e-04 , -4.26360632742869e-05 , 1.71576706180971e-04 ) - 24 ( 9.94892911463656e-01 , -9.04801848123271e-02 , 1.08392437997452e-02 , -4.34043968918623e-02 ) ( 4.08218962464344e-05 , 3.60686606780452e-04 , -4.32091299802860e-05 , 1.73025559869822e-04 ) - 25 ( 9.94865274497008e-01 , -9.05888500075216e-02 , 1.09769033218979e-02 , -4.37750322417940e-02 ) ( 4.10426139951310e-05 , 3.61113088545953e-04 , -4.37570789441720e-05 , 1.74499809774828e-04 ) - 26 ( 9.94842696775133e-01 , -9.06481847893688e-02 , 1.10954059422353e-02 , -4.41339691683329e-02 ) ( 4.12229254634621e-05 , 3.61344139392317e-04 , -4.42287942193370e-05 , 1.75927969701260e-04 ) - 27 ( 9.94824962048116e-01 , -9.06706488864391e-02 , 1.11829212623721e-02 , -4.44642619247934e-02 ) ( 4.13645585785194e-05 , 3.61429384974983e-04 , -4.45771195389264e-05 , 1.77242481863921e-04 ) - 28 ( 9.94811601036927e-01 , -9.06703674651151e-02 , 1.12293836982419e-02 , -4.47511323638196e-02 ) ( 4.14712617591352e-05 , 3.61425022578285e-04 , -4.47619257552785e-05 , 1.78384399194370e-04 ) - 29 ( 9.94801963555091e-01 , -9.06616843247956e-02 , 1.12270902231604e-02 , -4.49829384038806e-02 ) ( 4.15482279400340e-05 , 3.61388073059340e-04 , -4.47524941989370e-05 , 1.79307251474472e-04 ) - 30 ( 9.94795293173688e-01 , -9.06578422928237e-02 , 1.11710965045517e-02 , -4.51518207071648e-02 ) ( 4.16014983262487e-05 , 3.61371140630078e-04 , -4.45290973603736e-05 , 1.79979630419292e-04 ) - 31 ( 9.94790790369875e-01 , -9.06700109711078e-02 , 1.10594217982803e-02 , -4.52539688344244e-02 ) ( 4.16374581364648e-05 , 3.61418554057688e-04 , -4.40838177059692e-05 , 1.80386257885433e-04 ) - 32 ( 9.94787655103003e-01 , -9.07067883182348e-02 , 1.08930998886607e-02 , -4.52895151494764e-02 ) ( 4.16624966373904e-05 , 3.61564391012379e-04 , -4.34207527408272e-05 , 1.80527568750601e-04 ) - 33 ( 9.94785106318339e-01 , -9.07741836818644e-02 , 1.06761181594841e-02 , -4.52621290390331e-02 ) ( 4.16828514234531e-05 , 3.61832415325462e-04 , -4.25557737151859e-05 , 1.80418096959853e-04 ) - 34 ( 9.94782383326987e-01 , -9.08759671977928e-02 , 1.04152699871068e-02 , -4.51784302432211e-02 ) ( 4.17045974180370e-05 , 3.62237469779759e-04 , -4.15159383007289e-05 , 1.80084138464314e-04 ) - 35 ( 9.94778740636462e-01 , -9.10141757972667e-02 , 1.01199149985978e-02 , -4.50473562165450e-02 ) ( 4.17336881618950e-05 , 3.62787491302079e-04 , -4.03385356442665e-05 , 1.79561229978004e-04 ) - 36 ( 9.94773451641488e-01 , -9.11895285998344e-02 , 9.80161261516879e-03 , -4.48795964015018e-02 ) ( 4.17759263281172e-05 , 3.63485167001368e-04 , -3.90696262280471e-05 , 1.78891895192706e-04 ) - 37 ( 9.94765834654937e-01 , -9.14015536567541e-02 , 9.47358561494656e-03 , -4.46871499202457e-02 ) ( 4.18367558146745e-05 , 3.64328445106307e-04 , -3.77619042411093e-05 , 1.78123885156437e-04 ) - 38 ( 9.94755307047952e-01 , -9.16483517814180e-02 , 9.14999202764146e-03 , -4.44829895755552e-02 ) ( 4.19208293491576e-05 , 3.65309606419041e-04 , -3.64717959612317e-05 , 1.77308845149173e-04 ) - 39 ( 9.94741461700454e-01 , -9.19260830853272e-02 , 8.84503297238212e-03 , -4.42807521881895e-02 ) ( 4.20313979285352e-05 , 3.66413236480337e-04 , -3.52559039764323e-05 , 1.76501088466893e-04 ) - 40 ( 9.94724148740762e-01 , -9.22283983670171e-02 , 8.57198031977685e-03 , -4.40943488444842e-02 ) ( 4.21696580457610e-05 , 3.67613980120615e-04 , -3.41671313680286e-05 , 1.75756050918744e-04 ) + 20 ( 9.95047582247901e-01 , -8.94218407474711e-02 , 1.03501830154734e-02 , -4.21534953649891e-02 ) ( 3.95866076580436e-05 , 3.56504660282400e-04 , -4.12638394484893e-05 , 1.68056454879410e-04 ) + 21 ( 9.95003682839837e-01 , -8.97829885242213e-02 , 1.04393119624910e-02 , -4.23993734926744e-02 ) ( 3.99372197271322e-05 , 3.57933932898174e-04 , -4.16179506708815e-05 , 1.69031737037327e-04 ) + 22 ( 9.94962679614012e-01 , -9.00807729701850e-02 , 1.05578791084465e-02 , -4.26995515799716e-02 ) ( 4.02646961578782e-05 , 3.59111217849485e-04 , -4.20894792476610e-05 , 1.70223761008198e-04 ) + 23 ( 9.94925517922001e-01 , -9.03126986794675e-02 , 1.06952529221899e-02 , -4.30400024372660e-02 ) ( 4.05614879036287e-05 , 3.60026823523198e-04 , -4.26360632851805e-05 , 1.71576706138696e-04 ) + 24 ( 9.94892911461449e-01 , -9.04801848414051e-02 , 1.08392438023233e-02 , -4.34043968812029e-02 ) ( 4.08218962640658e-05 , 3.60686606895834e-04 , -4.32091299904993e-05 , 1.73025559827073e-04 ) + 25 ( 9.94865274494471e-01 , -9.05888500412821e-02 , 1.09769033233308e-02 , -4.37750322292276e-02 ) ( 4.10426140153920e-05 , 3.61113088679918e-04 , -4.37570789498096e-05 , 1.74499809724437e-04 ) + 26 ( 9.94842696773042e-01 , -9.06481848174512e-02 , 1.10954059447183e-02 , -4.41339691571599e-02 ) ( 4.12229254801604e-05 , 3.61344139503753e-04 , -4.42287942291727e-05 , 1.75927969656476e-04 ) + 27 ( 9.94824962046056e-01 , -9.06706489146701e-02 , 1.11829212647168e-02 , -4.44642619127326e-02 ) ( 4.13645585949729e-05 , 3.61429385087017e-04 , -4.45771195482112e-05 , 1.77242481815600e-04 ) + 28 ( 9.94811601034407e-01 , -9.06703674988958e-02 , 1.12293836999313e-02 , -4.47511323509693e-02 ) ( 4.14712617792593e-05 , 3.61425022712328e-04 , -4.47619257619370e-05 , 1.78384399142845e-04 ) + 29 ( 9.94801963553301e-01 , -9.06616843507634e-02 , 1.12270902259919e-02 , -4.49829383904157e-02 ) ( 4.15482279543266e-05 , 3.61388073162416e-04 , -4.47524942101701e-05 , 1.79307251420585e-04 ) + 30 ( 9.94795293171562e-01 , -9.06578423239697e-02 , 1.11710965065822e-02 , -4.51518206909619e-02 ) ( 4.16014983432260e-05 , 3.61371140753713e-04 , -4.45290973684036e-05 , 1.79979630354449e-04 ) + 31 ( 9.94790790368376e-01 , -9.06700109952209e-02 , 1.10594218017861e-02 , -4.52539688182038e-02 ) ( 4.16374581484353e-05 , 3.61418554153441e-04 , -4.40838177198993e-05 , 1.80386257820595e-04 ) + 32 ( 9.94787655101548e-01 , -9.07067883426823e-02 , 1.08930998924629e-02 , -4.52895151315648e-02 ) ( 4.16624966490124e-05 , 3.61564391109476e-04 , -4.34207527559406e-05 , 1.80527568679028e-04 ) + 33 ( 9.94785106316866e-01 , -9.07741837073836e-02 , 1.06761181635399e-02 , -4.52621290192839e-02 ) ( 4.16828514352205e-05 , 3.61832415426825e-04 , -4.25557737313109e-05 , 1.80418096880953e-04 ) + 34 ( 9.94782383325423e-01 , -9.08759672251909e-02 , 1.04152699913556e-02 , -4.51784302215533e-02 ) ( 4.17045974305217e-05 , 3.62237469888589e-04 , -4.15159383176215e-05 , 1.80084138377755e-04 ) + 35 ( 9.94778740634731e-01 , -9.10141758273820e-02 , 1.01199150029673e-02 , -4.50473561929485e-02 ) ( 4.17336881757203e-05 , 3.62787491421699e-04 , -4.03385356616366e-05 , 1.79561229883738e-04 ) + 36 ( 9.94773451639091e-01 , -9.11895286402353e-02 , 9.80161261834228e-03 , -4.48795963718487e-02 ) ( 4.17759263472595e-05 , 3.63485167161823e-04 , -3.90696262406339e-05 , 1.78891895074220e-04 ) + 37 ( 9.94765834652613e-01 , -9.14015536948658e-02 , 9.47358561936806e-03 , -4.46871498930807e-02 ) ( 4.18367558332307e-05 , 3.64328445257653e-04 , -3.77619042586746e-05 , 1.78123885047879e-04 ) + 38 ( 9.94755307045228e-01 , -9.16483518244586e-02 , 9.14999203197848e-03 , -4.44829895469045e-02 ) ( 4.19208293709127e-05 , 3.65309606589932e-04 , -3.64717959784524e-05 , 1.77308845034647e-04 ) + 39 ( 9.94741461697262e-01 , -9.19260831338689e-02 , 8.84503297656702e-03 , -4.42807521582896e-02 ) ( 4.20313979540273e-05 , 3.66413236673037e-04 , -3.52559039930375e-05 , 1.76501088347335e-04 ) + 40 ( 9.94724148736992e-01 , -9.22283984220502e-02 , 8.57198032337350e-03 , -4.40943488137254e-02 ) ( 4.21696580758678e-05 , 3.67613980339042e-04 , -3.41671313822781e-05 , 1.75756050795697e-04 ) diff --git a/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt b/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt +++ b/namd/tests/library/000_orientation_harmonic-ori-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out index 913368e3f..e51e7ce01 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -109,7 +105,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -120,26 +115,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped index 68355e27e..75d556e11 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.95047581774198e-01 , -8.94218449655825e-02 , 1.03501990061269e-02 , -4.21534936725870e-02 ) + x ( 9.95047581772214e-01 , -8.94218449921444e-02 , 1.03501990099413e-02 , -4.21534936621476e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.26088591477162e-03 + accumulatedWork 2.26088591477312e-03 } } diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj index 509adba31..c68dda8dd 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 0 ( 9.95725692918276e-01 , -7.96585470771598e-02 , 1.34264420545571e-02 , -4.47726589977838e-02 ) ( 3.41700762028735e-05 , 3.17725061894150e-04 , -5.35525350301741e-05 , 1.78579654954758e-04 ) 1.71094220294084e-05 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 - 1 ( 9.95703202497434e-01 , -7.99005029585730e-02 , 1.32741369737813e-02 , -4.48869630396400e-02 ) ( 2.83367138120423e-05 , 3.17696149303822e-04 , 3.90264420205889e-04 , 1.78477165769913e-04 ) 3.57367786265048e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.25751658795693e-05 - 2 ( 9.95678521556407e-01 , -8.01968009477312e-02 , 1.31263198967770e-02 , -4.49494666816481e-02 ) ( 2.10043163774406e-05 , 3.14124330884285e-04 , 9.28834252114772e-04 , 1.76063396271639e-04 ) 1.24105832996037e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.62928156880148e-04 - 3 ( 9.95652403677488e-01 , -8.05419873579345e-02 , 1.29777382869545e-02 , -4.49539501337857e-02 ) ( 1.18560940376575e-05 , 3.04619185568056e-04 , 1.56985791890468e-03 , 1.70021080023323e-04 ) 3.23286808547749e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.92924287234955e-04 - 4 ( 9.95625468031602e-01 , -8.09309981004511e-02 , 1.28228855771687e-02 , -4.48962644191386e-02 ) ( 7.70725693236790e-07 , 2.86357930588497e-04 , 2.30368856073467e-03 , 1.58856330355165e-04 ) 6.76777222122836e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.43830024565543e-04 - 5 ( 9.95598135259239e-01 , -8.13594234131779e-02 , 1.26568598023747e-02 , -4.47750063109274e-02 ) ( -1.19638357685023e-05 , 2.57128422733453e-04 , 3.09452499115324e-03 , 1.41506985517112e-04 ) 1.20779591337073e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.17743292406584e-03 - 6 ( 9.95570598990727e-01 , -8.18234327423189e-02 , 1.24760866963825e-02 , -4.45921017698568e-02 ) ( -2.55774576553760e-05 , 2.16780943542518e-04 , 3.88503951911507e-03 , 1.18141192226147e-04 ) 1.89439219877622e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.60702762768025e-03 - 7 ( 9.95542831933873e-01 , -8.23194903158855e-02 , 1.22788227118873e-02 , -4.43531488400399e-02 ) ( -3.90575682790280e-05 , 1.67766250719849e-04 , 4.61795501118427e-03 , 9.03912482932004e-05 ) 2.67041875895129e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.94669840769354e-03 - 8 ( 9.95514620234602e-01 , -8.28440057254391e-02 , 1.20654178024697e-02 , -4.40674177570056e-02 ) ( -5.15481325620161e-05 , 1.14015827333934e-04 , 5.25759497784956e-03 , 6.06487222586368e-05 ) 3.45770500468423e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.15860938064172e-03 - 9 ( 9.95485617111931e-01 , -8.33930326725034e-02 , 1.18383681499865e-02 , -4.37474715212837e-02 ) ( -6.25780827741211e-05 , 5.92548196854455e-05 , 5.79445555467542e-03 , 3.10847135979329e-05 ) 4.19801357307849e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.25291457221835e-03 - 10 ( 9.95455406045573e-01 , -8.39620811705810e-02 , 1.16022057593680e-02 , -4.34084360656384e-02 ) ( -7.20363521575908e-05 , 6.07593470320788e-06 , 6.23635565891445e-03 , 3.14126114343633e-06 ) 4.86217099062632e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 11 ( 9.95423564213814e-01 , -8.45460643347972e-02 , 1.13632560356581e-02 , -4.30670085521597e-02 ) ( -7.05611115363754e-05 , 5.99309127286019e-06 , 6.23732857268019e-03 , 3.05282706099796e-06 ) 4.86366147886625e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 12 ( 9.95389718481259e-01 , -8.51393646053625e-02 , 1.11292644683300e-02 , -4.27403370224198e-02 ) ( -6.91159591047267e-05 , 5.91174364473551e-06 , 6.23828095599262e-03 , 2.96772141696521e-06 ) 4.86512125722331e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 13 ( 9.95353590282289e-01 , -8.57359632682770e-02 , 1.09088825330022e-02 , -4.24449195605181e-02 ) ( -6.77542728844581e-05 , 5.83609473859762e-06 , 6.23917763573012e-03 , 2.88924929847956e-06 ) 4.86649632743153e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 14 ( 9.95315031170072e-01 , -8.63295442907098e-02 , 1.07110210230709e-02 , -4.21956459616350e-02 ) ( -6.65310885163908e-05 , 5.77063379223042e-06 , 6.23998242899872e-03 , 2.82053638151088e-06 ) 4.86773104444897e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 15 ( 9.95274053958565e-01 , -8.69134907370101e-02 , 1.05441161461300e-02 , -4.20050504045343e-02 ) ( -6.54985597796452e-05 , 5.71973964965100e-06 , 6.24066111879459e-03 , 2.76433440018415e-06 ) 4.86877270224177e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 16 ( 9.95230862266868e-01 , -8.74807574724623e-02 , 1.04153844293258e-02 , -4.18827844200880e-02 ) ( -6.47013396955228e-05 , 5.68724546298252e-06 , 6.24118446606660e-03 , 2.72285794673419e-06 ) 4.86957619519322e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 17 ( 9.95185874923942e-01 , -8.80237016490180e-02 , 1.03301482957764e-02 , -4.18352762159005e-02 ) ( -6.41723928153701e-05 , 5.67601661319342e-06 , 6.24153092939405e-03 , 2.69765663532097e-06 ) 4.87010824163727e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 18 ( 9.95139735945799e-01 , -8.85340217748383e-02 , 1.02912983197793e-02 , -4.18655241098357e-02 ) ( -6.39296531495683e-05 , 5.68759250541073e-06 , 6.24168882977397e-03 , 2.68952021368430e-06 ) 4.87035075381305e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 19 ( 9.95093299374205e-01 , -8.90029583343626e-02 , 1.02989334767443e-02 , -4.19729784210373e-02 ) ( -6.39737894420540e-05 , 5.72193232512286e-06 , 6.24165779846845e-03 , 2.69841077761449e-06 ) 4.87030309260599e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 20 ( 9.95047581774198e-01 , -8.94218449655825e-02 , 1.03501990061269e-02 , -4.21534936725870e-02 ) ( -6.42872031582073e-05 , 5.77729187968484e-06 , 6.24144943237969e-03 , 2.72341771508647e-06 ) 4.86998308194352e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 0 ( 9.95725692918276e-01 , -7.96585470771598e-02 , 1.34264420545571e-02 , -4.47726589977838e-02 ) ( 3.41700762028735e-05 , 3.17725061894150e-04 , -5.35525350301742e-05 , 1.78579654954758e-04 ) 1.71094220294084e-05 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 + 1 ( 9.95703202497441e-01 , -7.99005029584633e-02 , 1.32741369737848e-02 , -4.48869630396836e-02 ) ( 2.83367138119876e-05 , 3.17696149303388e-04 , 3.90264420205874e-04 , 1.78477165770087e-04 ) 3.57367786264763e-05 ( 9.93883734673619e-01 , 0.00000000000000e+00 , 1.10431526074847e-01 , 0.00000000000000e+00 ) 4.25751658795682e-05 + 2 ( 9.95678521556434e-01 , -8.01968009473040e-02 , 1.31263198967912e-02 , -4.49494666818169e-02 ) ( 2.10043163772193e-05 , 3.14124330882618e-04 , 9.28834252114706e-04 , 1.76063396272304e-04 ) 1.24105832995919e-04 ( 9.70142500145332e-01 , 0.00000000000000e+00 , 2.42535625036333e-01 , 0.00000000000000e+00 ) 1.62928156880146e-04 + 3 ( 9.95652403677545e-01 , -8.05419873570241e-02 , 1.29777382869849e-02 , -4.49539501341403e-02 ) ( 1.18560940371760e-05 , 3.04619185564628e-04 , 1.56985791890452e-03 , 1.70021080024672e-04 ) 3.23286808547484e-04 ( 9.19145030018058e-01 , 0.00000000000000e+00 , 3.93919298579168e-01 , 0.00000000000000e+00 ) 3.92924287234960e-04 + 4 ( 9.95625468031697e-01 , -8.09309980989665e-02 , 1.28228855772213e-02 , -4.48962644197014e-02 ) ( 7.70725692445905e-07 , 2.86357930583270e-04 , 2.30368856073438e-03 , 1.58856330357171e-04 ) 6.76777222122379e-04 ( 8.32050294337844e-01 , 0.00000000000000e+00 , 5.54700196225229e-01 , 0.00000000000000e+00 ) 7.43830024565586e-04 + 5 ( 9.95598135259372e-01 , -8.13594234111277e-02 , 1.26568598024581e-02 , -4.47750063116703e-02 ) ( -1.19638357695980e-05 , 2.57128422727014e-04 , 3.09452499115279e-03 , 1.41506985519482e-04 ) 1.20779591337005e-03 ( 7.07106781186547e-01 , 0.00000000000000e+00 , 7.07106781186547e-01 , 0.00000000000000e+00 ) 1.17743292406597e-03 + 6 ( 9.95570598990892e-01 , -8.18234327398263e-02 , 1.24760866965111e-02 , -4.45921017706951e-02 ) ( -2.55774576567467e-05 , 2.16780943535973e-04 , 3.88503951911439e-03 , 1.18141192228400e-04 ) 1.89439219877529e-03 ( 5.54700196225229e-01 , 0.00000000000000e+00 , 8.32050294337844e-01 , 0.00000000000000e+00 ) 1.60702762768054e-03 + 7 ( 9.95542831934058e-01 , -8.23194903131902e-02 , 1.22788227120833e-02 , -4.43531488408355e-02 ) ( -3.90575682806717e-05 , 1.67766250714442e-04 , 4.61795501118331e-03 , 9.03912482948679e-05 ) 2.67041875895001e-03 ( 3.93919298579168e-01 , 0.00000000000000e+00 , 9.19145030018058e-01 , 0.00000000000000e+00 ) 1.94669840769403e-03 + 8 ( 9.95514620234786e-01 , -8.28440057228855e-02 , 1.20654178027640e-02 , -4.40674177575778e-02 ) ( -5.15481325640461e-05 , 1.14015827330549e-04 , 5.25759497784824e-03 , 6.06487222594931e-05 ) 3.45770500468243e-03 ( 2.42535625036333e-01 , 0.00000000000000e+00 , 9.70142500145332e-01 , 0.00000000000000e+00 ) 2.15860938064247e-03 + 9 ( 9.95485617112086e-01 , -8.33930326705179e-02 , 1.18383681504187e-02 , -4.37474715214257e-02 ) ( -6.25780827768114e-05 , 5.92548196842370e-05 , 5.79445555467360e-03 , 3.10847135981400e-05 ) 4.19801357307588e-03 ( 1.10431526074847e-01 , 0.00000000000000e+00 , 9.93883734673619e-01 , 0.00000000000000e+00 ) 2.25291457221944e-03 + 10 ( 9.95455406045667e-01 , -8.39620811696408e-02 , 1.16022057599854e-02 , -4.34084360651368e-02 ) ( -7.20363521614028e-05 , 6.07593470346080e-06 , 6.23635565891194e-03 , 3.14126114356596e-06 ) 4.86217099062247e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 11 ( 9.95423564213811e-01 , -8.45460643353971e-02 , 1.13632560365135e-02 , -4.30670085508141e-02 ) ( -7.05611115416490e-05 , 5.99309127335064e-06 , 6.23732857267671e-03 , 3.05282706113075e-06 ) 4.86366147886091e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 12 ( 9.95389718481123e-01 , -8.51393646079810e-02 , 1.11292644694778e-02 , -4.27403370200617e-02 ) ( -6.91159591117955e-05 , 5.91174364552275e-06 , 6.23828095598795e-03 , 2.96772141710540e-06 ) 4.86512125721615e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 13 ( 9.95353590281985e-01 , -8.57359632733491e-02 , 1.09088825344929e-02 , -4.24449195570245e-02 ) ( -6.77542728936322e-05 , 5.83609473973489e-06 , 6.23917763572405e-03 , 2.88924929863384e-06 ) 4.86649632742223e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 14 ( 9.95315031169567e-01 , -8.63295442986035e-02 , 1.07110210249439e-02 , -4.21956459569390e-02 ) ( -6.65310885279126e-05 , 5.77063379376035e-06 , 6.23998242899110e-03 , 2.82053638168687e-06 ) 4.86773104443728e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 15 ( 9.95274053957830e-01 , -8.69134907480067e-02 , 1.05441161484066e-02 , -4.20050503986284e-02 ) ( -6.54985597936450e-05 , 5.71973965160146e-06 , 6.24066111878534e-03 , 2.76433440038838e-06 ) 4.86877270222756e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 16 ( 9.95230862265883e-01 , -8.74807574867389e-02 , 1.04153844320038e-02 , -4.18827844130215e-02 ) ( -6.47013397119858e-05 , 5.68724546536339e-06 , 6.24118446605571e-03 , 2.72285794697030e-06 ) 4.86957619517651e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 17 ( 9.95185874922694e-01 , -8.80237016666293e-02 , 1.03301482988283e-02 , -4.18352762077715e-02 ) ( -6.41723928341247e-05 , 5.67601661599500e-06 , 6.24153092938165e-03 , 2.69765663558857e-06 ) 4.87010824161822e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 18 ( 9.95139735944289e-01 , -8.85340217957036e-02 , 1.02912983231547e-02 , -4.18655241007787e-02 ) ( -6.39296531703027e-05 , 5.68759250860446e-06 , 6.24168882976025e-03 , 2.68952021397884e-06 ) 4.87035075379198e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 19 ( 9.95093299372444e-01 , -8.90029583582581e-02 , 1.02989334803762e-02 , -4.19729784112083e-02 ) ( -6.39737894643545e-05 , 5.72193232866381e-06 , 6.24165779845369e-03 , 2.69841077792800e-06 ) 4.87030309258332e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 20 ( 9.95047581772214e-01 , -8.94218449921444e-02 , 1.03501990099413e-02 , -4.21534936621476e-02 ) ( -6.42872031816166e-05 , 5.77729188351618e-06 , 6.24144943236418e-03 , 2.72341771540914e-06 ) 4.86998308191970e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out index 023407b4d..5455bcf82 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -109,7 +105,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -120,31 +115,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( 0.995048 , -0.0894218 , 0.0103502 , -0.0421535 ) colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped index 0d834a02a..80ded7bf8 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( 9.94724147282287e-01 , -9.22284123842412e-02 , 8.57202435943065e-03 , -4.40943438661931e-02 ) + x ( 9.94724147278495e-01 , -9.22284124393750e-02 , 8.57202436227895e-03 , -4.40943438358672e-02 ) } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) - accumulatedWork 2.26088591477162e-03 + accumulatedWork 2.26088591477312e-03 } } diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj index a8608cd4b..545a4a767 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 ( 9.95047581774198e-01 , -8.94218449655825e-02 , 1.03501990061269e-02 , -4.21534936725870e-02 ) ( -6.42872031582073e-05 , 5.77729187968484e-06 , 6.24144943237969e-03 , 2.72341771508647e-06 ) 4.86998308194352e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 21 ( 9.95003682334260e-01 , -8.97829929925345e-02 , 1.04393291863312e-02 , -4.23993716546049e-02 ) ( -6.48343047311814e-05 , 5.85024762290276e-06 , 6.24108712857907e-03 , 2.76273729542017e-06 ) 4.86942673646249e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 22 ( 9.94962679077155e-01 , -9.00807776816361e-02 , 1.05578975352894e-02 , -4.26995495938328e-02 ) ( -6.55630799832673e-05 , 5.93587413507200e-06 , 6.24060508570187e-03 , 2.81368743184070e-06 ) 4.86868668807296e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 23 ( 9.94925517353414e-01 , -9.03127036401896e-02 , 1.06952725287408e-02 , -4.30400002994432e-02 ) ( -6.64079280825436e-05 , 6.02806885909569e-06 , 6.24004647490369e-03 , 2.87277509190952e-06 ) 4.86782932654013e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 24 ( 9.94892910859826e-01 , -9.04801900685380e-02 , 1.08392645748153e-02 , -4.34043945874284e-02 ) ( -6.72936746700319e-05 , 6.11999985937453e-06 , 6.23946083147816e-03 , 2.93583477853088e-06 ) 4.86693074746560e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 25 ( 9.94865273858061e-01 , -9.05888555574097e-02 , 1.09769252601266e-02 , -4.37750297767849e-02 ) ( -6.81405121220271e-05 , 6.20463008653664e-06 , 6.23890081877020e-03 , 2.99824813020128e-06 ) 4.86607175534625e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 26 ( 9.94842696098306e-01 , -9.06481906689943e-02 , 1.10954290528118e-02 , -4.41339665385350e-02 ) ( -6.88694319684040e-05 , 6.27525278601464e-06 , 6.23841864350692e-03 , 3.05523799686328e-06 ) 4.86533236044889e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 27 ( 9.94824961330116e-01 , -9.06706551388669e-02 , 1.11829455661831e-02 , -4.44642591266877e-02 ) ( -6.94075830663685e-05 , 6.32596815807546e-06 , 6.23806249527008e-03 , 3.10221081977458e-06 ) 4.86478634363342e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 28 ( 9.94811600274131e-01 , -9.06703741379878e-02 , 1.12294092270974e-02 , -4.47511293948060e-02 ) ( -6.96929861680878e-05 , 6.35204608481931e-06 , 6.23787339223321e-03 , 3.13510602516003e-06 ) 4.86449646840391e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 29 ( 9.94801962743773e-01 , -9.06616914676642e-02 , 1.12271170184627e-02 , -4.49829352623114e-02 ) ( -6.96781856436282e-05 , 6.35015048766679e-06 , 6.23788272163551e-03 , 3.15070680536035e-06 ) 4.86451076872475e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 30 ( 9.94795292310257e-01 , -9.06578499543900e-02 , 1.11711246155064e-02 , -4.51518173922375e-02 ) ( -6.93326642576498e-05 , 6.31843588504616e-06 , 6.23811060337159e-03 , 3.14687435704348e-06 ) 4.86486009296005e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 31 ( 9.94790789451105e-01 , -9.06700191965351e-02 , 1.10594512797368e-02 , -4.52539653460176e-02 ) ( -6.86440920532849e-05 , 6.25655284528142e-06 , 6.23856504120304e-03 , 3.12268408184823e-06 ) 4.86555683503798e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 32 ( 9.94787654126230e-01 , -9.07067971467051e-02 , 1.08931307986771e-02 , -4.52895114880088e-02 ) ( -6.76186432835818e-05 , 6.16560784024465e-06 , 6.23924171412794e-03 , 3.07846132699065e-06 ) 4.86659461748473e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 33 ( 9.94785105281604e-01 , -9.07741931445759e-02 , 1.06761505567364e-02 , -4.52621252053962e-02 ) ( -6.62806416135132e-05 , 6.04811203105849e-06 , 6.24012423798566e-03 , 3.01572941078122e-06 ) 4.86794866290398e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 34 ( 9.94782382229110e-01 , -9.08759773165833e-02 , 1.04153039282901e-02 , -4.51784262387849e-02 ) ( -6.46716868136083e-05 , 5.90792805430392e-06 , 6.24118479330421e-03 , 2.93708964356536e-06 ) 4.86957669766956e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 35 ( 9.94778739477024e-01 , -9.10141865840077e-02 , 1.01199505360086e-02 , -4.50473520431876e-02 ) ( -6.28492246685917e-05 , 5.75019432326694e-06 , 6.24238513756400e-03 , 2.84605112366581e-06 ) 4.87142042443290e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 36 ( 9.94773450420717e-01 , -9.11895400566741e-02 , 9.80164979465735e-03 , -4.48795920616019e-02 ) ( -6.08843396302519e-05 , 5.58118526905689e-06 , 6.24367813620281e-03 , 2.74682072022538e-06 ) 4.87340778324529e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 37 ( 9.94765833373519e-01 , -9.14015657772049e-02 , 9.47362447441949e-03 , -4.46871454165775e-02 ) ( -5.88584935456410e-05 , 5.40806518365723e-06 , 6.24500998010697e-03 , 2.64405749758712e-06 ) 4.87545627651339e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 38 ( 9.94755305706783e-01 , -9.16483645522010e-02 , 9.15003259624412e-03 , -4.44829849110689e-02 ) ( -5.68590654435119e-05 , 5.23851476636451e-06 , 6.24632316888377e-03 , 2.54259608938115e-06 ) 4.87747749878614e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 39 ( 9.94741460300375e-01 , -9.19260964888404e-02 , 8.84507527042971e-03 , -4.42807473656820e-02 ) ( -5.49738529586110e-05 , 5.08024638875575e-06 , 6.24756014036145e-03 , 2.44715173914973e-06 ) 4.87938270367466e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 - 40 ( 9.94724147282287e-01 , -9.22284123842412e-02 , 8.57202435943065e-03 , -4.40943438661931e-02 ) ( -5.32850484997073e-05 , 4.94046056926641e-06 , 6.24866720237444e-03 , 2.36203097903292e-06 ) 4.88108888622058e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477162e-03 + 20 ( 9.95047581772214e-01 , -8.94218449921444e-02 , 1.03501990099413e-02 , -4.21534936621476e-02 ) ( -6.42872031816166e-05 , 5.77729188351618e-06 , 6.24144943236418e-03 , 2.72341771540914e-06 ) 4.86998308191970e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 21 ( 9.95003682332090e-01 , -8.97829930212753e-02 , 1.04393291902568e-02 , -4.23993716437056e-02 ) ( -6.48343047552602e-05 , 5.85024762696099e-06 , 6.24108712856311e-03 , 2.76273729574205e-06 ) 4.86942673643799e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 22 ( 9.94962679074848e-01 , -9.00807777119746e-02 , 1.05578975392661e-02 , -4.26995495825972e-02 ) ( -6.55630800076457e-05 , 5.93587413929206e-06 , 6.24060508568570e-03 , 2.81368743215307e-06 ) 4.86868668804814e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 23 ( 9.94925517351027e-01 , -9.03127036714925e-02 , 1.06952725327247e-02 , -4.30400002879546e-02 ) ( -6.64079281069542e-05 , 6.02806886341535e-06 , 6.24004647488748e-03 , 2.87277509220557e-06 ) 4.86782932651527e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 24 ( 9.94892910857417e-01 , -9.04801901001701e-02 , 1.08392645787803e-02 , -4.34043945757192e-02 ) ( -6.72936746943171e-05 , 6.11999986373752e-06 , 6.23946083146203e-03 , 2.93583477880549e-06 ) 4.86693074744086e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 25 ( 9.94865273855686e-01 , -9.05888555887877e-02 , 1.09769252640617e-02 , -4.37750297648312e-02 ) ( -6.81405121461231e-05 , 6.20463009089469e-06 , 6.23890081875418e-03 , 2.99824813044994e-06 ) 4.86607175532170e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 26 ( 9.94842696096015e-01 , -9.06481906996373e-02 , 1.10954290567160e-02 , -4.41339665262560e-02 ) ( -6.88694319923092e-05 , 6.27525279032860e-06 , 6.23841864349104e-03 , 3.05523799708078e-06 ) 4.86533236042453e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 27 ( 9.94824961327947e-01 , -9.06706551684395e-02 , 1.11829455700586e-02 , -4.44642591139523e-02 ) ( -6.94075830901017e-05 , 6.32596816231558e-06 , 6.23806249525430e-03 , 3.10221081995358e-06 ) 4.86478634360924e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 28 ( 9.94811600272105e-01 , -9.06703741663319e-02 , 1.12294092309447e-02 , -4.47511293814425e-02 ) ( -6.96929861916542e-05 , 6.35204608896586e-06 , 6.23787339221755e-03 , 3.13510602529034e-06 ) 4.86449646837991e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 29 ( 9.94801962741897e-01 , -9.06616914948174e-02 , 1.12271170222758e-02 , -4.49829352481218e-02 ) ( -6.96781856669942e-05 , 6.35015049171011e-06 , 6.23788272161999e-03 , 3.15070680542899e-06 ) 4.86451076870096e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 30 ( 9.94795292308519e-01 , -9.06578499805883e-02 , 1.11711246192723e-02 , -4.51518173770135e-02 ) ( -6.93326642807366e-05 , 6.31843588898705e-06 , 6.23811060335627e-03 , 3.14687435703579e-06 ) 4.86486009293656e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 31 ( 9.94790789449473e-01 , -9.06700192222035e-02 , 1.10594512834366e-02 , -4.52539653295560e-02 ) ( -6.86440920759764e-05 , 6.25655284913111e-06 , 6.23856504118798e-03 , 3.12268408174970e-06 ) 4.86555683501490e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 32 ( 9.94787654124658e-01 , -9.07067971724354e-02 , 1.08931308022897e-02 , -4.52895114701268e-02 ) ( -6.76186433057460e-05 , 6.16560784402434e-06 , 6.23924171411324e-03 , 3.07846132678909e-06 ) 4.86659461746219e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 33 ( 9.94785105280032e-01 , -9.07741931710955e-02 , 1.06761505602423e-02 , -4.52621251859446e-02 ) ( -6.62806416350276e-05 , 6.04811203479819e-06 , 6.24012423797141e-03 , 3.01572941046886e-06 ) 4.86794866288210e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 34 ( 9.94782382227464e-01 , -9.08759773447180e-02 , 1.04153039316759e-02 , -4.51784262176578e-02 ) ( -6.46716868343866e-05 , 5.90792805804091e-06 , 6.24118479329044e-03 , 2.93708964314039e-06 ) 4.86957669764842e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 35 ( 9.94778739475224e-01 , -9.10141866146385e-02 , 1.01199505392699e-02 , -4.50473520203313e-02 ) ( -6.28492246886030e-05 , 5.75019432704345e-06 , 6.24238513755075e-03 , 2.84605112313311e-06 ) 4.87142042441254e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 36 ( 9.94773450418677e-01 , -9.11895400906934e-02 , 9.80164979780012e-03 , -4.48795920370193e-02 ) ( -6.08843396495280e-05 , 5.58118527291748e-06 , 6.24367813619005e-03 , 2.74682071959611e-06 ) 4.87340778322567e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 37 ( 9.94765833371153e-01 , -9.14015658154700e-02 , 9.47362447745856e-03 , -4.46871453903308e-02 ) ( -5.88584935642695e-05 , 5.40806518764580e-06 , 6.24500998009463e-03 , 2.64405749687727e-06 ) 4.87545627649441e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 38 ( 9.94755305704011e-01 , -9.16483645954890e-02 , 9.15003259920000e-03 , -4.44829848832778e-02 ) ( -5.68590654616153e-05 , 5.23851477052131e-06 , 6.24632316887178e-03 , 2.54259608860927e-06 ) 4.87747749876768e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 39 ( 9.94741460297122e-01 , -9.19260965378052e-02 , 8.84507527332342e-03 , -4.42807473365176e-02 ) ( -5.49738529763158e-05 , 5.08024639311451e-06 , 6.24756014034971e-03 , 2.44715173833410e-06 ) 4.87938270365658e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 + 40 ( 9.94724147278495e-01 , -9.22284124393750e-02 , 8.57202436227895e-03 , -4.40943438358672e-02 ) ( -5.32850485171137e-05 , 4.94046057385252e-06 , 6.24866720236290e-03 , 2.36203097818903e-06 ) 4.88108888620278e-03 ( 0.00000000000000e+00 , 0.00000000000000e+00 , 1.00000000000000e+00 , 0.00000000000000e+00 ) 2.26088591477312e-03 diff --git a/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt b/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt +++ b/namd/tests/library/000_orientation_harmonic-ori-moving/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index e9a9f6185..22567fc90 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,28 +132,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 57a7f087b..174f4aa5e 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.50586699278142e+00 + x 2.50586699060249e+00 } restraint { diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 10296e333..9e8670803 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.34454807259353e+00 -1.29781922903741e-02 - 1 3.34456621005910e+00 -1.29782648402364e-02 - 2 3.33650183431222e+00 -1.29460073372489e-02 - 3 3.31967608166225e+00 -1.28787043266490e-02 - 4 3.29359679352004e+00 -1.27743871740802e-02 - 5 3.25804972932359e+00 -1.26321989172944e-02 - 6 3.21319557896124e+00 -1.24527823158450e-02 - 7 3.15964721748749e+00 -1.22385888699500e-02 - 8 3.09850657670722e+00 -1.19940263068289e-02 - 9 3.03134993698711e+00 -1.17253997479484e-02 - 10 2.96016041310420e+00 -1.14406416524168e-02 - 11 2.88721545965500e+00 -1.11488618386200e-02 - 12 2.81494477280673e+00 -1.08597790912269e-02 - 13 2.74578033381965e+00 -1.05831213352786e-02 - 14 2.68202224624271e+00 -1.03280889849708e-02 - 15 2.62573819607844e+00 -1.01029527843138e-02 - 16 2.57870029937537e+00 -9.91480119750147e-03 - 17 2.54234658740788e+00 -9.76938634963152e-03 - 18 2.51774460925550e+00 -9.67097843702200e-03 - 19 2.50553744233726e+00 -9.62214976934902e-03 - 20 2.50586699278142e+00 -9.62346797112569e-03 + 1 3.34456621006869e+00 -1.29782648402748e-02 + 2 3.33650183434893e+00 -1.29460073373957e-02 + 3 3.31967608173955e+00 -1.28787043269582e-02 + 4 3.29359679364577e+00 -1.27743871745831e-02 + 5 3.25804972949454e+00 -1.26321989179782e-02 + 6 3.21319557916635e+00 -1.24527823166654e-02 + 7 3.15964721770391e+00 -1.22385888708157e-02 + 8 3.09850657690298e+00 -1.19940263076119e-02 + 9 3.03134993712323e+00 -1.17253997484929e-02 + 10 2.96016041313917e+00 -1.14406416525567e-02 + 11 2.88721545954542e+00 -1.11488618381817e-02 + 12 2.81494477251460e+00 -1.08597790900584e-02 + 13 2.74578033330936e+00 -1.05831213332374e-02 + 14 2.68202224548980e+00 -1.03280889819592e-02 + 15 2.62573819506619e+00 -1.01029527802647e-02 + 16 2.57870029809758e+00 -9.91480119239031e-03 + 17 2.54234658587039e+00 -9.76938634348154e-03 + 18 2.51774460747483e+00 -9.67097842989931e-03 + 19 2.50553744033959e+00 -9.62214976135836e-03 + 20 2.50586699060249e+00 -9.62346796240996e-03 diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index e3acdcd80..706323615 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,33 +132,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 2.50587 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 86c2b39dd..92df7f52f 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 2.59806114483912e+00 + x 2.59806113934628e+00 } restraint { diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 64498a7a8..08b065f51 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 2.50586699278142e+00 -9.62346797112569e-03 - 21 2.51828912676855e+00 -9.67315650707419e-03 - 22 2.54171016632473e+00 -9.76684066529891e-03 - 23 2.57437672315441e+00 -9.89750689261763e-03 - 24 2.61394044202478e+00 -1.00557617680991e-02 - 25 2.65760032709751e+00 -1.02304013083901e-02 - 26 2.70230713671789e+00 -1.04092285468715e-02 - 27 2.74500166801146e+00 -1.05800066720458e-02 - 28 2.78285410384574e+00 -1.07314164153830e-02 - 29 2.81347402051205e+00 -1.08538960820482e-02 - 30 2.83506753731124e+00 -1.09402701492450e-02 - 31 2.84652760280228e+00 -1.09861104112091e-02 - 32 2.84745364262997e+00 -1.09898145705199e-02 - 33 2.83810685957546e+00 -1.09524274383019e-02 - 34 2.81931679148249e+00 -1.08772671659299e-02 - 35 2.79236160667317e+00 -1.07694464266927e-02 - 36 2.75884756305916e+00 -1.06353902522366e-02 - 37 2.72060909042328e+00 -1.04824363616931e-02 - 38 2.67964054352647e+00 -1.03185621741059e-02 - 39 2.63805615046828e+00 -1.01522246018731e-02 - 40 2.59806114483912e+00 -9.99224457935649e-03 + 20 2.50586699060249e+00 -9.62346796240996e-03 + 21 2.51828912444925e+00 -9.67315649779702e-03 + 22 2.54171016390634e+00 -9.76684065562536e-03 + 23 2.57437672068062e+00 -9.89750688272248e-03 + 24 2.61394043953042e+00 -1.00557617581217e-02 + 25 2.65760032461011e+00 -1.02304012984404e-02 + 26 2.70230713425706e+00 -1.04092285370282e-02 + 27 2.74500166558147e+00 -1.05800066623259e-02 + 28 2.78285410144146e+00 -1.07314164057658e-02 + 29 2.81347401811216e+00 -1.08538960724486e-02 + 30 2.83506753488489e+00 -1.09402701395396e-02 + 31 2.84652760030681e+00 -1.09861104012272e-02 + 32 2.84745364001396e+00 -1.09898145600559e-02 + 33 2.83810685678234e+00 -1.09524274271294e-02 + 34 2.81931678845251e+00 -1.08772671538101e-02 + 35 2.79236160334505e+00 -1.07694464133802e-02 + 36 2.75884755937459e+00 -1.06353902374984e-02 + 37 2.72060908633430e+00 -1.04824363453372e-02 + 38 2.67964053899086e+00 -1.03185621559634e-02 + 39 2.63805614546050e+00 -1.01522245818420e-02 + 40 2.59806113934628e+00 -9.99224455738511e-03 diff --git a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationangle-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out index 23e52329c..9e25d6b26 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,27 +114,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 3794713ae..b775835f5 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.14042524977569e+01 + x 1.14042525000436e+01 } restraint { diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj index 208ef8be6..362277f2e 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 1.05987658982707e+01 -4.19950635930827e-02 - 1 1.06266098865076e+01 -4.21064395460305e-02 - 2 1.06570380232944e+01 -4.22281520931778e-02 - 3 1.06891026494686e+01 -4.23564105978743e-02 - 4 1.07220322922544e+01 -4.24881291690175e-02 - 5 1.07553082614248e+01 -4.26212330456994e-02 - 6 1.07886956710148e+01 -4.27547826840591e-02 - 7 1.08222315380552e+01 -4.28889261522210e-02 - 8 1.08561787307268e+01 -4.30247149229071e-02 - 9 1.08909573892425e+01 -4.31638295569698e-02 - 10 1.09270659265304e+01 -4.33082637061217e-02 - 11 1.09650029613683e+01 -4.34600118454733e-02 - 12 1.10051994774624e+01 -4.36207979098498e-02 - 13 1.10479655806188e+01 -4.37918623224750e-02 - 14 1.10934497458239e+01 -4.39737989832956e-02 - 15 1.11416047500329e+01 -4.41664190001316e-02 - 16 1.11921570615955e+01 -4.43686282463821e-02 - 17 1.12445838365001e+01 -4.45783353460005e-02 - 18 1.12981079838905e+01 -4.47924319355620e-02 - 19 1.13517227431649e+01 -4.50068909726597e-02 - 20 1.14042524977569e+01 -4.52170099910277e-02 + 1 1.06266098864992e+01 -4.21064395459970e-02 + 2 1.06570380232614e+01 -4.22281520930457e-02 + 3 1.06891026493980e+01 -4.23564105975918e-02 + 4 1.07220322921382e+01 -4.24881291685529e-02 + 5 1.07553082612621e+01 -4.26212330450483e-02 + 6 1.07886956708129e+01 -4.27547826832515e-02 + 7 1.08222315378305e+01 -4.28889261513219e-02 + 8 1.08561787305042e+01 -4.30247149220168e-02 + 9 1.08909573890554e+01 -4.31638295562217e-02 + 10 1.09270659264173e+01 -4.33082637056690e-02 + 11 1.09650029613711e+01 -4.34600118454845e-02 + 12 1.10051994776244e+01 -4.36207979104977e-02 + 13 1.10479655809806e+01 -4.37918623239224e-02 + 14 1.10934497464229e+01 -4.39737989856916e-02 + 15 1.11416047509002e+01 -4.41664190036009e-02 + 16 1.11921570627529e+01 -4.43686282510115e-02 + 17 1.12445838379582e+01 -4.45783353518327e-02 + 18 1.12981079856473e+01 -4.47924319425893e-02 + 19 1.13517227452027e+01 -4.50068909808106e-02 + 20 1.14042525000436e+01 -4.52170100001743e-02 diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 8a00c0457..659cdc13a 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,32 +114,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 11.4043 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index d6e8c97ef..a902f9774 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 1.17634448022492e+01 + x 1.17634448064811e+01 } restraint { diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 4da52b8db..9b350dcb7 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 1.14042524977569e+01 -4.52170099910277e-02 - 21 1.14544480755564e+01 -4.54177923022257e-02 - 22 1.15011053897376e+01 -4.56044215589506e-02 - 23 1.15431885942609e+01 -4.57727543770436e-02 - 24 1.15799356423833e+01 -4.59197425695332e-02 - 25 1.16109269835055e+01 -4.60437079340218e-02 - 26 1.16361065785131e+01 -4.61444263140523e-02 - 27 1.16557559207023e+01 -4.62230236828094e-02 - 28 1.16704320370109e+01 -4.62817281480436e-02 - 29 1.16808864175993e+01 -4.63235456703971e-02 - 30 1.16879826712242e+01 -4.63519306848966e-02 - 31 1.16926277176089e+01 -4.63705108704357e-02 - 32 1.16957259267591e+01 -4.63829037070363e-02 - 33 1.16981585973899e+01 -4.63926343895594e-02 - 34 1.17007830899012e+01 -4.64031323596047e-02 - 35 1.17044386469586e+01 -4.64177545878343e-02 - 36 1.17099416836191e+01 -4.64397667344764e-02 - 37 1.17180555417655e+01 -4.64722221670619e-02 - 38 1.17294285106548e+01 -4.65177140426191e-02 - 39 1.17445071542025e+01 -4.65780286168101e-02 - 40 1.17634448022492e+01 -4.66537792089967e-02 + 20 1.14042525000436e+01 -4.52170100001743e-02 + 21 1.14544480780461e+01 -4.54177923121844e-02 + 22 1.15011053923729e+01 -4.56044215694917e-02 + 23 1.15431885969782e+01 -4.57727543879128e-02 + 24 1.15799356451165e+01 -4.59197425804660e-02 + 25 1.16109269861924e+01 -4.60437079447695e-02 + 26 1.16361065810996e+01 -4.61444263243983e-02 + 27 1.16557559231474e+01 -4.62230236925897e-02 + 28 1.16704320392906e+01 -4.62817281571624e-02 + 29 1.16808864197082e+01 -4.63235456788327e-02 + 30 1.16879826731775e+01 -4.63519306927099e-02 + 31 1.16926277194411e+01 -4.63705108777642e-02 + 32 1.16957259285228e+01 -4.63829037140912e-02 + 33 1.16981585991540e+01 -4.63926343966159e-02 + 34 1.17007830917475e+01 -4.64031323669901e-02 + 35 1.17044386489778e+01 -4.64177545959111e-02 + 36 1.17099416859060e+01 -4.64397667436240e-02 + 37 1.17180555444153e+01 -4.64722221776613e-02 + 38 1.17294285137575e+01 -4.65177140550300e-02 + 39 1.17445071578377e+01 -4.65780286313510e-02 + 40 1.17634448064811e+01 -4.66537792259242e-02 diff --git a/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationangle_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index e3dd29780..3159c4a1d 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,28 +132,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationProj colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 6aab80c05..8993379a3 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.99042890071513e-01 + x 9.99042890073178e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 6408cd312..52560e9b2 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 9.98296758220625e-01 -3.59318703288250e-03 - 1 9.98296730621305e-01 -3.59318692248522e-03 - 2 9.98304905164688e-01 -3.59321962065875e-03 - 3 9.98321909943251e-01 -3.59328763977300e-03 - 4 9.98348106341271e-01 -3.59339242536509e-03 - 5 9.98383489829552e-01 -3.59353395931821e-03 - 6 9.98427599823242e-01 -3.59371039929297e-03 - 7 9.98479469810032e-01 -3.59391787924013e-03 - 8 9.98537639417837e-01 -3.59415055767135e-03 - 9 9.98600233958691e-01 -3.59440093583477e-03 - 10 9.98665100608690e-01 -3.59466040243476e-03 - 11 9.98729977781407e-01 -3.59491991112563e-03 - 12 9.98792667791781e-01 -3.59517067116713e-03 - 13 9.98851182637630e-01 -3.59540473055052e-03 - 14 9.98903839987366e-01 -3.59561535994946e-03 - 15 9.98949300566769e-01 -3.59579720226708e-03 - 16 9.98986555615076e-01 -3.59594622246030e-03 - 17 9.99014887276758e-01 -3.59605954910703e-03 - 18 9.99033829853492e-01 -3.59613531941397e-03 - 19 9.99043154766428e-01 -3.59617261906571e-03 - 20 9.99042890071513e-01 -3.59617156028605e-03 + 1 9.98296730621296e-01 -3.59318692248518e-03 + 2 9.98304905164651e-01 -3.59321962065860e-03 + 3 9.98321909943172e-01 -3.59328763977269e-03 + 4 9.98348106341147e-01 -3.59339242536459e-03 + 5 9.98383489829382e-01 -3.59353395931753e-03 + 6 9.98427599823041e-01 -3.59371039929216e-03 + 7 9.98479469809825e-01 -3.59391787923930e-03 + 8 9.98537639417652e-01 -3.59415055767061e-03 + 9 9.98600233958565e-01 -3.59440093583426e-03 + 10 9.98665100608658e-01 -3.59466040243463e-03 + 11 9.98729977781503e-01 -3.59491991112601e-03 + 12 9.98792667792032e-01 -3.59517067116813e-03 + 13 9.98851182638057e-01 -3.59540473055223e-03 + 14 9.98903839987981e-01 -3.59561535995193e-03 + 15 9.98949300567580e-01 -3.59579720227032e-03 + 16 9.98986555616080e-01 -3.59594622246432e-03 + 17 9.99014887277948e-01 -3.59605954911179e-03 + 18 9.99033829854858e-01 -3.59613531941943e-03 + 19 9.99043154767953e-01 -3.59617261907181e-03 + 20 9.99042890073178e-01 -3.59617156029271e-03 diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index 8798aa21c..deb021ce1 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,33 +132,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationProj colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.999043 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 8b0add5c8..0f04cd392 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.98970741879346e-01 + x 9.98970741883698e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 32cfd70e2..7997c7579 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.99042890071513e-01 -3.59617156028605e-03 - 21 9.99033371043944e-01 -3.59613348417578e-03 - 22 9.99015305958516e-01 -3.59606122383406e-03 - 23 9.98989833767277e-01 -3.59595933506911e-03 - 24 9.98958548398355e-01 -3.59583419359342e-03 - 25 9.98923468752275e-01 -3.59569387500910e-03 - 26 9.98886942695769e-01 -3.59554777078308e-03 - 27 9.98851487059890e-01 -3.59540594823956e-03 - 28 9.98819580887699e-01 -3.59527832355080e-03 - 29 9.98793441988564e-01 -3.59517376795426e-03 - 30 9.98774823522244e-01 -3.59509929408898e-03 - 31 9.98764865062350e-01 -3.59505946024940e-03 - 32 9.98764021743129e-01 -3.59505608697251e-03 - 33 9.98772078283373e-01 -3.59508831313349e-03 - 34 9.98788236182522e-01 -3.59515294473009e-03 - 35 9.98811247689749e-01 -3.59524499075900e-03 - 36 9.98839563234612e-01 -3.59535825293845e-03 - 37 9.98871462837275e-01 -3.59548585134910e-03 - 38 9.98905154300893e-01 -3.59562061720357e-03 - 39 9.98938836852973e-01 -3.59575534741189e-03 - 40 9.98970741879346e-01 -3.59588296751738e-03 + 20 9.99042890073178e-01 -3.59617156029271e-03 + 21 9.99033371045725e-01 -3.59613348418290e-03 + 22 9.99015305960388e-01 -3.59606122384155e-03 + 23 9.98989833769218e-01 -3.59595933507687e-03 + 24 9.98958548400342e-01 -3.59583419360137e-03 + 25 9.98923468754291e-01 -3.59569387501716e-03 + 26 9.98886942697797e-01 -3.59554777079119e-03 + 27 9.98851487061923e-01 -3.59540594824769e-03 + 28 9.98819580889739e-01 -3.59527832355896e-03 + 29 9.98793441990623e-01 -3.59517376796249e-03 + 30 9.98774823524341e-01 -3.59509929409736e-03 + 31 9.98764865064516e-01 -3.59505946025807e-03 + 32 9.98764021745399e-01 -3.59505608698159e-03 + 33 9.98772078285790e-01 -3.59508831314316e-03 + 34 9.98788236185128e-01 -3.59515294474051e-03 + 35 9.98811247692583e-01 -3.59524499077033e-03 + 36 9.98839563237711e-01 -3.59535825295084e-03 + 37 9.98871462840668e-01 -3.59548585136267e-03 + 38 9.98905154304598e-01 -3.59562061721839e-03 + 39 9.98938836857002e-01 -3.59575534742801e-03 + 40 9.98970741883698e-01 -3.59588296753479e-03 diff --git a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationproj-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out index 15ba472df..0867faa1d 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,27 +114,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationProj colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped index dbd322f7c..fbbe4454a 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.80239375949467e-01 + x 9.80239375941569e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj index 2a3c28388..63a14b625 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 9.82939311075160e-01 -3.53175724430064e-03 - 1 9.82849734901045e-01 -3.53139893960418e-03 - 2 9.82751436474708e-01 -3.53100574589883e-03 - 3 9.82647417671745e-01 -3.53058967068698e-03 - 4 9.82540144796735e-01 -3.53016057918694e-03 - 5 9.82431293276323e-01 -3.52972517310529e-03 - 6 9.82321634339533e-01 -3.52928653735813e-03 - 7 9.82211059380067e-01 -3.52884423752027e-03 - 8 9.82098716903652e-01 -3.52839486761461e-03 - 9 9.81983226206096e-01 -3.52793290482439e-03 - 10 9.81862929059119e-01 -3.52745171623648e-03 - 11 9.81736142358021e-01 -3.52694456943208e-03 - 12 9.81601381064589e-01 -3.52640552425836e-03 - 13 9.81457536905773e-01 -3.52583014762309e-03 - 14 9.81304019863068e-01 -3.52521607945227e-03 - 15 9.81140882071682e-01 -3.52456352828673e-03 - 16 9.80968935309110e-01 -3.52387574123644e-03 - 17 9.80789847969960e-01 -3.52315939187984e-03 - 18 9.80606184563440e-01 -3.52242473825376e-03 - 19 9.80421345128356e-01 -3.52168538051342e-03 - 20 9.80239375949467e-01 -3.52095750379787e-03 + 1 9.82849734901072e-01 -3.53139893960429e-03 + 2 9.82751436474814e-01 -3.53100574589926e-03 + 3 9.82647417671973e-01 -3.53058967068789e-03 + 4 9.82540144797111e-01 -3.53016057918845e-03 + 5 9.82431293276853e-01 -3.52972517310741e-03 + 6 9.82321634340193e-01 -3.52928653736077e-03 + 7 9.82211059380804e-01 -3.52884423752322e-03 + 8 9.82098716904383e-01 -3.52839486761753e-03 + 9 9.81983226206714e-01 -3.52793290482686e-03 + 10 9.81862929059493e-01 -3.52745171623797e-03 + 11 9.81736142358011e-01 -3.52694456943204e-03 + 12 9.81601381064049e-01 -3.52640552425620e-03 + 13 9.81457536904562e-01 -3.52583014761825e-03 + 14 9.81304019861054e-01 -3.52521607944422e-03 + 15 9.81140882068755e-01 -3.52456352827502e-03 + 16 9.80968935305186e-01 -3.52387574122074e-03 + 17 9.80789847964994e-01 -3.52315939185998e-03 + 18 9.80606184557429e-01 -3.52242473822972e-03 + 19 9.80421345121349e-01 -3.52168538048540e-03 + 20 9.80239375941569e-01 -3.52095750376628e-03 diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out index 5af1ca243..821e0a8d3 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,32 +114,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - orientationProj colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.980239 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 32bda65e7..39341551b 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.78952248453755e-01 + x 9.78952248438667e-01 } restraint { diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj index f961e9ce6..36e1592b7 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.80239375949467e-01 -3.52095750379787e-03 - 21 9.80064651415975e-01 -3.52025860566390e-03 - 22 9.79901460938148e-01 -3.51960584375259e-03 - 23 9.79753565304145e-01 -3.51901426121658e-03 - 24 9.79623803009410e-01 -3.51849521203764e-03 - 25 9.79513820811740e-01 -3.51805528324696e-03 - 26 9.79423974214543e-01 -3.51769589685817e-03 - 27 9.79353401323632e-01 -3.51741360529453e-03 - 28 9.79300233731289e-01 -3.51720093492516e-03 - 29 9.79261883509026e-01 -3.51704753403610e-03 - 30 9.79235340258555e-01 -3.51694136103422e-03 - 31 9.79217422310898e-01 -3.51686968924359e-03 - 32 9.79204946067415e-01 -3.51681978426966e-03 - 33 9.79194803551154e-01 -3.51677921420462e-03 - 34 9.79183967865525e-01 -3.51673587146210e-03 - 35 9.79169472616686e-01 -3.51667789046674e-03 - 36 9.79148426614635e-01 -3.51659370645854e-03 - 37 9.79118117487522e-01 -3.51647246995009e-03 - 38 9.79076227155221e-01 -3.51630490862088e-03 - 39 9.79021136068235e-01 -3.51608454427294e-03 - 40 9.78952248453755e-01 -3.51580899381502e-03 + 20 9.80239375941569e-01 -3.52095750376628e-03 + 21 9.80064651407338e-01 -3.52025860562935e-03 + 22 9.79901460928968e-01 -3.51960584371587e-03 + 23 9.79753565294644e-01 -3.51901426117858e-03 + 24 9.79623802999823e-01 -3.51849521199929e-03 + 25 9.79513820802291e-01 -3.51805528320916e-03 + 26 9.79423974205426e-01 -3.51769589682171e-03 + 27 9.79353401314998e-01 -3.51741360525999e-03 + 28 9.79300233723229e-01 -3.51720093489292e-03 + 29 9.79261883501562e-01 -3.51704753400625e-03 + 30 9.79235340251636e-01 -3.51694136100655e-03 + 31 9.79217422304405e-01 -3.51686968921762e-03 + 32 9.79204946061162e-01 -3.51681978424465e-03 + 33 9.79194803544898e-01 -3.51677921417959e-03 + 34 9.79183967858975e-01 -3.51673587143590e-03 + 35 9.79169472609521e-01 -3.51667789043808e-03 + 36 9.79148426606516e-01 -3.51659370642606e-03 + 37 9.79118117478109e-01 -3.51647246991243e-03 + 38 9.79076227144190e-01 -3.51630490857676e-03 + 39 9.79021136055294e-01 -3.51608454422118e-03 + 40 9.78952248438667e-01 -3.51580899375467e-03 diff --git a/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt b/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt index 157cac038..129300d44 100644 --- a/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_orientationproj_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 188d105ae..e3e2b88a3 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -98,7 +94,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,27 +132,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 95457b174..a5b66188c 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.51992448739790e-01 + x 6.51992447935402e-01 } restraint { diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 9ff521cd9..20f9e8ab6 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 6.42446480928994e-01 -2.16978592371598e-03 - 1 6.41362151829732e-01 -2.16544860731893e-03 - 2 6.39964191531625e-01 -2.15985676612650e-03 - 3 6.38339929638892e-01 -2.15335971855557e-03 - 4 6.36588007574356e-01 -2.14635203029742e-03 - 5 6.34817335440207e-01 -2.13926934176083e-03 - 6 6.33145320204402e-01 -2.13258128081761e-03 - 7 6.31694089901779e-01 -2.12677635960711e-03 - 8 6.30583853252009e-01 -2.12233541300803e-03 - 9 6.29923415729674e-01 -2.11969366291869e-03 - 10 6.29798996911838e-01 -2.11919598764735e-03 - 11 6.30263472118592e-01 -2.12105388847437e-03 - 12 6.31328581658953e-01 -2.12531432663581e-03 - 13 6.32962276844382e-01 -2.13184910737753e-03 - 14 6.35092221778593e-01 -2.14036888711437e-03 - 15 6.37614971049963e-01 -2.15045988419985e-03 - 16 6.40409022430485e-01 -2.16163608972194e-03 - 17 6.43349209707525e-01 -2.17339683883010e-03 - 18 6.46319867665476e-01 -2.18527947066190e-03 - 19 6.49224738102162e-01 -2.19689895240865e-03 - 20 6.51992448739790e-01 -2.20796979495916e-03 + 0 6.42446480928998e-01 -2.16978592371599e-03 + 1 6.41362151827951e-01 -2.16544860731180e-03 + 2 6.39964191522473e-01 -2.15985676608989e-03 + 3 6.38339929621363e-01 -2.15335971848545e-03 + 4 6.36588007540679e-01 -2.14635203016272e-03 + 5 6.34817335398304e-01 -2.13926934159321e-03 + 6 6.33145320132662e-01 -2.13258128053065e-03 + 7 6.31694089805813e-01 -2.12677635922325e-03 + 8 6.30583853131960e-01 -2.12233541252784e-03 + 9 6.29923415581364e-01 -2.11969366232546e-03 + 10 6.29798996732227e-01 -2.11919598692891e-03 + 11 6.30263471904012e-01 -2.12105388761605e-03 + 12 6.31328581404817e-01 -2.12531432561927e-03 + 13 6.32962276627263e-01 -2.13184910650905e-03 + 14 6.35092221427288e-01 -2.14036888570915e-03 + 15 6.37614970671458e-01 -2.15045988268583e-03 + 16 6.40409021950152e-01 -2.16163608780061e-03 + 17 6.43349209139955e-01 -2.17339683655982e-03 + 18 6.46319867119914e-01 -2.18527946847966e-03 + 19 6.49224737403552e-01 -2.19689894961421e-03 + 20 6.51992447935402e-01 -2.20796979174161e-03 diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index f1030f219..d4194b991 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -98,7 +94,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -126,7 +122,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -137,32 +132,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.651992 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 2c5997d6d..57f5c66cf 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.75350774458524e-01 + x 6.75350774255469e-01 } restraint { diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index db5a45ae4..465a8190b 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 6.51992448739790e-01 -2.20796979495916e-03 - 21 6.54577359871602e-01 -2.21830943948641e-03 - 22 6.56956477797988e-01 -2.22782591119195e-03 - 23 6.59123837391726e-01 -2.23649534956690e-03 - 24 6.61084125660818e-01 -2.24433650264327e-03 - 25 6.62847214781938e-01 -2.25138885912775e-03 - 26 6.64424718041335e-01 -2.25769887216534e-03 - 27 6.65828841073339e-01 -2.26331536429336e-03 - 28 6.67072979054150e-01 -2.26829191621660e-03 - 29 6.68172991793991e-01 -2.27269196717596e-03 - 30 6.69147999050168e-01 -2.27659199620067e-03 - 31 6.70019872911646e-01 -2.28007949164658e-03 - 32 6.70811209861948e-01 -2.28324483944779e-03 - 33 6.71542241163152e-01 -2.28616896465261e-03 - 34 6.72227644663412e-01 -2.28891057865365e-03 - 35 6.72874369034013e-01 -2.29149747613605e-03 - 36 6.73481316803640e-01 -2.29392526721456e-03 - 37 6.74041160994404e-01 -2.29616464397762e-03 - 38 6.74543902662182e-01 -2.29817561064873e-03 - 39 6.74981259280343e-01 -2.29992503712137e-03 - 40 6.75350774458524e-01 -2.30140309783410e-03 + 20 6.51992447935402e-01 -2.20796979174161e-03 + 21 6.54577358969536e-01 -2.21830943587814e-03 + 22 6.56956476804603e-01 -2.22782590721841e-03 + 23 6.59123836309169e-01 -2.23649534523667e-03 + 24 6.61084124493515e-01 -2.24433649797406e-03 + 25 6.62847213541526e-01 -2.25138885416610e-03 + 26 6.64424716728470e-01 -2.25769886691388e-03 + 27 6.65828839710307e-01 -2.26331535884123e-03 + 28 6.67072977661715e-01 -2.26829191064686e-03 + 29 6.68172990385695e-01 -2.27269196154278e-03 + 30 6.69147997661702e-01 -2.27659199064681e-03 + 31 6.70019871557500e-01 -2.28007948623000e-03 + 32 6.70811208574338e-01 -2.28324483429735e-03 + 33 6.71542239966417e-01 -2.28616895986567e-03 + 34 6.72227643578755e-01 -2.28891057431502e-03 + 35 6.72874368078643e-01 -2.29149747231457e-03 + 36 6.73481315978386e-01 -2.29392526391354e-03 + 37 6.74041160330857e-01 -2.29616464132343e-03 + 38 6.74543902153436e-01 -2.29817560861374e-03 + 39 6.74981258926052e-01 -2.29992503570421e-03 + 40 6.75350774255469e-01 -2.30140309702188e-03 diff --git a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_rmsd-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out index 0df5ce6ef..66f42f578 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,13 +70,13 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,26 +114,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 59c145889..5965781f5 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.34779999706673e-01 + x 6.34779999776054e-01 } restraint { diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj index 0de897eb5..4aec974c6 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 6.13624515542194e-01 -2.05449806216878e-03 - 1 6.12490538024418e-01 -2.04996215209767e-03 - 2 6.11173746800116e-01 -2.04469498720046e-03 - 3 6.09786235548945e-01 -2.03914494219578e-03 - 4 6.08443934153914e-01 -2.03377573661566e-03 - 5 6.07262363747078e-01 -2.02904945498831e-03 - 6 6.06352646519890e-01 -2.02541058607956e-03 - 7 6.05817100403337e-01 -2.02326840161335e-03 - 8 6.05743803259169e-01 -2.02297521303668e-03 - 9 6.06199958858187e-01 -2.02479983543275e-03 - 10 6.07224667100095e-01 -2.02889866840038e-03 - 11 6.08822487970901e-01 -2.03528995188360e-03 - 12 6.10959603602463e-01 -2.04383841440985e-03 - 13 6.13564160848909e-01 -2.05425664339564e-03 - 14 6.16531504942698e-01 -2.06612601977079e-03 - 15 6.19733849273886e-01 -2.07893539709555e-03 - 16 6.23032907695619e-01 -2.09213163078248e-03 - 17 6.26293468659005e-01 -2.10517387463602e-03 - 18 6.29395874658527e-01 -2.11758349863411e-03 - 19 6.32245759582595e-01 -2.12898303833038e-03 - 20 6.34779999706673e-01 -2.13911999882669e-03 + 0 6.13624515542246e-01 -2.05449806216899e-03 + 1 6.12490538024335e-01 -2.04996215209734e-03 + 2 6.11173746799938e-01 -2.04469498719975e-03 + 3 6.09786235548445e-01 -2.03914494219378e-03 + 4 6.08443934153189e-01 -2.03377573661276e-03 + 5 6.07262363750067e-01 -2.02904945500027e-03 + 6 6.06352646518334e-01 -2.02541058607334e-03 + 7 6.05817100403672e-01 -2.02326840161469e-03 + 8 6.05743803262677e-01 -2.02297521305071e-03 + 9 6.06199958866108e-01 -2.02479983546443e-03 + 10 6.07224667113594e-01 -2.02889866845438e-03 + 11 6.08822487990989e-01 -2.03528995196396e-03 + 12 6.10959603629905e-01 -2.04383841451962e-03 + 13 6.13564160971268e-01 -2.05425664388507e-03 + 14 6.16531504985440e-01 -2.06612601994176e-03 + 15 6.19733849359571e-01 -2.07893539743829e-03 + 16 6.23032907749212e-01 -2.09213163099685e-03 + 17 6.26293468706736e-01 -2.10517387482694e-03 + 18 6.29395874814933e-01 -2.11758349925973e-03 + 19 6.32245759668358e-01 -2.12898303867343e-03 + 20 6.34779999776054e-01 -2.13911999910422e-03 diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out index c6589b658..46a799d77 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,13 +70,13 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -108,7 +104,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -119,31 +114,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.63478 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index c6c8eee84..1b15cce3c 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 6.57869102539559e-01 + x 6.57869102603360e-01 } restraint { diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 6131bf0e9..b53dc8777 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_rmsd_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 6.34779999706673e-01 -2.13911999882669e-03 - 21 6.36968499670390e-01 -2.14787399868156e-03 - 22 6.38812086586848e-01 -2.15524834634739e-03 - 23 6.40337357406265e-01 -2.16134942962506e-03 - 24 6.41589727219131e-01 -2.16635890887652e-03 - 25 6.42626037705784e-01 -2.17050415082314e-03 - 26 6.43507870289948e-01 -2.17403148115979e-03 - 27 6.44296238099800e-01 -2.17718495239920e-03 - 28 6.45047779413727e-01 -2.18019111765491e-03 - 29 6.45812131910624e-01 -2.18324852764250e-03 - 30 6.46629948954352e-01 -2.18651979581741e-03 - 31 6.47531080128373e-01 -2.19012432051349e-03 - 32 6.48532731402192e-01 -2.19413092560877e-03 - 33 6.49637836090191e-01 -2.19855134436077e-03 - 34 6.50834212189133e-01 -2.20333684875653e-03 - 35 6.52095178886227e-01 -2.20838071554491e-03 - 36 6.53382073051404e-01 -2.21352829220561e-03 - 37 6.54648626678558e-01 -2.21859450671423e-03 - 38 6.55846616450873e-01 -2.22338646580349e-03 - 39 6.56931804632144e-01 -2.22772721852858e-03 - 40 6.57869102539559e-01 -2.23147641015824e-03 + 20 6.34779999776054e-01 -2.13911999910422e-03 + 21 6.36968499730488e-01 -2.14787399892195e-03 + 22 6.38812086644733e-01 -2.15524834657893e-03 + 23 6.40337357461428e-01 -2.16134942984571e-03 + 24 6.41589727271310e-01 -2.16635890908524e-03 + 25 6.42626037763938e-01 -2.17050415105575e-03 + 26 6.43507870335777e-01 -2.17403148134311e-03 + 27 6.44296238145373e-01 -2.17718495258149e-03 + 28 6.45047779464950e-01 -2.18019111785980e-03 + 29 6.45812131951865e-01 -2.18324852780746e-03 + 30 6.46629949006064e-01 -2.18651979602426e-03 + 31 6.47531080168799e-01 -2.19012432067520e-03 + 32 6.48532731443661e-01 -2.19413092577464e-03 + 33 6.49637836133461e-01 -2.19855134453384e-03 + 34 6.50834212234814e-01 -2.20333684893926e-03 + 35 6.52095178934730e-01 -2.20838071573892e-03 + 36 6.53382073098997e-01 -2.21352829239599e-03 + 37 6.54648626732206e-01 -2.21859450692882e-03 + 38 6.55846616507654e-01 -2.22338646603062e-03 + 39 6.56931804692009e-01 -2.22772721876803e-03 + 40 6.57869102603360e-01 -2.23147641041344e-03 diff --git a/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt b/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_rmsd_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out index 61f83bfee..162de8092 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -107,7 +103,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -118,26 +113,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - selfCoordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 699308a19..b757a82d5 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.50086993007309e+00 + x 5.50086992991043e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj index 3eabd5c33..4497991fb 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 5.50064408080373e+00 -2.16025763232149e-02 - 1 5.50080703004882e+00 -2.16032281201953e-02 - 2 5.50068939069810e+00 -2.16027575627924e-02 - 3 5.50034727666126e+00 -2.16013891066450e-02 - 4 5.49985543899098e+00 -2.15994217559639e-02 - 5 5.49929900080157e+00 -2.15971960032063e-02 - 6 5.49876326013045e+00 -2.15950530405218e-02 - 7 5.49832342753577e+00 -2.15932937101431e-02 - 8 5.49803620216166e+00 -2.15921448086467e-02 - 9 5.49793456348608e+00 -2.15917382539443e-02 - 10 5.49802625415031e+00 -2.15921050166012e-02 - 11 5.49829556495176e+00 -2.15931822598070e-02 - 12 5.49870744203985e+00 -2.15948297681594e-02 - 13 5.49921283628923e+00 -2.15968513451569e-02 - 14 5.49975442850415e+00 -2.15990177140166e-02 - 15 5.50027220385344e+00 -2.16010888154138e-02 - 16 5.50070878638128e+00 -2.16028351455251e-02 - 17 5.50101460472211e+00 -2.16040584188884e-02 - 18 5.50115288500804e+00 -2.16046115400322e-02 - 19 5.50110418967735e+00 -2.16044167587094e-02 - 20 5.50086993007309e+00 -2.16034797202924e-02 + 1 5.50080703004843e+00 -2.16032281201937e-02 + 2 5.50068939069653e+00 -2.16027575627861e-02 + 3 5.50034727665768e+00 -2.16013891066307e-02 + 4 5.49985543898452e+00 -2.15994217559381e-02 + 5 5.49929900079136e+00 -2.15971960031654e-02 + 6 5.49876326011562e+00 -2.15950530404625e-02 + 7 5.49832342751543e+00 -2.15932937100617e-02 + 8 5.49803620213495e+00 -2.15921448085398e-02 + 9 5.49793456345215e+00 -2.15917382538086e-02 + 10 5.49802625410834e+00 -2.15921050164334e-02 + 11 5.49829556490095e+00 -2.15931822596038e-02 + 12 5.49870744197941e+00 -2.15948297679177e-02 + 13 5.49921283621840e+00 -2.15968513448736e-02 + 14 5.49975442842220e+00 -2.15990177136888e-02 + 15 5.50027220375965e+00 -2.16010888150386e-02 + 16 5.50070878627497e+00 -2.16028351450999e-02 + 17 5.50101460460263e+00 -2.16040584184105e-02 + 18 5.50115288487476e+00 -2.16046115394991e-02 + 19 5.50110418952966e+00 -2.16044167581187e-02 + 20 5.50086992991043e+00 -2.16034797196417e-02 diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out index 2b29746be..c7aa828f5 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -107,7 +103,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -118,31 +113,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - selfCoordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 5.50087 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 4e2699486..c26ac3859 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.52672800845913e+00 + x 5.52672800804253e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj index ae8c62635..2eae1fa46 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.50086993007309e+00 -2.16034797202924e-02 - 21 5.50047411702526e+00 -2.16018964681010e-02 - 22 5.49996271480815e+00 -2.15998508592326e-02 - 23 5.49940030464023e+00 -2.15976012185609e-02 - 24 5.49886427479469e+00 -2.15954570991788e-02 - 25 5.49843732358400e+00 -2.15937492943360e-02 - 26 5.49819952711805e+00 -2.15927981084722e-02 - 27 5.49822134791709e+00 -2.15928853916683e-02 - 28 5.49855877511631e+00 -2.15942351004652e-02 - 29 5.49925111600498e+00 -2.15970044640199e-02 - 30 5.50032111814578e+00 -2.16012844725831e-02 - 31 5.50177638755253e+00 -2.16071055502101e-02 - 32 5.50361077538265e+00 -2.16144431015306e-02 - 33 5.50580475246237e+00 -2.16232190098495e-02 - 34 5.50832462466879e+00 -2.16332984986752e-02 - 35 5.51112148850244e+00 -2.16444859540097e-02 - 36 5.51413136429316e+00 -2.16565254571726e-02 - 37 5.51727794304695e+00 -2.16691117721878e-02 - 38 5.52047847373687e+00 -2.16819138949475e-02 - 39 5.52365200686973e+00 -2.16946080274789e-02 - 40 5.52672800845913e+00 -2.17069120338365e-02 + 20 5.50086992991043e+00 -2.16034797196417e-02 + 21 5.50047411684707e+00 -2.16018964673883e-02 + 22 5.49996271461392e+00 -2.15998508584557e-02 + 23 5.49940030442948e+00 -2.15976012177179e-02 + 24 5.49886427456701e+00 -2.15954570982680e-02 + 25 5.49843732333905e+00 -2.15937492933562e-02 + 26 5.49819952685563e+00 -2.15927981074225e-02 + 27 5.49822134763710e+00 -2.15928853905484e-02 + 28 5.49855877481886e+00 -2.15942350992754e-02 + 29 5.49925111569040e+00 -2.15970044627616e-02 + 30 5.50032111781463e+00 -2.16012844712585e-02 + 31 5.50177638720568e+00 -2.16071055488227e-02 + 32 5.50361077502124e+00 -2.16144431000850e-02 + 33 5.50580475208785e+00 -2.16232190083514e-02 + 34 5.50832462428283e+00 -2.16332984971313e-02 + 35 5.51112148810689e+00 -2.16444859524276e-02 + 36 5.51413136388995e+00 -2.16565254555598e-02 + 37 5.51727794263797e+00 -2.16691117705519e-02 + 38 5.52047847332390e+00 -2.16819138932956e-02 + 39 5.52365200645431e+00 -2.16946080258172e-02 + 40 5.52672800804253e+00 -2.17069120321701e-02 diff --git a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt index 157cac038..b2949c9aa 100644 --- a/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-05-08. +colvars: Using NAMD interface, version 2018-04-29. diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out index 50bb8b9f3..541860fb0 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -106,7 +102,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -117,26 +112,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - selfCoordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped index f9e22915c..3d35609cc 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.50586098376003e+00 + x 5.50586098356346e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj index 429397ed3..85b262a41 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 5.50563763999570e+00 -2.16225505599828e-02 - 1 5.50579895884978e+00 -2.16231958353991e-02 - 2 5.50568249321270e+00 -2.16227299728508e-02 - 3 5.50534379589551e+00 -2.16213751835821e-02 - 4 5.50485687050173e+00 -2.16194274820069e-02 - 5 5.50430598899447e+00 -2.16172239559779e-02 - 6 5.50377559652656e+00 -2.16151023861063e-02 - 7 5.50334015165911e+00 -2.16133606066364e-02 - 8 5.50305578666305e+00 -2.16122231466522e-02 - 9 5.50295515134696e+00 -2.16118206053878e-02 - 10 5.50304591105647e+00 -2.16121836442259e-02 - 11 5.50331251381601e+00 -2.16132500552641e-02 - 12 5.50372025645284e+00 -2.16148810258114e-02 - 13 5.50422058047457e+00 -2.16168823218983e-02 - 14 5.50475674002052e+00 -2.16190269600821e-02 - 15 5.50526932054974e+00 -2.16210772821990e-02 - 16 5.50570152000281e+00 -2.16228060800113e-02 - 17 5.50600426285527e+00 -2.16240170514211e-02 - 18 5.50614114309177e+00 -2.16245645723671e-02 - 19 5.50609291762347e+00 -2.16243716704939e-02 - 20 5.50586098376003e+00 -2.16234439350401e-02 + 0 5.50563763999569e+00 -2.16225505599828e-02 + 1 5.50579895884940e+00 -2.16231958353976e-02 + 2 5.50568249321115e+00 -2.16227299728446e-02 + 3 5.50534379589073e+00 -2.16213751835629e-02 + 4 5.50485687049274e+00 -2.16194274819710e-02 + 5 5.50430598897902e+00 -2.16172239559161e-02 + 6 5.50377559650355e+00 -2.16151023860142e-02 + 7 5.50334015162730e+00 -2.16133606065092e-02 + 8 5.50305578662091e+00 -2.16122231464836e-02 + 9 5.50295515129356e+00 -2.16118206051742e-02 + 10 5.50304591099096e+00 -2.16121836439638e-02 + 11 5.50331251373771e+00 -2.16132500549508e-02 + 12 5.50372025636123e+00 -2.16148810254449e-02 + 13 5.50422058036933e+00 -2.16168823214773e-02 + 14 5.50475673990153e+00 -2.16190269596061e-02 + 15 5.50526932041704e+00 -2.16210772816681e-02 + 16 5.50570151985664e+00 -2.16228060794265e-02 + 17 5.50600426269577e+00 -2.16240170507831e-02 + 18 5.50614114291938e+00 -2.16245645716775e-02 + 19 5.50609291743878e+00 -2.16243716697551e-02 + 20 5.50586098356346e+00 -2.16234439342538e-02 diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out index 604f12633..6fe484f98 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. @@ -106,7 +102,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -117,31 +112,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - selfCoordNum colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 5.50586 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 2bc07b6b9..465216db6 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 5.53146030766424e+00 + x 5.53146030724717e+00 } restraint { diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 536d293f8..ccbfc7916 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 5.50586098376003e+00 -2.16234439350401e-02 - 21 5.50546911228746e+00 -2.16218764491499e-02 - 22 5.50496280789046e+00 -2.16198512315618e-02 - 23 5.50440600602358e+00 -2.16176240240943e-02 - 24 5.50387532112795e+00 -2.16155012845118e-02 - 25 5.50345262459281e+00 -2.16138104983712e-02 - 26 5.50321719184149e+00 -2.16128687673660e-02 - 27 5.50323878086140e+00 -2.16129551234456e-02 - 28 5.50357282100607e+00 -2.16142912840243e-02 - 29 5.50425822661691e+00 -2.16170329064677e-02 - 30 5.50531751791649e+00 -2.16212700716660e-02 - 31 5.50675822499661e+00 -2.16270328999864e-02 - 32 5.50857426063415e+00 -2.16342970425366e-02 - 33 5.51074629106000e+00 -2.16429851642400e-02 - 34 5.51324095917529e+00 -2.16529638367011e-02 - 35 5.51600985055786e+00 -2.16640394022315e-02 - 36 5.51898962532829e+00 -2.16759585013131e-02 - 37 5.52210473752456e+00 -2.16884189500983e-02 - 38 5.52527326352281e+00 -2.17010930540912e-02 - 39 5.52841506317671e+00 -2.17136602527069e-02 - 40 5.53146030766424e+00 -2.17258412306570e-02 + 20 5.50586098356346e+00 -2.16234439342538e-02 + 21 5.50546911207949e+00 -2.16218764483180e-02 + 22 5.50496280767144e+00 -2.16198512306858e-02 + 23 5.50440600579367e+00 -2.16176240231747e-02 + 24 5.50387532088709e+00 -2.16155012835484e-02 + 25 5.50345262434073e+00 -2.16138104973629e-02 + 26 5.50321719157780e+00 -2.16128687663112e-02 + 27 5.50323878058562e+00 -2.16129551223425e-02 + 28 5.50357282071772e+00 -2.16142912828709e-02 + 29 5.50425822631558e+00 -2.16170329052623e-02 + 30 5.50531751760189e+00 -2.16212700704076e-02 + 31 5.50675822466860e+00 -2.16270328986744e-02 + 32 5.50857426029279e+00 -2.16342970411712e-02 + 33 5.51074629070554e+00 -2.16429851628222e-02 + 34 5.51324095880821e+00 -2.16529638352328e-02 + 35 5.51600985017893e+00 -2.16640394007157e-02 + 36 5.51898962493855e+00 -2.16759584997542e-02 + 37 5.52210473712539e+00 -2.16884189485016e-02 + 38 5.52527326311583e+00 -2.17010930524633e-02 + 39 5.52841506276376e+00 -2.17136602510550e-02 + 40 5.53146030724717e+00 -2.17258412289887e-02 diff --git a/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt b/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_selfcoordnum_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 90d795b91..97875d855 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,17 +88,17 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -128,7 +124,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -139,28 +134,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - spinAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 7b11d47e8..2c69fa7d4 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.56417643630365e+00 + x -1.56417643615813e+00 } restraint { diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 813c43c6c..7fdccd94c 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 -1.84067203510482e+00 7.76268814041928e-03 - 1 -1.84826917190189e+00 7.79307668760756e-03 - 2 -1.85122278124429e+00 7.80489112497715e-03 - 3 -1.84852747918889e+00 7.79410991675556e-03 - 4 -1.83943263506144e+00 7.75773054024574e-03 - 5 -1.82355826066059e+00 7.69423304264234e-03 - 6 -1.80098250081617e+00 7.60393000326468e-03 - 7 -1.77228476375142e+00 7.48913905500567e-03 - 8 -1.73853720797388e+00 7.35414883189552e-03 - 9 -1.70124617189668e+00 7.20498468758673e-03 - 10 -1.66225195279233e+00 7.04900781116932e-03 - 11 -1.62359992640856e+00 6.89439970563425e-03 - 12 -1.58739844252513e+00 6.74959377010052e-03 - 13 -1.55567854108748e+00 6.62271416434992e-03 - 14 -1.53026683719969e+00 6.52106734879876e-03 - 15 -1.51267765483671e+00 6.45071061934683e-03 - 16 -1.50402646523430e+00 6.41610586093720e-03 - 17 -1.50496521246286e+00 6.41986084985144e-03 - 18 -1.51564034674263e+00 6.46256138697051e-03 - 19 -1.53567491271986e+00 6.54269965087945e-03 - 20 -1.56417643630365e+00 6.65670574521461e-03 + 1 -1.84826917190272e+00 7.79307668761089e-03 + 2 -1.85122278124769e+00 7.80489112499078e-03 + 3 -1.84852747919607e+00 7.79410991678428e-03 + 4 -1.83943263507235e+00 7.75773054028941e-03 + 5 -1.82355826067355e+00 7.69423304269421e-03 + 6 -1.80098250082777e+00 7.60393000331108e-03 + 7 -1.77228476375683e+00 7.48913905502733e-03 + 8 -1.73853720796757e+00 7.35414883187027e-03 + 9 -1.70124617187310e+00 7.20498468749239e-03 + 10 -1.66225195274677e+00 7.04900781098710e-03 + 11 -1.62359992633788e+00 6.89439970535152e-03 + 12 -1.58739844242825e+00 6.74959376971300e-03 + 13 -1.55567854096568e+00 6.62271416386271e-03 + 14 -1.53026683705662e+00 6.52106734822649e-03 + 15 -1.51267765467802e+00 6.45071061871208e-03 + 16 -1.50402646506685e+00 6.41610586026742e-03 + 17 -1.50496521229370e+00 6.41986084917482e-03 + 18 -1.51564034657794e+00 6.46256138631175e-03 + 19 -1.53567491256393e+00 6.54269965025573e-03 + 20 -1.56417643615813e+00 6.65670574463252e-03 diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index b11e0344c..ddf8c7f74 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,17 +88,17 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -128,7 +124,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -139,33 +134,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - spinAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -1.56418 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 00ee63db3..6e327970d 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -1.67720949927313e+00 + x -1.67720949787628e+00 } restraint { diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index 0a68c54fa..5c8d1aff8 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -1.56417643630365e+00 6.65670574521461e-03 - 21 -1.59977280229335e+00 6.79909120917339e-03 - 22 -1.64067849467003e+00 6.96271397868011e-03 - 23 -1.68479233914237e+00 7.13916935656949e-03 - 24 -1.72982439584738e+00 7.31929758338951e-03 - 25 -1.77344385042163e+00 7.49377540168654e-03 - 26 -1.81343393777301e+00 7.65373575109205e-03 - 27 -1.84783676714212e+00 7.79134706856848e-03 - 28 -1.87507204676182e+00 7.90028818704729e-03 - 29 -1.89401880707755e+00 7.97607522831020e-03 - 30 -1.90405601824540e+00 8.01622407298159e-03 - 31 -1.90506463947095e+00 8.02025855788378e-03 - 32 -1.89739864549939e+00 7.98959458199754e-03 - 33 -1.88183530385872e+00 7.92734121543490e-03 - 34 -1.85951507145392e+00 7.83806028581570e-03 - 35 -1.83187886015785e+00 7.72751544063142e-03 - 36 -1.80060563931043e+00 7.60242255724172e-03 - 37 -1.76754822452589e+00 7.47019289810355e-03 - 38 -1.73466169550726e+00 7.33864678202902e-03 - 39 -1.70391870996803e+00 7.21567483987211e-03 - 40 -1.67720949927313e+00 7.10883799709252e-03 + 20 -1.56417643615813e+00 6.65670574463252e-03 + 21 -1.59977280215672e+00 6.79909120862687e-03 + 22 -1.64067849453734e+00 6.96271397814937e-03 + 23 -1.68479233900518e+00 7.13916935602071e-03 + 24 -1.72982439569390e+00 7.31929758277560e-03 + 25 -1.77344385023716e+00 7.49377540094865e-03 + 26 -1.81343393754057e+00 7.65373575016229e-03 + 27 -1.84783676684341e+00 7.79134706737363e-03 + 28 -1.87507204637838e+00 7.90028818551353e-03 + 29 -1.89401880659213e+00 7.97607522636850e-03 + 30 -1.90405601764340e+00 8.01622407057361e-03 + 31 -1.90506463874174e+00 8.02025855496697e-03 + 32 -1.89739864463758e+00 7.98959457855033e-03 + 33 -1.88183530286499e+00 7.92734121145994e-03 + 34 -1.85951507033553e+00 7.83806028134214e-03 + 35 -1.83187885892875e+00 7.72751543571502e-03 + 36 -1.80060563799079e+00 7.60242255196314e-03 + 37 -1.76754822314118e+00 7.47019289256470e-03 + 38 -1.73466169408694e+00 7.33864677634775e-03 + 39 -1.70391870854367e+00 7.21567483417467e-03 + 40 -1.67720949787628e+00 7.10883799150512e-03 diff --git a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..832c6a06f 100644 --- a/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_spinangle-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-14. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out index 21561ed31..38bb57ee5 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,17 +70,17 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 3 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -110,7 +106,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.000111111 according to the specified width (3). colvars: ---------------------------------------------------------------------- @@ -121,27 +116,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - spinAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 448e93eef..79a2a90e4 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -6.52196175536141e+00 + x -6.52196175528559e+00 } restraint { diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj index b5f5b8fe8..b65c4790b 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 -6.74120349419055e+00 7.60133721576728e-04 - 1 -6.74680409124828e+00 7.60756010138697e-04 - 2 -6.74928398676149e+00 7.61031554084610e-04 - 3 -6.74760118854074e+00 7.60844576504527e-04 - 4 -6.74089237392950e+00 7.60099152658834e-04 - 5 -6.72859795234419e+00 7.58733105816021e-04 - 6 -6.71056189835939e+00 7.56729099817710e-04 - 7 -6.68709018460270e+00 7.54121131622523e-04 - 8 -6.65896053827068e+00 7.50995615363409e-04 - 9 -6.62738484679749e+00 7.47487205199721e-04 - 10 -6.59393151686784e+00 7.43770168540871e-04 - 11 -6.56041836906667e+00 7.40046485451852e-04 - 12 -6.52878782065636e+00 7.36531980072929e-04 - 13 -6.50097576076332e+00 7.33441751195925e-04 - 14 -6.47878371985369e+00 7.30975968872632e-04 - 15 -6.46376168616761e+00 7.29306854018624e-04 - 16 -6.45710716430512e+00 7.28567462700569e-04 - 17 -6.45958482192202e+00 7.28842757991336e-04 - 18 -6.47146995375796e+00 7.30163328195329e-04 - 19 -6.49251798076206e+00 7.32501997862452e-04 - 20 -6.52196175536141e+00 7.35773528373490e-04 + 0 -6.74120349418967e+00 7.60133721576629e-04 + 1 -6.74680409124886e+00 7.60756010138763e-04 + 2 -6.74928398676683e+00 7.61031554085203e-04 + 3 -6.74760118854837e+00 7.60844576505375e-04 + 4 -6.74089237394015e+00 7.60099152660017e-04 + 5 -6.72859795268796e+00 7.58733105854218e-04 + 6 -6.71056189836587e+00 7.56729099818430e-04 + 7 -6.68709018460367e+00 7.54121131622629e-04 + 8 -6.65896053826554e+00 7.50995615362838e-04 + 9 -6.62738484678158e+00 7.47487205197953e-04 + 10 -6.59393151683697e+00 7.43770168537441e-04 + 11 -6.56041836901761e+00 7.40046485446401e-04 + 12 -6.52878782058752e+00 7.36531980065280e-04 + 13 -6.50097576071506e+00 7.33441751190562e-04 + 14 -6.47878371974444e+00 7.30975968860493e-04 + 15 -6.46376168610113e+00 7.29306854011237e-04 + 16 -6.45710716417506e+00 7.28567462686117e-04 + 17 -6.45958482166641e+00 7.28842757962935e-04 + 18 -6.47146995371894e+00 7.30163328190994e-04 + 19 -6.49251798066684e+00 7.32501997851872e-04 + 20 -6.52196175528559e+00 7.35773528365066e-04 diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out index 58c424da8..62bc7782b 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,17 +70,17 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 3 -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -110,7 +106,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.000111111 according to the specified width (3). colvars: ---------------------------------------------------------------------- @@ -121,32 +116,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - spinAngle colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: -6.52196 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 311efe354..e4d09163e 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x -6.64191475499626e+00 + x -6.64191475373326e+00 } restraint { diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj index e9ee60f48..59936cd90 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 -6.52196175536141e+00 7.35773528373490e-04 - 21 -6.55853866136453e+00 7.39837629040503e-04 - 22 -6.60054957188598e+00 7.44505507987332e-04 - 23 -6.64595045368826e+00 7.49550050409807e-04 - 24 -6.69247420112553e+00 7.54719355680614e-04 - 25 -6.73777528462053e+00 7.59752809402281e-04 - 26 -6.77958465048355e+00 7.64398294498173e-04 - 27 -6.81585908066260e+00 7.68428786740289e-04 - 28 -6.84490920657793e+00 7.71656578508659e-04 - 29 -6.86549395871066e+00 7.73943773190073e-04 - 30 -6.87687521064447e+00 7.75208356738274e-04 - 31 -6.87883312849994e+00 7.75425903166660e-04 - 32 -6.87164844230811e+00 7.74627604700902e-04 - 33 -6.85606123102412e+00 7.72895692336013e-04 - 34 -6.83321600017101e+00 7.70357333352334e-04 - 35 -6.80460002005342e+00 7.67177780005936e-04 - 36 -6.77197706433820e+00 7.63553007148689e-04 - 37 -6.73731414663200e+00 7.59701571848000e-04 - 38 -6.70269652304925e+00 7.55855169227695e-04 - 39 -6.67022757555205e+00 7.52247508394672e-04 - 40 -6.64191475499626e+00 7.49101639444029e-04 + 20 -6.52196175528559e+00 7.35773528365066e-04 + 21 -6.55853866126809e+00 7.39837629029787e-04 + 22 -6.60054957179227e+00 7.44505507976919e-04 + 23 -6.64595045358898e+00 7.49550050398775e-04 + 24 -6.69247420100935e+00 7.54719355667705e-04 + 25 -6.73777528436304e+00 7.59752809373671e-04 + 26 -6.77958465029172e+00 7.64398294476858e-04 + 27 -6.81585908038471e+00 7.68428786709412e-04 + 28 -6.84490920631285e+00 7.71656578479206e-04 + 29 -6.86549395828653e+00 7.73943773142947e-04 + 30 -6.87687521003861e+00 7.75208356670957e-04 + 31 -6.87883312782949e+00 7.75425903092165e-04 + 32 -6.87164844151262e+00 7.74627604612513e-04 + 33 -6.85606123010451e+00 7.72895692233834e-04 + 34 -6.83321599913451e+00 7.70357333237168e-04 + 35 -6.80460001891363e+00 7.67177779879293e-04 + 36 -6.77197706280820e+00 7.63553006978689e-04 + 37 -6.73731414535818e+00 7.59701571706465e-04 + 38 -6.70269652174944e+00 7.55855169083271e-04 + 39 -6.67022757425629e+00 7.52247508250699e-04 + 40 -6.64191475373326e+00 7.49101639303696e-04 diff --git a/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt b/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_spinangle_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out index 0b71aa10e..69afc9ed5 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -128,7 +124,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -139,28 +134,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - tilt colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 21771cc4e..1c8f75a13 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.99415492547103e-01 + x 9.99415492548698e-01 } restraint { diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj index 257bb1412..a797dc77d 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 9.98812440566840e-01 -3.59524976226736e-03 - 1 9.98816680233361e-01 -3.59526672093344e-03 - 2 9.98826523073495e-01 -3.59530609229398e-03 - 3 9.98842018672579e-01 -3.59536807469031e-03 - 4 9.98863121611601e-01 -3.59545248644640e-03 - 5 9.98889669016434e-01 -3.59555867606574e-03 - 6 9.98921340687004e-01 -3.59568536274802e-03 - 7 9.98957619944279e-01 -3.59583047977712e-03 - 8 9.98997773201826e-01 -3.59599109280730e-03 - 9 9.99040860340336e-01 -3.59616344136134e-03 - 10 9.99085779266818e-01 -3.59634311706727e-03 - 11 9.99131338939409e-01 -3.59652535575764e-03 - 12 9.99176347610903e-01 -3.59670539044361e-03 - 13 9.99219697607167e-01 -3.59687879042867e-03 - 14 9.99260427488015e-01 -3.59704170995206e-03 - 15 9.99297748982546e-01 -3.59719099593018e-03 - 16 9.99331038661138e-01 -3.59732415464455e-03 - 17 9.99359807085313e-01 -3.59743922834125e-03 - 18 9.99383664673950e-01 -3.59753465869580e-03 - 19 9.99402301732208e-01 -3.59760920692883e-03 - 20 9.99415492547103e-01 -3.59766197018841e-03 + 1 9.98816680233352e-01 -3.59526672093341e-03 + 2 9.98826523073460e-01 -3.59530609229384e-03 + 3 9.98842018672504e-01 -3.59536807469002e-03 + 4 9.98863121611482e-01 -3.59545248644593e-03 + 5 9.98889669016271e-01 -3.59555867606508e-03 + 6 9.98921340686809e-01 -3.59568536274724e-03 + 7 9.98957619944074e-01 -3.59583047977630e-03 + 8 9.98997773201637e-01 -3.59599109280655e-03 + 9 9.99040860340198e-01 -3.59616344136079e-03 + 10 9.99085779266763e-01 -3.59634311706705e-03 + 11 9.99131338939470e-01 -3.59652535575788e-03 + 12 9.99176347611108e-01 -3.59670539044443e-03 + 13 9.99219697607536e-01 -3.59687879043014e-03 + 14 9.99260427488563e-01 -3.59704170995425e-03 + 15 9.99297748983282e-01 -3.59719099593313e-03 + 16 9.99331038662066e-01 -3.59732415464826e-03 + 17 9.99359807086426e-01 -3.59743922834570e-03 + 18 9.99383664675241e-01 -3.59753465870096e-03 + 19 9.99402301733660e-01 -3.59760920693464e-03 + 20 9.99415492548698e-01 -3.59766197019479e-03 diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out index 35a5c40ee..0ed6ee7d8 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,25 +55,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -92,7 +88,7 @@ colvars: Atom group "atoms" defined with 10 atoms requested: total mass = colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -128,7 +124,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -139,33 +134,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - tilt colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.999415 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index 71c119b43..50c49fa3e 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.99399210038338e-01 + x 9.99399210041976e-01 } restraint { diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj index c3db036ec..86fc22b8b 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.99415492547103e-01 -3.59766197018841e-03 - 21 9.99423124211601e-01 -3.59769249684640e-03 - 22 9.99425243203459e-01 -3.59770097281383e-03 - 23 9.99422108246234e-01 -3.59768843298494e-03 - 24 9.99414235597450e-01 -3.59765694238980e-03 - 25 9.99402422546063e-01 -3.59760969018425e-03 - 26 9.99387736076906e-01 -3.59755094430763e-03 - 27 9.99371458556963e-01 -3.59748583422785e-03 - 28 9.99354991188822e-01 -3.59741996475529e-03 - 29 9.99339727176955e-01 -3.59735890870782e-03 - 30 9.99326916410865e-01 -3.59730766564346e-03 - 31 9.99317547849854e-01 -3.59727019139942e-03 - 32 9.99312272722288e-01 -3.59724909088915e-03 - 33 9.99311381509340e-01 -3.59724552603736e-03 - 34 9.99314833116121e-01 -3.59725933246448e-03 - 35 9.99322320512548e-01 -3.59728928205019e-03 - 36 9.99333348005097e-01 -3.59733339202039e-03 - 37 9.99347295864453e-01 -3.59738918345781e-03 - 38 9.99363457668243e-01 -3.59745383067297e-03 - 39 9.99381050365372e-01 -3.59752420146149e-03 - 40 9.99399210038338e-01 -3.59759684015335e-03 + 20 9.99415492548698e-01 -3.59766197019479e-03 + 21 9.99423124213315e-01 -3.59769249685326e-03 + 22 9.99425243205266e-01 -3.59770097282107e-03 + 23 9.99422108248105e-01 -3.59768843299242e-03 + 24 9.99414235599357e-01 -3.59765694239743e-03 + 25 9.99402422547979e-01 -3.59760969019192e-03 + 26 9.99387736078806e-01 -3.59755094431523e-03 + 27 9.99371458558828e-01 -3.59748583423531e-03 + 28 9.99354991190644e-01 -3.59741996476258e-03 + 29 9.99339727178734e-01 -3.59735890871494e-03 + 30 9.99326916412614e-01 -3.59730766565046e-03 + 31 9.99317547851597e-01 -3.59727019140639e-03 + 32 9.99312272724061e-01 -3.59724909089624e-03 + 33 9.99311381511187e-01 -3.59724552604475e-03 + 34 9.99314833118093e-01 -3.59725933247237e-03 + 35 9.99322320514697e-01 -3.59728928205879e-03 + 36 9.99333348007473e-01 -3.59733339202989e-03 + 37 9.99347295867101e-01 -3.59738918346840e-03 + 38 9.99363457671199e-01 -3.59745383068479e-03 + 39 9.99381050368662e-01 -3.59752420147465e-03 + 40 9.99399210041976e-01 -3.59759684016791e-03 diff --git a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt index 157cac038..832c6a06f 100644 --- a/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_tilt-fitgroup_harmonic-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2018-12-14. +colvars: Using NAMD interface, version 2018-08-29. diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out index 466786003..ffac56dd2 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -110,7 +106,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.4 according to the specified width (0.05). colvars: ---------------------------------------------------------------------- @@ -121,27 +116,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - tilt colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped index 22e226ed8..776f51f15 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.86667458349930e-01 + x 9.86667458341471e-01 } restraint { diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj index be7100171..036a31008 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 9.89817622562351e-01 -3.55927049024940e-01 - 1 9.89739193890686e-01 -3.55895677556274e-01 - 2 9.89645626534388e-01 -3.55858250613755e-01 - 3 9.89537793456435e-01 -3.55815117382574e-01 - 4 9.89416411924999e-01 -3.55766564770000e-01 - 5 9.89282053848009e-01 -3.55712821539204e-01 - 6 9.89135240737646e-01 -3.55654096295058e-01 - 7 9.88976581441553e-01 -3.55590632576621e-01 - 8 9.88806911283522e-01 -3.55522764513409e-01 - 9 9.88627402346676e-01 -3.55450960938670e-01 - 10 9.88439627708785e-01 -3.55375851083514e-01 - 11 9.88245572588250e-01 -3.55298229035300e-01 - 12 9.88047593326962e-01 -3.55219037330785e-01 - 13 9.87848337461123e-01 -3.55139334984449e-01 - 14 9.87650651623308e-01 -3.55060260649323e-01 - 15 9.87457507491825e-01 -3.54983002996730e-01 - 16 9.87271960375771e-01 -3.54908784150308e-01 - 17 9.87097125290053e-01 -3.54838850116021e-01 - 18 9.86936130482758e-01 -3.54774452193103e-01 - 19 9.86792003048169e-01 -3.54716801219267e-01 - 20 9.86667458349930e-01 -3.54666983339972e-01 + 0 9.89817622562340e-01 -3.55927049024936e-01 + 1 9.89739193890710e-01 -3.55895677556284e-01 + 2 9.89645626534500e-01 -3.55858250613800e-01 + 3 9.89537793456669e-01 -3.55815117382668e-01 + 4 9.89416411925387e-01 -3.55766564770155e-01 + 5 9.89282053848041e-01 -3.55712821539216e-01 + 6 9.89135240738356e-01 -3.55654096295342e-01 + 7 9.88976581442317e-01 -3.55590632576927e-01 + 8 9.88806911284239e-01 -3.55522764513695e-01 + 9 9.88627402347221e-01 -3.55450960938888e-01 + 10 9.88439627709016e-01 -3.55375851083606e-01 + 11 9.88245572588017e-01 -3.55298229035207e-01 + 12 9.88047593326122e-01 -3.55219037330449e-01 + 13 9.87848337457110e-01 -3.55139334982844e-01 + 14 9.87650651620881e-01 -3.55060260648352e-01 + 15 9.87457507486578e-01 -3.54983002994631e-01 + 16 9.87271960371439e-01 -3.54908784148575e-01 + 17 9.87097125283486e-01 -3.54838850113394e-01 + 18 9.86936130473010e-01 -3.54774452189204e-01 + 19 9.86792003040408e-01 -3.54716801216163e-01 + 20 9.86667458341471e-01 -3.54666983336588e-01 diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out index 790ae8ec1..8e045427a 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "RMSD_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -74,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: # axis = ( 1 , -3 , 4 ) colvars: Normalizing rotation axis to ( 0.196116 , -0.588348 , 0.784465 ). @@ -110,7 +106,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.4 according to the specified width (0.05). colvars: ---------------------------------------------------------------------- @@ -121,32 +116,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - orientation colvar component: -colvars: - tilt colvar component (derived from orientation): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 0.986667 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped index ffcadedd3..33ffc6902 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 9.85614564530977e-01 + x 9.85614564513385e-01 } restraint { diff --git a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj index b5e56c253..e9303a790 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 9.86667458349930e-01 -3.54666983339972e-01 - 21 9.86564598798781e-01 -3.54625839519512e-01 - 22 9.86484566772892e-01 -3.54593826709157e-01 - 23 9.86427228496625e-01 -3.54570891398650e-01 - 24 9.86390977455002e-01 -3.54556390982001e-01 - 25 9.86372728522180e-01 -3.54549091408872e-01 - 26 9.86368130550494e-01 -3.54547252220198e-01 - 27 9.86371969386892e-01 -3.54548787754757e-01 - 28 9.86378686084241e-01 -3.54551474433696e-01 - 29 9.86382912477289e-01 -3.54553164990916e-01 - 30 9.86379931734801e-01 -3.54551972693920e-01 - 31 9.86365997688778e-01 -3.54546399075511e-01 - 32 9.86338483201464e-01 -3.54535393280585e-01 - 33 9.86295866427772e-01 -3.54518346571109e-01 - 34 9.86237598508030e-01 -3.54495039403212e-01 - 35 9.86163919711047e-01 -3.54465567884419e-01 - 36 9.86075697598078e-01 -3.54430279039231e-01 - 37 9.85974343825943e-01 -3.54389737530377e-01 - 38 9.85861830034088e-01 -3.54344732013635e-01 - 39 9.85740778424268e-01 -3.54296311369707e-01 - 40 9.85614564530977e-01 -3.54245825812391e-01 + 20 9.86667458341471e-01 -3.54666983336588e-01 + 21 9.86564598790534e-01 -3.54625839516214e-01 + 22 9.86484566764204e-01 -3.54593826705681e-01 + 23 9.86427228487669e-01 -3.54570891395068e-01 + 24 9.86390977445951e-01 -3.54556390978380e-01 + 25 9.86372728511522e-01 -3.54549091404609e-01 + 26 9.86368130541750e-01 -3.54547252216700e-01 + 27 9.86371969378090e-01 -3.54548787751236e-01 + 28 9.86378686073627e-01 -3.54551474429451e-01 + 29 9.86382912469260e-01 -3.54553164987704e-01 + 30 9.86379931725049e-01 -3.54551972690020e-01 + 31 9.86365997681395e-01 -3.54546399072558e-01 + 32 9.86338483193996e-01 -3.54535393277598e-01 + 33 9.86295866419978e-01 -3.54518346567991e-01 + 34 9.86237598499642e-01 -3.54495039399857e-01 + 35 9.86163919701783e-01 -3.54465567880713e-01 + 36 9.86075697585368e-01 -3.54430279034147e-01 + 37 9.85974343814067e-01 -3.54389737525627e-01 + 38 9.85861830020574e-01 -3.54344732008230e-01 + 39 9.85740778408907e-01 -3.54296311363563e-01 + 40 9.85614564513385e-01 -3.54245825805354e-01 diff --git a/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt b/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt +++ b/namd/tests/library/000_tilt_harmonic-fixed/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out index 9990cc125..bb4bac866 100644 --- a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out +++ b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsdA" @@ -27,14 +25,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 8 atoms requested: total mass = 43.069, total charge = -0.09. @@ -42,7 +40,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -78,14 +76,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] @@ -131,14 +129,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = off [default] +colvars: # centerReference = on +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] @@ -183,14 +181,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = on +colvars: # centerReference = off [default] +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] @@ -236,14 +234,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off -colvars: # rotateToReference = off +colvars: # centerReference = off +colvars: # rotateReference = off colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 8 atoms requested: total mass = 43.069, total charge = -0.09. @@ -288,7 +286,6 @@ colvars: # centers = { 0, 0, 0, 0, 0 } colvars: # targetCenters = { 0, 0, 0, 0, 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsdA" will be rescaled to 1 according to the specified width (1). colvars: The force constant for colvar "rmsdB" will be rescaled to 1 according to the specified width (1). @@ -303,7 +300,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 5 in total. colvars: ---------------------------------------------------------------------- @@ -317,7 +313,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -336,7 +331,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -355,7 +349,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -374,7 +367,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -393,7 +385,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -409,34 +400,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdB":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdC":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdD":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdE":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (8 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdB":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. colvars: Re-initialized atom group for variable "rmsdC":0/0. 8 atoms: total mass = 43.069, total charge = -0.09. diff --git a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj index 266bf3e21..9c94197c3 100644 --- a/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj +++ b/namd/tests/library/001_10ala_RMSD/AutoDiff/test.colvars.traj @@ -1,2 +1,2 @@ -# step rmsdA ft_rmsdA rmsdB ft_rmsdB rmsdC ft_rmsdC rmsdD ft_rmsdD rmsdE ft_rmsdE - 0 2.61009345658189e-01 0.00000000000000e+00 1.27145912684355e+01 0.00000000000000e+00 6.68502465870546e-01 0.00000000000000e+00 9.31703240469482e-01 0.00000000000000e+00 1.24224459145532e+00 0.00000000000000e+00 +# step rmsdA ft_rmsdA rmsdB ft_rmsdB rmsdC ft_rmsdC rmsdD ft_rmsdD rmsdE ft_rmsdE + 0 2.61009345658189e-01 0.00000000000000e+00 1.27145912684355e+01 0.00000000000000e+00 6.68502465870546e-01 0.00000000000000e+00 9.31703240469482e-01 0.00000000000000e+00 1.24224459145532e+00 0.00000000000000e+00 diff --git a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out index a4dfd6895..aae270fda 100644 --- a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out +++ b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "eigenvector_Ca" @@ -57,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,20 +70,19 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating the vector projection: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: # vector = [default] colvars: # vectorFile = "../Common/da.xyz" colvars: # vectorCol = "" [default] colvars: Geometric center of the provided vector: ( 0.9999 , 2 , 3 ) colvars: # differenceVector = on -colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = x_vec - x_ref. -colvars: # normalizeVector = off [default] -colvars: Normalizing the vector so that the norm of the projection |v ⋅ (x_vec - x_ref)| = 1. +colvars: "differenceVector" is on: subtracting the reference positions from the provided vector: v = v - x0. +colvars: "differenceVector" is on: normalizing the vector. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -113,7 +110,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "eigenvector_Ca" will be rescaled to 10 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -124,28 +120,13 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - eigenvector colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "eigenvector_Ca":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "eigenvector_Ca":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj index d319abefa..a10b71b97 100644 --- a/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj +++ b/namd/tests/library/002_10ala_fit_gradients/AutoDiff/test.colvars.traj @@ -1,2 +1,2 @@ # step eigenvector_Ca ft_eigenvector_Ca fa_eigenvector_Ca - 0 9.99999999999999e-01 0.00000000000000e+00 -9.99999999999999e+00 + 0 1.00000000000000e+00 0.00000000000000e+00 -1.00000000000000e+01 diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out index 5b4640743..832cffd51 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -57,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -112,7 +110,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd" will be rescaled to 10000 according to the specified width (0.01). colvars: ---------------------------------------------------------------------- @@ -123,7 +120,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -137,7 +133,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -152,30 +147,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped index e621f3ff5..20535536d 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name rmsd - x 1.39198635632537e+00 + x 1.39198635631904e+00 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 1.00000000000000e-01 - accumulatedWork -1.79849880092255e+03 + accumulatedWork -1.79849880092103e+03 } } diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj index 88056a153..62e3fc7d4 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step rmsd ft_rmsd fa_rmsd E_harmonic1 x0_rmsd W_harmonic1 0 2.17249057079325e+00 0.00000000000000e+00 -2.17456306136404e+04 2.35985764009279e+04 0.00000000000000e+00 0.00000000000000e+00 - 1 2.16345956010640e+00 -2.17419903526924e+04 -2.15552301966651e+04 2.31869403850683e+04 1.00000000000000e-02 -2.15345956010640e+02 - 2 2.13583213462443e+00 -2.14389529078214e+04 -2.11786796675906e+04 2.23837281095469e+04 2.00000000000000e-02 -4.26929169473084e+02 - 3 2.09038365006932e+00 -2.07262996388757e+04 -2.06237403371939e+04 2.12259039273649e+04 3.00000000000000e-02 -6.32967534480016e+02 - 4 2.02806882503406e+00 -1.96255637093855e+04 -1.98999689385910e+04 1.97620882653616e+04 4.00000000000000e-02 -8.31774416983422e+02 - 5 1.95030623811202e+00 -1.81667585436761e+04 -1.90215654435014e+04 1.80558189930374e+04 5.00000000000000e-02 -1.02180504079462e+03 - 6 1.85875201230836e+00 -1.63966970219124e+04 -1.80051076432067e+04 1.61775440089168e+04 6.00000000000000e-02 -1.20168024202546e+03 - 7 1.75513110974568e+00 -1.43781737213953e+04 -1.68678624085543e+04 1.41983342851636e+04 7.00000000000000e-02 -1.37019335300003e+03 - 8 1.64142178718387e+00 -1.21888818488311e+04 -1.56296320897105e+04 1.21901899874623e+04 8.00000000000000e-02 -1.52633553171842e+03 - 9 1.51964633571603e+00 -9.89848282368767e+03 -1.43106598205174e+04 1.02194432261313e+04 9.00000000000000e-02 -1.66930016529002e+03 - 10 1.39198635632537e+00 -7.49967017329654e+03 -1.29327834268169e+04 8.34614372465450e+03 1.00000000000000e-01 -1.79849880092255e+03 + 1 2.16345956010639e+00 -2.17419903527299e+04 -2.15552301966649e+04 2.31869403850679e+04 1.00000000000000e-02 -2.15345956010639e+02 + 2 2.13583213462437e+00 -2.14389529078606e+04 -2.11786796675899e+04 2.23837281095455e+04 2.00000000000000e-02 -4.26929169473075e+02 + 3 2.09038365006916e+00 -2.07262996389219e+04 -2.06237403371923e+04 2.12259039273616e+04 3.00000000000000e-02 -6.32967534479991e+02 + 4 2.02806882503376e+00 -1.96255637094443e+04 -1.98999689385880e+04 1.97620882653556e+04 4.00000000000000e-02 -8.31774416983368e+02 + 5 1.95030623811151e+00 -1.81667585437567e+04 -1.90215654434962e+04 1.80558189930276e+04 5.00000000000000e-02 -1.02180504079452e+03 + 6 1.85875201230753e+00 -1.63966970220336e+04 -1.80051076431984e+04 1.61775440089019e+04 6.00000000000000e-02 -1.20168024202527e+03 + 7 1.75513110974436e+00 -1.43781737215985e+04 -1.68678624085410e+04 1.41983342851413e+04 7.00000000000000e-02 -1.37019335299971e+03 + 8 1.64142178718173e+00 -1.21888818492009e+04 -1.56296320896891e+04 1.21901899874289e+04 8.00000000000000e-02 -1.52633553171788e+03 + 9 1.51964633571245e+00 -9.89848282440100e+03 -1.43106598204816e+04 1.02194432260802e+04 9.00000000000000e-02 -1.66930016528913e+03 + 10 1.39198635631904e+00 -7.49967017479936e+03 -1.29327834267536e+04 8.34614372457276e+03 1.00000000000000e-01 -1.79849880092103e+03 diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out index 1539c97b7..460e18798 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -57,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/pi-ideal.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -112,7 +110,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd" will be rescaled to 10000 according to the specified width (0.01). colvars: ---------------------------------------------------------------------- @@ -123,7 +120,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -137,7 +133,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -152,36 +147,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "rmsd" from value: 1.39199 colvars: Restarting harmonic bias "harmonic1" from step number 10. colvars: Restarting harmonicwalls bias "rmsdw" from step number 10. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testres.colvars.state". colvars: The final output state file will be "testres.colvars.state". +colvars: Opening trajectory file "testres.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The restart output state file will be "testres.colvars.state". colvars: The final output state file will be "testres.colvars.state". diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped index e2cb96809..0329bdfbc 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name rmsd - x 3.58513981869359e-01 + x 3.58513981358481e-01 } restraint { @@ -14,7 +14,7 @@ restraint { name harmonic1 firstStep 0 centers 2.00000000000000e-01 - accumulatedWork -2.38254491368653e+03 + accumulatedWork -2.38254491346066e+03 } } diff --git a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj index cfd59f064..afd7851c5 100644 --- a/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj +++ b/namd/tests/library/003_10ala_SMD_restart/AutoDiff/testres.colvars.traj @@ -1,12 +1,12 @@ # step rmsd ft_rmsd fa_rmsd E_harmonic1 x0_rmsd W_harmonic1 - 10 1.39198635632537e+00 0.00000000000000e+00 -1.29327834268169e+04 8.34614372465450e+03 1.00000000000000e-01 -1.79849880092255e+03 - 11 1.26066443054501e+00 -5.04906136264293e+03 -1.15182509497555e+04 6.62014315860736e+03 1.10000000000000e-01 -1.91356524397705e+03 - 12 1.12800176084383e+00 -2.47793069174467e+03 -1.00902976260468e+04 5.08033774932134e+03 1.20000000000000e-01 -2.01436542006143e+03 - 13 9.96492050953577e-01 3.15682479164454e+02 -8.67388543004531e+03 3.75404237182868e+03 1.30000000000000e-01 -2.10101462515679e+03 - 14 8.68461409598148e-01 2.99293971896176e+03 -7.29229871007746e+03 2.65328012636860e+03 1.40000000000000e-01 -2.17386076611661e+03 - 15 7.47100495226679e-01 6.43619261578947e+03 -5.97747595721906e+03 1.78264500699973e+03 1.50000000000000e-01 -2.23357081563928e+03 - 16 6.35910083193821e-01 1.00836160874306e+04 -4.76445993277015e+03 1.13245203642775e+03 1.60000000000000e-01 -2.28116182395866e+03 - 17 5.38589382317609e-01 1.33134883220103e+04 -3.69027971699926e+03 6.79290663786381e+02 1.70000000000000e-01 -2.31802076219042e+03 - 18 4.58478968346367e-01 1.57771913409965e+04 -2.78837447314713e+03 3.87752679056283e+02 1.80000000000000e-01 -2.34586865902505e+03 - 19 3.98248564745421e-01 1.64627514687814e+04 -2.08546813310166e+03 2.16837323592639e+02 1.90000000000000e-01 -2.36669351549960e+03 - 20 3.58513981869359e-01 1.49916694393498e+04 -1.58772495851228e+03 1.25633412240397e+02 2.00000000000000e-01 -2.38254491368653e+03 + 10 1.39198635631904e+00 0.00000000000000e+00 -1.29327834267536e+04 8.34614372457276e+03 1.00000000000000e-01 -1.79849880092103e+03 + 11 1.26066443053330e+00 -5.04906136565955e+03 -1.15182509496383e+04 6.62014315847261e+03 1.10000000000000e-01 -1.91356524397436e+03 + 12 1.12800176082188e+00 -2.47793069731417e+03 -1.00902976258270e+04 5.08033774910002e+03 1.20000000000000e-01 -2.01436542005655e+03 + 13 9.96492050911879e-01 3.15682468320502e+02 -8.67388542962791e+03 3.75404237146737e+03 1.30000000000000e-01 -2.10101462514774e+03 + 14 8.68461409518928e-01 2.99293969889592e+03 -7.29229870928447e+03 2.65328012579152e+03 1.40000000000000e-01 -2.17386076609963e+03 + 15 7.47100495082919e-01 6.43619258679187e+03 -5.97747595578002e+03 1.78264500614134e+03 1.50000000000000e-01 -2.23357081560792e+03 + 16 6.35910082961470e-01 1.00836160673481e+04 -4.76445993044432e+03 1.13245203532197e+03 1.60000000000000e-01 -2.28116182390407e+03 + 17 5.38589381992358e-01 1.33134883328259e+04 -3.69027971374350e+03 6.79290662587542e+02 1.70000000000000e-01 -2.31802076210330e+03 + 18 4.58478967939376e-01 1.57771913740319e+04 -2.78837446907315e+03 3.87752677922900e+02 1.80000000000000e-01 -2.34586865889724e+03 + 19 3.98248564275675e-01 1.64627515062483e+04 -2.08546812839950e+03 2.16837322614399e+02 1.90000000000000e-01 -2.36669351532481e+03 + 20 3.58513981358481e-01 1.49916694678179e+04 -1.58772495339839e+03 1.25633411430584e+02 2.00000000000000e-01 -2.38254491346066e+03 diff --git a/namd/tests/library/003_10ala_SMD_restart/namd-version.txt b/namd/tests/library/003_10ala_SMD_restart/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/003_10ala_SMD_restart/namd-version.txt +++ b/namd/tests/library/003_10ala_SMD_restart/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out index 24596243b..80cd2d40b 100644 --- a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out +++ b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -27,56 +25,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.011, total charge = 0.51. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -86,10 +84,10 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] -colvars: # lowerBoundary = -180 [default] -colvars: # upperBoundary = 180 [default] -colvars: # hardLowerBoundary = on [default] -colvars: # hardUpperBoundary = on [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -118,7 +116,6 @@ colvars: # targetNumStages = 36 colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 10 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -129,39 +126,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. colvars: Re-initialized atom group for variable "d":0/3. 1 atoms: total mass = 14.007, total charge = -0.47. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "previous.colvars.state". -colvars: This state file was generated with version +colvars: Restarting from file "previous.colvars.state". colvars: Restarting collective variable "d" from value: -137.21 colvars: Restarting harmonic bias "harmonic1" from step number 8000. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testr.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/2. 1 atoms: total mass = 12.011, total charge = 0.51. diff --git a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj index 4ec655cd6..1cecbe504 100644 --- a/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj +++ b/namd/tests/library/004_10ala_moving_restart/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step d fa_d 8000 -1.37210258611294e+02 2.21025861129385e+01 - 8002 -1.36437406938754e+02 1.43740693875392e+01 - 8004 -1.32448586831542e+02 -2.55141316845757e+01 - 8006 -1.34451844766900e+02 -5.48155233099777e+00 - 8008 -1.37758781619839e+02 2.75878161983877e+01 - 8010 -1.35039285402134e+02 3.92854021337428e-01 - 8012 -1.32417992183404e+02 -2.58200781659573e+01 - 8014 -1.35927148506493e+02 9.27148506492500e+00 - 8016 -1.37371418693785e+02 2.37141869378459e+01 - 8018 -1.33415236151160e+02 -1.58476384884008e+01 - 8020 -1.33332063901251e+02 -1.66793609874881e+01 + 8002 -1.36437406938780e+02 1.43740693877973e+01 + 8004 -1.32448586831588e+02 -2.55141316841204e+01 + 8006 -1.34451844766881e+02 -5.48155233119189e+00 + 8008 -1.37758781619817e+02 2.75878161981655e+01 + 8010 -1.35039285402271e+02 3.92854022709912e-01 + 8012 -1.32417992183434e+02 -2.58200781656637e+01 + 8014 -1.35927148506204e+02 9.27148506203707e+00 + 8016 -1.37371418693973e+02 2.37141869397252e+01 + 8018 -1.33415236151821e+02 -1.58476384817905e+01 + 8020 -1.33332063900607e+02 -1.66793609939288e+01 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out b/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out index 477048315..f8428a56e 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.Tcl.out @@ -1,4 +1,4 @@ -TCL: Running Colvars version 2023-07-21 +TCL: Running Colvars version 2020-04-09 TCL: Running cv units real TCL: TCL: d = 0.00000000000000e+00 @@ -13,7 +13,7 @@ TCL: E(harmonic1) = 18000 TCL: Original numsteps 20 will be ignored. TCL: Running for 20 steps TCL: d = 1.28684277602119e+01 -TCL: E(abf1) = 32.885 +TCL: E(abf1) = 0 TCL: E(harmonic1) = 94.2708 TCL: Running cv bias harm2 getconfig TCL: @@ -27,7 +27,7 @@ TCL: TCL: Running cv bias harm2 energy TCL: 17.8166 TCL: Running cv bias harm2 update -TCL: 1.78166082981433e+01 +TCL: 17.8166 TCL: Running for 20 steps TCL: Running cv bias harm2 energy TCL: 13.4817 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out index ca61c96ea..d3135664a 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -27,28 +25,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -106,7 +104,6 @@ colvars: # centers = { 12 } colvars: # targetCenters = { 12 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 250 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -117,35 +114,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Prepared sample and gradient buffers at step 0. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). +colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. +colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". colvars: ---------------------------------------------------------------------- @@ -156,7 +135,6 @@ colvars: # colvarsTrajFrequency = 2 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -173,7 +151,6 @@ colvars: # centers = { 13 } colvars: # targetCenters = { 13 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 25 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -184,296 +161,271 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Saving collective variables state to "test.colvars.state". -colvars: Features of "colvar d" (refcount) -colvars: - ON active (3) -colvars: - awake -colvars: - ON gradient (3) -colvars: - collect_gradient -colvars: - collect_atom_ids -colvars: - velocity_from_finite_differences -colvars: - ON total_force (3) -colvars: - ON total_force_calculation (1) -colvars: - ON subtract_applied_force_from_total_force -colvars: - ON Jacobian_derivative (1) -colvars: - hide_Jacobian_force -colvars: - extended_Lagrangian -colvars: - external -colvars: - Langevin_dynamics -colvars: - output_energy -colvars: - ON output_value -colvars: - output_velocity -colvars: - ON output_applied_force -colvars: - ON output_total_force -colvars: - ON lower_boundary -colvars: - ON upper_boundary -colvars: - hard_lower_boundary -colvars: - hard_upper_boundary -colvars: - reflecting_lower_boundary -colvars: - reflecting_upper_boundary -colvars: - ON grid -colvars: - running_average -colvars: - correlation_function -colvars: - scripted -colvars: - custom_function -colvars: - periodic -colvars: - ON single_component -colvars: - ON scalar (7) -colvars: - ON linear (2) -colvars: - ON homogeneous -colvars: - multiple_timestep +colvars: Features of "colvar d" ON/OFF (refcount) +colvars: - active ON (4) +colvars: - awake ON (0) +colvars: - gradient ON (3) +colvars: - collect_gradient OFF (0) +colvars: - velocity_from_finite_differences OFF (0) +colvars: - total_force ON (3) +colvars: - total_force_calculation ON (1) +colvars: - subtract_applied_force_from_total_force ON (0) +colvars: - Jacobian_derivative ON (1) +colvars: - hide_Jacobian_force OFF (0) +colvars: - extended_Lagrangian OFF (0) +colvars: - Langevin_dynamics OFF (0) +colvars: - output_energy OFF (0) +colvars: - output_value ON (0) +colvars: - output_velocity OFF (0) +colvars: - output_applied_force ON (0) +colvars: - output_total_force ON (0) +colvars: - lower_boundary ON (1) +colvars: - upper_boundary ON (1) +colvars: - hard_lower_boundary OFF (0) +colvars: - hard_upper_boundary OFF (0) +colvars: - reflecting_lower_boundary OFF (0) +colvars: - reflecting_upper_boundary OFF (0) +colvars: - grid ON (0) +colvars: - running_average OFF (0) +colvars: - correlation_function OFF (0) +colvars: - scripted OFF (0) +colvars: - custom_function OFF (0) +colvars: - periodic OFF (0) +colvars: - single_component ON (0) +colvars: - scalar ON (6) +colvars: - linear ON (2) +colvars: - homogeneous ON (0) +colvars: - multiple_timestep OFF (0) colvars: * child 1 -colvars: Features of "cvc distance0001" (refcount) -colvars: - ON active -colvars: - scalar -colvars: - periodic -colvars: - defined_width -colvars: - ON defined_lower_boundary -colvars: - defined_upper_boundary -colvars: - ON gradient (2) -colvars: - explicit_gradient -colvars: - ON inverse_gradient (2) -colvars: - ON Jacobian_derivative (1) -colvars: - total_force_from_one_group -colvars: - debug_gradient -colvars: - ON use_minimum-image_with_PBCs -colvars: - ON function_of_centers_of_mass (1) -colvars: - ON scalable_calculation (1) -colvars: - ON scalable_calculation_of_centers_of_mass -colvars: - collect_atom_ids +colvars: Features of "cvc distance0001" ON/OFF (refcount) +colvars: - active ON (0) +colvars: - scalar OFF (0) +colvars: - periodic OFF (0) +colvars: - defined_width OFF (0) +colvars: - defined_lower_boundary ON (0) +colvars: - defined_upper_boundary OFF (0) +colvars: - gradient ON (2) +colvars: - explicit_gradient ON (0) +colvars: - inverse_gradient ON (2) +colvars: - Jacobian_derivative ON (1) +colvars: - total_force_from_one_group OFF (0) +colvars: - debug_gradient OFF (0) +colvars: - use_minimum-image_with_PBCs ON (0) +colvars: - function_of_centers_of_mass ON (1) +colvars: - scalable_calculation ON (0) +colvars: - scalable_calculation_of_centers_of_mass ON (1) colvars: * child 1 -colvars: Features of "atom group group1" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids +colvars: Features of "atom group group1" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) colvars: * child 2 -colvars: Features of "atom group group2" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids -colvars: Features of "bias harmonic1" (refcount) -colvars: - ON active -colvars: - awake -colvars: - step_zero_data -colvars: - ON apply_force -colvars: - bypass_extended_Lagrangian_coordinates -colvars: - obtain_total_force -colvars: - output_accumulated_work -colvars: - history_dependent -colvars: - time_dependent -colvars: - require_scalar_variables -colvars: - calculate_a_PMF -colvars: - calculate_TI_samples -colvars: - write_TI_samples_ -colvars: - write_TI_PMF -colvars: - scale_biasing_force +colvars: Features of "atom group group2" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) +colvars: Features of "bias harmonic1" ON/OFF (refcount) +colvars: - active ON (1) +colvars: - awake ON (0) +colvars: - step_zero_data OFF (0) +colvars: - apply_force ON (0) +colvars: - bypass_extended_Lagrangian_coordinates OFF (0) +colvars: - obtain_total_force OFF (0) +colvars: - output_accumulated_work OFF (0) +colvars: - history_dependent OFF (0) +colvars: - time_dependent OFF (0) +colvars: - require_scalar_variables OFF (0) +colvars: - calculate_a_PMF OFF (0) +colvars: - calculate_TI_samples OFF (0) +colvars: - write_TI_samples_ OFF (0) +colvars: - write_TI_PMF OFF (0) colvars: * child 1 -colvars: Features of "colvar d" (refcount) -colvars: - ON active (3) -colvars: - awake -colvars: - ON gradient (3) -colvars: - collect_gradient -colvars: - collect_atom_ids -colvars: - velocity_from_finite_differences -colvars: - ON total_force (3) -colvars: - ON total_force_calculation (1) -colvars: - ON subtract_applied_force_from_total_force -colvars: - ON Jacobian_derivative (1) -colvars: - hide_Jacobian_force -colvars: - extended_Lagrangian -colvars: - external -colvars: - Langevin_dynamics -colvars: - output_energy -colvars: - ON output_value -colvars: - output_velocity -colvars: - ON output_applied_force -colvars: - ON output_total_force -colvars: - ON lower_boundary -colvars: - ON upper_boundary -colvars: - hard_lower_boundary -colvars: - hard_upper_boundary -colvars: - reflecting_lower_boundary -colvars: - reflecting_upper_boundary -colvars: - ON grid -colvars: - running_average -colvars: - correlation_function -colvars: - scripted -colvars: - custom_function -colvars: - periodic -colvars: - ON single_component -colvars: - ON scalar (7) -colvars: - ON linear (2) -colvars: - ON homogeneous -colvars: - multiple_timestep +colvars: Features of "colvar d" ON/OFF (refcount) +colvars: - active ON (4) +colvars: - awake ON (0) +colvars: - gradient ON (3) +colvars: - collect_gradient OFF (0) +colvars: - velocity_from_finite_differences OFF (0) +colvars: - total_force ON (3) +colvars: - total_force_calculation ON (1) +colvars: - subtract_applied_force_from_total_force ON (0) +colvars: - Jacobian_derivative ON (1) +colvars: - hide_Jacobian_force OFF (0) +colvars: - extended_Lagrangian OFF (0) +colvars: - Langevin_dynamics OFF (0) +colvars: - output_energy OFF (0) +colvars: - output_value ON (0) +colvars: - output_velocity OFF (0) +colvars: - output_applied_force ON (0) +colvars: - output_total_force ON (0) +colvars: - lower_boundary ON (1) +colvars: - upper_boundary ON (1) +colvars: - hard_lower_boundary OFF (0) +colvars: - hard_upper_boundary OFF (0) +colvars: - reflecting_lower_boundary OFF (0) +colvars: - reflecting_upper_boundary OFF (0) +colvars: - grid ON (0) +colvars: - running_average OFF (0) +colvars: - correlation_function OFF (0) +colvars: - scripted OFF (0) +colvars: - custom_function OFF (0) +colvars: - periodic OFF (0) +colvars: - single_component ON (0) +colvars: - scalar ON (6) +colvars: - linear ON (2) +colvars: - homogeneous ON (0) +colvars: - multiple_timestep OFF (0) colvars: * child 1 -colvars: Features of "cvc distance0001" (refcount) -colvars: - ON active -colvars: - scalar -colvars: - periodic -colvars: - defined_width -colvars: - ON defined_lower_boundary -colvars: - defined_upper_boundary -colvars: - ON gradient (2) -colvars: - explicit_gradient -colvars: - ON inverse_gradient (2) -colvars: - ON Jacobian_derivative (1) -colvars: - total_force_from_one_group -colvars: - debug_gradient -colvars: - ON use_minimum-image_with_PBCs -colvars: - ON function_of_centers_of_mass (1) -colvars: - ON scalable_calculation (1) -colvars: - ON scalable_calculation_of_centers_of_mass -colvars: - collect_atom_ids +colvars: Features of "cvc distance0001" ON/OFF (refcount) +colvars: - active ON (0) +colvars: - scalar OFF (0) +colvars: - periodic OFF (0) +colvars: - defined_width OFF (0) +colvars: - defined_lower_boundary ON (0) +colvars: - defined_upper_boundary OFF (0) +colvars: - gradient ON (2) +colvars: - explicit_gradient ON (0) +colvars: - inverse_gradient ON (2) +colvars: - Jacobian_derivative ON (1) +colvars: - total_force_from_one_group OFF (0) +colvars: - debug_gradient OFF (0) +colvars: - use_minimum-image_with_PBCs ON (0) +colvars: - function_of_centers_of_mass ON (1) +colvars: - scalable_calculation ON (0) +colvars: - scalable_calculation_of_centers_of_mass ON (1) colvars: * child 1 -colvars: Features of "atom group group1" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids +colvars: Features of "atom group group1" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) colvars: * child 2 -colvars: Features of "atom group group2" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids +colvars: Features of "atom group group2" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) colvars: Saving collective variables state to "test.colvars.state". -colvars: Features of "bias harm2" (refcount) -colvars: - ON active -colvars: - awake -colvars: - step_zero_data -colvars: - ON apply_force -colvars: - bypass_extended_Lagrangian_coordinates -colvars: - obtain_total_force -colvars: - output_accumulated_work -colvars: - history_dependent -colvars: - time_dependent -colvars: - require_scalar_variables -colvars: - calculate_a_PMF -colvars: - calculate_TI_samples -colvars: - write_TI_samples_ -colvars: - write_TI_PMF -colvars: - scale_biasing_force +colvars: Features of "bias harm2" ON/OFF (refcount) +colvars: - active ON (1) +colvars: - awake ON (0) +colvars: - step_zero_data OFF (0) +colvars: - apply_force ON (0) +colvars: - bypass_extended_Lagrangian_coordinates OFF (0) +colvars: - obtain_total_force OFF (0) +colvars: - output_accumulated_work OFF (0) +colvars: - history_dependent OFF (0) +colvars: - time_dependent OFF (0) +colvars: - require_scalar_variables OFF (0) +colvars: - calculate_a_PMF OFF (0) +colvars: - calculate_TI_samples OFF (0) +colvars: - write_TI_samples_ OFF (0) +colvars: - write_TI_PMF OFF (0) colvars: * child 1 -colvars: Features of "colvar d" (refcount) -colvars: - ON active (2) -colvars: - awake -colvars: - ON gradient (2) -colvars: - collect_gradient -colvars: - collect_atom_ids -colvars: - velocity_from_finite_differences -colvars: - ON total_force (3) -colvars: - ON total_force_calculation (1) -colvars: - ON subtract_applied_force_from_total_force -colvars: - ON Jacobian_derivative (1) -colvars: - hide_Jacobian_force -colvars: - extended_Lagrangian -colvars: - external -colvars: - Langevin_dynamics -colvars: - output_energy -colvars: - ON output_value -colvars: - output_velocity -colvars: - ON output_applied_force -colvars: - ON output_total_force -colvars: - ON lower_boundary -colvars: - ON upper_boundary -colvars: - hard_lower_boundary -colvars: - hard_upper_boundary -colvars: - reflecting_lower_boundary -colvars: - reflecting_upper_boundary -colvars: - ON grid -colvars: - running_average -colvars: - correlation_function -colvars: - scripted -colvars: - custom_function -colvars: - periodic -colvars: - ON single_component -colvars: - ON scalar (7) -colvars: - ON linear (2) -colvars: - ON homogeneous -colvars: - multiple_timestep +colvars: Features of "colvar d" ON/OFF (refcount) +colvars: - active ON (3) +colvars: - awake ON (0) +colvars: - gradient ON (2) +colvars: - collect_gradient OFF (0) +colvars: - velocity_from_finite_differences OFF (0) +colvars: - total_force ON (3) +colvars: - total_force_calculation ON (1) +colvars: - subtract_applied_force_from_total_force ON (0) +colvars: - Jacobian_derivative ON (1) +colvars: - hide_Jacobian_force OFF (0) +colvars: - extended_Lagrangian OFF (0) +colvars: - Langevin_dynamics OFF (0) +colvars: - output_energy OFF (0) +colvars: - output_value ON (0) +colvars: - output_velocity OFF (0) +colvars: - output_applied_force ON (0) +colvars: - output_total_force ON (0) +colvars: - lower_boundary ON (1) +colvars: - upper_boundary ON (1) +colvars: - hard_lower_boundary OFF (0) +colvars: - hard_upper_boundary OFF (0) +colvars: - reflecting_lower_boundary OFF (0) +colvars: - reflecting_upper_boundary OFF (0) +colvars: - grid ON (0) +colvars: - running_average OFF (0) +colvars: - correlation_function OFF (0) +colvars: - scripted OFF (0) +colvars: - custom_function OFF (0) +colvars: - periodic OFF (0) +colvars: - single_component ON (0) +colvars: - scalar ON (6) +colvars: - linear ON (2) +colvars: - homogeneous ON (0) +colvars: - multiple_timestep OFF (0) colvars: * child 1 -colvars: Features of "cvc distance0001" (refcount) -colvars: - ON active -colvars: - scalar -colvars: - periodic -colvars: - defined_width -colvars: - ON defined_lower_boundary -colvars: - defined_upper_boundary -colvars: - ON gradient (2) -colvars: - explicit_gradient -colvars: - ON inverse_gradient (2) -colvars: - ON Jacobian_derivative (1) -colvars: - total_force_from_one_group -colvars: - debug_gradient -colvars: - ON use_minimum-image_with_PBCs -colvars: - ON function_of_centers_of_mass (1) -colvars: - ON scalable_calculation (1) -colvars: - ON scalable_calculation_of_centers_of_mass -colvars: - collect_atom_ids +colvars: Features of "cvc distance0001" ON/OFF (refcount) +colvars: - active ON (0) +colvars: - scalar OFF (0) +colvars: - periodic OFF (0) +colvars: - defined_width OFF (0) +colvars: - defined_lower_boundary ON (0) +colvars: - defined_upper_boundary OFF (0) +colvars: - gradient ON (2) +colvars: - explicit_gradient ON (0) +colvars: - inverse_gradient ON (2) +colvars: - Jacobian_derivative ON (1) +colvars: - total_force_from_one_group OFF (0) +colvars: - debug_gradient OFF (0) +colvars: - use_minimum-image_with_PBCs ON (0) +colvars: - function_of_centers_of_mass ON (1) +colvars: - scalable_calculation ON (0) +colvars: - scalable_calculation_of_centers_of_mass ON (1) colvars: * child 1 -colvars: Features of "atom group group1" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids +colvars: Features of "atom group group1" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) colvars: * child 2 -colvars: Features of "atom group group2" (refcount) -colvars: - active -colvars: - center_to_reference -colvars: - center_to_origin -colvars: - rotate_to_origin -colvars: - fitting_group -colvars: - explicit_atom_gradient -colvars: - fit_gradients -colvars: - atomic_forces -colvars: - ON scalable_group (1) -colvars: - ON scalable_group_center_of_mass -colvars: - collect_atom_ids +colvars: Features of "atom group group2" ON/OFF (refcount) +colvars: - active OFF (0) +colvars: - translational_fit OFF (0) +colvars: - rotational_fit OFF (0) +colvars: - fitting_group OFF (0) +colvars: - explicit_atom_gradient ON (1) +colvars: - fit_gradients OFF (0) +colvars: - atomic_forces OFF (0) +colvars: - scalable_group ON (0) +colvars: - scalable_group_center_of_mass ON (1) colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". colvars: The final output state file will be "test.colvars.state". colvars: Saving collective variables state to "test.colvars.state". colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "d" from value: 11.9615 colvars: Restarting abf bias "abf1" from step number 60. colvars: ---------------------------------------------------------------------- @@ -486,7 +438,6 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -500,32 +451,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 1 atoms requested. +colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 1 atoms requested. +colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. @@ -579,7 +530,6 @@ colvars: # centers = { 12 } colvars: # targetCenters = { 12 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 10 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 250 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -590,7 +540,5 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Warning: before deleting colvar d, deleting related bias harmonic1 colvars: Warning: before deleting colvar d, deleting related bias abf1 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj index 31374c82a..f029f1ae9 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.colvars.traj @@ -1,38 +1,38 @@ # step d ft_d fa_d E_harmonic1 - 0 0.00000000000000e+00 0.00000000000000e+00 3.00000000000000e+03 1.80000000000000e+04 + 0 0.00000000000000e+00 0.00000000000000e+00 3.00000000000000e+03 1.80000000000000e+04 # step d ft_d fa_d E_harmonic1 - 0 1.42467449615693e+01 0.00000000000000e+00 -5.61686240392322e+02 6.30982865292123e+02 - 2 1.42282559728026e+01 5.32933601659170e+00 -5.59529927201590e+02 6.20640585041297e+02 - 4 1.41727662460742e+01 3.36254334328178e+01 -5.43191561518562e+02 5.90114145009947e+02 - 6 1.40831323320984e+01 8.13697353990825e+01 -5.89087882335502e+02 5.42430039129236e+02 - 8 1.39609835871958e+01 1.43683712679872e+02 -4.90245896798950e+02 4.80682078656413e+02 - 10 1.38136915830204e+01 2.11747525531865e+02 -6.48260269443340e+02 4.11184644789902e+02 - 12 1.36437184346286e+01 2.81640059890150e+02 -6.92569668547312e+02 3.37726286542257e+02 - 14 1.34588898265283e+01 3.45729335505761e+02 -7.10451792137843e+02 2.66044940743482e+02 - 16 1.32645132385707e+01 4.00985013285219e+02 -7.17113322927902e+02 1.99874216315080e+02 - 18 1.30658878095359e+01 4.46271310489825e+02 -7.12743262873798e+02 1.42014602814653e+02 - 20 1.28684277602119e+01 4.80580458032557e+02 -6.97687398085530e+02 9.42708468383301e+01 + 0 1.42467449615693e+01 0.00000000000000e+00 -5.61686240392322e+02 6.30982865292123e+02 + 2 1.42282559728026e+01 5.32933601891204e+00 -5.59529927203773e+02 6.20640585041317e+02 + 4 1.41727662460744e+01 3.36254334374946e+01 -5.43191561518601e+02 5.90114145010033e+02 + 6 1.40831323320990e+01 8.13697354080271e+01 -5.89087882343440e+02 5.42430039129534e+02 + 8 1.39609835871970e+01 1.43683712693643e+02 -4.90245896799256e+02 4.80682078657013e+02 + 10 1.38136915830229e+01 2.11747525548495e+02 -6.48260269460101e+02 4.11184644791030e+02 + 12 1.36437184346326e+01 2.81640059905252e+02 -6.92569668563411e+02 3.37726286543895e+02 + 14 1.34588898265340e+01 3.45729335512429e+02 -7.10451792145928e+02 2.66044940745548e+02 + 16 1.32645132385777e+01 4.00985013276056e+02 -7.17113322920477e+02 1.99874216317278e+02 + 18 1.30658878095430e+01 4.46271310459046e+02 -7.12743262844788e+02 1.42014602816538e+02 + 20 1.28684277602171e+01 4.80580457979151e+02 -6.97687398033433e+02 9.42708468394674e+01 # step d ft_d fa_d E_harmonic1 E_harm2 - 20 1.28684277602119e+01 4.91888943214004e+02 -7.00052334681550e+02 9.42708468383301e+01 2.16390678535748e-01 - 22 1.26751474320465e+01 5.03084201979406e+02 -6.63749745792196e+02 5.69780068748745e+01 1.31911488632471e+00 - 24 1.24888492973171e+01 5.15335038410192e+02 -6.24768595172394e+02 2.98717044359277e+01 3.26593801066529e+00 - 26 1.23139243019797e+01 5.23015189146873e+02 -5.84344372191302e+02 1.23185584216834e+01 5.88374829267482e+00 - 28 1.21466432034073e+01 5.30527139882848e+02 -1.53268809370116e+01 2.68802863819490e+00 9.10272277863661e+00 - 30 1.19993450538088e+01 5.38695710631225e+02 2.51801102025817e+01 5.36193141719397e-05 1.25163790167116e+01 - 32 1.18850444891885e+01 5.34994463767922e+02 5.66127654731507e+01 1.65184618324038e+00 1.55390723886105e+01 - 34 1.18115458382762e+01 5.01682268034594e+02 7.68248944740457e+01 4.43937138387764e+00 1.76552911814828e+01 - 36 1.17769967624676e+01 4.41508793838497e+02 8.63258903213991e+01 6.21630549373929e+00 1.86967114876829e+01 - 38 1.17769542143717e+01 3.61640408513788e+02 8.63375910477925e+01 6.21867781082023e+00 1.86980124217904e+01 - 40 1.18061287071667e+01 2.69866690242884e+02 7.83146055291581e+01 4.69825977310700e+00 1.78166082981433e+01 + 20 1.28684277602171e+01 4.91888943151427e+02 -7.00052334624999e+02 9.42708468394674e+01 2.16390678518517e-01 + 22 1.26751474320475e+01 5.03084201909373e+02 -6.63749745722433e+02 5.69780068750397e+01 1.31911488631676e+00 + 24 1.24888492973110e+01 5.15335038327460e+02 -6.24768595087998e+02 2.98717044351878e+01 3.26593801074265e+00 + 26 1.23139243019631e+01 5.23015189033541e+02 -5.84344372073400e+02 1.23185584203791e+01 5.88374829295988e+00 + 28 1.21466432033769e+01 5.30527139707869e+02 -1.53268809286588e+01 2.68802863708136e+00 9.10272277928461e+00 + 30 1.19993450537562e+01 5.38695710361251e+02 2.51801102170466e+01 5.36193227844337e-05 1.25163790180274e+01 + 32 1.18850444890963e+01 5.34994463383540e+02 5.66127654985307e+01 1.65184618589271e+00 1.55390723911830e+01 + 34 1.18115458381165e+01 5.01682267555293e+02 7.68248945179519e+01 4.43937139139973e+00 1.76552911862265e+01 + 36 1.17769967622096e+01 4.41508793313709e+02 8.63258903923681e+01 6.21630550812685e+00 1.86967114955734e+01 + 38 1.17769542139854e+01 3.61640408006584e+02 8.63375911540067e+01 6.21867783235716e+00 1.86980124336000e+01 + 40 1.18061287066284e+01 2.69866689808628e+02 7.83146056771794e+01 4.69825979919525e+00 1.78166083142086e+01 # step d ft_d fa_d E_harm2 - 40 1.18061287071667e+01 2.21949532598602e+02 2.98467823208325e+01 1.78166082981433e+01 - 42 1.18555777465383e+01 1.74464231066044e+02 2.86105563365434e+01 1.63712786777305e+01 - 44 1.19176677655463e+01 8.22937406521174e+01 2.70583058613429e+01 1.46430383217196e+01 - 46 1.19851813921025e+01 -6.16868558833627e+00 2.53704651974387e+01 1.28732100866889e+01 - 48 1.20415309220875e+01 -8.97664353399688e+01 -3.04621864232869e+02 1.14832871664300e+01 - 50 1.20655400395174e+01 -1.50412424652567e+02 -1.19070572819524e+02 1.09151927218147e+01 - 52 1.20686235856919e+01 -1.88148861256361e+02 -2.70255157819366e+01 1.08432753141169e+01 - 54 1.20571466482814e+01 -2.05067811724940e+02 2.93687990810595e+01 1.11121555355867e+01 - 56 1.20332538295850e+01 -2.00399870515217e+02 6.58114559546446e+01 1.16824769751521e+01 - 58 1.20000609190792e+01 -1.75170570569691e+02 8.83273233309201e+01 1.24984770694101e+01 - 60 1.19614725567188e+01 -1.36757725642476e+02 2.59631860820309e+01 1.34817406306033e+01 + 40 1.18061287066284e+01 2.21949532217238e+02 2.98467823342890e+01 1.78166083142086e+01 + 42 1.18555777458287e+01 1.74464230745251e+02 2.86105563542814e+01 1.63712786980303e+01 + 44 1.19176677646512e+01 8.22937404700844e+01 2.70583058837192e+01 1.46430383459383e+01 + 46 1.19851813910175e+01 -6.16868563783110e+00 2.53704652245623e+01 1.28732101142145e+01 + 48 1.20415309208210e+01 -8.97664352869559e+01 -3.04621864055419e+02 1.14832871967769e+01 + 50 1.20655400380907e+01 -1.50412424518311e+02 -1.19070572741895e+02 1.09151927551443e+01 + 52 1.20686235841253e+01 -1.88148861003765e+02 -2.70255157752960e+01 1.08432753505955e+01 + 54 1.20571466466005e+01 -2.05067811286631e+02 2.93687990112175e+01 1.11121555752091e+01 + 56 1.20332538278214e+01 -2.00399869950163e+02 6.58114558084562e+01 1.16824770177739e+01 + 58 1.20000609172601e+01 -1.75170570145191e+02 8.83273231404457e+01 1.24984771148846e+01 + 60 1.19614725548519e+01 -1.36757725550194e+02 2.59631861287023e+01 1.34817406790728e+01 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.grad b/namd/tests/library/005_Tcl_script/AutoDiff/test.grad index 09257e021..2a30d2884 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.grad +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.grad @@ -1,18 +1,18 @@ # 1 # 1.20000000000000e+01 2.00000000000000e-01 100 0 - 1.21000000000000e+01 6.99836010424488e+01 - 1.23000000000000e+01 -5.26375313539263e+02 - 1.25000000000000e+01 -5.16708952033009e+02 - 1.27000000000000e+01 -5.05977066295794e+02 - 1.29000000000000e+01 -4.88119448153522e+02 - 1.31000000000000e+01 -4.54995001246909e+02 - 1.33000000000000e+01 -4.12314411202659e+02 - 1.35000000000000e+01 -3.59715820938218e+02 - 1.37000000000000e+01 -2.97680997031215e+02 - 1.39000000000000e+01 -2.12126120219850e+02 - 1.41000000000000e+01 -9.78647224947473e+01 - 1.43000000000000e+01 -1.38644228493632e+01 + 1.21000000000000e+01 6.99836008077528e+01 + 1.23000000000000e+01 -5.26375313396654e+02 + 1.25000000000000e+01 -5.16708951944646e+02 + 1.27000000000000e+01 -5.05977066222890e+02 + 1.29000000000000e+01 -4.88119448094002e+02 + 1.31000000000000e+01 -4.54995001210363e+02 + 1.33000000000000e+01 -4.12314411188385e+02 + 1.35000000000000e+01 -3.59715820941386e+02 + 1.37000000000000e+01 -2.97680997044662e+02 + 1.39000000000000e+01 -2.12126120236132e+02 + 1.41000000000000e+01 -9.78647225049371e+01 + 1.43000000000000e+01 -1.38644228524206e+01 1.45000000000000e+01 0.00000000000000e+00 1.47000000000000e+01 0.00000000000000e+00 1.49000000000000e+01 0.00000000000000e+00 diff --git a/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf b/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf index 53f87f0d2..edf8b154a 100644 --- a/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf +++ b/namd/tests/library/005_Tcl_script/AutoDiff/test.pmf @@ -1,18 +1,18 @@ # 1 # 1.19000000000000e+01 2.00000000000000e-01 101 0 - 1.20000000000000e+01 7.63151734992420e+02 - 1.22000000000000e+01 7.77148455200910e+02 - 1.24000000000000e+01 6.71873392493057e+02 - 1.26000000000000e+01 5.68531602086455e+02 - 1.28000000000000e+01 4.67336188827297e+02 - 1.30000000000000e+01 3.69712299196592e+02 - 1.32000000000000e+01 2.78713298947211e+02 - 1.34000000000000e+01 1.96250416706679e+02 - 1.36000000000000e+01 1.24307252519035e+02 - 1.38000000000000e+01 6.47710531127921e+01 - 1.40000000000000e+01 2.23458290688221e+01 - 1.42000000000000e+01 2.77288456987264e+00 + 1.20000000000000e+01 7.63151734965745e+02 + 1.22000000000000e+01 7.77148455127296e+02 + 1.24000000000000e+01 6.71873392447965e+02 + 1.26000000000000e+01 5.68531602059036e+02 + 1.28000000000000e+01 4.67336188814458e+02 + 1.30000000000000e+01 3.69712299195657e+02 + 1.32000000000000e+01 2.78713298953585e+02 + 1.34000000000000e+01 1.96250416715908e+02 + 1.36000000000000e+01 1.24307252527630e+02 + 1.38000000000000e+01 6.47710531186980e+01 + 1.40000000000000e+01 2.23458290714716e+01 + 1.42000000000000e+01 2.77288457048417e+00 1.44000000000000e+01 0.00000000000000e+00 1.46000000000000e+01 0.00000000000000e+00 1.48000000000000e+01 0.00000000000000e+00 diff --git a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out index dbb4752af..ed14c521a 100644 --- a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out +++ b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsdA" @@ -57,14 +55,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. @@ -72,7 +70,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -108,21 +106,21 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] -colvars: Enabling "centerToReference" and "rotateToReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. +colvars: Enabling "centerReference" and "rotateReference", to minimize RMSD before calculating it as a variable: if this is not the desired behavior, disable them explicitly within the "atoms" block. colvars: This is a standard minimum RMSD, derivatives of the optimal rotation will not be computed as they cancel out in the gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -161,7 +159,6 @@ colvars: # centers = { 0, 0 } colvars: # targetCenters = { 0, 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsdA" will be rescaled to 1 according to the specified width (1). colvars: The force constant for colvar "rmsdB" will be rescaled to 1 according to the specified width (1). @@ -173,7 +170,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- @@ -187,7 +183,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -206,7 +201,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } colvars: # upperWalls = { 5 } @@ -222,30 +216,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - harmonicWalls colvar bias implementation: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "rmsdB":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "rmsdA":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: Re-initialized atom group for variable "rmsdB":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj index c60285dcf..ddcb476b2 100644 --- a/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj +++ b/namd/tests/library/006_10ala_groups/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step rmsdA ft_rmsdA rmsdB ft_rmsdB - 0 4.84870372257743e-01 0.00000000000000e+00 4.84870372257743e-01 0.00000000000000e+00 - 1 4.84397558390959e-01 2.73671250705184e+01 4.84397558390959e-01 2.73671250705184e+01 - 2 4.83907428259633e-01 2.16076116033336e+01 4.83907428259633e-01 2.16076116033336e+01 - 3 4.83522392477099e-01 1.48700273529640e+01 4.83522392477099e-01 1.48700273529640e+01 - 4 4.83083112857061e-01 9.62041735404308e+00 4.83083112857061e-01 9.62041735404308e+00 - 5 4.82621016611279e-01 6.75848681260943e+00 4.82621016611279e-01 6.75848681260943e+00 - 6 4.82181848616836e-01 3.55598529366702e+00 4.82181848616836e-01 3.55598529366702e+00 - 7 4.81645520126582e-01 3.84568150780596e+00 4.81645520126582e-01 3.84568150780596e+00 - 8 4.81136761646141e-01 7.38903469459440e+00 4.81136761646141e-01 7.38903469459440e+00 - 9 4.80598465151405e-01 1.31715075709571e+01 4.80598465151405e-01 1.31715075709571e+01 - 10 4.80094226696681e-01 2.27871464954793e+01 4.80094226696681e-01 2.27871464954793e+01 - 11 4.79704703210026e-01 3.33000067642520e+01 4.79704703210026e-01 3.33000067642520e+01 - 12 4.79506792185437e-01 4.04751300688640e+01 4.79506792185437e-01 4.04751300688640e+01 - 13 4.79327275852122e-01 4.50913689853400e+01 4.79327275852122e-01 4.50913689853400e+01 - 14 4.79314968876482e-01 4.98879888654564e+01 4.79314968876482e-01 4.98879888654564e+01 - 15 4.79397379649694e-01 4.87227323912461e+01 4.79397379649694e-01 4.87227323912461e+01 - 16 4.79394129019021e-01 4.65370310291944e+01 4.79394129019021e-01 4.65370310291944e+01 - 17 4.79404085663536e-01 4.25674541281252e+01 4.79404085663536e-01 4.25674541281252e+01 - 18 4.79306164129660e-01 3.79497992181814e+01 4.79306164129660e-01 3.79497992181814e+01 - 19 4.79258291381186e-01 3.40970490306029e+01 4.79258291381186e-01 3.40970490306029e+01 - 20 4.79299937829629e-01 2.83439956536282e+01 4.79299937829629e-01 2.83439956536282e+01 +# step rmsdA ft_rmsdA rmsdB ft_rmsdB + 0 4.84870372257743e-01 0.00000000000000e+00 4.84870372257743e-01 0.00000000000000e+00 + 1 4.84397558390947e-01 2.73671250418532e+01 4.84397558390947e-01 2.73671250418532e+01 + 2 4.83907428259583e-01 2.16076115744649e+01 4.83907428259583e-01 2.16076115744649e+01 + 3 4.83522392476985e-01 1.48700273236137e+01 4.83522392476985e-01 1.48700273236137e+01 + 4 4.83083112856857e-01 9.62041732419351e+00 4.83083112856857e-01 9.62041732419351e+00 + 5 4.82621016610959e-01 6.75848678249268e+00 4.82621016610959e-01 6.75848678249268e+00 + 6 4.82181848616375e-01 3.55598526400234e+00 4.82181848616375e-01 3.55598526400234e+00 + 7 4.81645520125956e-01 3.84568147972637e+00 4.81645520125956e-01 3.84568147972637e+00 + 8 4.81136761645330e-01 7.38903466954419e+00 4.81136761645330e-01 7.38903466954419e+00 + 9 4.80598465150393e-01 1.31715075507452e+01 4.80598465150393e-01 1.31715075507452e+01 + 10 4.80094226695461e-01 2.27871464821819e+01 4.80094226695461e-01 2.27871464821819e+01 + 11 4.79704703208599e-01 3.33000067601667e+01 4.79704703208599e-01 3.33000067601667e+01 + 12 4.79506792183813e-01 4.04751300762086e+01 4.79506792183813e-01 4.04751300762086e+01 + 13 4.79327275850325e-01 4.50913690064303e+01 4.79327275850325e-01 4.50913690064303e+01 + 14 4.79314968874545e-01 4.98879889015527e+01 4.79314968874545e-01 4.98879889015527e+01 + 15 4.79397379647665e-01 4.87227324434123e+01 4.79397379647665e-01 4.87227324434123e+01 + 16 4.79394129016958e-01 4.65370310981482e+01 4.79394129016958e-01 4.65370310981482e+01 + 17 4.79404085661514e-01 4.25674542132686e+01 4.79404085661514e-01 4.25674542132686e+01 + 18 4.79306164127760e-01 3.79497993178883e+01 4.79306164127760e-01 3.79497993178883e+01 + 19 4.79258291379496e-01 3.40970491422707e+01 4.79258291379496e-01 3.40970491422707e+01 + 20 4.79299937828241e-01 2.83439957758912e+01 4.79299937828241e-01 2.83439957758912e+01 diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out index 4ffa0e954..0e9b1d0ff 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.Tcl.out @@ -4,4 +4,4 @@ TCL: Running for 20 steps TCL: Resetting colvars with scripted config TCL: Reinitializing atom data TCL: Running for 20 steps -TCL: { 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1.} {0.803041923852589 -0.044335223471426634 -0.5942710294931693 -0.803041923852589 0.044335223471426634 0.5942710294931693 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.} +TCL: { 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1.} {0.8030419238525889 -0.044335223471426655 -0.5942710294931696 -0.8030419238525889 0.044335223471426655 0.5942710294931696 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.} diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out index 7d1128cfc..4169f3a81 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "unscripted.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -27,28 +25,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -87,14 +85,14 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "atoms" defined with 104 atoms requested: total mass = 727.821, total charge = 6.70552e-08. @@ -102,7 +100,7 @@ colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -1.09169 , -2.08869 , -2.98243 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] @@ -134,7 +132,6 @@ colvars: # centers = { 18 } colvars: # targetCenters = { 18 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 500 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "d" will be rescaled to 500 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -147,7 +144,6 @@ colvars: # colvarsTrajFrequency = 2 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- @@ -161,7 +157,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -178,33 +173,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (104 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "o":0/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (104 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "o":0/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08. @@ -219,7 +196,6 @@ colvars: # colvarsTrajFrequency = 2 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "ds" @@ -233,32 +209,32 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 1 atoms requested. +colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 1 atoms requested. +colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. @@ -297,17 +273,17 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] -colvars: Atom group "atoms" defined with 2 atoms requested. +colvars: Atom group "atoms" defined with 2 atoms requested: total mass = 24.022, total charge = -0.03. colvars: # useX = on [default] colvars: # useY = on [default] colvars: # useZ = on [default] @@ -321,21 +297,21 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] -colvars: Atom group "atoms" defined with 104 atoms requested. +colvars: Atom group "atoms" defined with 104 atoms requested: total mass = 727.821, total charge = 6.70552e-08. colvars: # refPositions = [default] colvars: # refPositionsFile = "../Common/da.xyz" colvars: # refPositionsCol = "" [default] -colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -1.09169 , -2.08869 , -2.98243 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry. colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] colvars: All components initialized. colvars: This colvar uses scripted function "vector". @@ -370,7 +346,6 @@ colvars: # colvarsTrajFrequency = 2 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = on [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- @@ -384,7 +359,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -401,26 +375,4 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (104 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - cartesian colvar component: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: - orientation colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Scripted functions (Tcl): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped index f2e2c8800..b8c350fb2 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name ds - x 1.91635808809322e+01 + x 1.91635808809730e+01 } colvar { name vec - x ( 1.91635808809322e+01 , 9.74600371905328e-01 , 2.12939348562529e-01 , -1.24954463293996e-03 , -6.93497480454941e-02 ) + x ( 1.91635808809730e+01 , 9.74600371909626e-01 , 2.12939348547346e-01 , -1.24954463323046e-03 , -6.93497480317003e-02 ) } restraint { diff --git a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj index 219a7e69d..bc74a2043 100644 --- a/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj +++ b/namd/tests/library/007_scripted_cv_biases/AutoDiff/test.colvars.traj @@ -1,24 +1,24 @@ -# step d fa_d o - 0 1.42467449615693e+01 1.87662751921536e+03 ( 9.99999748638998e-01 , 6.84042724576856e-04 , 5.12508171642993e-05 , -1.79390207161577e-04 ) - 2 1.45977275439174e+01 1.70113622804129e+03 ( 9.99985973761768e-01 , 5.11485913752449e-03 , -3.32731800435062e-05 , -1.37455033649980e-03 ) - 4 1.50626713340642e+01 1.46866433296788e+03 ( 9.99843158592009e-01 , 1.70395625511364e-02 , -1.43866916458119e-04 , -4.82605709994617e-03 ) - 6 1.56168085965040e+01 1.19159570174801e+03 ( 9.99321288192689e-01 , 3.53760784420164e-02 , -2.78427047982270e-04 , -1.02673520124943e-02 ) - 8 1.62291266298058e+01 8.85436685097112e+02 ( 9.98133542942750e-01 , 5.85622743078173e-02 , -4.51475701501585e-04 , -1.73114600811307e-02 ) - 10 1.68643388381556e+01 5.67830580922218e+02 ( 9.96054934943680e-01 , 8.49744253320995e-02 , -6.83720355286896e-04 , -2.55625925973094e-02 ) - 12 1.74846635628564e+01 2.57668218571810e+02 ( 9.92972839556575e-01 , 1.13139164128729e-01 , -9.51259109789660e-04 , -3.46924278382252e-02 ) - 14 1.80530624332013e+01 -2.65312166006630e+01 ( 9.88977962065000e-01 , 1.41311479847713e-01 , -1.14108783882053e-03 , -4.41854515825400e-02 ) - 16 1.85372200961635e+01 -2.68610048081769e+02 ( 9.84381327963322e-01 , 1.67770992143166e-01 , -1.20902908627445e-03 , -5.33369815525160e-02 ) - 18 1.89124918771599e+01 -4.56245938579931e+02 ( 9.79545563652526e-01 , 1.91522263376275e-01 , -1.22366955068550e-03 , -6.17107283437381e-02 ) - 20 1.91635808809322e+01 -5.81790440466119e+02 ( 9.74600371905327e-01 , 2.12939348562529e-01 , -1.24954463293998e-03 , -6.93497480454941e-02 ) -# step ds fa_ds vec fa_vec - 20 1.42467449615693e+01 0.00000000000000e+00 ( 1.42467449615693e+01 , 9.99999748638998e-01 , 6.84042724576856e-04 , 5.12508171642993e-05 , -1.79390207161577e-04 ) ( 1.87662751921535e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 22 1.45977275439174e+01 0.00000000000000e+00 ( 1.45977275439174e+01 , 9.99985973761768e-01 , 5.11485913752449e-03 , -3.32731800435062e-05 , -1.37455033649980e-03 ) ( 1.70113622804130e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 24 1.50626713340642e+01 0.00000000000000e+00 ( 1.50626713340642e+01 , 9.99843158592009e-01 , 1.70395625511364e-02 , -1.43866916458118e-04 , -4.82605709994616e-03 ) ( 1.46866433296790e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 26 1.56168085965040e+01 0.00000000000000e+00 ( 1.56168085965040e+01 , 9.99321288192689e-01 , 3.53760784420164e-02 , -2.78427047982271e-04 , -1.02673520124943e-02 ) ( 1.19159570174800e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 28 1.62291266298058e+01 0.00000000000000e+00 ( 1.62291266298058e+01 , 9.98133542942750e-01 , 5.85622743078173e-02 , -4.51475701501585e-04 , -1.73114600811307e-02 ) ( 8.85436685097099e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 30 1.68643388381556e+01 0.00000000000000e+00 ( 1.68643388381556e+01 , 9.96054934943680e-01 , 8.49744253320995e-02 , -6.83720355286896e-04 , -2.55625925973094e-02 ) ( 5.67830580922200e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 32 1.74846635628564e+01 0.00000000000000e+00 ( 1.74846635628564e+01 , 9.92972839556575e-01 , 1.13139164128729e-01 , -9.51259109789661e-04 , -3.46924278382252e-02 ) ( 2.57668218571800e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 34 1.80530624332013e+01 0.00000000000000e+00 ( 1.80530624332013e+01 , 9.88977962065000e-01 , 1.41311479847713e-01 , -1.14108783882053e-03 , -4.41854515825400e-02 ) ( -2.65312166006506e+01 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 36 1.85372200961635e+01 0.00000000000000e+00 ( 1.85372200961635e+01 , 9.84381327963322e-01 , 1.67770992143166e-01 , -1.20902908627445e-03 , -5.33369815525160e-02 ) ( -2.68610048081751e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 38 1.89124918771599e+01 0.00000000000000e+00 ( 1.89124918771599e+01 , 9.79545563652526e-01 , 1.91522263376275e-01 , -1.22366955068550e-03 , -6.17107283437381e-02 ) ( -4.56245938579951e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) - 40 1.91635808809322e+01 0.00000000000000e+00 ( 1.91635808809322e+01 , 9.74600371905328e-01 , 2.12939348562529e-01 , -1.24954463293996e-03 , -6.93497480454941e-02 ) ( -5.81790440466101e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) +# step d fa_d o + 0 1.42467449615693e+01 1.87662751921536e+03 ( 9.99999748638998e-01 , 6.84042724576832e-04 , 5.12508171643214e-05 , -1.79390207161565e-04 ) + 2 1.45977275439175e+01 1.70113622804125e+03 ( 9.99985973761768e-01 , 5.11485913744026e-03 , -3.32731800417789e-05 , -1.37455033645004e-03 ) + 4 1.50626713340646e+01 1.46866433296768e+03 ( 9.99843158592016e-01 , 1.70395625507908e-02 , -1.43866916456290e-04 , -4.82605709972753e-03 ) + 6 1.56168085965048e+01 1.19159570174758e+03 ( 9.99321288192724e-01 , 3.53760784411667e-02 , -2.78427047992860e-04 , -1.02673520119492e-02 ) + 8 1.62291266298068e+01 8.85436685096593e+02 ( 9.98133542942867e-01 , 5.85622743061378e-02 , -4.51475701577846e-04 , -1.73114600800356e-02 ) + 10 1.68643388381563e+01 5.67830580921871e+02 ( 9.96054934943978e-01 , 8.49744253292275e-02 , -6.83720355648298e-04 , -2.55625925952464e-02 ) + 12 1.74846635628575e+01 2.57668218571256e+02 ( 9.92972839557288e-01 , 1.13139164123728e-01 , -9.51259111211344e-04 , -3.46924278340861e-02 ) + 14 1.80530624332059e+01 -2.65312166029723e+01 ( 9.88977962066854e-01 , 1.41311479837272e-01 , -1.14108784183725e-03 , -4.41854515743639e-02 ) + 16 1.85372200961765e+01 -2.68610048088240e+02 ( 9.84381327967116e-01 , 1.67770992125046e-01 , -1.20902908935363e-03 , -5.33369815394103e-02 ) + 18 1.89124918771857e+01 -4.56245938592827e+02 ( 9.79545563657221e-01 , 1.91522263357025e-01 , -1.22366955206206e-03 , -6.17107283289307e-02 ) + 20 1.91635808809730e+01 -5.81790440486497e+02 ( 9.74600371909626e-01 , 2.12939348547346e-01 , -1.24954463323043e-03 , -6.93497480317004e-02 ) +# step ds fa_ds vec fa_vec + 20 1.42467449615693e+01 0.00000000000000e+00 ( 1.42467449615693e+01 , 9.99999748638998e-01 , 6.84042724576832e-04 , 5.12508171643214e-05 , -1.79390207161565e-04 ) ( 1.87662751921535e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 22 1.45977275439175e+01 0.00000000000000e+00 ( 1.45977275439175e+01 , 9.99985973761768e-01 , 5.11485913744027e-03 , -3.32731800417788e-05 , -1.37455033645004e-03 ) ( 1.70113622804125e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 24 1.50626713340646e+01 0.00000000000000e+00 ( 1.50626713340647e+01 , 9.99843158592016e-01 , 1.70395625507908e-02 , -1.43866916456290e-04 , -4.82605709972753e-03 ) ( 1.46866433296765e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 26 1.56168085965049e+01 0.00000000000000e+00 ( 1.56168085965048e+01 , 9.99321288192724e-01 , 3.53760784411667e-02 , -2.78427047992838e-04 , -1.02673520119492e-02 ) ( 1.19159570174760e+03 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 28 1.62291266298068e+01 0.00000000000000e+00 ( 1.62291266298068e+01 , 9.98133542942867e-01 , 5.85622743061378e-02 , -4.51475701577845e-04 , -1.73114600800356e-02 ) ( 8.85436685096600e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 30 1.68643388381563e+01 0.00000000000000e+00 ( 1.68643388381563e+01 , 9.96054934943978e-01 , 8.49744253292276e-02 , -6.83720355648297e-04 , -2.55625925952464e-02 ) ( 5.67830580921850e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 32 1.74846635628575e+01 0.00000000000000e+00 ( 1.74846635628575e+01 , 9.92972839557288e-01 , 1.13139164123728e-01 , -9.51259111211365e-04 , -3.46924278340861e-02 ) ( 2.57668218571251e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 34 1.80530624332059e+01 0.00000000000000e+00 ( 1.80530624332059e+01 , 9.88977962066854e-01 , 1.41311479837272e-01 , -1.14108784183723e-03 , -4.41854515743639e-02 ) ( -2.65312166029492e+01 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 36 1.85372200961765e+01 0.00000000000000e+00 ( 1.85372200961765e+01 , 9.84381327967116e-01 , 1.67770992125046e-01 , -1.20902908935363e-03 , -5.33369815394102e-02 ) ( -2.68610048088250e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 38 1.89124918771856e+01 0.00000000000000e+00 ( 1.89124918771856e+01 , 9.79545563657221e-01 , 1.91522263357025e-01 , -1.22366955206212e-03 , -6.17107283289307e-02 ) ( -4.56245938592801e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 40 1.91635808809730e+01 0.00000000000000e+00 ( 1.91635808809730e+01 , 9.74600371909626e-01 , 2.12939348547346e-01 , -1.24954463323041e-03 , -6.93497480317004e-02 ) ( -5.81790440486500e+02 , 0.00000000000000e+00 , 1.00000000000000e+05 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/namd/tests/library/007_scripted_cv_biases/namd-version.txt b/namd/tests/library/007_scripted_cv_biases/namd-version.txt index 157cac038..3851f0163 100644 --- a/namd/tests/library/007_scripted_cv_biases/namd-version.txt +++ b/namd/tests/library/007_scripted_cv_biases/namd-version.txt @@ -1,3 +1,5 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2016-11-28-namd-2-12. +colvars: Using NAMD interface, version 2016-11-23. + +Wall-compatible restart information added later. diff --git a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out index 6a9e4c603..bc3b30e0e 100644 --- a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out +++ b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "dmat" @@ -57,27 +55,27 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1_2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 2 atoms requested: total mass = 24.022, total charge = -0.03. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_9_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 2 atoms requested: total mass = 24.022, total charge = 0.14. @@ -114,7 +112,6 @@ colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = off [default] colvars: # outputCenters = on colvars: # forceConstant = 1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "dmat" will be rescaled to 25 according to the specified width (0.2). colvars: ---------------------------------------------------------------------- @@ -125,31 +122,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - distancePairs colvar component: -colvars: Shen2015 https://doi.org/10.1371/journal.pcbi.1004368 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "dmat":0/0. 2 atoms: total mass = 24.022, total charge = -0.03. colvars: Re-initialized atom group for variable "dmat":0/1. 2 atoms: total mass = 24.022, total charge = 0.14. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (4 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "dmat":0/0. 2 atoms: total mass = 24.022, total charge = -0.03. colvars: Re-initialized atom group for variable "dmat":0/1. 2 atoms: total mass = 24.022, total charge = 0.14. colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj index 82cfa8cb8..4da3a5ad0 100644 --- a/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj +++ b/namd/tests/library/008_distance_pairs/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step dmat fa_dmat x0_dmat 0 ( 1.21777809554943e+01 , 1.42467449615693e+01 , 1.04037423074584e+01 , 1.19921066122679e+01 ) ( -4.44452388735783e+00 , -6.16862403923228e+00 , -1.00935576864602e+01 , 1.97334693301965e-01 ) ( 1.20000000000000e+01 , 1.40000000000000e+01 , 1.00000000000000e+01 , 1.20000000000000e+01 ) - 1 ( 1.21756207147491e+01 , 1.42470238788079e+01 , 1.04051155961944e+01 , 1.19946270847732e+01 ) ( -4.56551786872810e+00 , -6.40059697019808e+00 , -1.02528899048608e+01 , -4.06771193291355e-02 ) ( 1.19930000000000e+01 , 1.39910000000000e+01 , 9.99500000000000e+00 , 1.19930000000000e+01 ) - 2 ( 1.21730460027225e+01 , 1.42474017558768e+01 , 1.04061807237121e+01 , 1.19973140354256e+01 ) ( -4.67615006806166e+00 , -6.63504389691996e+00 , -1.04045180928018e+01 , -2.82850885640329e-01 ) ( 1.19860000000000e+01 , 1.39820000000000e+01 , 9.99000000000000e+00 , 1.19860000000000e+01 ) - 3 ( 1.21706185978867e+01 , 1.42476454576843e+01 , 1.04071659086200e+01 , 1.19998189022153e+01 ) ( -4.79046494716631e+00 , -6.86613644210809e+00 , -1.05541477154994e+01 , -5.20472555383211e-01 ) ( 1.19790000000000e+01 , 1.39730000000000e+01 , 9.98500000000000e+00 , 1.19790000000000e+01 ) - 4 ( 1.21683952007753e+01 , 1.42481001273688e+01 , 1.04075924776308e+01 , 1.20018588027655e+01 ) ( -4.90988001938302e+00 , -7.10250318422005e+00 , -1.06898119407688e+01 , -7.46470069137661e-01 ) ( 1.19720000000000e+01 , 1.39640000000000e+01 , 9.98000000000000e+00 , 1.19720000000000e+01 ) - 5 ( 1.21663636501510e+01 , 1.42484947491514e+01 , 1.04077166779264e+01 , 1.20033662039908e+01 ) ( -5.03409125377492e+00 , -7.33736872878623e+00 , -1.08179169481593e+01 , -9.59155099770514e-01 ) ( 1.19650000000000e+01 , 1.39550000000000e+01 , 9.97500000000000e+00 , 1.19650000000000e+01 ) - 6 ( 1.21637914428202e+01 , 1.42488413632141e+01 , 1.04074400269771e+01 , 1.20048328024046e+01 ) ( -5.14478607050619e+00 , -7.57103408035369e+00 , -1.09360006744287e+01 , -1.17082006011526e+00 ) ( 1.19580000000000e+01 , 1.39460000000000e+01 , 9.97000000000000e+00 , 1.19580000000000e+01 ) - 7 ( 1.21606504826560e+01 , 1.42491108211546e+01 , 1.04064186711875e+01 , 1.20059438853592e+01 ) ( -5.24126206639965e+00 , -7.80277052886533e+00 , -1.10354667796874e+01 , -1.37359713397900e+00 ) ( 1.19510000000000e+01 , 1.39370000000000e+01 , 9.96500000000000e+00 , 1.19510000000000e+01 ) - 8 ( 1.21578350901329e+01 , 1.42493400866675e+01 , 1.04052750916551e+01 , 1.20066641446701e+01 ) ( -5.34587725332165e+00 , -8.03350216668708e+00 , -1.11318772913779e+01 , -1.56660361675320e+00 ) ( 1.19440000000000e+01 , 1.39280000000000e+01 , 9.96000000000000e+00 , 1.19440000000000e+01 ) - 9 ( 1.21551529536114e+01 , 1.42495154307442e+01 , 1.04038460769366e+01 , 1.20069492651864e+01 ) ( -5.45382384028512e+00 , -8.26288576860619e+00 , -1.12211519234160e+01 , -1.74873162966009e+00 ) ( 1.19370000000000e+01 , 1.39190000000000e+01 , 9.95500000000000e+00 , 1.19370000000000e+01 ) - 10 ( 1.21523782650640e+01 , 1.42496785499675e+01 , 1.04020777830207e+01 , 1.20068009867444e+01 ) ( -5.55945662659898e+00 , -8.49196374918688e+00 , -1.13019445755174e+01 , -1.92002466861112e+00 ) ( 1.19300000000000e+01 , 1.39100000000000e+01 , 9.95000000000000e+00 , 1.19300000000000e+01 ) + 1 ( 1.21756207147491e+01 , 1.42470238788079e+01 , 1.04051155961944e+01 , 1.19946270847732e+01 ) ( -4.56551786872841e+00 , -6.40059697019852e+00 , -1.02528899048611e+01 , -4.06771193293132e-02 ) ( 1.19930000000000e+01 , 1.39910000000000e+01 , 9.99500000000000e+00 , 1.19930000000000e+01 ) + 2 ( 1.21730460027225e+01 , 1.42474017558769e+01 , 1.04061807237121e+01 , 1.19973140354256e+01 ) ( -4.67615006806308e+00 , -6.63504389692182e+00 , -1.04045180928033e+01 , -2.82850885641173e-01 ) ( 1.19860000000000e+01 , 1.39820000000000e+01 , 9.99000000000000e+00 , 1.19860000000000e+01 ) + 3 ( 1.21706185978868e+01 , 1.42476454576845e+01 , 1.04071659086201e+01 , 1.19998189022154e+01 ) ( -4.79046494716990e+00 , -6.86613644211285e+00 , -1.05541477155027e+01 , -5.20472555385387e-01 ) ( 1.19790000000000e+01 , 1.39730000000000e+01 , 9.98500000000000e+00 , 1.19790000000000e+01 ) + 4 ( 1.21683952007756e+01 , 1.42481001273692e+01 , 1.04075924776310e+01 , 1.20018588027657e+01 ) ( -4.90988001939003e+00 , -7.10250318422965e+00 , -1.06898119407748e+01 , -7.46470069142058e-01 ) ( 1.19720000000000e+01 , 1.39640000000000e+01 , 9.98000000000000e+00 , 1.19720000000000e+01 ) + 5 ( 1.21663636501515e+01 , 1.42484947491521e+01 , 1.04077166779268e+01 , 1.20033662039911e+01 ) ( -5.03409125378686e+00 , -7.33736872880351e+00 , -1.08179169481691e+01 , -9.59155099778552e-01 ) ( 1.19650000000000e+01 , 1.39550000000000e+01 , 9.97500000000000e+00 , 1.19650000000000e+01 ) + 6 ( 1.21637914428210e+01 , 1.42488413632153e+01 , 1.04074400269777e+01 , 1.20048328024051e+01 ) ( -5.14478607052502e+00 , -7.57103408038215e+00 , -1.09360006744432e+01 , -1.17082006012863e+00 ) ( 1.19580000000000e+01 , 1.39460000000000e+01 , 9.97000000000000e+00 , 1.19580000000000e+01 ) + 7 ( 1.21606504826571e+01 , 1.42491108211564e+01 , 1.04064186711883e+01 , 1.20059438853600e+01 ) ( -5.24126206642750e+00 , -7.80277052890939e+00 , -1.10354667797074e+01 , -1.37359713399947e+00 ) ( 1.19510000000000e+01 , 1.39370000000000e+01 , 9.96499999999999e+00 , 1.19510000000000e+01 ) + 8 ( 1.21578350901344e+01 , 1.42493400866701e+01 , 1.04052750916562e+01 , 1.20066641446713e+01 ) ( -5.34587725336086e+00 , -8.03350216675169e+00 , -1.11318772914041e+01 , -1.56660361678274e+00 ) ( 1.19440000000000e+01 , 1.39280000000000e+01 , 9.95999999999999e+00 , 1.19440000000000e+01 ) + 9 ( 1.21551529536135e+01 , 1.42495154307479e+01 , 1.04038460769379e+01 , 1.20069492651880e+01 ) ( -5.45382384033828e+00 , -8.26288576869678e+00 , -1.12211519234485e+01 , -1.74873162970037e+00 ) ( 1.19370000000000e+01 , 1.39190000000000e+01 , 9.95499999999999e+00 , 1.19370000000000e+01 ) + 10 ( 1.21523782650667e+01 , 1.42496785499723e+01 , 1.04020777830222e+01 , 1.20068009867465e+01 ) ( -5.55945662666826e+00 , -8.49196374930874e+00 , -1.13019445755558e+01 , -1.92002466866330e+00 ) ( 1.19300000000000e+01 , 1.39100000000000e+01 , 9.94999999999999e+00 , 1.19300000000000e+01 ) diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out index 157b9cded..49ea4044e 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -27,28 +25,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -109,30 +107,14 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped index 56cddbb67..d0176330c 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 1.42698565162752e+01 + x 1.42698565162903e+01 } metadynamics { @@ -43,9 +43,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 8.33855405317537e-07 - 3.00574542330873e-04 8.54334028864708e-03 1.91497791865179e-02 - 3.38510199591916e-03 4.71875402354643e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 8.33855405052094e-07 + 3.00574542266188e-04 8.54334028777445e-03 1.91497791869240e-02 + 3.38510199644364e-03 4.71875402495671e-05 0.00000000000000e+00 0.00000000000000e+00 hills_energy_gradients grid_parameters { @@ -77,9 +77,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 2.98417493776893e-05 - 6.93917949849616e-03 8.87295997392777e-02 -4.43203926802213e-02 - -5.08263278082148e-02 -1.30782612378422e-03 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 2.98417493685997e-05 + 6.93917949716513e-03 8.87295997352626e-02 -4.43203926688531e-02 + -5.08263278137392e-02 -1.30782612413995e-03 0.00000000000000e+00 0.00000000000000e+00 } diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj index eabe053dd..ce3224f94 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step d 0 1.42467449615693e+01 1 1.42470955327846e+01 - 2 1.42476939547290e+01 - 3 1.42483110732973e+01 - 4 1.42492943585134e+01 - 5 1.42503736285743e+01 - 6 1.42515602222322e+01 - 7 1.42528228624278e+01 - 8 1.42541950327196e+01 - 9 1.42556585606043e+01 - 10 1.42572498626143e+01 - 11 1.42590470996029e+01 - 12 1.42605989324670e+01 - 13 1.42621615963588e+01 - 14 1.42637368066246e+01 - 15 1.42651402747104e+01 - 16 1.42662547203247e+01 - 17 1.42670733056670e+01 - 18 1.42680933124105e+01 - 19 1.42689260104905e+01 - 20 1.42698565162752e+01 + 2 1.42476939547291e+01 + 3 1.42483110732975e+01 + 4 1.42492943585138e+01 + 5 1.42503736285750e+01 + 6 1.42515602222333e+01 + 7 1.42528228624295e+01 + 8 1.42541950327222e+01 + 9 1.42556585606080e+01 + 10 1.42572498626192e+01 + 11 1.42590470996093e+01 + 12 1.42605989324750e+01 + 13 1.42621615963684e+01 + 14 1.42637368066359e+01 + 15 1.42651402747233e+01 + 16 1.42662547203391e+01 + 17 1.42670733056824e+01 + 18 1.42680933124264e+01 + 19 1.42689260105063e+01 + 20 1.42698565162903e+01 diff --git a/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf b/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf index 7af5ed5c9..f07621e5c 100644 --- a/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf +++ b/namd/tests/library/009_mtd_expand/AutoDiff/test.pmf @@ -1,79 +1,79 @@ # 1 # 0.00000000000000e+00 2.00000000000000e-01 76 0 - 1.00000000000000e-01 1.91497791865179e-02 - 3.00000000000000e-01 1.91497791865179e-02 - 5.00000000000000e-01 1.91497791865179e-02 - 7.00000000000000e-01 1.91497791865179e-02 - 9.00000000000000e-01 1.91497791865179e-02 - 1.10000000000000e+00 1.91497791865179e-02 - 1.30000000000000e+00 1.91497791865179e-02 - 1.50000000000000e+00 1.91497791865179e-02 - 1.70000000000000e+00 1.91497791865179e-02 - 1.90000000000000e+00 1.91497791865179e-02 - 2.10000000000000e+00 1.91497791865179e-02 - 2.30000000000000e+00 1.91497791865179e-02 - 2.50000000000000e+00 1.91497791865179e-02 - 2.70000000000000e+00 1.91497791865179e-02 - 2.90000000000000e+00 1.91497791865179e-02 - 3.10000000000000e+00 1.91497791865179e-02 - 3.30000000000000e+00 1.91497791865179e-02 - 3.50000000000000e+00 1.91497791865179e-02 - 3.70000000000000e+00 1.91497791865179e-02 - 3.90000000000000e+00 1.91497791865179e-02 - 4.10000000000000e+00 1.91497791865179e-02 - 4.30000000000000e+00 1.91497791865179e-02 - 4.50000000000000e+00 1.91497791865179e-02 - 4.70000000000000e+00 1.91497791865179e-02 - 4.90000000000000e+00 1.91497791865179e-02 - 5.10000000000000e+00 1.91497791865179e-02 - 5.30000000000000e+00 1.91497791865179e-02 - 5.50000000000000e+00 1.91497791865179e-02 - 5.70000000000000e+00 1.91497791865179e-02 - 5.90000000000000e+00 1.91497791865179e-02 - 6.10000000000000e+00 1.91497791865179e-02 - 6.30000000000000e+00 1.91497791865179e-02 - 6.50000000000000e+00 1.91497791865179e-02 - 6.70000000000000e+00 1.91497791865179e-02 - 6.90000000000000e+00 1.91497791865179e-02 - 7.10000000000000e+00 1.91497791865179e-02 - 7.30000000000000e+00 1.91497791865179e-02 - 7.50000000000000e+00 1.91497791865179e-02 - 7.70000000000000e+00 1.91497791865179e-02 - 7.90000000000000e+00 1.91497791865179e-02 - 8.10000000000000e+00 1.91497791865179e-02 - 8.30000000000000e+00 1.91497791865179e-02 - 8.50000000000000e+00 1.91497791865179e-02 - 8.70000000000000e+00 1.91497791865179e-02 - 8.90000000000000e+00 1.91497791865179e-02 - 9.10000000000000e+00 1.91497791865179e-02 - 9.30000000000000e+00 1.91497791865179e-02 - 9.50000000000000e+00 1.91497791865179e-02 - 9.70000000000000e+00 1.91497791865179e-02 - 9.90000000000000e+00 1.91497791865179e-02 - 1.01000000000000e+01 1.91497791865179e-02 - 1.03000000000000e+01 1.91497791865179e-02 - 1.05000000000000e+01 1.91497791865179e-02 - 1.07000000000000e+01 1.91497791865179e-02 - 1.09000000000000e+01 1.91497791865179e-02 - 1.11000000000000e+01 1.91497791865179e-02 - 1.13000000000000e+01 1.91497791865179e-02 - 1.15000000000000e+01 1.91497791865179e-02 - 1.17000000000000e+01 1.91497791865179e-02 - 1.19000000000000e+01 1.91497791865179e-02 - 1.21000000000000e+01 1.91497791865179e-02 - 1.23000000000000e+01 1.91497791865179e-02 - 1.25000000000000e+01 1.91497791865179e-02 - 1.27000000000000e+01 1.91497791865179e-02 - 1.29000000000000e+01 1.91497791865179e-02 - 1.31000000000000e+01 1.91497791865179e-02 - 1.33000000000000e+01 1.91497791865179e-02 - 1.35000000000000e+01 1.91497791865179e-02 - 1.37000000000000e+01 1.91489453311125e-02 - 1.39000000000000e+01 1.88492046441870e-02 - 1.41000000000000e+01 1.06064388978708e-02 + 1.00000000000000e-01 1.91497791869240e-02 + 3.00000000000000e-01 1.91497791869240e-02 + 5.00000000000000e-01 1.91497791869240e-02 + 7.00000000000000e-01 1.91497791869240e-02 + 9.00000000000000e-01 1.91497791869240e-02 + 1.10000000000000e+00 1.91497791869240e-02 + 1.30000000000000e+00 1.91497791869240e-02 + 1.50000000000000e+00 1.91497791869240e-02 + 1.70000000000000e+00 1.91497791869240e-02 + 1.90000000000000e+00 1.91497791869240e-02 + 2.10000000000000e+00 1.91497791869240e-02 + 2.30000000000000e+00 1.91497791869240e-02 + 2.50000000000000e+00 1.91497791869240e-02 + 2.70000000000000e+00 1.91497791869240e-02 + 2.90000000000000e+00 1.91497791869240e-02 + 3.10000000000000e+00 1.91497791869240e-02 + 3.30000000000000e+00 1.91497791869240e-02 + 3.50000000000000e+00 1.91497791869240e-02 + 3.70000000000000e+00 1.91497791869240e-02 + 3.90000000000000e+00 1.91497791869240e-02 + 4.10000000000000e+00 1.91497791869240e-02 + 4.30000000000000e+00 1.91497791869240e-02 + 4.50000000000000e+00 1.91497791869240e-02 + 4.70000000000000e+00 1.91497791869240e-02 + 4.90000000000000e+00 1.91497791869240e-02 + 5.10000000000000e+00 1.91497791869240e-02 + 5.30000000000000e+00 1.91497791869240e-02 + 5.50000000000000e+00 1.91497791869240e-02 + 5.70000000000000e+00 1.91497791869240e-02 + 5.90000000000000e+00 1.91497791869240e-02 + 6.10000000000000e+00 1.91497791869240e-02 + 6.30000000000000e+00 1.91497791869240e-02 + 6.50000000000000e+00 1.91497791869240e-02 + 6.70000000000000e+00 1.91497791869240e-02 + 6.90000000000000e+00 1.91497791869240e-02 + 7.10000000000000e+00 1.91497791869240e-02 + 7.30000000000000e+00 1.91497791869240e-02 + 7.50000000000000e+00 1.91497791869240e-02 + 7.70000000000000e+00 1.91497791869240e-02 + 7.90000000000000e+00 1.91497791869240e-02 + 8.10000000000000e+00 1.91497791869240e-02 + 8.30000000000000e+00 1.91497791869240e-02 + 8.50000000000000e+00 1.91497791869240e-02 + 8.70000000000000e+00 1.91497791869240e-02 + 8.90000000000000e+00 1.91497791869240e-02 + 9.10000000000000e+00 1.91497791869240e-02 + 9.30000000000000e+00 1.91497791869240e-02 + 9.50000000000000e+00 1.91497791869240e-02 + 9.70000000000000e+00 1.91497791869240e-02 + 9.90000000000000e+00 1.91497791869240e-02 + 1.01000000000000e+01 1.91497791869240e-02 + 1.03000000000000e+01 1.91497791869240e-02 + 1.05000000000000e+01 1.91497791869240e-02 + 1.07000000000000e+01 1.91497791869240e-02 + 1.09000000000000e+01 1.91497791869240e-02 + 1.11000000000000e+01 1.91497791869240e-02 + 1.13000000000000e+01 1.91497791869240e-02 + 1.15000000000000e+01 1.91497791869240e-02 + 1.17000000000000e+01 1.91497791869240e-02 + 1.19000000000000e+01 1.91497791869240e-02 + 1.21000000000000e+01 1.91497791869240e-02 + 1.23000000000000e+01 1.91497791869240e-02 + 1.25000000000000e+01 1.91497791869240e-02 + 1.27000000000000e+01 1.91497791869240e-02 + 1.29000000000000e+01 1.91497791869240e-02 + 1.31000000000000e+01 1.91497791869240e-02 + 1.33000000000000e+01 1.91497791869240e-02 + 1.35000000000000e+01 1.91497791869240e-02 + 1.37000000000000e+01 1.91489453315190e-02 + 1.39000000000000e+01 1.88492046446579e-02 + 1.41000000000000e+01 1.06064388991496e-02 1.43000000000000e+01 -0.00000000000000e+00 - 1.45000000000000e+01 1.57646771905987e-02 - 1.47000000000000e+01 1.91025916462824e-02 - 1.49000000000000e+01 1.91497791865179e-02 - 1.51000000000000e+01 1.91497791865179e-02 + 1.45000000000000e+01 1.57646771904804e-02 + 1.47000000000000e+01 1.91025916466745e-02 + 1.49000000000000e+01 1.91497791869240e-02 + 1.51000000000000e+01 1.91497791869240e-02 diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out index 51c6085f0..791e3e5d1 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "angle" @@ -57,42 +55,42 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] @@ -128,56 +126,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_5" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_6" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_7" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -220,6 +218,11 @@ colvars: # historyFreq = 5 colvars: # shared = off [default] colvars: # maxForce = [default] colvars: # integrate = on [default] +colvars: # pABFintegrateFreq = 0 [default] +colvars: # integrateInitMaxIterations = 10000 [default] +colvars: # integrateInitTol = 1e-06 [default] +colvars: # integrateMaxIterations = 100 [default] +colvars: # integrateTol = 0.0001 [default] colvars: Finished ABF setup. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. @@ -229,29 +232,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (7 scalable groups, 7 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - angle colvar component: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - Poisson integration of 2D/3D free energy surfaces: -colvars: Henin2021 https://doi.org/10.1021/acs.jctc.1c00593 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "angle":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "angle":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "angle":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. @@ -260,11 +240,11 @@ colvars: Re-initialized atom group for variable "dihedral":0/1. 1 atoms: total m colvars: Re-initialized atom group for variable "dihedral":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "dihedral":0/3. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (7 scalable groups, 7 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "angle":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "angle":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "angle":0/2. 1 atoms: total mass = 12.011, total charge = 0.07. diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped index cf8ab20fa..8e53a7a8c 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name angle - x 9.71572414999404e+01 + x 9.71572414998837e+01 } colvar { name dihedral - x 4.76248133822394e+01 + x 4.76248133821808e+01 } abf { @@ -256,8 +256,8 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 3.86055080717640e-01 -1.47156688763172e+00 - 1.21510007787258e-01 -3.46687391789233e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 3.86055079861384e-01 -1.47156688632534e+00 + 1.21510007293019e-01 -3.46687391825760e-01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj index 7fe21a71e..dfd38fd88 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step angle ft_angle fa_angle dihedral ft_dihedral fa_dihedral 0 9.68498695196423e+01 0.00000000000000e+00 0.00000000000000e+00 4.86056572577460e+01 0.00000000000000e+00 0.00000000000000e+00 - 1 9.68581311788645e+01 -1.84451708831746e-02 1.84451708831746e-02 4.84876896364246e+01 -2.26204233738360e-02 2.26204233738360e-02 - 2 9.68825903830917e+01 -1.75928069494324e-02 2.72415743578908e-02 4.83727459141996e+01 1.09239386526311e-01 -3.19992698893197e-02 - 3 9.69105533161851e+01 -3.36465334818358e-02 3.84570855185028e-02 4.82565768693385e+01 1.87476845825581e-01 -9.44915518311800e-02 - 4 9.69406101257451e+01 -8.90986866663562e-02 6.07317571850918e-02 4.81501282214520e+01 2.91829502654487e-01 -1.67448927494802e-01 - 5 9.69674902853217e+01 -1.44712759388158e-01 8.96743090627233e-02 4.80499450162547e+01 4.19420612850755e-01 -2.51333050064953e-01 - 6 9.69953149267565e+01 -1.91014192347208e-01 0.00000000000000e+00 4.79483470270909e+01 5.72126050345682e-01 0.00000000000000e+00 - 7 9.70261917919329e+01 -3.39026775359731e-01 3.39026775359731e-01 4.78551169384050e+01 1.09938746010351e+00 -1.09938746010351e+00 - 8 9.70529963144370e+01 -4.61821781835164e-02 3.62117864451490e-01 4.77722438820884e+01 2.55842716309053e-01 -1.22730881825804e+00 - 9 9.70984141114596e+01 -2.94041075882280e-02 3.71919233647566e-01 4.76919701530931e+01 3.67640478945815e-01 -1.34985564457331e+00 - 10 9.71572414999404e+01 -5.65433882802956e-02 3.86055080717640e-01 4.76248133822394e+01 4.86844972233643e-01 -1.47156688763172e+00 + 1 9.68581311788660e+01 -1.84451705170512e-02 1.84451705170512e-02 4.84876896364254e+01 -2.26204229896581e-02 2.26204229896581e-02 + 2 9.68825903830946e+01 -1.75928069356493e-02 2.72415739848758e-02 4.83727459141994e+01 1.09239386473433e-01 -3.19992702470586e-02 + 3 9.69105533161889e+01 -3.36465334276460e-02 3.84570851274245e-02 4.82565768693354e+01 1.87476845673922e-01 -9.44915521383659e-02 + 4 9.69406101257489e+01 -8.90986865550939e-02 6.07317567661980e-02 4.81501282214438e+01 2.91829502364863e-01 -1.67448927729582e-01 + 5 9.69674902853240e+01 -1.44712759211668e-01 8.96743086085316e-02 4.80499450162389e+01 4.19420612395337e-01 -2.51333050208649e-01 + 6 9.69953149267550e+01 -1.91014192106924e-01 0.00000000000000e+00 4.79483470270649e+01 5.72126049702663e-01 0.00000000000000e+00 + 7 9.70261917919283e+01 -3.39026774573669e-01 3.39026774573669e-01 4.78551169383663e+01 1.09938745929832e+00 -1.09938745929832e+00 + 8 9.70529963144229e+01 -4.61821781161425e-02 3.62117863631741e-01 4.77722438820399e+01 2.55842715985027e-01 -1.22730881729084e+00 + 9 9.70984141114285e+01 -2.94041075150722e-02 3.71919232803431e-01 4.76919701530380e+01 3.67640478440557e-01 -1.34985564343769e+00 + 10 9.71572414998837e+01 -5.65433882318097e-02 3.86055079861384e-01 4.76248133821808e+01 4.86844971550587e-01 -1.47156688632534e+00 diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad b/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad index 81d482591..02118c831 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.hist.grad @@ -506,7 +506,7 @@ 9.90000000000000e+01 3.30000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 3.90000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 4.50000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 - 9.90000000000000e+01 5.10000000000000e+01 8.96743090627233e-02 -2.51333050064953e-01 + 9.90000000000000e+01 5.10000000000000e+01 8.96743086085316e-02 -2.51333050208651e-01 9.90000000000000e+01 5.70000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 6.30000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 6.90000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 @@ -1439,8 +1439,8 @@ 9.90000000000000e+01 2.70000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 3.30000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 3.90000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 - 9.90000000000000e+01 4.50000000000000e+01 3.86055080717640e-01 -1.47156688763172e+00 - 9.90000000000000e+01 5.10000000000000e+01 1.21510007787258e-01 -3.46687391789233e-01 + 9.90000000000000e+01 4.50000000000000e+01 3.86055079861383e-01 -1.47156688632533e+00 + 9.90000000000000e+01 5.10000000000000e+01 1.21510007293019e-01 -3.46687391825762e-01 9.90000000000000e+01 5.70000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 6.30000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 9.90000000000000e+01 6.90000000000000e+01 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/010_angle_dihedral/AutoDiff/test.pmf b/namd/tests/library/010_angle_dihedral/AutoDiff/test.pmf index 2e2ed113b..7c4062cb5 100644 --- a/namd/tests/library/010_angle_dihedral/AutoDiff/test.pmf +++ b/namd/tests/library/010_angle_dihedral/AutoDiff/test.pmf @@ -2,994 +2,994 @@ # -3.00000000000000e+00 6.00000000000000e+00 31 0 # -3.00000000000000e+00 6.00000000000000e+00 31 0 - 0.00000000000000e+00 0.00000000000000e+00 1.51009815876327e+00 - 0.00000000000000e+00 6.00000000000000e+00 1.50899655857926e+00 - 0.00000000000000e+00 1.20000000000000e+01 1.50573250552505e+00 - 0.00000000000000e+00 1.80000000000000e+01 1.50042663768510e+00 - 0.00000000000000e+00 2.40000000000000e+01 1.49327637922519e+00 - 0.00000000000000e+00 3.00000000000000e+01 1.48454794014076e+00 - 0.00000000000000e+00 3.60000000000000e+01 1.47456435406080e+00 - 0.00000000000000e+00 4.20000000000000e+01 1.46368875273805e+00 - 0.00000000000000e+00 4.80000000000000e+01 1.45230209151690e+00 - 0.00000000000000e+00 5.40000000000000e+01 1.44077854855034e+00 - 0.00000000000000e+00 6.00000000000000e+01 1.42946157001708e+00 - 0.00000000000000e+00 6.60000000000000e+01 1.41864385459838e+00 - 0.00000000000000e+00 7.20000000000000e+01 1.40855356791195e+00 - 0.00000000000000e+00 7.80000000000000e+01 1.39934925462895e+00 - 0.00000000000000e+00 8.40000000000000e+01 1.39112230499060e+00 - 0.00000000000000e+00 9.00000000000000e+01 1.38390435486459e+00 - 0.00000000000000e+00 9.60000000000000e+01 1.37767823773271e+00 - 0.00000000000000e+00 1.02000000000000e+02 1.37239071363859e+00 - 0.00000000000000e+00 1.08000000000000e+02 1.36796467001035e+00 - 0.00000000000000e+00 1.14000000000000e+02 1.36430923187549e+00 - 0.00000000000000e+00 1.20000000000000e+02 1.36132859440307e+00 - 0.00000000000000e+00 1.26000000000000e+02 1.35892795858837e+00 - 0.00000000000000e+00 1.32000000000000e+02 1.35701801187453e+00 - 0.00000000000000e+00 1.38000000000000e+02 1.35551761039734e+00 - 0.00000000000000e+00 1.44000000000000e+02 1.35435559814837e+00 - 0.00000000000000e+00 1.50000000000000e+02 1.35347095168579e+00 - 0.00000000000000e+00 1.56000000000000e+02 1.35281330593119e+00 - 0.00000000000000e+00 1.62000000000000e+02 1.35234234180210e+00 - 0.00000000000000e+00 1.68000000000000e+02 1.35202738996321e+00 - 0.00000000000000e+00 1.74000000000000e+02 1.35184684773466e+00 - 0.00000000000000e+00 1.80000000000000e+02 1.35178806116327e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.51009815636836e+00 + 0.00000000000000e+00 6.00000000000000e+00 1.50899655618504e+00 + 0.00000000000000e+00 1.20000000000000e+01 1.50573250313282e+00 + 0.00000000000000e+00 1.80000000000000e+01 1.50042663529605e+00 + 0.00000000000000e+00 2.40000000000000e+01 1.49327637684030e+00 + 0.00000000000000e+00 3.00000000000000e+01 1.48454793776074e+00 + 0.00000000000000e+00 3.60000000000000e+01 1.47456435168608e+00 + 0.00000000000000e+00 4.20000000000000e+01 1.46368875036872e+00 + 0.00000000000000e+00 4.80000000000000e+01 1.45230208915275e+00 + 0.00000000000000e+00 5.40000000000000e+01 1.44077854619086e+00 + 0.00000000000000e+00 6.00000000000000e+01 1.42946156766158e+00 + 0.00000000000000e+00 6.60000000000000e+01 1.41864385224600e+00 + 0.00000000000000e+00 7.20000000000000e+01 1.40855356556177e+00 + 0.00000000000000e+00 7.80000000000000e+01 1.39934925228003e+00 + 0.00000000000000e+00 8.40000000000000e+01 1.39112230264205e+00 + 0.00000000000000e+00 9.00000000000000e+01 1.38390435251564e+00 + 0.00000000000000e+00 9.60000000000000e+01 1.37767823538270e+00 + 0.00000000000000e+00 1.02000000000000e+02 1.37239071128698e+00 + 0.00000000000000e+00 1.08000000000000e+02 1.36796466765676e+00 + 0.00000000000000e+00 1.14000000000000e+02 1.36430922951965e+00 + 0.00000000000000e+00 1.20000000000000e+02 1.36132859204485e+00 + 0.00000000000000e+00 1.26000000000000e+02 1.35892795622774e+00 + 0.00000000000000e+00 1.32000000000000e+02 1.35701800951155e+00 + 0.00000000000000e+00 1.38000000000000e+02 1.35551760803214e+00 + 0.00000000000000e+00 1.44000000000000e+02 1.35435559578114e+00 + 0.00000000000000e+00 1.50000000000000e+02 1.35347094931678e+00 + 0.00000000000000e+00 1.56000000000000e+02 1.35281330356067e+00 + 0.00000000000000e+00 1.62000000000000e+02 1.35234233943039e+00 + 0.00000000000000e+00 1.68000000000000e+02 1.35202738759063e+00 + 0.00000000000000e+00 1.74000000000000e+02 1.35184684536156e+00 + 0.00000000000000e+00 1.80000000000000e+02 1.35178805878998e+00 - 6.00000000000000e+00 0.00000000000000e+00 1.51119937084531e+00 - 6.00000000000000e+00 6.00000000000000e+00 1.51007748368520e+00 - 6.00000000000000e+00 1.20000000000000e+01 1.50675316060219e+00 - 6.00000000000000e+00 1.80000000000000e+01 1.50134901773917e+00 - 6.00000000000000e+00 2.40000000000000e+01 1.49406574169698e+00 - 6.00000000000000e+00 3.00000000000000e+01 1.48517563873370e+00 - 6.00000000000000e+00 3.60000000000000e+01 1.47501056537712e+00 - 6.00000000000000e+00 4.20000000000000e+01 1.46394448109528e+00 - 6.00000000000000e+00 4.80000000000000e+01 1.45237066937222e+00 - 6.00000000000000e+00 5.40000000000000e+01 1.44067542824489e+00 - 6.00000000000000e+00 6.00000000000000e+01 1.42921217918408e+00 - 6.00000000000000e+00 6.60000000000000e+01 1.41828012223120e+00 - 6.00000000000000e+00 7.20000000000000e+01 1.40811032873877e+00 - 6.00000000000000e+00 7.80000000000000e+01 1.39886044299830e+00 - 6.00000000000000e+00 8.40000000000000e+01 1.39061783763075e+00 - 6.00000000000000e+00 9.00000000000000e+01 1.38340846280514e+00 - 6.00000000000000e+00 9.60000000000000e+01 1.37720888665793e+00 - 6.00000000000000e+00 1.02000000000000e+02 1.37196005001064e+00 - 6.00000000000000e+00 1.08000000000000e+02 1.36757934508754e+00 - 6.00000000000000e+00 1.14000000000000e+02 1.36397196305022e+00 - 6.00000000000000e+00 1.20000000000000e+02 1.36103864684035e+00 - 6.00000000000000e+00 1.26000000000000e+02 1.35868264070495e+00 - 6.00000000000000e+00 1.32000000000000e+02 1.35681303845279e+00 - 6.00000000000000e+00 1.38000000000000e+02 1.35534827015054e+00 - 6.00000000000000e+00 1.44000000000000e+02 1.35421661085036e+00 - 6.00000000000000e+00 1.50000000000000e+02 1.35335728348555e+00 - 6.00000000000000e+00 1.56000000000000e+02 1.35271975789688e+00 - 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1.39405569373783e+00 + 1.80000000000000e+02 1.44000000000000e+02 1.39039153489000e+00 + 1.80000000000000e+02 1.50000000000000e+02 1.38745617270075e+00 + 1.80000000000000e+02 1.56000000000000e+02 1.38516474450159e+00 + 1.80000000000000e+02 1.62000000000000e+02 1.38344975278396e+00 + 1.80000000000000e+02 1.68000000000000e+02 1.38226031224452e+00 + 1.80000000000000e+02 1.74000000000000e+02 1.38156058387008e+00 + 1.80000000000000e+02 1.80000000000000e+02 1.38132948034468e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state index ceba9352b..38b541ee8 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.metadynamics1.rep1.state @@ -20,9 +20,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.53403286720768e-06 8.43235276972864e-04 - 3.21927751514002e-02 9.90603521389808e-02 2.46033419259411e-02 - 4.93589875891209e-04 4.23052788302019e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.53403289508330e-06 8.43235284919676e-04 + 3.21927752810740e-02 9.90603520983741e-02 2.46033418312340e-02 + 4.93589872784461e-04 4.23052788272303e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -45,9 +45,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 2.26292238292108e-05 8.26704499874479e-03 - 1.53420242499276e-01 -2.66708902934347e-02 -1.30444282639589e-01 - -5.10069715433551e-03 -6.37695701865853e-06 0.00000000000000e+00 + 0.00000000000000e+00 2.26292242192221e-05 8.26704506678145e-03 + 1.53420242800061e-01 -2.66708910635591e-02 -1.30444282281981e-01 + -5.10069712416846e-03 -6.37695701821339e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out index f11fa72fe..c68838faf 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep1.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -145,7 +143,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -159,7 +156,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -174,33 +170,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Multiple-walker metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep1r.colvars.state". colvars: The final output state file will be "test.rep1.colvars.state". +colvars: Opening trajectory file "test.rep1.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep1r.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped index 094d10a53..b96d93fd6 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 1.41656974969458e+01 + x 1.41656974949034e+01 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.53403286720768e-06 8.43235276972864e-04 - 3.21927751514002e-02 9.90603521389808e-02 2.46033419259411e-02 - 4.93589875891209e-04 4.23052788302019e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.53403289508330e-06 8.43235284919676e-04 + 3.21927752810740e-02 9.90603520983741e-02 2.46033418312340e-02 + 4.93589872784461e-04 4.23052788272303e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -55,9 +55,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 2.26292238292108e-05 8.26704499874479e-03 - 1.53420242499276e-01 -2.66708902934347e-02 -1.30444282639589e-01 - -5.10069715433551e-03 -6.37695701865853e-06 0.00000000000000e+00 + 0.00000000000000e+00 2.26292242192221e-05 8.26704506678145e-03 + 1.53420242800061e-01 -2.66708910635591e-02 -1.30444282281981e-01 + -5.10069712416846e-03 -6.37695701821339e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj index 5731bc76e..441edf82b 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.colvars.traj @@ -2,101 +2,101 @@ 0 1.42467449615693e+01 0.00000000000000e+00 1 1.42470955327846e+01 0.00000000000000e+00 2 1.42476657799120e+01 0.00000000000000e+00 - 3 1.42485380098359e+01 0.00000000000000e+00 - 4 1.42499968808362e+01 0.00000000000000e+00 - 5 1.42516048130991e+01 0.00000000000000e+00 - 6 1.42535349212359e+01 0.00000000000000e+00 - 7 1.42555542781170e+01 0.00000000000000e+00 - 8 1.42579210999817e+01 0.00000000000000e+00 - 9 1.42607955979351e+01 0.00000000000000e+00 - 10 1.42638739176583e+01 -1.41180095141270e-03 - 11 1.42668375588355e+01 -1.41180095141270e-03 - 12 1.42696059392625e+01 -1.41180095141270e-03 - 13 1.42727236830683e+01 -1.41180095141270e-03 - 14 1.42758764946660e+01 -1.41180095141270e-03 - 15 1.42787429047727e+01 -1.41180095141270e-03 - 16 1.42810489912705e+01 -1.41180095141270e-03 - 17 1.42825584062025e+01 -1.41180095141270e-03 - 18 1.42834947131625e+01 -1.41180095141270e-03 - 19 1.42840554431827e+01 -1.41180095141270e-03 - 20 1.42836137141448e+01 -4.81601991180831e-03 - 21 1.42824534007361e+01 -4.81601991180831e-03 - 22 1.42809048150996e+01 -4.81601991180831e-03 - 23 1.42792649819969e+01 -4.81601991180831e-03 - 24 1.42777803318197e+01 -4.81601991180831e-03 - 25 1.42752531196685e+01 -4.81601991180831e-03 - 26 1.42721001284968e+01 -4.81601991180831e-03 - 27 1.42684964153165e+01 -4.81601991180831e-03 - 28 1.42647910498589e+01 -4.81601991180831e-03 - 29 1.42606805882796e+01 -4.81601991180831e-03 - 30 1.42569926418712e+01 -5.52810721041820e-03 - 31 1.42531586691654e+01 -5.52810721041820e-03 - 32 1.42495999936203e+01 -5.52810721041820e-03 - 33 1.42462931131815e+01 -5.52810721041820e-03 - 34 1.42426029444897e+01 -5.52810721041820e-03 - 35 1.42381298876351e+01 -5.52810721041820e-03 - 36 1.42340878762643e+01 -5.52810721041820e-03 - 37 1.42306974076639e+01 -5.52810721041820e-03 - 38 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1.42012327627117e+01 2.92915634676080e-03 - 60 1.42036332173818e+01 7.60060814309682e-03 - 61 1.42058762807719e+01 7.60060814309682e-03 - 62 1.42077667923895e+01 7.60060814309682e-03 - 63 1.42098444758797e+01 7.60060814309682e-03 - 64 1.42116396739042e+01 7.60060814309682e-03 - 65 1.42136940032780e+01 7.60060814309682e-03 - 66 1.42154217558442e+01 7.60060814309682e-03 - 67 1.42168868960268e+01 7.60060814309682e-03 - 68 1.42178935094514e+01 7.60060814309682e-03 - 69 1.42184230283353e+01 7.60060814309682e-03 - 70 1.42187771926287e+01 1.07651861772312e-02 - 71 1.42193777496991e+01 1.07651861772312e-02 - 72 1.42195540781285e+01 1.07651861772312e-02 - 73 1.42196083093533e+01 1.07651861772312e-02 - 74 1.42197149208802e+01 1.07651861772312e-02 - 75 1.42202788377849e+01 1.07651861772312e-02 - 76 1.42213115704096e+01 1.07651861772312e-02 - 77 1.42222264813178e+01 1.07651861772312e-02 - 78 1.42228883735255e+01 1.07651861772312e-02 - 79 1.42232741606514e+01 1.07651861772312e-02 - 80 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1.42777803318261e+01 -4.81601991397794e-03 + 25 1.42752531196695e+01 -4.81601991397794e-03 + 26 1.42721001284912e+01 -4.81601991397794e-03 + 27 1.42684964153029e+01 -4.81601991397794e-03 + 28 1.42647910498358e+01 -4.81601991397794e-03 + 29 1.42606805882456e+01 -4.81601991397794e-03 + 30 1.42569926418246e+01 -5.52810720784699e-03 + 31 1.42531586691047e+01 -5.52810720784699e-03 + 32 1.42495999935438e+01 -5.52810720784699e-03 + 33 1.42462931130875e+01 -5.52810720784699e-03 + 34 1.42426029443764e+01 -5.52810720784699e-03 + 35 1.42381298875008e+01 -5.52810720784699e-03 + 36 1.42340878761072e+01 -5.52810720784699e-03 + 37 1.42306974074822e+01 -5.52810720784699e-03 + 38 1.42272038093346e+01 -5.52810720784699e-03 + 39 1.42243354344263e+01 -5.52810720784699e-03 + 40 1.42218646485599e+01 -2.67379444822040e-03 + 41 1.42190777077468e+01 -2.67379444822040e-03 + 42 1.42160211302678e+01 -2.67379444822040e-03 + 43 1.42124278513310e+01 -2.67379444822040e-03 + 44 1.42090572659494e+01 -2.67379444822040e-03 + 45 1.42058271938036e+01 -2.67379444822040e-03 + 46 1.42033823263127e+01 -2.67379444822040e-03 + 47 1.42003268228049e+01 -2.67379444822040e-03 + 48 1.41976446229193e+01 -2.67379444822040e-03 + 49 1.41956578972582e+01 -2.67379444822040e-03 + 50 1.41941111007313e+01 2.92915643758184e-03 + 51 1.41926279960324e+01 2.92915643758184e-03 + 52 1.41926027090037e+01 2.92915643758184e-03 + 53 1.41928452081821e+01 2.92915643758184e-03 + 54 1.41932447289925e+01 2.92915643758184e-03 + 55 1.41940166338356e+01 2.92915643758184e-03 + 56 1.41951734095904e+01 2.92915643758184e-03 + 57 1.41967411062606e+01 2.92915643758184e-03 + 58 1.41989912324301e+01 2.92915643758184e-03 + 59 1.42012327617553e+01 2.92915643758184e-03 + 60 1.42036332163974e+01 7.60060833091658e-03 + 61 1.42058762797617e+01 7.60060833091658e-03 + 62 1.42077667913556e+01 7.60060833091658e-03 + 63 1.42098444748241e+01 7.60060833091658e-03 + 64 1.42116396728290e+01 7.60060833091658e-03 + 65 1.42136940021851e+01 7.60060833091658e-03 + 66 1.42154217547355e+01 7.60060833091658e-03 + 67 1.42168868949041e+01 7.60060833091658e-03 + 68 1.42178935083162e+01 7.60060833091658e-03 + 69 1.42184230271890e+01 7.60060833091658e-03 + 70 1.42187771914724e+01 1.07651864810836e-02 + 71 1.42193777485337e+01 1.07651864810836e-02 + 72 1.42195540769546e+01 1.07651864810836e-02 + 73 1.42196083081712e+01 1.07651864810836e-02 + 74 1.42197149196897e+01 1.07651864810836e-02 + 75 1.42202788365857e+01 1.07651864810836e-02 + 76 1.42213115692008e+01 1.07651864810836e-02 + 77 1.42222264800984e+01 1.07651864810836e-02 + 78 1.42228883722939e+01 1.07651864810836e-02 + 79 1.42232741594059e+01 1.07651864810836e-02 + 80 1.42237439344237e+01 1.34302339631847e-02 + 81 1.42241333527676e+01 1.34302339631847e-02 + 82 1.42242035696691e+01 1.34302339631847e-02 + 83 1.42237365420353e+01 1.34302339631847e-02 + 84 1.42227422602652e+01 1.34302339631847e-02 + 85 1.42207685317808e+01 1.34302339631847e-02 + 86 1.42180863416851e+01 1.34302339631847e-02 + 87 1.42142852895987e+01 1.34302339631847e-02 + 88 1.42099549129055e+01 1.34302339631847e-02 + 89 1.42054325297988e+01 1.34302339631847e-02 + 90 1.42007097380791e+01 1.83891584072187e-02 + 91 1.41956149687583e+01 1.83891584072187e-02 + 92 1.41905358606444e+01 1.83891584072187e-02 + 93 1.41851130561985e+01 1.83891584072187e-02 + 94 1.41798559764745e+01 1.83891584072187e-02 + 95 1.41754225260859e+01 1.83891584072187e-02 + 96 1.41724186121957e+01 1.83891584072187e-02 + 97 1.41698989963895e+01 1.83891584072187e-02 + 98 1.41682594906300e+01 1.83891584072187e-02 + 99 1.41669592353631e+01 1.83891584072187e-02 + 100 1.41656974949034e+01 2.66708910635591e-02 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf index b2d0a8859..8e7f46287 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep1.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 9.90603521389808e-02 - 7.50000000000000e-01 9.90603521389808e-02 - 1.25000000000000e+00 9.90603521389808e-02 - 1.75000000000000e+00 9.90603521389808e-02 - 2.25000000000000e+00 9.90603521389808e-02 - 2.75000000000000e+00 9.90603521389808e-02 - 3.25000000000000e+00 9.90603521389808e-02 - 3.75000000000000e+00 9.90603521389808e-02 - 4.25000000000000e+00 9.90603521389808e-02 - 4.75000000000000e+00 9.90603521389808e-02 - 5.25000000000000e+00 9.90603521389808e-02 - 5.75000000000000e+00 9.90603521389808e-02 - 6.25000000000000e+00 9.90603521389808e-02 - 6.75000000000000e+00 9.90603521389808e-02 - 7.25000000000000e+00 9.90603521389808e-02 - 7.75000000000000e+00 9.90603521389808e-02 - 8.25000000000000e+00 9.90603521389808e-02 - 8.75000000000000e+00 9.90603521389808e-02 - 9.25000000000000e+00 9.90603521389808e-02 - 9.75000000000000e+00 9.90603521389808e-02 - 1.02500000000000e+01 9.90603521389808e-02 - 1.07500000000000e+01 9.90603521389808e-02 - 1.12500000000000e+01 9.90603521389808e-02 - 1.17500000000000e+01 9.90603521389808e-02 - 1.22500000000000e+01 9.90603521389808e-02 - 1.27500000000000e+01 9.90588181061136e-02 - 1.32500000000000e+01 9.82171168620079e-02 - 1.37500000000000e+01 6.68675769875805e-02 + 2.50000000000000e-01 9.90603520983742e-02 + 7.50000000000000e-01 9.90603520983742e-02 + 1.25000000000000e+00 9.90603520983742e-02 + 1.75000000000000e+00 9.90603520983742e-02 + 2.25000000000000e+00 9.90603520983742e-02 + 2.75000000000000e+00 9.90603520983742e-02 + 3.25000000000000e+00 9.90603520983742e-02 + 3.75000000000000e+00 9.90603520983742e-02 + 4.25000000000000e+00 9.90603520983742e-02 + 4.75000000000000e+00 9.90603520983742e-02 + 5.25000000000000e+00 9.90603520983742e-02 + 5.75000000000000e+00 9.90603520983742e-02 + 6.25000000000000e+00 9.90603520983742e-02 + 6.75000000000000e+00 9.90603520983742e-02 + 7.25000000000000e+00 9.90603520983742e-02 + 7.75000000000000e+00 9.90603520983742e-02 + 8.25000000000000e+00 9.90603520983742e-02 + 8.75000000000000e+00 9.90603520983742e-02 + 9.25000000000000e+00 9.90603520983742e-02 + 9.75000000000000e+00 9.90603520983742e-02 + 1.02500000000000e+01 9.90603520983742e-02 + 1.07500000000000e+01 9.90603520983742e-02 + 1.12500000000000e+01 9.90603520983742e-02 + 1.17500000000000e+01 9.90603520983742e-02 + 1.22500000000000e+01 9.90603520983742e-02 + 1.27500000000000e+01 9.90588180654791e-02 + 1.32500000000000e+01 9.82171168134545e-02 + 1.37500000000000e+01 6.68675768173003e-02 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 7.44570102130396e-02 - 1.52500000000000e+01 9.85667622630896e-02 - 1.57500000000000e+01 9.90599290861925e-02 - 1.62500000000000e+01 9.90603521389808e-02 - 1.67500000000000e+01 9.90603521389808e-02 - 1.72500000000000e+01 9.90603521389808e-02 - 1.77500000000000e+01 9.90603521389808e-02 - 1.82500000000000e+01 9.90603521389808e-02 - 1.87500000000000e+01 9.90603521389808e-02 - 1.92500000000000e+01 9.90603521389808e-02 - 1.97500000000000e+01 9.90603521389808e-02 - 2.02500000000000e+01 9.90603521389808e-02 - 2.07500000000000e+01 9.90603521389808e-02 - 2.12500000000000e+01 9.90603521389808e-02 - 2.17500000000000e+01 9.90603521389808e-02 - 2.22500000000000e+01 9.90603521389808e-02 - 2.27500000000000e+01 9.90603521389808e-02 - 2.32500000000000e+01 9.90603521389808e-02 - 2.37500000000000e+01 9.90603521389808e-02 - 2.42500000000000e+01 9.90603521389808e-02 - 2.47500000000000e+01 9.90603521389808e-02 + 1.47500000000000e+01 7.44570102671401e-02 + 1.52500000000000e+01 9.85667622255897e-02 + 1.57500000000000e+01 9.90599290455859e-02 + 1.62500000000000e+01 9.90603520983742e-02 + 1.67500000000000e+01 9.90603520983742e-02 + 1.72500000000000e+01 9.90603520983742e-02 + 1.77500000000000e+01 9.90603520983742e-02 + 1.82500000000000e+01 9.90603520983742e-02 + 1.87500000000000e+01 9.90603520983742e-02 + 1.92500000000000e+01 9.90603520983742e-02 + 1.97500000000000e+01 9.90603520983742e-02 + 2.02500000000000e+01 9.90603520983742e-02 + 2.07500000000000e+01 9.90603520983742e-02 + 2.12500000000000e+01 9.90603520983742e-02 + 2.17500000000000e+01 9.90603520983742e-02 + 2.22500000000000e+01 9.90603520983742e-02 + 2.27500000000000e+01 9.90603520983742e-02 + 2.32500000000000e+01 9.90603520983742e-02 + 2.37500000000000e+01 9.90603520983742e-02 + 2.42500000000000e+01 9.90603520983742e-02 + 2.47500000000000e+01 9.90603520983742e-02 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state index f6e1b5a1e..f25418e7c 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.metadynamics1.rep2.state @@ -17,9 +17,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 5.90367888432614e-05 - 7.72360342049122e-03 7.98103713126329e-02 6.51481918280550e-02 - 4.20150496559186e-03 2.14098483126557e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 5.90367895903547e-05 + 7.72360347936990e-03 7.98103714989791e-02 6.51481916206231e-02 + 4.20150492815907e-03 2.14098479953629e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -42,9 +42,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 7.25346801924767e-04 - 5.56809955469972e-02 1.70182689379045e-01 -1.91812601541206e-01 - -3.36985920842485e-02 -2.80399679154532e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 7.25346810525990e-04 + 5.56809958916884e-02 1.70182688913198e-01 -1.91812601663509e-01 + -3.36985918329314e-02 -2.80399675255803e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out index c53fc7f3d..239d8d6d2 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep2.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -145,7 +143,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -159,7 +156,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -174,42 +170,22 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Multiple-walker metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep2r.colvars.state". colvars: The final output state file will be "test.rep2.colvars.state". +colvars: Opening trajectory file "test.rep2.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "test.rep2r.colvars.state". colvars: The final output state file will be "test.rep2.colvars.state". colvars: Metadynamics bias "metadynamics1": accessing replica "rep1". -colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". -colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep1.colvars.metadynamics1.rep1.state". colvars: Restarting metadynamics bias "metadynamics1" from step number 100. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: Synchronizing (emptying the buffer of) trajectory file "test.rep2.colvars.traj". colvars: Saving collective variables state to "test.rep2.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped index a6354098b..22c1a118b 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 9.94700459880913e+00 + x 9.94700459588437e+00 } metadynamics { @@ -27,9 +27,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 5.90367888432614e-05 - 7.72360342049122e-03 7.98103713126329e-02 6.51481918280550e-02 - 4.20150496559186e-03 2.14098483126557e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 5.90367895903547e-05 + 7.72360347936990e-03 7.98103714989791e-02 6.51481916206231e-02 + 4.20150492815907e-03 2.14098479953629e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -52,9 +52,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 7.25346801924767e-04 - 5.56809955469972e-02 1.70182689379045e-01 -1.91812601541206e-01 - -3.36985920842485e-02 -2.80399679154532e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 7.25346810525990e-04 + 5.56809958916884e-02 1.70182688913198e-01 -1.91812601663509e-01 + -3.36985918329314e-02 -2.80399675255803e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj index 87c724e96..7ebb8134c 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.colvars.traj @@ -1,102 +1,102 @@ # step d fa_d 0 9.92876155419194e+00 0.00000000000000e+00 - 1 9.92863721108117e+00 0.00000000000000e+00 - 2 9.92825734340718e+00 0.00000000000000e+00 - 3 9.92755127525950e+00 0.00000000000000e+00 - 4 9.92667471909311e+00 0.00000000000000e+00 - 5 9.92575034311276e+00 0.00000000000000e+00 - 6 9.92495620963959e+00 0.00000000000000e+00 - 7 9.92461789359752e+00 0.00000000000000e+00 - 8 9.92536305405157e+00 0.00000000000000e+00 - 9 9.92598579851022e+00 0.00000000000000e+00 - 10 9.92698489552914e+00 -1.53692716384904e-02 - 11 9.92813713186745e+00 -1.53692716384904e-02 - 12 9.92958955154718e+00 -1.53692716384904e-02 - 13 9.93146245533469e+00 -1.53692716384904e-02 - 14 9.93387956305109e+00 -1.53692716384904e-02 - 15 9.93625622414012e+00 -1.53692716384904e-02 - 16 9.93875399313412e+00 -1.53692716384904e-02 - 17 9.94136244546042e+00 -1.53692716384904e-02 - 18 9.94440242008114e+00 -1.53692716384904e-02 - 19 9.94723046489032e+00 -1.53692716384904e-02 - 20 9.95024031483397e+00 -3.19982334686605e-02 - 21 9.95290175147503e+00 -3.19982334686605e-02 - 22 9.95500360291990e+00 -3.19982334686605e-02 - 23 9.95625077342743e+00 -3.19982334686605e-02 - 24 9.95679355590983e+00 -3.19982334686605e-02 - 25 9.95732344685766e+00 -3.19982334686605e-02 - 26 9.95731470350271e+00 -3.19982334686605e-02 - 27 9.95681072299199e+00 -3.19982334686605e-02 - 28 9.95602536365077e+00 -3.19982334686605e-02 - 29 9.95531430839414e+00 -3.19982334686605e-02 - 30 9.95424975105506e+00 -4.88206365730334e-02 - 31 9.95332421152467e+00 -4.88206365730334e-02 - 32 9.95229914723985e+00 -4.88206365730334e-02 - 33 9.95131483147978e+00 -4.88206365730334e-02 - 34 9.95060259370787e+00 -4.88206365730334e-02 - 35 9.94987218183758e+00 -4.88206365730334e-02 - 36 9.94977154513057e+00 -4.88206365730334e-02 - 37 9.95025457677085e+00 -4.88206365730334e-02 - 38 9.95141923918344e+00 -4.88206365730334e-02 - 39 9.95216006978580e+00 -4.88206365730334e-02 - 40 9.95360310850276e+00 -6.56123202550344e-02 - 41 9.95547794209557e+00 -6.56123202550344e-02 - 42 9.95752449941017e+00 -6.56123202550344e-02 - 43 9.95986469077451e+00 -6.56123202550344e-02 - 44 9.96229115270165e+00 -6.56123202550344e-02 - 45 9.96422304181782e+00 -6.56123202550344e-02 - 46 9.96619104731396e+00 -6.56123202550344e-02 - 47 9.96771829749829e+00 -6.56123202550344e-02 - 48 9.96865300857455e+00 -6.56123202550344e-02 - 49 9.96983842022116e+00 -6.56123202550344e-02 - 50 9.97072851638560e+00 -8.31549680361093e-02 - 51 9.97176839583889e+00 -8.31549680361093e-02 - 52 9.97294474948930e+00 -8.31549680361093e-02 - 53 9.97393162178829e+00 -8.31549680361093e-02 - 54 9.97422213976697e+00 -8.31549680361093e-02 - 55 9.97427923345291e+00 -8.31549680361093e-02 - 56 9.97509912850479e+00 -8.31549680361093e-02 - 57 9.97598939132573e+00 -8.31549680361093e-02 - 58 9.97736094478977e+00 -8.31549680361093e-02 - 59 9.97908316200223e+00 -8.31549680361093e-02 - 60 9.98144866321475e+00 -1.01101051065911e-01 - 61 9.98418248507440e+00 -1.01101051065911e-01 - 62 9.98724279063945e+00 -1.01101051065911e-01 - 63 9.98983902620720e+00 -1.01101051065911e-01 - 64 9.99205502549511e+00 -1.01101051065911e-01 - 65 9.99396375834268e+00 -1.01101051065911e-01 - 66 9.99521991233981e+00 -1.01101051065911e-01 - 67 9.99552925406132e+00 -1.01101051065911e-01 - 68 9.99539402401249e+00 -1.01101051065911e-01 - 69 9.99477561290164e+00 -1.01101051065911e-01 - 70 9.99375663938557e+00 -1.19446772057086e-01 - 71 9.99241934438575e+00 -1.19446772057086e-01 - 72 9.99028414356615e+00 -1.19446772057086e-01 - 73 9.98782436656130e+00 -1.19446772057086e-01 - 74 9.98501318847694e+00 -1.19446772057086e-01 - 75 9.98166896908869e+00 -1.19446772057086e-01 - 76 9.97818649901180e+00 -1.19446772057086e-01 - 77 9.97405361956510e+00 -1.19446772057086e-01 - 78 9.97043749036436e+00 -1.19446772057086e-01 - 79 9.96680015701972e+00 -1.19446772057086e-01 - 80 9.96387279717675e+00 -1.36704453464043e-01 - 81 9.96115537712523e+00 -1.36704453464043e-01 - 82 9.95917142515307e+00 -1.36704453464043e-01 - 83 9.95805513531301e+00 -1.36704453464043e-01 - 84 9.95728144936743e+00 -1.36704453464043e-01 - 85 9.95684688548056e+00 -1.36704453464043e-01 - 86 9.95695270593551e+00 -1.36704453464043e-01 - 87 9.95764400234754e+00 -1.36704453464043e-01 - 88 9.95799943403282e+00 -1.36704453464043e-01 - 89 9.95808582547394e+00 -1.36704453464043e-01 - 90 9.95829827009459e+00 -1.53714986499153e-01 - 91 9.95900434623497e+00 -1.53714986499153e-01 - 92 9.95935452195446e+00 -1.53714986499153e-01 - 93 9.95926444820010e+00 -1.53714986499153e-01 - 94 9.95895383355610e+00 -1.53714986499153e-01 - 95 9.95787595556106e+00 -1.53714986499153e-01 - 96 9.95651093462575e+00 -1.53714986499153e-01 - 97 9.95450882105866e+00 -1.53714986499153e-01 - 98 9.95215317348883e+00 -1.53714986499153e-01 - 99 9.94953653719804e+00 -1.53714986499153e-01 - 100 9.94700459880913e+00 -1.70182689379045e-01 + 1 9.92863721108118e+00 0.00000000000000e+00 + 2 9.92825734340721e+00 0.00000000000000e+00 + 3 9.92755127525955e+00 0.00000000000000e+00 + 4 9.92667471909320e+00 0.00000000000000e+00 + 5 9.92575034311287e+00 0.00000000000000e+00 + 6 9.92495620963971e+00 0.00000000000000e+00 + 7 9.92461789359763e+00 0.00000000000000e+00 + 8 9.92536305405160e+00 0.00000000000000e+00 + 9 9.92598579851009e+00 0.00000000000000e+00 + 10 9.92698489552874e+00 -1.53692716384669e-02 + 11 9.92813713186662e+00 -1.53692716384669e-02 + 12 9.92958955154570e+00 -1.53692716384669e-02 + 13 9.93146245533227e+00 -1.53692716384669e-02 + 14 9.93387956304736e+00 -1.53692716384669e-02 + 15 9.93625622413464e+00 -1.53692716384669e-02 + 16 9.93875399312634e+00 -1.53692716384669e-02 + 17 9.94136244544969e+00 -1.53692716384669e-02 + 18 9.94440242006668e+00 -1.53692716384669e-02 + 19 9.94723046487128e+00 -1.53692716384669e-02 + 20 9.95024031480938e+00 -3.19982334674286e-02 + 21 9.95290175144380e+00 -3.19982334674286e-02 + 22 9.95500360288087e+00 -3.19982334674286e-02 + 23 9.95625077337936e+00 -3.19982334674286e-02 + 24 9.95679355585141e+00 -3.19982334674286e-02 + 25 9.95732344678751e+00 -3.19982334674286e-02 + 26 9.95731470341938e+00 -3.19982334674286e-02 + 27 9.95681072289397e+00 -3.19982334674286e-02 + 28 9.95602536353651e+00 -3.19982334674286e-02 + 29 9.95531430826202e+00 -3.19982334674286e-02 + 30 9.95424975090340e+00 -4.88206365646183e-02 + 31 9.95332421135175e+00 -4.88206365646183e-02 + 32 9.95229914704390e+00 -4.88206365646183e-02 + 33 9.95131483125902e+00 -4.88206365646183e-02 + 34 9.95060259346046e+00 -4.88206365646183e-02 + 35 9.94987218156172e+00 -4.88206365646183e-02 + 36 9.94977154482446e+00 -4.88206365646183e-02 + 37 9.95025457643273e+00 -4.88206365646183e-02 + 38 9.95141923881165e+00 -4.88206365646183e-02 + 39 9.95216006937876e+00 -4.88206365646183e-02 + 40 9.95360310805905e+00 -6.56123202254770e-02 + 41 9.95547794161392e+00 -6.56123202254770e-02 + 42 9.95752449888952e+00 -6.56123202254770e-02 + 43 9.95986469021403e+00 -6.56123202254770e-02 + 44 9.96229115210074e+00 -6.56123202254770e-02 + 45 9.96422304117613e+00 -6.56123202254770e-02 + 46 9.96619104663140e+00 -6.56123202254770e-02 + 47 9.96771829677501e+00 -6.56123202254770e-02 + 48 9.96865300781088e+00 -6.56123202254770e-02 + 49 9.96983841941765e+00 -6.56123202254770e-02 + 50 9.97072851554298e+00 -8.31549679728180e-02 + 51 9.97176839495805e+00 -8.31549679728180e-02 + 52 9.97294474857124e+00 -8.31549679728180e-02 + 53 9.97393162083410e+00 -8.31549679728180e-02 + 54 9.97422213877777e+00 -8.31549679728180e-02 + 55 9.97427923242988e+00 -8.31549679728180e-02 + 56 9.97509912744913e+00 -8.31549679728180e-02 + 57 9.97598939023862e+00 -8.31549679728180e-02 + 58 9.97736094367233e+00 -8.31549679728180e-02 + 59 9.97908316085552e+00 -8.31549679728180e-02 + 60 9.98144866203979e+00 -1.01101050961226e-01 + 61 9.98418248387209e+00 -1.01101050961226e-01 + 62 9.98724278941060e+00 -1.01101050961226e-01 + 63 9.98983902495251e+00 -1.01101050961226e-01 + 64 9.99205502421520e+00 -1.01101050961226e-01 + 65 9.99396375703816e+00 -1.01101050961226e-01 + 66 9.99521991101117e+00 -1.01101050961226e-01 + 67 9.99552925270898e+00 -1.01101050961226e-01 + 68 9.99539402263682e+00 -1.01101050961226e-01 + 69 9.99477561150299e+00 -1.01101050961226e-01 + 70 9.99375663796423e+00 -1.19446771910169e-01 + 71 9.99241934294185e+00 -1.19446771910169e-01 + 72 9.99028414209973e+00 -1.19446771910169e-01 + 73 9.98782436507227e+00 -1.19446771910169e-01 + 74 9.98501318696502e+00 -1.19446771910169e-01 + 75 9.98166896755343e+00 -1.19446771910169e-01 + 76 9.97818649745244e+00 -1.19446771910169e-01 + 77 9.97405361798055e+00 -1.19446771910169e-01 + 78 9.97043748875320e+00 -1.19446771910169e-01 + 79 9.96680015538000e+00 -1.19446771910169e-01 + 80 9.96387279550620e+00 -1.36704453245133e-01 + 81 9.96115537542108e+00 -1.36704453245133e-01 + 82 9.95917142341217e+00 -1.36704453245133e-01 + 83 9.95805513353189e+00 -1.36704453245133e-01 + 84 9.95728144754225e+00 -1.36704453245133e-01 + 85 9.95684688360727e+00 -1.36704453245133e-01 + 86 9.95695270400995e+00 -1.36704453245133e-01 + 87 9.95764400036554e+00 -1.36704453245133e-01 + 88 9.95799943199032e+00 -1.36704453245133e-01 + 89 9.95808582336709e+00 -1.36704453245133e-01 + 90 9.95829826791995e+00 -1.53714986181138e-01 + 91 9.95900434398949e+00 -1.53714986181138e-01 + 92 9.95935451963563e+00 -1.53714986181138e-01 + 93 9.95926444580604e+00 -1.53714986181138e-01 + 94 9.95895383108549e+00 -1.53714986181138e-01 + 95 9.95787595301329e+00 -1.53714986181138e-01 + 96 9.95651093200075e+00 -1.53714986181138e-01 + 97 9.95450881835695e+00 -1.53714986181138e-01 + 98 9.95215317071137e+00 -1.53714986181138e-01 + 99 9.94953653434610e+00 -1.53714986181138e-01 + 100 9.94700459588437e+00 -1.70182688913198e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf index 2f5afd073..5f62fc1ee 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/test.rep2.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 9.90603521389808e-02 - 7.50000000000000e-01 9.90603521389808e-02 - 1.25000000000000e+00 9.90603521389808e-02 - 1.75000000000000e+00 9.90603521389808e-02 - 2.25000000000000e+00 9.90603521389808e-02 - 2.75000000000000e+00 9.90603521389808e-02 - 3.25000000000000e+00 9.90603521389808e-02 - 3.75000000000000e+00 9.90603521389808e-02 - 4.25000000000000e+00 9.90603521389808e-02 - 4.75000000000000e+00 9.90603521389808e-02 - 5.25000000000000e+00 9.90603521389808e-02 - 5.75000000000000e+00 9.90603521389808e-02 - 6.25000000000000e+00 9.90603521389808e-02 - 6.75000000000000e+00 9.90603521389808e-02 - 7.25000000000000e+00 9.90603521389808e-02 - 7.75000000000000e+00 9.90603521389808e-02 - 8.25000000000000e+00 9.90603521389808e-02 - 8.75000000000000e+00 9.90013153501375e-02 - 9.25000000000000e+00 9.13367487184896e-02 - 9.75000000000000e+00 1.92499808263479e-02 - 1.02500000000000e+01 3.39121603109258e-02 - 1.07500000000000e+01 9.48588471733889e-02 - 1.12500000000000e+01 9.90389422906681e-02 - 1.17500000000000e+01 9.90603521389808e-02 - 1.22500000000000e+01 9.90603521389808e-02 - 1.27500000000000e+01 9.90588181061136e-02 - 1.32500000000000e+01 9.82171168620079e-02 - 1.37500000000000e+01 6.68675769875806e-02 + 2.50000000000000e-01 9.90603520983742e-02 + 7.50000000000000e-01 9.90603520983742e-02 + 1.25000000000000e+00 9.90603520983742e-02 + 1.75000000000000e+00 9.90603520983742e-02 + 2.25000000000000e+00 9.90603520983742e-02 + 2.75000000000000e+00 9.90603520983742e-02 + 3.25000000000000e+00 9.90603520983742e-02 + 3.75000000000000e+00 9.90603520983742e-02 + 4.25000000000000e+00 9.90603520983742e-02 + 4.75000000000000e+00 9.90603520983742e-02 + 5.25000000000000e+00 9.90603520983742e-02 + 5.75000000000000e+00 9.90603520983742e-02 + 6.25000000000000e+00 9.90603520983742e-02 + 6.75000000000000e+00 9.90603520983742e-02 + 7.25000000000000e+00 9.90603520983742e-02 + 7.75000000000000e+00 9.90603520983742e-02 + 8.25000000000000e+00 9.90603520983742e-02 + 8.75000000000000e+00 9.90013153087839e-02 + 9.25000000000000e+00 9.13367486190043e-02 + 9.75000000000000e+00 1.92499805993951e-02 + 1.02500000000000e+01 3.39121604777511e-02 + 1.07500000000000e+01 9.48588471702151e-02 + 1.12500000000000e+01 9.90389422503788e-02 + 1.17500000000000e+01 9.90603520983742e-02 + 1.22500000000000e+01 9.90603520983742e-02 + 1.27500000000000e+01 9.90588180654791e-02 + 1.32500000000000e+01 9.82171168134545e-02 + 1.37500000000000e+01 6.68675768173003e-02 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 7.44570102130397e-02 - 1.52500000000000e+01 9.85667622630896e-02 - 1.57500000000000e+01 9.90599290861925e-02 - 1.62500000000000e+01 9.90603521389808e-02 - 1.67500000000000e+01 9.90603521389808e-02 - 1.72500000000000e+01 9.90603521389808e-02 - 1.77500000000000e+01 9.90603521389808e-02 - 1.82500000000000e+01 9.90603521389808e-02 - 1.87500000000000e+01 9.90603521389808e-02 - 1.92500000000000e+01 9.90603521389808e-02 - 1.97500000000000e+01 9.90603521389808e-02 - 2.02500000000000e+01 9.90603521389808e-02 - 2.07500000000000e+01 9.90603521389808e-02 - 2.12500000000000e+01 9.90603521389808e-02 - 2.17500000000000e+01 9.90603521389808e-02 - 2.22500000000000e+01 9.90603521389808e-02 - 2.27500000000000e+01 9.90603521389808e-02 - 2.32500000000000e+01 9.90603521389808e-02 - 2.37500000000000e+01 9.90603521389808e-02 - 2.42500000000000e+01 9.90603521389808e-02 - 2.47500000000000e+01 9.90603521389808e-02 + 1.47500000000000e+01 7.44570102671402e-02 + 1.52500000000000e+01 9.85667622255897e-02 + 1.57500000000000e+01 9.90599290455859e-02 + 1.62500000000000e+01 9.90603520983742e-02 + 1.67500000000000e+01 9.90603520983742e-02 + 1.72500000000000e+01 9.90603520983742e-02 + 1.77500000000000e+01 9.90603520983742e-02 + 1.82500000000000e+01 9.90603520983742e-02 + 1.87500000000000e+01 9.90603520983742e-02 + 1.92500000000000e+01 9.90603520983742e-02 + 1.97500000000000e+01 9.90603520983742e-02 + 2.02500000000000e+01 9.90603520983742e-02 + 2.07500000000000e+01 9.90603520983742e-02 + 2.12500000000000e+01 9.90603520983742e-02 + 2.17500000000000e+01 9.90603520983742e-02 + 2.22500000000000e+01 9.90603520983742e-02 + 2.27500000000000e+01 9.90603520983742e-02 + 2.32500000000000e+01 9.90603520983742e-02 + 2.37500000000000e+01 9.90603520983742e-02 + 2.42500000000000e+01 9.90603520983742e-02 + 2.47500000000000e+01 9.90603520983742e-02 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state index 0f90b9de5..30662bcfc 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.metadynamics1.rep1.state @@ -20,9 +20,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.25323465171985e-05 3.48877739229281e-03 - 8.48743669974108e-02 1.87767103667070e-01 3.74493273101570e-02 - 6.54251825834146e-04 4.23052788302019e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.25323473186721e-05 3.48877751270849e-03 + 8.48743679843641e-02 1.87767102998601e-01 3.74493268741002e-02 + 6.54251815918406e-04 4.23052788272303e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -45,9 +45,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.70780739637743e-04 3.06678366244801e-02 - 3.38095245919524e-01 -1.52211785481214e-01 -2.11534386688208e-01 - -6.90290108238559e-03 -6.37695701865853e-06 0.00000000000000e+00 + 0.00000000000000e+00 1.70780749827028e-04 3.06678375007270e-02 + 3.38095246589823e-01 -1.52211789178683e-01 -2.11534384625674e-01 + -6.90290098044747e-03 -6.37695701821339e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out index 051450ff0..2c9517acb 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep1.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -145,7 +143,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -159,7 +156,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -174,49 +170,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Multiple-walker metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.rep1.colvars.state". +colvars: Restarting from file "test.rep1.colvars.state". colvars: Restarting collective variable "d" from value: 14.1657 colvars: Restarting metadynamics bias "metadynamics1" from step number 100. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: Restarting harmonicwalls bias "dw" from step number 100. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testres.rep1r.colvars.state". colvars: The final output state file will be "testres.rep1.colvars.state". +colvars: Opening trajectory file "testres.rep1.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "testres.rep1r.colvars.state". colvars: The final output state file will be "testres.rep1.colvars.state". colvars: Metadynamics bias "metadynamics1": accessing replica "rep2". -colvars: Metadynamics bias "metadynamics1": replica "rep2" has supplied a new state file, "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". -colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep2" from file "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". +colvars: Metadynamics bias "metadynamics1": replica "rep2" has supplied a new state file, "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". +colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep2" from file "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/test.rep2.colvars.metadynamics1.rep2.state". colvars: Restarting metadynamics bias "metadynamics1" from step number 100. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: Saving collective variables state to "testres.rep1.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped index 3af8b69d2..19d64ce2c 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 1.40671697483701e+01 + x 1.40671697413825e+01 } metadynamics { @@ -30,9 +30,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.25323465171985e-05 3.48877739229281e-03 - 8.48743669974108e-02 1.87767103667070e-01 3.74493273101570e-02 - 6.54251825834146e-04 4.23052788302019e-07 0.00000000000000e+00 + 0.00000000000000e+00 1.25323473186721e-05 3.48877751270849e-03 + 8.48743679843641e-02 1.87767102998601e-01 3.74493268741002e-02 + 6.54251815918406e-04 4.23052788272303e-07 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -55,9 +55,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 1.70780739637743e-04 3.06678366244801e-02 - 3.38095245919524e-01 -1.52211785481214e-01 -2.11534386688208e-01 - -6.90290108238559e-03 -6.37695701865853e-06 0.00000000000000e+00 + 0.00000000000000e+00 1.70780749827028e-04 3.06678375007270e-02 + 3.38095246589823e-01 -1.52211789178683e-01 -2.11534384625674e-01 + -6.90290098044747e-03 -6.37695701821339e-06 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj index ba8e3a579..62aa833b8 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.colvars.traj @@ -1,102 +1,102 @@ # step d fa_d - 100 1.41656974969458e+01 2.66708902934347e-02 - 101 1.41645168177934e+01 2.66708902934347e-02 - 102 1.41639313723197e+01 2.66708902934347e-02 - 103 1.41639423493949e+01 2.66708902934347e-02 - 104 1.41647561707625e+01 2.66708902934347e-02 - 105 1.41658632142319e+01 2.66708902934347e-02 - 106 1.41673787387882e+01 2.66708902934347e-02 - 107 1.41690285541915e+01 2.66708902934347e-02 - 108 1.41710437199635e+01 2.66708902934347e-02 - 109 1.41735809954887e+01 2.66708902934347e-02 - 110 1.41763514579746e+01 3.39682706157757e-02 - 111 1.41790650979264e+01 3.39682706157757e-02 - 112 1.41816844532206e+01 3.39682706157757e-02 - 113 1.41848030101558e+01 3.39682706157757e-02 - 114 1.41881572686952e+01 3.39682706157757e-02 - 115 1.41914710994669e+01 3.39682706157757e-02 - 116 1.41945076521072e+01 3.39682706157757e-02 - 117 1.41970530487971e+01 3.39682706157757e-02 - 118 1.41993348384181e+01 3.39682706157757e-02 - 119 1.42015324362938e+01 3.39682706157757e-02 - 120 1.42029799155388e+01 3.87040708124342e-02 - 121 1.42039018573139e+01 3.87040708124342e-02 - 122 1.42045497524016e+01 3.87040708124342e-02 - 123 1.42051279143509e+01 3.87040708124342e-02 - 124 1.42057799825133e+01 3.87040708124342e-02 - 125 1.42052035543398e+01 3.87040708124342e-02 - 126 1.42037125406107e+01 3.87040708124342e-02 - 127 1.42013876753793e+01 3.87040708124342e-02 - 128 1.41985000504608e+01 3.87040708124342e-02 - 129 1.41946867955086e+01 3.87040708124342e-02 - 130 1.41907407040072e+01 4.46331785411240e-02 - 131 1.41860814711741e+01 4.46331785411240e-02 - 132 1.41811502776628e+01 4.46331785411240e-02 - 133 1.41759651349297e+01 4.46331785411240e-02 - 134 1.41699530857131e+01 4.46331785411240e-02 - 135 1.41627941484716e+01 4.46331785411240e-02 - 136 1.41557931733251e+01 4.46331785411240e-02 - 137 1.41492699069035e+01 4.46331785411240e-02 - 138 1.41425596947339e+01 4.46331785411240e-02 - 139 1.41364771205764e+01 4.46331785411240e-02 - 140 1.41308683076945e+01 5.59216758917605e-02 - 141 1.41250693714429e+01 5.59216758917605e-02 - 142 1.41191585710561e+01 5.59216758917605e-02 - 143 1.41128806964629e+01 5.59216758917605e-02 - 144 1.41069776769885e+01 5.59216758917605e-02 - 145 1.41013330433959e+01 5.59216758917605e-02 - 146 1.40965351247715e+01 5.59216758917605e-02 - 147 1.40911236046535e+01 5.59216758917605e-02 - 148 1.40860174228665e+01 5.59216758917605e-02 - 149 1.40814707023824e+01 5.59216758917605e-02 - 150 1.40771721143455e+01 7.10415197980919e-02 - 151 1.40727022571165e+01 7.10415197980919e-02 - 152 1.40694284519236e+01 7.10415197980919e-02 - 153 1.40661582239069e+01 7.10415197980919e-02 - 154 1.40627979791840e+01 7.10415197980919e-02 - 155 1.40596112342542e+01 7.10415197980919e-02 - 156 1.40566695308391e+01 7.10415197980919e-02 - 157 1.40540744563696e+01 7.10415197980919e-02 - 158 1.40521880941470e+01 7.10415197980919e-02 - 159 1.40504169101966e+01 7.10415197980919e-02 - 160 1.40490177872330e+01 8.77068087997524e-02 - 161 1.40477627185972e+01 8.77068087997524e-02 - 162 1.40465343759200e+01 8.77068087997524e-02 - 163 1.40459238443624e+01 8.77068087997524e-02 - 164 1.40454989023081e+01 8.77068087997524e-02 - 165 1.40458141277865e+01 8.77068087997524e-02 - 166 1.40462783872865e+01 8.77068087997524e-02 - 167 1.40469230273499e+01 8.77068087997524e-02 - 168 1.40475066692391e+01 8.77068087997524e-02 - 169 1.40479434669772e+01 8.77068087997524e-02 - 170 1.40484684779552e+01 1.04398839016414e-01 - 171 1.40494304130099e+01 1.04398839016414e-01 - 172 1.40500894456774e+01 1.04398839016414e-01 - 173 1.40506811271051e+01 1.04398839016414e-01 - 174 1.40513374594737e+01 1.04398839016414e-01 - 175 1.40524333189262e+01 1.04398839016414e-01 - 176 1.40539698807596e+01 1.04398839016414e-01 - 177 1.40553742441127e+01 1.04398839016414e-01 - 178 1.40565462753219e+01 1.04398839016414e-01 - 179 1.40575157791768e+01 1.04398839016414e-01 - 180 1.40587097821679e+01 1.20570595809343e-01 - 181 1.40600393183434e+01 1.20570595809343e-01 - 182 1.40613410361508e+01 1.20570595809343e-01 - 183 1.40624671262692e+01 1.20570595809343e-01 - 184 1.40634905316866e+01 1.20570595809343e-01 - 185 1.40640000721401e+01 1.20570595809343e-01 - 186 1.40642859325702e+01 1.20570595809343e-01 - 187 1.40639315897108e+01 1.20570595809343e-01 - 188 1.40634945893112e+01 1.20570595809343e-01 - 189 1.40632564819739e+01 1.20570595809343e-01 - 190 1.40631238625021e+01 1.36504067884959e-01 - 191 1.40628238911534e+01 1.36504067884959e-01 - 192 1.40626278632898e+01 1.36504067884959e-01 - 193 1.40620533099285e+01 1.36504067884959e-01 - 194 1.40614884998255e+01 1.36504067884959e-01 - 195 1.40614791769245e+01 1.36504067884959e-01 - 196 1.40625287964965e+01 1.36504067884959e-01 - 197 1.40636172394048e+01 1.36504067884959e-01 - 198 1.40650874989452e+01 1.36504067884959e-01 - 199 1.40663704991439e+01 1.36504067884959e-01 - 200 1.40671697483701e+01 1.52211785481214e-01 + 100 1.41656974949034e+01 2.66708910635591e-02 + 101 1.41645168157006e+01 2.66708910635591e-02 + 102 1.41639313701771e+01 2.66708910635591e-02 + 103 1.41639423472033e+01 2.66708910635591e-02 + 104 1.41647561685229e+01 2.66708910635591e-02 + 105 1.41658632119453e+01 2.66708910635591e-02 + 106 1.41673787364561e+01 2.66708910635591e-02 + 107 1.41690285518153e+01 2.66708910635591e-02 + 108 1.41710437175448e+01 2.66708910635591e-02 + 109 1.41735809930291e+01 2.66708910635591e-02 + 110 1.41763514554758e+01 3.39682716198089e-02 + 111 1.41790650953902e+01 3.39682716198089e-02 + 112 1.41816844506487e+01 3.39682716198089e-02 + 113 1.41848030075499e+01 3.39682716198089e-02 + 114 1.41881572660568e+01 3.39682716198089e-02 + 115 1.41914710967974e+01 3.39682716198089e-02 + 116 1.41945076494076e+01 3.39682716198089e-02 + 117 1.41970530460683e+01 3.39682716198089e-02 + 118 1.41993348356605e+01 3.39682716198089e-02 + 119 1.42015324335073e+01 3.39682716198089e-02 + 120 1.42029799127233e+01 3.87040720936605e-02 + 121 1.42039018544684e+01 3.87040720936605e-02 + 122 1.42045497495248e+01 3.87040720936605e-02 + 123 1.42051279114412e+01 3.87040720936605e-02 + 124 1.42057799795685e+01 3.87040720936605e-02 + 125 1.42052035513576e+01 3.87040720936605e-02 + 126 1.42037125375882e+01 3.87040720936605e-02 + 127 1.42013876723135e+01 3.87040720936605e-02 + 128 1.41985000473486e+01 3.87040720936605e-02 + 129 1.41946867923467e+01 3.87040720936605e-02 + 130 1.41907407007924e+01 4.46331801324967e-02 + 131 1.41860814679033e+01 4.46331801324967e-02 + 132 1.41811502743331e+01 4.46331801324967e-02 + 133 1.41759651315384e+01 4.46331801324967e-02 + 134 1.41699530822577e+01 4.46331801324967e-02 + 135 1.41627941449498e+01 4.46331801324967e-02 + 136 1.41557931697353e+01 4.46331801324967e-02 + 137 1.41492699032442e+01 4.46331801324967e-02 + 138 1.41425596910040e+01 4.46331801324967e-02 + 139 1.41364771167751e+01 4.46331801324967e-02 + 140 1.41308683038212e+01 5.59216777970916e-02 + 141 1.41250693674976e+01 5.59216777970916e-02 + 142 1.41191585670391e+01 5.59216777970916e-02 + 143 1.41128806923745e+01 5.59216777970916e-02 + 144 1.41069776728295e+01 5.59216777970916e-02 + 145 1.41013330391674e+01 5.59216777970916e-02 + 146 1.40965351204746e+01 5.59216777970916e-02 + 147 1.40911236002896e+01 5.59216777970916e-02 + 148 1.40860174184372e+01 5.59216777970916e-02 + 149 1.40814706978895e+01 5.59216777970916e-02 + 150 1.40771721097910e+01 7.10415219806404e-02 + 151 1.40727022525028e+01 7.10415219806404e-02 + 152 1.40694284472531e+01 7.10415219806404e-02 + 153 1.40661582191822e+01 7.10415219806404e-02 + 154 1.40627979744080e+01 7.10415219806404e-02 + 155 1.40596112294300e+01 7.10415219806404e-02 + 156 1.40566695259700e+01 7.10415219806404e-02 + 157 1.40540744514590e+01 7.10415219806404e-02 + 158 1.40521880891984e+01 7.10415219806404e-02 + 159 1.40504169052137e+01 7.10415219806404e-02 + 160 1.40490177822194e+01 8.77068112269737e-02 + 161 1.40477627135566e+01 8.77068112269737e-02 + 162 1.40465343708561e+01 8.77068112269737e-02 + 163 1.40459238392784e+01 8.77068112269737e-02 + 164 1.40454988972072e+01 8.77068112269737e-02 + 165 1.40458141226713e+01 8.77068112269737e-02 + 166 1.40462783821594e+01 8.77068112269737e-02 + 167 1.40469230222126e+01 8.77068112269737e-02 + 168 1.40475066640928e+01 8.77068112269737e-02 + 169 1.40479434618223e+01 8.77068112269737e-02 + 170 1.40484684727914e+01 1.04398841694391e-01 + 171 1.40494304078364e+01 1.04398841694391e-01 + 172 1.40500894404924e+01 1.04398841694391e-01 + 173 1.40506811219062e+01 1.04398841694391e-01 + 174 1.40513374542578e+01 1.04398841694391e-01 + 175 1.40524333136897e+01 1.04398841694391e-01 + 176 1.40539698754981e+01 1.04398841694391e-01 + 177 1.40553742388214e+01 1.04398841694391e-01 + 178 1.40565462699957e+01 1.04398841694391e-01 + 179 1.40575157738103e+01 1.04398841694391e-01 + 180 1.40587097767556e+01 1.20570598774338e-01 + 181 1.40600393128797e+01 1.20570598774338e-01 + 182 1.40613410306303e+01 1.20570598774338e-01 + 183 1.40624671206865e+01 1.20570598774338e-01 + 184 1.40634905260370e+01 1.20570598774338e-01 + 185 1.40640000664191e+01 1.20570598774338e-01 + 186 1.40642859267739e+01 1.20570598774338e-01 + 187 1.40639315838357e+01 1.20570598774338e-01 + 188 1.40634945833543e+01 1.20570598774338e-01 + 189 1.40632564759331e+01 1.20570598774338e-01 + 190 1.40631238563757e+01 1.36504071186495e-01 + 191 1.40628238849401e+01 1.36504071186495e-01 + 192 1.40626278569889e+01 1.36504071186495e-01 + 193 1.40620533035397e+01 1.36504071186495e-01 + 194 1.40614884933489e+01 1.36504071186495e-01 + 195 1.40614791703604e+01 1.36504071186495e-01 + 196 1.40625287898456e+01 1.36504071186495e-01 + 197 1.40636172326678e+01 1.36504071186495e-01 + 198 1.40650874921233e+01 1.36504071186495e-01 + 199 1.40663704922385e+01 1.36504071186495e-01 + 200 1.40671697413825e+01 1.52211789178683e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf index 5728a51c7..6256d0183 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep1.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 1.87767103667070e-01 - 7.50000000000000e-01 1.87767103667070e-01 - 1.25000000000000e+00 1.87767103667070e-01 - 1.75000000000000e+00 1.87767103667070e-01 - 2.25000000000000e+00 1.87767103667070e-01 - 2.75000000000000e+00 1.87767103667070e-01 - 3.25000000000000e+00 1.87767103667070e-01 - 3.75000000000000e+00 1.87767103667070e-01 - 4.25000000000000e+00 1.87767103667070e-01 - 4.75000000000000e+00 1.87767103667070e-01 - 5.25000000000000e+00 1.87767103667070e-01 - 5.75000000000000e+00 1.87767103667070e-01 - 6.25000000000000e+00 1.87767103667070e-01 - 6.75000000000000e+00 1.87767103667070e-01 - 7.25000000000000e+00 1.87767103667070e-01 - 7.75000000000000e+00 1.87767103667070e-01 - 8.25000000000000e+00 1.87767103667070e-01 - 8.75000000000000e+00 1.87708066878227e-01 - 9.25000000000000e+00 1.80043500246579e-01 - 9.75000000000000e+00 1.07956732354437e-01 - 1.02500000000000e+01 1.22618911839015e-01 - 1.07500000000000e+01 1.83565598701478e-01 - 1.12500000000000e+01 1.87745693818758e-01 - 1.17500000000000e+01 1.87767103667070e-01 - 1.22500000000000e+01 1.87767103667070e-01 - 1.27500000000000e+01 1.87754571320553e-01 - 1.32500000000000e+01 1.84278326274777e-01 - 1.37500000000000e+01 1.02892736669659e-01 + 2.50000000000000e-01 1.87767102998601e-01 + 7.50000000000000e-01 1.87767102998601e-01 + 1.25000000000000e+00 1.87767102998601e-01 + 1.75000000000000e+00 1.87767102998601e-01 + 2.25000000000000e+00 1.87767102998601e-01 + 2.75000000000000e+00 1.87767102998601e-01 + 3.25000000000000e+00 1.87767102998601e-01 + 3.75000000000000e+00 1.87767102998601e-01 + 4.25000000000000e+00 1.87767102998601e-01 + 4.75000000000000e+00 1.87767102998601e-01 + 5.25000000000000e+00 1.87767102998601e-01 + 5.75000000000000e+00 1.87767102998601e-01 + 6.25000000000000e+00 1.87767102998601e-01 + 6.75000000000000e+00 1.87767102998601e-01 + 7.25000000000000e+00 1.87767102998601e-01 + 7.75000000000000e+00 1.87767102998601e-01 + 8.25000000000000e+00 1.87767102998601e-01 + 8.75000000000000e+00 1.87708066209011e-01 + 9.25000000000000e+00 1.80043499519231e-01 + 9.75000000000000e+00 1.07956731499622e-01 + 1.02500000000000e+01 1.22618911377978e-01 + 1.07500000000000e+01 1.83565598070442e-01 + 1.12500000000000e+01 1.87745693150606e-01 + 1.17500000000000e+01 1.87767102998601e-01 + 1.22500000000000e+01 1.87767102998601e-01 + 1.27500000000000e+01 1.87754570651283e-01 + 1.32500000000000e+01 1.84278325485893e-01 + 1.37500000000000e+01 1.02892735014237e-01 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 1.50317776356913e-01 - 1.52500000000000e+01 1.87112851841236e-01 - 1.57500000000000e+01 1.87766680614282e-01 - 1.62500000000000e+01 1.87767103667070e-01 - 1.67500000000000e+01 1.87767103667070e-01 - 1.72500000000000e+01 1.87767103667070e-01 - 1.77500000000000e+01 1.87767103667070e-01 - 1.82500000000000e+01 1.87767103667070e-01 - 1.87500000000000e+01 1.87767103667070e-01 - 1.92500000000000e+01 1.87767103667070e-01 - 1.97500000000000e+01 1.87767103667070e-01 - 2.02500000000000e+01 1.87767103667070e-01 - 2.07500000000000e+01 1.87767103667070e-01 - 2.12500000000000e+01 1.87767103667070e-01 - 2.17500000000000e+01 1.87767103667070e-01 - 2.22500000000000e+01 1.87767103667070e-01 - 2.27500000000000e+01 1.87767103667070e-01 - 2.32500000000000e+01 1.87767103667070e-01 - 2.37500000000000e+01 1.87767103667070e-01 - 2.42500000000000e+01 1.87767103667070e-01 - 2.47500000000000e+01 1.87767103667070e-01 + 1.47500000000000e+01 1.50317776124501e-01 + 1.52500000000000e+01 1.87112851182683e-01 + 1.57500000000000e+01 1.87766679945813e-01 + 1.62500000000000e+01 1.87767102998601e-01 + 1.67500000000000e+01 1.87767102998601e-01 + 1.72500000000000e+01 1.87767102998601e-01 + 1.77500000000000e+01 1.87767102998601e-01 + 1.82500000000000e+01 1.87767102998601e-01 + 1.87500000000000e+01 1.87767102998601e-01 + 1.92500000000000e+01 1.87767102998601e-01 + 1.97500000000000e+01 1.87767102998601e-01 + 2.02500000000000e+01 1.87767102998601e-01 + 2.07500000000000e+01 1.87767102998601e-01 + 2.12500000000000e+01 1.87767102998601e-01 + 2.17500000000000e+01 1.87767102998601e-01 + 2.22500000000000e+01 1.87767102998601e-01 + 2.27500000000000e+01 1.87767102998601e-01 + 2.32500000000000e+01 1.87767102998601e-01 + 2.37500000000000e+01 1.87767102998601e-01 + 2.42500000000000e+01 1.87767102998601e-01 + 2.47500000000000e+01 1.87767102998601e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state index c2787a073..b13fd85e3 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.metadynamics1.rep2.state @@ -17,9 +17,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 4.94688027692718e-07 4.73585964068546e-04 - 2.87475263076380e-02 1.74745280192386e-01 1.04414172539260e-01 - 5.69106166051415e-03 2.62455924536695e-05 0.00000000000000e+00 + 0.00000000000000e+00 4.94688080523780e-07 4.73585992341132e-04 + 2.87475270508744e-02 1.74745280616823e-01 1.04414171448857e-01 + 5.69106155906453e-03 2.62455918518392e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -42,9 +42,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 7.40502444565457e-06 4.99357118645503e-03 - 1.69663403453012e-01 2.28926007806402e-01 -3.54750303020055e-01 - -4.70268703518904e-02 -3.46867177951536e-04 0.00000000000000e+00 + 0.00000000000000e+00 7.40502520045617e-06 4.99357144931863e-03 + 1.69663406152221e-01 2.28926002246273e-01 -3.54750301243893e-01 + -4.70268695839609e-02 -3.46867170320607e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out index 373c73703..213231cf9 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.rep2.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "Protein_C-alpha_10" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -145,7 +143,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 40000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -159,7 +156,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0 } [default] colvars: Lower walls were not provided. @@ -174,49 +170,27 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Metadynamics colvar bias implementation: -colvars: - Multiple-walker metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - harmonicWalls colvar bias implementation: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.rep2.colvars.state". +colvars: Restarting from file "test.rep2.colvars.state". colvars: Restarting collective variable "d" from value: 9.947 colvars: Restarting metadynamics bias "metadynamics1" from step number 100. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: Restarting harmonicwalls bias "dw" from step number 100. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "testres.rep2r.colvars.state". colvars: The final output state file will be "testres.rep2.colvars.state". +colvars: Opening trajectory file "testres.rep2.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "d":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: The restart output state file will be "testres.rep2r.colvars.state". colvars: The final output state file will be "testres.rep2.colvars.state". colvars: Metadynamics bias "metadynamics1": accessing replica "rep1". -colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". -colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/data/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": replica "rep1" has supplied a new state file, "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". +colvars: Metadynamics bias "metadynamics1": reading the state of replica "rep1" from file "/home/jhenin/Projects/colvars/namd/tests/library/011_multiple_walker_mtd/testres.rep1.colvars.metadynamics1.rep1.state". colvars: Restarting metadynamics bias "metadynamics1" from step number 200. -colvars: read biasing energy and forces from grids. -colvars: read 0 additional explicit hills. colvars: Saving collective variables state to "testres.rep2.colvars.state". diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped index ce8f94f06..5f3f08a24 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name d - x 9.71175738936231e+00 + x 9.71175738207289e+00 } metadynamics { @@ -27,9 +27,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 4.94688027692718e-07 4.73585964068546e-04 - 2.87475263076380e-02 1.74745280192386e-01 1.04414172539260e-01 - 5.69106166051415e-03 2.62455924536695e-05 0.00000000000000e+00 + 0.00000000000000e+00 4.94688080523780e-07 4.73585992341132e-04 + 2.87475270508744e-02 1.74745280616823e-01 1.04414171448857e-01 + 5.69106155906453e-03 2.62455918518392e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -52,9 +52,9 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 7.40502444565457e-06 4.99357118645503e-03 - 1.69663403453012e-01 2.28926007806402e-01 -3.54750303020055e-01 - -4.70268703518904e-02 -3.46867177951536e-04 0.00000000000000e+00 + 0.00000000000000e+00 7.40502520045617e-06 4.99357144931863e-03 + 1.69663406152221e-01 2.28926002246273e-01 -3.54750301243893e-01 + -4.70268695839609e-02 -3.46867170320607e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj index 968ab38c3..c28a19f9f 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.colvars.traj @@ -1,102 +1,102 @@ # step d fa_d - 100 9.94700459880913e+00 -1.70182689379045e-01 - 101 9.94458508072563e+00 -1.70182689379045e-01 - 102 9.94237837820968e+00 -1.70182689379045e-01 - 103 9.94046458309169e+00 -1.70182689379045e-01 - 104 9.93917797308190e+00 -1.70182689379045e-01 - 105 9.93831816374525e+00 -1.70182689379045e-01 - 106 9.93730879096641e+00 -1.70182689379045e-01 - 107 9.93672533958771e+00 -1.70182689379045e-01 - 108 9.93648376433042e+00 -1.70182689379045e-01 - 109 9.93652762126550e+00 -1.70182689379045e-01 - 110 9.93706371051391e+00 -1.86126457809144e-01 - 111 9.93776112437344e+00 -1.86126457809144e-01 - 112 9.93854506396815e+00 -1.86126457809144e-01 - 113 9.93918085558668e+00 -1.86126457809144e-01 - 114 9.93937655776149e+00 -1.86126457809144e-01 - 115 9.93893038769523e+00 -1.86126457809144e-01 - 116 9.93789380597970e+00 -1.86126457809144e-01 - 117 9.93662177237539e+00 -1.86126457809144e-01 - 118 9.93489575202623e+00 -1.86126457809144e-01 - 119 9.93264204575408e+00 -1.86126457809144e-01 - 120 9.93021576158670e+00 -2.01684582122971e-01 - 121 9.92745577074879e+00 -2.01684582122971e-01 - 122 9.92406367525066e+00 -2.01684582122971e-01 - 123 9.91986260614685e+00 -2.01684582122971e-01 - 124 9.91533757230742e+00 -2.01684582122971e-01 - 125 9.91093484659609e+00 -2.01684582122971e-01 - 126 9.90665292000386e+00 -2.01684582122971e-01 - 127 9.90211123575625e+00 -2.01684582122971e-01 - 128 9.89781300639078e+00 -2.01684582122971e-01 - 129 9.89406397314085e+00 -2.01684582122971e-01 - 130 9.89014114097385e+00 -2.14600526453355e-01 - 131 9.88640594807955e+00 -2.14600526453355e-01 - 132 9.88226178935358e+00 -2.14600526453355e-01 - 133 9.87820929751591e+00 -2.14600526453355e-01 - 134 9.87355012903898e+00 -2.14600526453355e-01 - 135 9.86875345004836e+00 -2.14600526453355e-01 - 136 9.86400574623842e+00 -2.14600526453355e-01 - 137 9.85896120473937e+00 -2.14600526453355e-01 - 138 9.85422081110592e+00 -2.14600526453355e-01 - 139 9.84970384401704e+00 -2.14600526453355e-01 - 140 9.84571930818557e+00 -2.23905911190324e-01 - 141 9.84162990967742e+00 -2.23905911190324e-01 - 142 9.83714753185596e+00 -2.23905911190324e-01 - 143 9.83237840767275e+00 -2.23905911190324e-01 - 144 9.82753784272710e+00 -2.23905911190324e-01 - 145 9.82322257656238e+00 -2.23905911190324e-01 - 146 9.81960403664628e+00 -2.23905911190324e-01 - 147 9.81638215506584e+00 -2.23905911190324e-01 - 148 9.81411815808055e+00 -2.23905911190324e-01 - 149 9.81186120705696e+00 -2.23905911190324e-01 - 150 9.81023976272379e+00 -2.29929522719298e-01 - 151 9.80895196959333e+00 -2.29929522719298e-01 - 152 9.80803347824830e+00 -2.29929522719298e-01 - 153 9.80725710064431e+00 -2.29929522719298e-01 - 154 9.80685628798525e+00 -2.29929522719298e-01 - 155 9.80643124588796e+00 -2.29929522719298e-01 - 156 9.80651929639905e+00 -2.29929522719298e-01 - 157 9.80658366325459e+00 -2.29929522719298e-01 - 158 9.80608274963996e+00 -2.29929522719298e-01 - 159 9.80533154240805e+00 -2.29929522719298e-01 - 160 9.80408986198415e+00 -2.35357584210514e-01 - 161 9.80243195992594e+00 -2.35357584210514e-01 - 162 9.80032235880316e+00 -2.35357584210514e-01 - 163 9.79828002793355e+00 -2.35357584210514e-01 - 164 9.79526929328518e+00 -2.35357584210514e-01 - 165 9.79205900623106e+00 -2.35357584210514e-01 - 166 9.78836209103374e+00 -2.35357584210514e-01 - 167 9.78427949895649e+00 -2.35357584210514e-01 - 168 9.77985340851435e+00 -2.35357584210514e-01 - 169 9.77597577391508e+00 -2.35357584210514e-01 - 170 9.77231657346676e+00 -2.37624973314339e-01 - 171 9.76872765210230e+00 -2.37624973314339e-01 - 172 9.76445832601357e+00 -2.37624973314339e-01 - 173 9.76039938432572e+00 -2.37624973314339e-01 - 174 9.75645215032161e+00 -2.37624973314339e-01 - 175 9.75287082046772e+00 -2.37624973314339e-01 - 176 9.74968666704269e+00 -2.37624973314339e-01 - 177 9.74684973756385e+00 -2.37624973314339e-01 - 178 9.74348360020917e+00 -2.37624973314339e-01 - 179 9.74030680111914e+00 -2.37624973314339e-01 - 180 9.73711488499836e+00 -2.36313615584043e-01 - 181 9.73433465068754e+00 -2.36313615584043e-01 - 182 9.73173780573565e+00 -2.36313615584043e-01 - 183 9.72947843607525e+00 -2.36313615584043e-01 - 184 9.72710977792195e+00 -2.36313615584043e-01 - 185 9.72467706469478e+00 -2.36313615584043e-01 - 186 9.72244089654436e+00 -2.36313615584043e-01 - 187 9.72029112628186e+00 -2.36313615584043e-01 - 188 9.71845562836040e+00 -2.36313615584043e-01 - 189 9.71680424007266e+00 -2.36313615584043e-01 - 190 9.71521749525137e+00 -2.32792461579337e-01 - 191 9.71413765244917e+00 -2.32792461579337e-01 - 192 9.71307166808760e+00 -2.32792461579337e-01 - 193 9.71195901360456e+00 -2.32792461579337e-01 - 194 9.71186724904802e+00 -2.32792461579337e-01 - 195 9.71169950721007e+00 -2.32792461579337e-01 - 196 9.71157180660297e+00 -2.32792461579337e-01 - 197 9.71177699982444e+00 -2.32792461579337e-01 - 198 9.71199162310558e+00 -2.32792461579337e-01 - 199 9.71215449719626e+00 -2.32792461579337e-01 - 200 9.71175738936231e+00 -2.28926007806402e-01 + 100 9.94700459588437e+00 -1.70182688913198e-01 + 101 9.94458507772995e+00 -1.70182688913198e-01 + 102 9.94237837514508e+00 -1.70182688913198e-01 + 103 9.94046457996010e+00 -1.70182688913198e-01 + 104 9.93917796988520e+00 -1.70182688913198e-01 + 105 9.93831816048514e+00 -1.70182688913198e-01 + 106 9.93730878764442e+00 -1.70182688913198e-01 + 107 9.93672533620511e+00 -1.70182688913198e-01 + 108 9.93648376088839e+00 -1.70182688913198e-01 + 109 9.93652761776498e+00 -1.70182688913198e-01 + 110 9.93706370695588e+00 -1.86126457148131e-01 + 111 9.93776112075882e+00 -1.86126457148131e-01 + 112 9.93854506029798e+00 -1.86126457148131e-01 + 113 9.93918085186220e+00 -1.86126457148131e-01 + 114 9.93937655398418e+00 -1.86126457148131e-01 + 115 9.93893038386686e+00 -1.86126457148131e-01 + 116 9.93789380210237e+00 -1.86126457148131e-01 + 117 9.93662176845159e+00 -1.86126457148131e-01 + 118 9.93489574805879e+00 -1.86126457148131e-01 + 119 9.93264204174611e+00 -1.86126457148131e-01 + 120 9.93021575754143e+00 -2.01684581228258e-01 + 121 9.92745576666947e+00 -2.01684581228258e-01 + 122 9.92406367114035e+00 -2.01684581228258e-01 + 123 9.91986260200830e+00 -2.01684581228258e-01 + 124 9.91533756814292e+00 -2.01684581228258e-01 + 125 9.91093484240737e+00 -2.01684581228258e-01 + 126 9.90665291579182e+00 -2.01684581228258e-01 + 127 9.90211123152112e+00 -2.01684581228258e-01 + 128 9.89781300213203e+00 -2.01684581228258e-01 + 129 9.89406396885698e+00 -2.01684581228258e-01 + 130 9.89014113666249e+00 -2.14600525240779e-01 + 131 9.88640594373758e+00 -2.14600525240779e-01 + 132 9.88226178497735e+00 -2.14600525240779e-01 + 133 9.87820929310142e+00 -2.14600525240779e-01 + 134 9.87355012458204e+00 -2.14600525240779e-01 + 135 9.86875344554473e+00 -2.14600525240779e-01 + 136 9.86400574168410e+00 -2.14600525240779e-01 + 137 9.85896120013053e+00 -2.14600525240779e-01 + 138 9.85422080643946e+00 -2.14600525240779e-01 + 139 9.84970383929048e+00 -2.14600525240779e-01 + 140 9.84571930339719e+00 -2.23905909555689e-01 + 141 9.84162990482619e+00 -2.23905909555689e-01 + 142 9.83714752694151e+00 -2.23905909555689e-01 + 143 9.83237840269532e+00 -2.23905909555689e-01 + 144 9.82753783768742e+00 -2.23905909555689e-01 + 145 9.82322257146133e+00 -2.23905909555689e-01 + 146 9.81960403148490e+00 -2.23905909555689e-01 + 147 9.81638214984508e+00 -2.23905909555689e-01 + 148 9.81411815280101e+00 -2.23905909555689e-01 + 149 9.81186120171889e+00 -2.23905909555689e-01 + 150 9.81023975732696e+00 -2.29929520564960e-01 + 151 9.80895196413704e+00 -2.29929520564960e-01 + 152 9.80803347273143e+00 -2.29929520564960e-01 + 153 9.80725709506516e+00 -2.29929520564960e-01 + 154 9.80685628234177e+00 -2.29929520564960e-01 + 155 9.80643124017792e+00 -2.29929520564960e-01 + 156 9.80651929062019e+00 -2.29929520564960e-01 + 157 9.80658365740485e+00 -2.29929520564960e-01 + 158 9.80608274371768e+00 -2.29929520564960e-01 + 159 9.80533153641205e+00 -2.29929520564960e-01 + 160 9.80408985591389e+00 -2.35357581465163e-01 + 161 9.80243195378187e+00 -2.35357581465163e-01 + 162 9.80032235258663e+00 -2.35357581465163e-01 + 163 9.79828002164672e+00 -2.35357581465163e-01 + 164 9.79526928693096e+00 -2.35357581465163e-01 + 165 9.79205899981332e+00 -2.35357581465163e-01 + 166 9.78836208455697e+00 -2.35357581465163e-01 + 167 9.78427949242546e+00 -2.35357581465163e-01 + 168 9.77985340193428e+00 -2.35357581465163e-01 + 169 9.77597576729126e+00 -2.35357581465163e-01 + 170 9.77231656680436e+00 -2.37624969895514e-01 + 171 9.76872764540608e+00 -2.37624969895514e-01 + 172 9.76445831928769e+00 -2.37624969895514e-01 + 173 9.76039937757358e+00 -2.37624969895514e-01 + 174 9.75645214354585e+00 -2.37624969895514e-01 + 175 9.75287081367028e+00 -2.37624969895514e-01 + 176 9.74968666022476e+00 -2.37624969895514e-01 + 177 9.74684973072586e+00 -2.37624969895514e-01 + 178 9.74348359335075e+00 -2.37624969895514e-01 + 179 9.74030679423950e+00 -2.37624969895514e-01 + 180 9.73711487809642e+00 -2.36313611463974e-01 + 181 9.73433464376223e+00 -2.36313611463974e-01 + 182 9.73173779878573e+00 -2.36313611463974e-01 + 183 9.72947842909980e+00 -2.36313611463974e-01 + 184 9.72710977092031e+00 -2.36313611463974e-01 + 185 9.72467705766697e+00 -2.36313611463974e-01 + 186 9.72244088949095e+00 -2.36313611463974e-01 + 187 9.72029111920384e+00 -2.36313611463974e-01 + 188 9.71845562125918e+00 -2.36313611463974e-01 + 189 9.71680423295022e+00 -2.36313611463974e-01 + 190 9.71521748810981e+00 -2.32792456745213e-01 + 191 9.71413764529071e+00 -2.32792456745213e-01 + 192 9.71307166091424e+00 -2.32792456745213e-01 + 193 9.71195900641790e+00 -2.32792456745213e-01 + 194 9.71186724184931e+00 -2.32792456745213e-01 + 195 9.71169949999982e+00 -2.32792456745213e-01 + 196 9.71157179938086e+00 -2.32792456745213e-01 + 197 9.71177699258930e+00 -2.32792456745213e-01 + 198 9.71199161585537e+00 -2.32792456745213e-01 + 199 9.71215448992823e+00 -2.32792456745213e-01 + 200 9.71175738207289e+00 -2.28926002246273e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf index 403599903..f66c76153 100644 --- a/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf +++ b/namd/tests/library/011_multiple_walker_mtd/AutoDiff/testres.rep2.pmf @@ -1,53 +1,53 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 50 0 - 2.50000000000000e-01 1.87767103667070e-01 - 7.50000000000000e-01 1.87767103667070e-01 - 1.25000000000000e+00 1.87767103667070e-01 - 1.75000000000000e+00 1.87767103667070e-01 - 2.25000000000000e+00 1.87767103667070e-01 - 2.75000000000000e+00 1.87767103667070e-01 - 3.25000000000000e+00 1.87767103667070e-01 - 3.75000000000000e+00 1.87767103667070e-01 - 4.25000000000000e+00 1.87767103667070e-01 - 4.75000000000000e+00 1.87767103667070e-01 - 5.25000000000000e+00 1.87767103667070e-01 - 5.75000000000000e+00 1.87767103667070e-01 - 6.25000000000000e+00 1.87767103667070e-01 - 6.75000000000000e+00 1.87767103667070e-01 - 7.25000000000000e+00 1.87767103667070e-01 - 7.75000000000000e+00 1.87767103667070e-01 - 8.25000000000000e+00 1.87766608979042e-01 - 8.75000000000000e+00 1.87293517703001e-01 - 9.25000000000000e+00 1.59019577359432e-01 - 9.75000000000000e+00 1.30218234746837e-02 - 1.02500000000000e+01 8.33529311278102e-02 - 1.07500000000000e+01 1.82076042006556e-01 - 1.12500000000000e+01 1.87740858074616e-01 - 1.17500000000000e+01 1.87767103667070e-01 - 1.22500000000000e+01 1.87767103667070e-01 - 1.27500000000000e+01 1.87754571320553e-01 - 1.32500000000000e+01 1.84278326274777e-01 - 1.37500000000000e+01 1.02892736669659e-01 + 2.50000000000000e-01 1.87767102998601e-01 + 7.50000000000000e-01 1.87767102998601e-01 + 1.25000000000000e+00 1.87767102998601e-01 + 1.75000000000000e+00 1.87767102998601e-01 + 2.25000000000000e+00 1.87767102998601e-01 + 2.75000000000000e+00 1.87767102998601e-01 + 3.25000000000000e+00 1.87767102998601e-01 + 3.75000000000000e+00 1.87767102998601e-01 + 4.25000000000000e+00 1.87767102998601e-01 + 4.75000000000000e+00 1.87767102998601e-01 + 5.25000000000000e+00 1.87767102998601e-01 + 5.75000000000000e+00 1.87767102998601e-01 + 6.25000000000000e+00 1.87767102998601e-01 + 6.75000000000000e+00 1.87767102998601e-01 + 7.25000000000000e+00 1.87767102998601e-01 + 7.75000000000000e+00 1.87767102998601e-01 + 8.25000000000000e+00 1.87766608310520e-01 + 8.75000000000000e+00 1.87293517006260e-01 + 9.25000000000000e+00 1.59019575947726e-01 + 9.75000000000000e+00 1.30218223817775e-02 + 1.02500000000000e+01 8.33529315497443e-02 + 1.07500000000000e+01 1.82076041439536e-01 + 1.12500000000000e+01 1.87740857406749e-01 + 1.17500000000000e+01 1.87767102998601e-01 + 1.22500000000000e+01 1.87767102998601e-01 + 1.27500000000000e+01 1.87754570651282e-01 + 1.32500000000000e+01 1.84278325485893e-01 + 1.37500000000000e+01 1.02892735014237e-01 1.42500000000000e+01 -0.00000000000000e+00 - 1.47500000000000e+01 1.50317776356913e-01 - 1.52500000000000e+01 1.87112851841236e-01 - 1.57500000000000e+01 1.87766680614282e-01 - 1.62500000000000e+01 1.87767103667070e-01 - 1.67500000000000e+01 1.87767103667070e-01 - 1.72500000000000e+01 1.87767103667070e-01 - 1.77500000000000e+01 1.87767103667070e-01 - 1.82500000000000e+01 1.87767103667070e-01 - 1.87500000000000e+01 1.87767103667070e-01 - 1.92500000000000e+01 1.87767103667070e-01 - 1.97500000000000e+01 1.87767103667070e-01 - 2.02500000000000e+01 1.87767103667070e-01 - 2.07500000000000e+01 1.87767103667070e-01 - 2.12500000000000e+01 1.87767103667070e-01 - 2.17500000000000e+01 1.87767103667070e-01 - 2.22500000000000e+01 1.87767103667070e-01 - 2.27500000000000e+01 1.87767103667070e-01 - 2.32500000000000e+01 1.87767103667070e-01 - 2.37500000000000e+01 1.87767103667070e-01 - 2.42500000000000e+01 1.87767103667070e-01 - 2.47500000000000e+01 1.87767103667070e-01 + 1.47500000000000e+01 1.50317776124501e-01 + 1.52500000000000e+01 1.87112851182683e-01 + 1.57500000000000e+01 1.87766679945813e-01 + 1.62500000000000e+01 1.87767102998601e-01 + 1.67500000000000e+01 1.87767102998601e-01 + 1.72500000000000e+01 1.87767102998601e-01 + 1.77500000000000e+01 1.87767102998601e-01 + 1.82500000000000e+01 1.87767102998601e-01 + 1.87500000000000e+01 1.87767102998601e-01 + 1.92500000000000e+01 1.87767102998601e-01 + 1.97500000000000e+01 1.87767102998601e-01 + 2.02500000000000e+01 1.87767102998601e-01 + 2.07500000000000e+01 1.87767102998601e-01 + 2.12500000000000e+01 1.87767102998601e-01 + 2.17500000000000e+01 1.87767102998601e-01 + 2.22500000000000e+01 1.87767102998601e-01 + 2.27500000000000e+01 1.87767102998601e-01 + 2.32500000000000e+01 1.87767102998601e-01 + 2.37500000000000e+01 1.87767102998601e-01 + 2.42500000000000e+01 1.87767102998601e-01 + 2.47500000000000e+01 1.87767102998601e-01 diff --git a/namd/tests/library/011_multiple_walker_mtd/namd-version.txt b/namd/tests/library/011_multiple_walker_mtd/namd-version.txt index 157cac038..e2b19c981 100644 --- a/namd/tests/library/011_multiple_walker_mtd/namd-version.txt +++ b/namd/tests/library/011_multiple_walker_mtd/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-04-09". +colvars: Using NAMD interface, version "2020-04-07". diff --git a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out index 3ff945377..6f057103a 100644 --- a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out +++ b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: Warning: no collective variables defined. colvars: Collective variables initialized, 0 in total. colvars: No collective variables biases were defined. @@ -21,6 +19,8 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration: colvars: # units = "" [default] @@ -29,7 +29,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "d0" @@ -43,28 +42,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -75,7 +74,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -100,28 +99,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -138,28 +137,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 2 atoms requested: total mass = 15.015, total charge = -0.31. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -176,28 +175,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 3 atoms requested: total mass = 16.023, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -208,7 +207,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -233,28 +232,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 14.007, total charge = -0.62. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -271,28 +270,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 2 atoms requested: total mass = 15.015, total charge = -0.31. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -309,28 +308,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 3 atoms requested: total mass = 16.023, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -347,28 +346,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 28.034, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -385,28 +384,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 5 atoms requested: total mass = 29.042, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -423,28 +422,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 6 atoms requested: total mass = 41.053, total charge = -0.27. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -461,28 +460,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 7 atoms requested: total mass = 42.061, total charge = -0.18. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -493,7 +492,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -514,26 +513,9 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (14 scalable groups, 56 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (14 scalable groups, 56 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "d0":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. colvars: Re-initialized atom group for variable "d0":0/1. 1 atoms: total mass = 1.008, total charge = 0.09. colvars: Re-initialized atom group for variable "d1":0/0. 1 atoms: total mass = 14.007, total charge = -0.62. diff --git a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj index e61993948..764d968c2 100644 --- a/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj +++ b/namd/tests/library/012_cvc_loop/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step d0 d1 d2 0 9.68028971673885e+00 2.83439401925857e+01 6.55272039460079e+01 - 1 9.68459329037158e+00 2.83503517848776e+01 6.55348311139462e+01 - 2 9.68863510077707e+00 2.83568986120102e+01 6.55435199472898e+01 - 3 9.69270450128096e+00 2.83637753155840e+01 6.55522671059708e+01 - 4 9.69567146225122e+00 2.83683142733353e+01 6.55581718660859e+01 - 5 9.69861372974800e+00 2.83728360758402e+01 6.55643117777301e+01 - 6 9.69989691772941e+00 2.83755769999054e+01 6.55687963597424e+01 - 7 9.69881248545288e+00 2.83761329500648e+01 6.55711659392461e+01 - 8 9.69696590303006e+00 2.83755659867833e+01 6.55723453523354e+01 - 9 9.69437508769387e+00 2.83738021775598e+01 6.55721051237738e+01 - 10 9.69142876298948e+00 2.83713870793780e+01 6.55715234769294e+01 - 11 9.68736616543871e+00 2.83668242786358e+01 6.55679613897708e+01 - 12 9.68269170466530e+00 2.83619773538931e+01 6.55640905410330e+01 - 13 9.67603219488243e+00 2.83539684890163e+01 6.55557350085058e+01 - 14 9.67131225666176e+00 2.83481344963114e+01 6.55501180057890e+01 - 15 9.66613278096313e+00 2.83417789198344e+01 6.55442094171420e+01 - 16 9.66208835184987e+00 2.83361112760016e+01 6.55383049475210e+01 - 17 9.65853060611532e+00 2.83296225776533e+01 6.55305098868216e+01 - 18 9.65562060404079e+00 2.83230675648197e+01 6.55226790315196e+01 - 19 9.65479770157889e+00 2.83184820767205e+01 6.55167907309241e+01 - 20 9.65474241851144e+00 2.83146389464743e+01 6.55122068151385e+01 + 1 9.68459329037381e+00 2.83503517848797e+01 6.55348311139484e+01 + 2 9.68863510078556e+00 2.83568986120180e+01 6.55435199472981e+01 + 3 9.69270450129925e+00 2.83637753156007e+01 6.55522671059886e+01 + 4 9.69567146228222e+00 2.83683142733634e+01 6.55581718661156e+01 + 5 9.69861372979398e+00 2.83728360758814e+01 6.55643117777734e+01 + 6 9.69989691779190e+00 2.83755769999609e+01 6.55687963598000e+01 + 7 9.69881248553272e+00 2.83761329501348e+01 6.55711659393180e+01 + 8 9.69696590312749e+00 2.83755659868676e+01 6.55723453524207e+01 + 9 9.69437508780854e+00 2.83738021776574e+01 6.55721051238709e+01 + 10 9.69142876312061e+00 2.83713870794876e+01 6.55715234770360e+01 + 11 9.68736616558516e+00 2.83668242787558e+01 6.55679613898842e+01 + 12 9.68269170482564e+00 2.83619773540213e+01 6.55640905411503e+01 + 13 9.67603219505517e+00 2.83539684891505e+01 6.55557350086236e+01 + 14 9.67131225684547e+00 2.83481344964496e+01 6.55501180059041e+01 + 15 9.66613278115654e+00 2.83417789199746e+01 6.55442094172513e+01 + 16 9.66208835205202e+00 2.83361112761420e+01 6.55383049476216e+01 + 17 9.65853060632552e+00 2.83296225777924e+01 6.55305098869110e+01 + 18 9.65562060425861e+00 2.83230675649562e+01 6.55226790315953e+01 + 19 9.65479770180415e+00 2.83184820768533e+01 6.55167907309839e+01 + 20 9.65474241874427e+00 2.83146389466025e+01 6.55122068151804e+01 diff --git a/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out b/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out index 2c7067791..bc4c60690 100644 --- a/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out +++ b/namd/tests/library/014_refposgroup/AutoDiff/test.Tcl.out @@ -1,100 +1,40 @@ -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013848072 0.0000000003878053 0.0000000094410965 } -TCL: TOTAL TORQUE: { 0.0000000096171986 -0.0000000667110256 0.0000000013296057 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013845900 0.0000000003876409 0.0000000094405268 } -TCL: TOTAL TORQUE: { 0.0000000095852526 -0.0000000666977762 0.0000000013328793 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013847470 0.0000000003876303 0.0000000094408976 } -TCL: TOTAL TORQUE: { 0.0000000095511905 -0.0000000666894295 0.0000000013372524 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013847025 0.0000000003881038 0.0000000094419481 } -TCL: TOTAL TORQUE: { 0.0000000095191286 -0.0000000666852835 0.0000000013450220 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013846686 0.0000000003885957 0.0000000094430159 } -TCL: TOTAL TORQUE: { 0.0000000094870103 -0.0000000666864186 0.0000000013531377 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013843890 0.0000000003892623 0.0000000094432095 } -TCL: TOTAL TORQUE: { 0.0000000094558161 -0.0000000666831221 0.0000000013625325 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013839316 0.0000000003896171 0.0000000094426439 } -TCL: TOTAL TORQUE: { 0.0000000094239665 -0.0000000666716580 0.0000000013697786 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013834814 0.0000000003898117 0.0000000094412102 } -TCL: TOTAL TORQUE: { 0.0000000093931183 -0.0000000666537403 0.0000000013755888 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013832539 0.0000000003898992 0.0000000094391743 } -TCL: TOTAL TORQUE: { 0.0000000093661994 -0.0000000666327935 0.0000000013798055 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013832885 0.0000000003903983 0.0000000094360750 } -TCL: TOTAL TORQUE: { 0.0000000093368824 -0.0000000666050974 0.0000000013869035 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013836644 0.0000000003910720 0.0000000094315508 } -TCL: TOTAL TORQUE: { 0.0000000093077337 -0.0000000665692967 0.0000000013947463 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013839568 0.0000000003916391 0.0000000094269754 } -TCL: TOTAL TORQUE: { 0.0000000092818309 -0.0000000665320030 0.0000000014013880 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013839793 0.0000000003921171 0.0000000094227682 } -TCL: TOTAL TORQUE: { 0.0000000092568291 -0.0000000664963768 0.0000000014075589 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013838283 0.0000000003926106 0.0000000094177920 } -TCL: TOTAL TORQUE: { 0.0000000092346419 -0.0000000664554638 0.0000000014134884 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013835781 0.0000000003927679 0.0000000094127447 } -TCL: TOTAL TORQUE: { 0.0000000092166221 -0.0000000664099504 0.0000000014163500 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013833556 0.0000000003930108 0.0000000094071154 } -TCL: TOTAL TORQUE: { 0.0000000091982395 -0.0000000663596005 0.0000000014197321 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013832197 0.0000000003935579 0.0000000094012935 } -TCL: TOTAL TORQUE: { 0.0000000091779127 -0.0000000663086817 0.0000000014254637 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013833440 0.0000000003940628 0.0000000093949191 } -TCL: TOTAL TORQUE: { 0.0000000091557357 -0.0000000662538246 0.0000000014308384 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013834062 0.0000000003941312 0.0000000093895322 } -TCL: TOTAL TORQUE: { 0.0000000091350936 -0.0000000662080812 0.0000000014332043 } -TCL: NUM. ATOMS REQUESTED: 6 -TCL: NUM. ATOMS USED: 6 -TCL: NUM. ATOM GROUPS USED: 0 -TCL: TOTAL FORCE: { 0.0000000013834729 0.0000000003936539 0.0000000093840155 } -TCL: TOTAL TORQUE: { 0.0000000091166648 -0.0000000661598230 0.0000000014313052 } +TCL: TOTAL FORCE: ( 1.384807019055856e-9 3.878058707496024e-10 9.441096737727861e-9 ) +TCL: TOTAL TORQUE: ( 9.617198148959005e-9 -6.671102603661438e-8 1.3296069245605224e-9 ) +TCL: TOTAL FORCE: ( 1.3845898871878148e-9 3.876407805858406e-10 9.440526915760472e-9 ) +TCL: TOTAL TORQUE: ( 9.58525481209449e-9 -6.669777796730614e-8 1.3328811387935957e-9 ) +TCL: TOTAL FORCE: ( 1.384747011501375e-9 3.876299281557749e-10 9.440897230650336e-9 ) +TCL: TOTAL TORQUE: ( 9.551191837431361e-9 -6.668942509335807e-8 1.3372550289325602e-9 ) +TCL: TOTAL FORCE: ( 1.3847027136026924e-9 3.8810379909826054e-10 9.441948223276597e-9 ) +TCL: TOTAL TORQUE: ( 9.519129040569396e-9 -6.668528440556543e-8 1.3450211500121156e-9 ) +TCL: TOTAL FORCE: ( 1.3846692126229243e-9 3.8859587769835e-10 9.44301592475938e-9 ) +TCL: TOTAL TORQUE: ( 9.487008512110151e-9 -6.668641860940738e-8 1.3531361586771595e-9 ) +TCL: TOTAL FORCE: ( 1.3843895196874456e-9 3.892627331580911e-10 9.443209769699479e-9 ) +TCL: TOTAL TORQUE: ( 9.455814797831863e-9 -6.668312035884583e-8 1.3625308659115376e-9 ) +TCL: TOTAL FORCE: ( 1.3839312196228803e-9 3.896173383921564e-10 9.442643722490374e-9 ) +TCL: TOTAL TORQUE: ( 9.423963831522997e-9 -6.66716588604288e-8 1.3697779022159295e-9 ) +TCL: TOTAL FORCE: ( 1.3834813572533022e-9 3.8981154415473895e-10 9.441210035987524e-9 ) +TCL: TOTAL TORQUE: ( 9.39311961545286e-9 -6.665373897263294e-8 1.375589642194086e-9 ) +TCL: TOTAL FORCE: ( 1.383253483977498e-9 3.8989927952925996e-10 9.43917471962763e-9 ) +TCL: TOTAL TORQUE: ( 9.36619892755175e-9 -6.663279394913957e-8 1.3798079900873006e-9 ) +TCL: TOTAL FORCE: ( 1.383288567025076e-9 3.903983525344046e-10 9.43607558756554e-9 ) +TCL: TOTAL TORQUE: ( 9.336882378363498e-9 -6.660509610512122e-8 1.3869025372592603e-9 ) +TCL: TOTAL FORCE: ( 1.3836645162967898e-9 3.910716472876885e-10 9.431551373229041e-9 ) +TCL: TOTAL TORQUE: ( 9.307735915342619e-9 -6.656929452120153e-8 1.3947462074170858e-9 ) +TCL: TOTAL FORCE: ( 1.383956810263598e-9 3.916388602309695e-10 9.426974978410385e-9 ) +TCL: TOTAL TORQUE: ( 9.281833523999694e-9 -6.653200479433963e-8 1.4013895599518378e-9 ) +TCL: TOTAL FORCE: ( 1.3839795143244515e-9 3.9211683899864624e-10 9.422767954792022e-9 ) +TCL: TOTAL TORQUE: ( 9.256830413306716e-9 -6.64963777374794e-8 1.4075592358331335e-9 ) +TCL: TOTAL FORCE: ( 1.3838287182821318e-9 3.9261055517769705e-10 9.417791990706803e-9 ) +TCL: TOTAL TORQUE: ( 9.234642384114977e-9 -6.64554629103975e-8 1.4134880488292367e-9 ) +TCL: TOTAL FORCE: ( 1.3835778911452934e-9 3.927678460247108e-10 9.412744972348008e-9 ) +TCL: TOTAL TORQUE: ( 9.216622132157681e-9 -6.640994820727997e-8 1.4163497041863593e-9 ) +TCL: TOTAL FORCE: ( 1.3833555689846122e-9 3.9301065180019634e-10 9.407115364457042e-9 ) +TCL: TOTAL TORQUE: ( 9.198239947494358e-9 -6.635960181355927e-8 1.4197321096531823e-9 ) +TCL: TOTAL FORCE: ( 1.3832198719754274e-9 3.9355749215097546e-10 9.401293632471663e-9 ) +TCL: TOTAL TORQUE: ( 9.17791531662715e-9 -6.630868121249023e-8 1.425466855664581e-9 ) +TCL: TOTAL FORCE: ( 1.3833443557320635e-9 3.940626436271799e-10 9.394919009420022e-9 ) +TCL: TOTAL TORQUE: ( 9.155735281041189e-9 -6.625382553693271e-8 1.4308377815908102e-9 ) +TCL: TOTAL FORCE: ( 1.383406056376657e-9 3.941313664324042e-10 9.38953176321533e-9 ) +TCL: TOTAL TORQUE: ( 9.135093126388938e-9 -6.620808390422894e-8 1.4332044995235549e-9 ) +TCL: TOTAL FORCE: ( 1.3834732248696469e-9 3.936540260429666e-10 9.384015065005968e-9 ) +TCL: TOTAL TORQUE: ( 9.11666298009095e-9 -6.615982339752691e-8 1.4313049634395725e-9 ) diff --git a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out index 90737e554..c84bb7e88 100644 --- a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out +++ b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 0 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "r" @@ -27,25 +25,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 5 atoms requested: total mass = 60.055, total charge = 0.35. @@ -66,7 +64,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -94,7 +92,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.1 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "r" will be rescaled to 0.1 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -105,29 +102,13 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (6 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "r":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (6 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "r":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: The final output state file will be "test.colvars.state". colvars: Debugging gradients for cvc rmsd0001 @@ -151,11 +132,11 @@ colvars: dx(interp) = -1.35149604087641e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.75153e-07 colvars: refPosGroup atom 0, component 0: colvars: dx(actual) = -1.32256818830001e-08 -colvars: dx(interp) = -1.32256806784028e-08 +colvars: dx(interp) = -1.32256806784027e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.10802e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.65148816633609e-09 -colvars: dx(interp) = 5.65148916474421e-09 +colvars: dx(interp) = 5.65148916474418e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.76663e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70015094119935e-08 @@ -183,7 +164,7 @@ colvars: dx(interp) = 1.64047652855846e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.00693e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44798905777589e-09 -colvars: dx(interp) = 9.44799082028362e-09 +colvars: dx(interp) = 9.44799082028361e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.86548e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.49833905283003e-08 @@ -209,7 +190,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02938776286510e-08 colvars: dx(interp) = 3.02938806702505e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.00403e-07. -colvars: Gradient sum: ( 0.973323 , -0.185412 , -0.13515 ) Fit gradient sum: ( -0.973323 , 0.185412 , 0.13515 ) Total ( -3.33067e-16 , 3.05311e-16 , 5.55112e-17 ) +colvars: Gradient sum: ( 0.973323 , -0.185412 , -0.13515 ) Fit gradient sum: ( -0.973323 , 0.185412 , 0.13515 ) Total ( -1.11022e-16 , -5.55112e-17 , -2.22045e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234785 , 0.269301 , -0.173026 ) @@ -251,7 +232,7 @@ colvars: dx(interp) = 8.53838213116278e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.71227e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.15095546613520e-10 -colvars: dx(interp) = 8.15096690566031e-10 +colvars: dx(interp) = 8.15096690566021e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.40346e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26069001693941e-08 @@ -271,11 +252,11 @@ colvars: dx(interp) = -1.49873663013446e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.94117e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.07673869820246e-09 -colvars: dx(interp) = 1.07674116921778e-09 +colvars: dx(interp) = 1.07674116921777e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.29491e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.95859750219097e-09 -colvars: dx(interp) = 9.95860073923380e-09 +colvars: dx(interp) = 9.95860073923379e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.25050e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43292595566891e-08 @@ -289,7 +270,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02918081729331e-08 colvars: dx(interp) = 3.02918110782712e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.59117e-08. -colvars: Gradient sum: ( 0.973303 , -0.185528 , -0.135131 ) Fit gradient sum: ( -0.973303 , 0.185528 , 0.135131 ) Total ( 0 , -2.22045e-16 , 1.94289e-16 ) +colvars: Gradient sum: ( 0.973303 , -0.185528 , -0.135131 ) Fit gradient sum: ( -0.973303 , 0.185528 , 0.135131 ) Total ( 1.11022e-16 , -1.11022e-16 , 2.77556e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234756 , 0.269374 , -0.172978 ) @@ -331,7 +312,7 @@ colvars: dx(interp) = 8.53613239284918e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.92870e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.18408452119002e-10 -colvars: dx(interp) = 8.18402186831441e-10 +colvars: dx(interp) = 8.18402186831449e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.65545e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26106322951136e-08 @@ -343,7 +324,7 @@ colvars: dx(interp) = 1.64127071165021e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.64922e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44612565945135e-09 -colvars: dx(interp) = 9.44611973805957e-09 +colvars: dx(interp) = 9.44611973805956e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.26859e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.49949652694659e-08 @@ -351,7 +332,7 @@ colvars: dx(interp) = -1.49949667603800e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.94276e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.08642161933403e-09 -colvars: dx(interp) = 1.08642112294382e-09 +colvars: dx(interp) = 1.08642112294384e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.56904e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.95594184871607e-09 @@ -359,7 +340,7 @@ colvars: dx(interp) = 9.95594165715356e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.92410e-08. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43341960523458e-08 -colvars: dx(interp) = 1.43341893744116e-08 +colvars: dx(interp) = 1.43341893744115e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.65874e-07. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.30965638334146e-08 @@ -369,7 +350,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02961637999033e-08 colvars: dx(interp) = 3.02961588118116e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.64644e-07. -colvars: Gradient sum: ( 0.973277 , -0.185665 , -0.135133 ) Fit gradient sum: ( -0.973277 , 0.185665 , 0.135133 ) Total ( 0 , -2.77556e-17 , -1.66533e-16 ) +colvars: Gradient sum: ( 0.973277 , -0.185665 , -0.135133 ) Fit gradient sum: ( -0.973277 , 0.185665 , 0.135133 ) Total ( 0 , 2.77556e-16 , -5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234717 , 0.269457 , -0.172922 ) @@ -391,11 +372,11 @@ colvars: dx(interp) = -1.35095571144321e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.93919e-08 colvars: refPosGroup atom 0, component 0: colvars: dx(actual) = -1.32276785080876e-08 -colvars: dx(interp) = -1.32276807821041e-08 +colvars: dx(interp) = -1.32276807821042e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.71914e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.61136204169088e-09 -colvars: dx(interp) = 5.61135643011218e-09 +colvars: dx(interp) = 5.61135643011219e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.00004e-06. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70074335620529e-08 @@ -403,19 +384,19 @@ colvars: dx(interp) = -3.70074373671765e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.02821e-07. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.08169099128008e-08 -colvars: dx(interp) = -3.08169108969143e-08 +colvars: dx(interp) = -3.08169108969144e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.19342e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53347614793165e-09 -colvars: dx(interp) = 8.53347204237835e-09 +colvars: dx(interp) = 8.53347204237836e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.81111e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.19884604652543e-10 -colvars: dx(interp) = 8.19880913108474e-10 +colvars: dx(interp) = 8.19880913108477e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.50252e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26149719348723e-08 -colvars: dx(interp) = -5.26149677696460e-08 +colvars: dx(interp) = -5.26149677696461e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.91643e-08. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64202287322723e-08 @@ -423,7 +404,7 @@ colvars: dx(interp) = 1.64202293878008e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.99220e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44173628170120e-09 -colvars: dx(interp) = 9.44173782371806e-09 +colvars: dx(interp) = 9.44173782371807e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.63319e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50037209323273e-08 @@ -449,7 +430,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03022300585098e-08 colvars: dx(interp) = 3.03022309014118e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.78165e-08. -colvars: Gradient sum: ( 0.973258 , -0.185792 , -0.135096 ) Fit gradient sum: ( -0.973258 , 0.185792 , 0.135096 ) Total ( 0 , -1.38778e-16 , -5.55112e-17 ) +colvars: Gradient sum: ( 0.973258 , -0.185792 , -0.135096 ) Fit gradient sum: ( -0.973258 , 0.185792 , 0.135096 ) Total ( -2.22045e-16 , -2.77556e-17 , 0 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234673 , 0.269532 , -0.172868 ) @@ -479,11 +460,11 @@ colvars: dx(interp) = 5.59468663743374e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.84774e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70104338287547e-08 -colvars: dx(interp) = -3.70104348510150e-08 +colvars: dx(interp) = -3.70104348510151e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.76209e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.08071026466905e-08 -colvars: dx(interp) = -3.08070979989617e-08 +colvars: dx(interp) = -3.08070979989616e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.50865e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53082937624094e-09 @@ -491,11 +472,11 @@ colvars: dx(interp) = 8.53082896971171e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.76541e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.21989587507232e-10 -colvars: dx(interp) = 8.21992304895591e-10 +colvars: dx(interp) = 8.21992304895594e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.30587e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26181160864780e-08 -colvars: dx(interp) = -5.26181139628721e-08 +colvars: dx(interp) = -5.26181139628722e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.03588e-08. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64276485747905e-08 @@ -503,7 +484,7 @@ colvars: dx(interp) = 1.64276457374503e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.72717e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43767197725265e-09 -colvars: dx(interp) = 9.43767316290166e-09 +colvars: dx(interp) = 9.43767316290167e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.25629e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50121302056050e-08 @@ -511,11 +492,11 @@ colvars: dx(interp) = -1.50121288821272e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.81606e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.10627063065749e-09 -colvars: dx(interp) = 1.10626880712029e-09 +colvars: dx(interp) = 1.10626880712028e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.64836e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94974769241708e-09 -colvars: dx(interp) = 9.94974605686307e-09 +colvars: dx(interp) = 9.94974605686308e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.64381e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43403262597985e-08 @@ -529,7 +510,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03069658258437e-08 colvars: dx(interp) = 3.03069655364643e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.54828e-09. -colvars: Gradient sum: ( 0.973239 , -0.185915 , -0.135059 ) Fit gradient sum: ( -0.973239 , 0.185915 , 0.135059 ) Total ( 0 , 2.22045e-16 , -1.38778e-16 ) +colvars: Gradient sum: ( 0.973239 , -0.185915 , -0.135059 ) Fit gradient sum: ( -0.973239 , 0.185915 , 0.135059 ) Total ( -2.22045e-16 , 2.77556e-17 , -1.11022e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234607 , 0.269564 , -0.172831 ) @@ -555,7 +536,7 @@ colvars: dx(interp) = -1.32278620619718e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.45370e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.58072343892491e-09 -colvars: dx(interp) = 5.58072846304628e-09 +colvars: dx(interp) = 5.58072846304627e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.00263e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.70086290502059e-08 @@ -567,11 +548,11 @@ colvars: dx(interp) = -3.07984711538700e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.33569e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.52902282133527e-09 -colvars: dx(interp) = 8.52902381842602e-09 +colvars: dx(interp) = 8.52902381842601e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.16906e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.21517076587952e-10 -colvars: dx(interp) = 8.21520935813326e-10 +colvars: dx(interp) = 8.21520935813319e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.69768e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26158636660057e-08 @@ -583,7 +564,7 @@ colvars: dx(interp) = 1.64322611396739e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.85733e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43348865689586e-09 -colvars: dx(interp) = 9.43349355322967e-09 +colvars: dx(interp) = 9.43349355322966e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.19037e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50185890390730e-08 @@ -591,7 +572,7 @@ colvars: dx(interp) = -1.50185908462051e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.20326e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.11479359077293e-09 -colvars: dx(interp) = 1.11479734212101e-09 +colvars: dx(interp) = 1.11479734212100e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.36506e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94741355953010e-09 @@ -609,7 +590,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03068983242838e-08 colvars: dx(interp) = 3.03068956667397e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.76878e-08. -colvars: Gradient sum: ( 0.973222 , -0.186041 , -0.135007 ) Fit gradient sum: ( -0.973222 , 0.186041 , 0.135007 ) Total ( -1.11022e-16 , 1.66533e-16 , 1.11022e-16 ) +colvars: Gradient sum: ( 0.973222 , -0.186041 , -0.135007 ) Fit gradient sum: ( -0.973222 , 0.186041 , 0.135007 ) Total ( -1.11022e-16 , -2.498e-16 , 0 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234537 , 0.269561 , -0.17281 ) @@ -647,11 +628,11 @@ colvars: dx(interp) = -3.07916615664810e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.56497e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.52869419531999e-09 -colvars: dx(interp) = 8.52868892238300e-09 +colvars: dx(interp) = 8.52868892238299e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.18258e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.19877499225186e-10 -colvars: dx(interp) = 8.19875243528284e-10 +colvars: dx(interp) = 8.19875243528287e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.75126e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26105150555622e-08 @@ -683,13 +664,13 @@ colvars: dx(interp) = 1.43339758956300e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.78098e-09. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.30378747797977e-08 -colvars: dx(interp) = -1.30378745728901e-08 +colvars: dx(interp) = -1.30378745728902e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.58697e-08. colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03053191430536e-08 colvars: dx(interp) = 3.03053173599431e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.88382e-08. -colvars: Gradient sum: ( 0.973204 , -0.186178 , -0.134953 ) Fit gradient sum: ( -0.973204 , 0.186178 , 0.134953 ) Total ( 0 , 0 , -4.16334e-16 ) +colvars: Gradient sum: ( 0.973204 , -0.186178 , -0.134953 ) Fit gradient sum: ( -0.973204 , 0.186178 , 0.134953 ) Total ( 3.33067e-16 , -1.66533e-16 , -1.94289e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234465 , 0.26953 , -0.172803 ) @@ -727,11 +708,11 @@ colvars: dx(interp) = -3.07862418575286e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.39617e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.52950954310927e-09 -colvars: dx(interp) = 8.52950262791878e-09 +colvars: dx(interp) = 8.52950262791877e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.10737e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.18326739704389e-10 -colvars: dx(interp) = 8.18323711303208e-10 +colvars: dx(interp) = 8.18323711303201e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.70072e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.26022727598274e-08 @@ -743,7 +724,7 @@ colvars: dx(interp) = 1.64395237187071e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.28199e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.42581479534965e-09 -colvars: dx(interp) = 9.42581605591191e-09 +colvars: dx(interp) = 9.42581605591192e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.33735e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50253089969965e-08 @@ -751,7 +732,7 @@ colvars: dx(interp) = -1.50253124431236e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.29355e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.12816245234626e-09 -colvars: dx(interp) = 1.12815789618417e-09 +colvars: dx(interp) = 1.12815789618418e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.03857e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94434401491162e-09 @@ -769,7 +750,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.03002405388497e-08 colvars: dx(interp) = 3.03002411548953e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.03314e-08. -colvars: Gradient sum: ( 0.973182 , -0.186322 , -0.134914 ) Fit gradient sum: ( -0.973182 , 0.186322 , 0.134914 ) Total ( -2.22045e-16 , 8.32667e-17 , 0 ) +colvars: Gradient sum: ( 0.973182 , -0.186322 , -0.134914 ) Fit gradient sum: ( -0.973182 , 0.186322 , 0.134914 ) Total ( -3.33067e-16 , 1.38778e-16 , -8.32667e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.2344 , 0.269471 , -0.172812 ) @@ -795,7 +776,7 @@ colvars: dx(interp) = -1.32356119387801e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.51720e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.55776402677566e-09 -colvars: dx(interp) = 5.55776415678252e-09 +colvars: dx(interp) = 5.55776415678251e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.33919e-08. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.69885455597796e-08 @@ -803,15 +784,15 @@ colvars: dx(interp) = -3.69885421692242e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.16650e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.07832497270510e-08 -colvars: dx(interp) = -3.07832430368368e-08 +colvars: dx(interp) = -3.07832430368367e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.17333e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53208881324008e-09 -colvars: dx(interp) = 8.53209051317432e-09 +colvars: dx(interp) = 8.53209051317431e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.99240e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.16180900642394e-10 -colvars: dx(interp) = 8.16182049051563e-10 +colvars: dx(interp) = 8.16182049051574e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.40705e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25918135707570e-08 @@ -827,7 +808,7 @@ colvars: dx(interp) = 9.42484522140630e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.10575e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50250638597527e-08 -colvars: dx(interp) = -1.50250574958697e-08 +colvars: dx(interp) = -1.50250574958698e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.23551e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.13177911487128e-09 @@ -835,11 +816,11 @@ colvars: dx(interp) = 1.13178194955547e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.50463e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94482007854458e-09 -colvars: dx(interp) = 9.94482275879587e-09 +colvars: dx(interp) = 9.94482275879586e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.69512e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43201948077376e-08 -colvars: dx(interp) = 1.43202002666372e-08 +colvars: dx(interp) = 1.43202002666371e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.81203e-07. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.30169226508769e-08 @@ -849,7 +830,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02934708429348e-08 colvars: dx(interp) = 3.02934722035031e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.49129e-08. -colvars: Gradient sum: ( 0.973155 , -0.186464 , -0.134908 ) Fit gradient sum: ( -0.973155 , 0.186464 , 0.134908 ) Total ( -1.11022e-16 , 1.11022e-16 , 2.77556e-16 ) +colvars: Gradient sum: ( 0.973155 , -0.186464 , -0.134908 ) Fit gradient sum: ( -0.973155 , 0.186464 , 0.134908 ) Total ( 3.33067e-16 , 0 , -5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234296 , 0.269417 , -0.172808 ) @@ -875,7 +856,7 @@ colvars: dx(interp) = -1.32422526736177e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.36098e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.55336931995498e-09 -colvars: dx(interp) = 5.55337024450270e-09 +colvars: dx(interp) = 5.55337024450271e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.66484e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.69760897456217e-08 @@ -887,11 +868,11 @@ colvars: dx(interp) = -3.07767415223223e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.03519e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53379233944906e-09 -colvars: dx(interp) = 8.53379552462336e-09 +colvars: dx(interp) = 8.53379552462335e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.73243e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.17991008261743e-10 -colvars: dx(interp) = 8.17993039794563e-10 +colvars: dx(interp) = 8.17993039794562e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.48356e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25781533866621e-08 @@ -903,7 +884,7 @@ colvars: dx(interp) = 1.64451465632283e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.31202e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.42628552991209e-09 -colvars: dx(interp) = 9.42628948602318e-09 +colvars: dx(interp) = 9.42628948602319e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.19689e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50267567278206e-08 @@ -911,11 +892,11 @@ colvars: dx(interp) = -1.50267515866314e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.42136e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.13714904159679e-09 -colvars: dx(interp) = 1.13714937112551e-09 +colvars: dx(interp) = 1.13714937112552e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.89785e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94296200929057e-09 -colvars: dx(interp) = 9.94296464169271e-09 +colvars: dx(interp) = 9.94296464169270e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.64750e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43117819817462e-08 @@ -929,7 +910,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02822567022076e-08 colvars: dx(interp) = 3.02822597447637e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.00473e-07. -colvars: Gradient sum: ( 0.973121 , -0.186623 , -0.134934 ) Fit gradient sum: ( -0.973121 , 0.186623 , 0.134934 ) Total ( -2.22045e-16 , 1.11022e-16 , -8.32667e-17 ) +colvars: Gradient sum: ( 0.973121 , -0.186623 , -0.134934 ) Fit gradient sum: ( -0.973121 , 0.186623 , 0.134934 ) Total ( -1.11022e-16 , 1.11022e-16 , -3.88578e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234174 , 0.269337 , -0.172813 ) @@ -963,15 +944,15 @@ colvars: dx(interp) = -3.69593977936285e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.28040e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.07704990376578e-08 -colvars: dx(interp) = -3.07704988193405e-08 +colvars: dx(interp) = -3.07704988193406e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.09502e-09. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53549586565805e-09 -colvars: dx(interp) = 8.53549862619538e-09 +colvars: dx(interp) = 8.53549862619539e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.23419e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.20783441213280e-10 -colvars: dx(interp) = 8.20780197348801e-10 +colvars: dx(interp) = 8.20780197348790e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.95216e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25603880419112e-08 @@ -983,7 +964,7 @@ colvars: dx(interp) = 1.64463866462574e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.80441e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43124334185086e-09 -colvars: dx(interp) = 9.43124625857663e-09 +colvars: dx(interp) = 9.43124625857664e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.09262e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50269396925751e-08 @@ -995,7 +976,7 @@ colvars: dx(interp) = 1.14190518785238e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.20873e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94215909599916e-09 -colvars: dx(interp) = 9.94215964550208e-09 +colvars: dx(interp) = 9.94215964550207e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.52700e-08. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.43026106513844e-08 @@ -1009,7 +990,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02664240336981e-08 colvars: dx(interp) = 3.02664253559446e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.36869e-08. -colvars: Gradient sum: ( 0.973081 , -0.186777 , -0.135012 ) Fit gradient sum: ( -0.973081 , 0.186777 , 0.135012 ) Total ( 1.11022e-16 , 8.32667e-17 , 2.498e-16 ) +colvars: Gradient sum: ( 0.973081 , -0.186777 , -0.135012 ) Fit gradient sum: ( -0.973081 , 0.186777 , 0.135012 ) Total ( 0 , 2.77556e-16 , -2.22045e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.234049 , 0.269251 , -0.172818 ) @@ -1035,7 +1016,7 @@ colvars: dx(interp) = -1.32624504625399e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.50484e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.54771517613517e-09 -colvars: dx(interp) = 5.54771226834331e-09 +colvars: dx(interp) = 5.54771226834333e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.24142e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.69424064672330e-08 @@ -1047,11 +1028,11 @@ colvars: dx(interp) = -3.07644895154988e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.47710e-09. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53744630546771e-09 -colvars: dx(interp) = 8.53744794265352e-09 +colvars: dx(interp) = 8.53744794265350e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.91765e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.23895618395909e-10 -colvars: dx(interp) = 8.23894751207842e-10 +colvars: dx(interp) = 8.23894751207838e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.05255e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25424947994679e-08 @@ -1063,7 +1044,7 @@ colvars: dx(interp) = 1.64481466417069e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.82325e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43529698815837e-09 -colvars: dx(interp) = 9.43529750666335e-09 +colvars: dx(interp) = 9.43529750666334e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.49538e-08. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50270977883338e-08 @@ -1075,7 +1056,7 @@ colvars: dx(interp) = 1.14616428729916e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.44466e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.94072202331608e-09 -colvars: dx(interp) = 9.94071820020490e-09 +colvars: dx(interp) = 9.94071820020491e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.84591e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42922811363633e-08 @@ -1089,7 +1070,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02509981509047e-08 colvars: dx(interp) = 3.02509964189633e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.72524e-08. -colvars: Gradient sum: ( 0.973043 , -0.186923 , -0.135085 ) Fit gradient sum: ( -0.973043 , 0.186923 , 0.135085 ) Total ( -1.11022e-16 , 5.55112e-17 , 5.55112e-17 ) +colvars: Gradient sum: ( 0.973043 , -0.186923 , -0.135085 ) Fit gradient sum: ( -0.973043 , 0.186923 , 0.135085 ) Total ( 1.11022e-16 , 2.22045e-16 , 2.77556e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233924 , 0.269169 , -0.17282 ) @@ -1127,11 +1108,11 @@ colvars: dx(interp) = -3.07585788706113e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.46834e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53809289935725e-09 -colvars: dx(interp) = 8.53808936876943e-09 +colvars: dx(interp) = 8.53808936876944e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.13510e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.26105406304123e-10 -colvars: dx(interp) = 8.26104904082130e-10 +colvars: dx(interp) = 8.26104904082126e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.07939e-07. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25262713324537e-08 @@ -1143,7 +1124,7 @@ colvars: dx(interp) = 1.64489014094928e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.75055e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43667011199523e-09 -colvars: dx(interp) = 9.43666776859373e-09 +colvars: dx(interp) = 9.43666776859372e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.48329e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50279149124799e-08 @@ -1151,7 +1132,7 @@ colvars: dx(interp) = -1.50279164684174e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.03536e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.15079323848022e-09 -colvars: dx(interp) = 1.15079570362507e-09 +colvars: dx(interp) = 1.15079570362508e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.14213e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.93875737265171e-09 @@ -1169,7 +1150,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02379525862762e-08 colvars: dx(interp) = 3.02379521612961e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.40545e-08. -colvars: Gradient sum: ( 0.973014 , -0.187041 , -0.135129 ) Fit gradient sum: ( -0.973014 , 0.187041 , 0.135129 ) Total ( 1.11022e-16 , -1.11022e-16 , 0 ) +colvars: Gradient sum: ( 0.973014 , -0.187041 , -0.135129 ) Fit gradient sum: ( -0.973014 , 0.187041 , 0.135129 ) Total ( 0 , 8.32667e-17 , 1.11022e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233783 , 0.269072 , -0.172824 ) @@ -1211,7 +1192,7 @@ colvars: dx(interp) = 8.53851757305771e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.45711e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.28652702011823e-10 -colvars: dx(interp) = 8.28651094684910e-10 +colvars: dx(interp) = 8.28651094684908e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.93969e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.25080263713562e-08 @@ -1219,7 +1200,7 @@ colvars: dx(interp) = -5.25080262626950e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.06942e-09. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64482276687750e-08 -colvars: dx(interp) = 1.64482285289397e-08 +colvars: dx(interp) = 1.64482285289396e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.22953e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43820843701815e-09 @@ -1243,13 +1224,13 @@ colvars: dx(interp) = 1.42696604177533e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.65875e-07. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.29644650570526e-08 -colvars: dx(interp) = -1.29644631624477e-08 +colvars: dx(interp) = -1.29644631624476e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.46138e-07. colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02220222181404e-08 colvars: dx(interp) = 3.02220270034202e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.58338e-07. -colvars: Gradient sum: ( 0.972987 , -0.187152 , -0.135166 ) Fit gradient sum: ( -0.972987 , 0.187152 , 0.135166 ) Total ( -1.11022e-16 , 5.55112e-17 , -8.32667e-17 ) +colvars: Gradient sum: ( 0.972987 , -0.187152 , -0.135166 ) Fit gradient sum: ( -0.972987 , 0.187152 , 0.135166 ) Total ( -2.22045e-16 , 5.55112e-17 , -2.498e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233652 , 0.268975 , -0.172829 ) @@ -1275,7 +1256,7 @@ colvars: dx(interp) = -1.32848260553267e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.79536e-08. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.53572121475554e-09 -colvars: dx(interp) = 5.53571877378612e-09 +colvars: dx(interp) = 5.53571877378613e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.40949e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68913646298097e-08 @@ -1287,11 +1268,11 @@ colvars: dx(interp) = -3.07470135653119e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.93636e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.53970405501059e-09 -colvars: dx(interp) = 8.53970370599940e-09 +colvars: dx(interp) = 8.53970370599939e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.08692e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.31423818681287e-10 -colvars: dx(interp) = 8.31424273287314e-10 +colvars: dx(interp) = 8.31424273287319e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.46780e-07. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24915630961686e-08 @@ -1303,7 +1284,7 @@ colvars: dx(interp) = 1.64490443312681e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.36057e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43796862884483e-09 -colvars: dx(interp) = 9.43796707135715e-09 +colvars: dx(interp) = 9.43796707135716e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.65024e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50295562661995e-08 @@ -1315,7 +1296,7 @@ colvars: dx(interp) = 1.15783892166374e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.03950e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.93288296058381e-09 -colvars: dx(interp) = 9.93288148106967e-09 +colvars: dx(interp) = 9.93288148106965e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.48951e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42566420890944e-08 @@ -1329,7 +1310,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.02093123849545e-08 colvars: dx(interp) = 3.02093113112382e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.55426e-08. -colvars: Gradient sum: ( 0.972963 , -0.187251 , -0.135202 ) Fit gradient sum: ( -0.972963 , 0.187251 , 0.135202 ) Total ( 0 , 0 , 5.55112e-17 ) +colvars: Gradient sum: ( 0.972963 , -0.187251 , -0.135202 ) Fit gradient sum: ( -0.972963 , 0.187251 , 0.135202 ) Total ( 0 , -2.77556e-17 , -5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233501 , 0.268891 , -0.17282 ) @@ -1383,7 +1364,7 @@ colvars: dx(interp) = 1.64524625852538e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.02999e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.43822975330022e-09 -colvars: dx(interp) = 9.43822725654554e-09 +colvars: dx(interp) = 9.43822725654555e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.64536e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50321763925376e-08 @@ -1400,7 +1381,7 @@ colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.12540e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42431844096791e-08 colvars: dx(interp) = 1.42431843748016e-08 -colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.44872e-09. +colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.44871e-09. colvars: refPosGroup atom 4, component 1: colvars: dx(actual) = -1.29516273261743e-08 colvars: dx(interp) = -1.29516244952331e-08 @@ -1409,7 +1390,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01953040349190e-08 colvars: dx(interp) = 3.01953067756868e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.07680e-08. -colvars: Gradient sum: ( 0.972936 , -0.18736 , -0.135247 ) Fit gradient sum: ( -0.972936 , 0.18736 , 0.135247 ) Total ( -1.11022e-16 , 1.11022e-16 , -5.55112e-17 ) +colvars: Gradient sum: ( 0.972936 , -0.18736 , -0.135247 ) Fit gradient sum: ( -0.972936 , 0.18736 , 0.135247 ) Total ( -3.33067e-16 , 1.94289e-16 , 2.77556e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233334 , 0.268839 , -0.172792 ) @@ -1435,7 +1416,7 @@ colvars: dx(interp) = -1.32982975870102e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.68116e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.52796031172420e-09 -colvars: dx(interp) = 5.52796395730564e-09 +colvars: dx(interp) = 5.52796395730563e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.59480e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68559884833530e-08 @@ -1451,7 +1432,7 @@ colvars: dx(interp) = 8.54029141083031e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.23973e-08. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.48276116016677e-10 -colvars: dx(interp) = 8.48275187664032e-10 +colvars: dx(interp) = 8.48275187664044e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.09440e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24580787697460e-08 @@ -1463,7 +1444,7 @@ colvars: dx(interp) = 1.64581994897726e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.86623e-08. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44032407801387e-09 -colvars: dx(interp) = 9.44032745458435e-09 +colvars: dx(interp) = 9.44032745458434e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.57675e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50375996099683e-08 @@ -1471,7 +1452,7 @@ colvars: dx(interp) = -1.50376008458710e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 8.21875e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.16808074324126e-09 -colvars: dx(interp) = 1.16807984581743e-09 +colvars: dx(interp) = 1.16807984581744e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.68289e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.91784787629513e-09 @@ -1489,7 +1470,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01791249768257e-08 colvars: dx(interp) = 3.01791291797173e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.39265e-07. -colvars: Gradient sum: ( 0.972906 , -0.187482 , -0.135296 ) Fit gradient sum: ( -0.972906 , 0.187482 , 0.135296 ) Total ( -1.11022e-16 , -1.66533e-16 , 5.55112e-17 ) +colvars: Gradient sum: ( 0.972906 , -0.187482 , -0.135296 ) Fit gradient sum: ( -0.972906 , 0.187482 , 0.135296 ) Total ( -3.33067e-16 , 1.66533e-16 , -5.55112e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233163 , 0.26881 , -0.172755 ) @@ -1515,7 +1496,7 @@ colvars: dx(interp) = -1.33079579182108e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.61708e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.52538281795023e-09 -colvars: dx(interp) = 5.52538365273264e-09 +colvars: dx(interp) = 5.52538365273265e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.51081e-07. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68380721482708e-08 @@ -1527,11 +1508,11 @@ colvars: dx(interp) = -3.07143629147814e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.96154e-09. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.54108606063164e-09 -colvars: dx(interp) = 8.54108462786948e-09 +colvars: dx(interp) = 8.54108462786949e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.67749e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.63986215904333e-10 -colvars: dx(interp) = 8.63984483685957e-10 +colvars: dx(interp) = 8.63984483685953e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.00491e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24407806068439e-08 @@ -1551,7 +1532,7 @@ colvars: dx(interp) = -1.50443213074023e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.15626e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.17551302025731e-09 -colvars: dx(interp) = 1.17551172995610e-09 +colvars: dx(interp) = 1.17551172995609e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.09765e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.90585391491550e-09 @@ -1569,7 +1550,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01599225593918e-08 colvars: dx(interp) = 3.01599231791652e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.05496e-08. -colvars: Gradient sum: ( 0.972861 , -0.187655 , -0.135377 ) Fit gradient sum: ( -0.972861 , 0.187655 , 0.135377 ) Total ( 0 , -1.66533e-16 , -2.22045e-16 ) +colvars: Gradient sum: ( 0.972861 , -0.187655 , -0.135377 ) Fit gradient sum: ( -0.972861 , 0.187655 , 0.135377 ) Total ( -4.44089e-16 , -2.77556e-17 , -8.32667e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.233016 , 0.268793 , -0.172714 ) @@ -1603,7 +1584,7 @@ colvars: dx(interp) = -3.68237786462595e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.36274e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.07013916511778e-08 -colvars: dx(interp) = -3.07013933891594e-08 +colvars: dx(interp) = -3.07013933891593e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.66092e-08. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.54437764985505e-09 @@ -1611,11 +1592,11 @@ colvars: dx(interp) = 8.54437233935429e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.21520e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 8.80977069073197e-10 -colvars: dx(interp) = 8.80974516357789e-10 +colvars: dx(interp) = 8.80974516357787e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.89760e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.24269960777701e-08 -colvars: dx(interp) = -5.24269988263056e-08 +colvars: dx(interp) = -5.24269988263055e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.24260e-08. colvars: refPosGroup atom 2, component 1: colvars: dx(actual) = 1.64836180260863e-08 @@ -1623,7 +1604,7 @@ colvars: dx(interp) = 1.64836152925342e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.65834e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.44961797699762e-09 -colvars: dx(interp) = 9.44961894491783e-09 +colvars: dx(interp) = 9.44961894491784e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.02430e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50513521646189e-08 @@ -1631,11 +1612,11 @@ colvars: dx(interp) = -1.50513524198364e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.69564e-08. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.18215304212299e-09 -colvars: dx(interp) = 1.18215354891988e-09 +colvars: dx(interp) = 1.18215354891989e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.28707e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.89235360293605e-09 -colvars: dx(interp) = 9.89235145488877e-09 +colvars: dx(interp) = 9.89235145488878e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.17142e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.42107428047211e-08 @@ -1649,7 +1630,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01451859030522e-08 colvars: dx(interp) = 3.01451822120947e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.22439e-07. -colvars: Gradient sum: ( 0.972812 , -0.187862 , -0.135443 ) Fit gradient sum: ( -0.972812 , 0.187862 , 0.135443 ) Total ( -3.33067e-16 , 2.22045e-16 , -3.88578e-16 ) +colvars: Gradient sum: ( 0.972812 , -0.187862 , -0.135443 ) Fit gradient sum: ( -0.972812 , 0.187862 , 0.135443 ) Total ( 0 , 8.32667e-17 , -2.77556e-17 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.232895 , 0.268756 , -0.172689 ) @@ -1675,7 +1656,7 @@ colvars: dx(interp) = -1.33145349553423e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.89118e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.53619017296114e-09 -colvars: dx(interp) = 5.53619602088125e-09 +colvars: dx(interp) = 5.53619602088123e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.05631e-06. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.68101620296102e-08 @@ -1703,7 +1684,7 @@ colvars: dx(interp) = 1.64991576726264e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.27652e-07. colvars: refPosGroup atom 2, component 2: colvars: dx(actual) = 9.45344957870020e-09 -colvars: dx(interp) = 9.45345422358396e-09 +colvars: dx(interp) = 9.45345422358397e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.91343e-07. colvars: refPosGroup atom 3, component 0: colvars: dx(actual) = -1.50559547051898e-08 @@ -1711,7 +1692,7 @@ colvars: dx(interp) = -1.50559499577201e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 3.15322e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.18710907770492e-09 -colvars: dx(interp) = 1.18711101841253e-09 +colvars: dx(interp) = 1.18711101841254e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.63482e-06. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.88098136645021e-09 @@ -1729,7 +1710,7 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01317442108484e-08 colvars: dx(interp) = 3.01317461182275e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 6.33013e-08. -colvars: Gradient sum: ( 0.972755 , -0.188099 , -0.135521 ) Fit gradient sum: ( -0.972755 , 0.188099 , 0.135521 ) Total ( 0 , 2.77556e-17 , 8.32667e-17 ) +colvars: Gradient sum: ( 0.972755 , -0.188099 , -0.135521 ) Fit gradient sum: ( -0.972755 , 0.188099 , 0.135521 ) Total ( -1.11022e-16 , -8.32667e-17 , 2.77556e-16 ) colvars: Debugging gradients for cvc rmsd0001 colvars: Fit gradients: colvars: refPosGroup[0] = ( -0.232767 , 0.268736 , -0.172656 ) @@ -1755,7 +1736,7 @@ colvars: dx(interp) = -1.33169569565328e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.26978e-07. colvars: refPosGroup atom 0, component 1: colvars: dx(actual) = 5.54423351672995e-09 -colvars: dx(interp) = 5.54423349146830e-09 +colvars: dx(interp) = 5.54423349146829e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 4.55638e-09. colvars: refPosGroup atom 0, component 2: colvars: dx(actual) = -3.67969441583682e-08 @@ -1763,15 +1744,15 @@ colvars: dx(interp) = -3.67969415711082e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 7.03118e-08. colvars: refPosGroup atom 1, component 0: colvars: dx(actual) = -3.06796579252477e-08 -colvars: dx(interp) = -3.06796542496762e-08 +colvars: dx(interp) = -3.06796542496761e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.19805e-07. colvars: refPosGroup atom 1, component 1: colvars: dx(actual) = 8.55582804604182e-09 -colvars: dx(interp) = 8.55583619604505e-09 +colvars: dx(interp) = 8.55583619604507e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 9.52567e-07. colvars: refPosGroup atom 1, component 2: colvars: dx(actual) = 9.12068642833219e-10 -colvars: dx(interp) = 9.12071277135839e-10 +colvars: dx(interp) = 9.12071277135838e-10 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.88827e-06. colvars: refPosGroup atom 2, component 0: colvars: dx(actual) = -5.23999084123261e-08 @@ -1791,11 +1772,11 @@ colvars: dx(interp) = -1.50616518663852e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 2.10329e-07. colvars: refPosGroup atom 3, component 1: colvars: dx(actual) = 1.19267085096908e-09 -colvars: dx(interp) = 1.19267017999369e-09 +colvars: dx(interp) = 1.19267017999368e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.62582e-07. colvars: refPosGroup atom 3, component 2: colvars: dx(actual) = 9.86899095778426e-09 -colvars: dx(interp) = 9.86899596501447e-09 +colvars: dx(interp) = 9.86899596501446e-09 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 5.07370e-07. colvars: refPosGroup atom 4, component 0: colvars: dx(actual) = 1.41884619608845e-08 @@ -1809,5 +1790,5 @@ colvars: refPosGroup atom 4, component 2: colvars: dx(actual) = 3.01179419182063e-08 colvars: dx(interp) = 3.01179465384051e-08 colvars: |dx(actual) - dx(interp)|/|dx(actual)| = 1.53404e-07. -colvars: Gradient sum: ( 0.972697 , -0.188344 , -0.135599 ) Fit gradient sum: ( -0.972697 , 0.188344 , 0.135599 ) Total ( -2.22045e-16 , 1.11022e-16 , -1.11022e-16 ) +colvars: Gradient sum: ( 0.972697 , -0.188344 , -0.135599 ) Fit gradient sum: ( -0.972697 , 0.188344 , 0.135599 ) Total ( 0 , -8.32667e-17 , -3.05311e-16 ) colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj index 0aee73595..92e7f7f59 100644 --- a/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj +++ b/namd/tests/library/014_refposgroup/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step r fa_r 0 1.42934254297405e+01 -1.42934254297405e+00 - 1 1.42933316010584e+01 -1.42933316010584e+00 - 2 1.42929135723284e+01 -1.42929135723284e+00 - 3 1.42923486101213e+01 -1.42923486101213e+00 - 4 1.42923026875853e+01 -1.42923026875853e+00 - 5 1.42924344310511e+01 -1.42924344310511e+00 - 6 1.42922522296169e+01 -1.42922522296169e+00 - 7 1.42921269629819e+01 -1.42921269629819e+00 - 8 1.42921521124067e+01 -1.42921521124067e+00 - 9 1.42925995746785e+01 -1.42925995746785e+00 - 10 1.42932888390403e+01 -1.42932888390403e+00 - 11 1.42938611783336e+01 -1.42938611783336e+00 - 12 1.42940308415500e+01 -1.42940308415500e+00 - 13 1.42939753495075e+01 -1.42939753495075e+00 - 14 1.42930019085500e+01 -1.42930019085500e+00 - 15 1.42917673901443e+01 -1.42917673901443e+00 - 16 1.42906595563889e+01 -1.42906595563889e+00 - 17 1.42898165380577e+01 -1.42898165380577e+00 - 18 1.42887881291995e+01 -1.42887881291995e+00 - 19 1.42873640416024e+01 -1.42873640416024e+00 - 20 1.42859393553853e+01 -1.42859393553853e+00 + 1 1.42933316010585e+01 -1.42933316010585e+00 + 2 1.42929135723286e+01 -1.42929135723286e+00 + 3 1.42923486101217e+01 -1.42923486101217e+00 + 4 1.42923026875859e+01 -1.42923026875859e+00 + 5 1.42924344310521e+01 -1.42924344310521e+00 + 6 1.42922522296184e+01 -1.42922522296184e+00 + 7 1.42921269629840e+01 -1.42921269629840e+00 + 8 1.42921521124096e+01 -1.42921521124096e+00 + 9 1.42925995746822e+01 -1.42925995746822e+00 + 10 1.42932888390452e+01 -1.42932888390452e+00 + 11 1.42938611783395e+01 -1.42938611783396e+00 + 12 1.42940308415572e+01 -1.42940308415572e+00 + 13 1.42939753495160e+01 -1.42939753495160e+00 + 14 1.42930019085598e+01 -1.42930019085598e+00 + 15 1.42917673901553e+01 -1.42917673901553e+00 + 16 1.42906595564010e+01 -1.42906595564010e+00 + 17 1.42898165380707e+01 -1.42898165380707e+00 + 18 1.42887881292130e+01 -1.42887881292130e+00 + 19 1.42873640416160e+01 -1.42873640416160e+00 + 20 1.42859393553985e+01 -1.42859393553985e+00 diff --git a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped index 8c6776e10..b42918a80 100644 --- a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name angle - x 9.03916964165211e+01 + x 9.03916964164922e+01 } restraint { diff --git a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj index b71ea85f2..5e9454d4b 100644 --- a/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj +++ b/namd/tests/library/015_dummy_atom/AutoDiff/test.colvars.traj @@ -1,12 +1,12 @@ # step angle fa_angle 0 8.94641033519923e+01 2.92663795777991e+00 - 1 8.94912729262455e+01 2.91909085382069e+00 - 2 8.95442152151541e+01 2.90438466245720e+00 - 3 8.96073749974988e+01 2.88684027847255e+00 - 4 8.96877844443296e+01 2.86450432101956e+00 - 5 8.97771650948167e+01 2.83967636255091e+00 - 6 8.98769301106577e+01 2.81196385815065e+00 - 7 8.99890383094453e+01 2.78082269182076e+00 - 8 9.01041412594469e+01 2.74884965015365e+00 - 9 9.02399071760806e+01 2.71113689553318e+00 - 10 9.03916964165211e+01 2.66897321763303e+00 + 1 8.94912729262462e+01 2.91909085382051e+00 + 2 8.95442152151567e+01 2.90438466245647e+00 + 3 8.96073749975041e+01 2.88684027847108e+00 + 4 8.96877844443377e+01 2.86450432101732e+00 + 5 8.97771650948268e+01 2.83967636254810e+00 + 6 8.98769301106680e+01 2.81196385814778e+00 + 7 8.99890383094529e+01 2.78082269181864e+00 + 8 9.01041412594477e+01 2.74884965015340e+00 + 9 9.02399071760696e+01 2.71113689553622e+00 + 10 9.03916964164922e+01 2.66897321764106e+00 diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out index 8b2c94159..6bf9ea6a6 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 0 colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,27 +125,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped index f96f926f7..f7587bf73 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21685416853788e+00 + x 3.21685416874363e+00 } restraint { diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj index 450a1752e..8aaf17fd1 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hp_one - 0 3.20554673468334e+00 -4.96887477549335e-02 1.92888410426048e-02 - 1 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 - 2 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 - 3 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 - 4 3.20472669829003e+00 -4.96756271726405e-02 1.92786557421498e-02 - 5 3.20472669829003e+00 0.00000000000000e+00 1.92786557421498e-02 - 6 3.20472669829003e+00 0.00000000000000e+00 1.92786557421498e-02 - 7 3.20472669829003e+00 0.00000000000000e+00 1.92786557421498e-02 - 8 3.21245897755043e+00 -4.97993436408069e-02 1.93748017738685e-02 - 9 3.21245897755043e+00 0.00000000000000e+00 1.93748017738685e-02 - 10 3.21245897755043e+00 0.00000000000000e+00 1.93748017738685e-02 - 11 3.21245897755043e+00 0.00000000000000e+00 1.93748017738685e-02 - 12 3.22129314143762e+00 -4.99406902630019e-02 1.94849417495711e-02 - 13 3.22129314143762e+00 0.00000000000000e+00 1.94849417495711e-02 - 14 3.22129314143762e+00 0.00000000000000e+00 1.94849417495711e-02 - 15 3.22129314143762e+00 0.00000000000000e+00 1.94849417495711e-02 - 16 3.22320461230820e+00 -4.99712737969313e-02 1.95088141006865e-02 - 17 3.22320461230820e+00 0.00000000000000e+00 1.95088141006865e-02 - 18 3.22320461230820e+00 0.00000000000000e+00 1.95088141006865e-02 - 19 3.22320461230820e+00 0.00000000000000e+00 1.95088141006865e-02 - 20 3.21685416853788e+00 -4.98696666966061e-02 1.94295598158639e-02 + 0 3.20554673468334e+00 -4.96887477549335e-02 1.92888410426048e-02 + 1 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 + 2 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 + 3 3.20554673468334e+00 0.00000000000000e+00 1.92888410426048e-02 + 4 3.20472669830023e+00 -4.96756271728037e-02 1.92786557422765e-02 + 5 3.20472669830023e+00 0.00000000000000e+00 1.92786557422765e-02 + 6 3.20472669830023e+00 0.00000000000000e+00 1.92786557422765e-02 + 7 3.20472669830023e+00 0.00000000000000e+00 1.92786557422765e-02 + 8 3.21245897759072e+00 -4.97993436414515e-02 1.93748017743701e-02 + 9 3.21245897759072e+00 0.00000000000000e+00 1.93748017743701e-02 + 10 3.21245897759072e+00 0.00000000000000e+00 1.93748017743701e-02 + 11 3.21245897759072e+00 0.00000000000000e+00 1.93748017743701e-02 + 12 3.22129314152384e+00 -4.99406902643814e-02 1.94849417506475e-02 + 13 3.22129314152384e+00 0.00000000000000e+00 1.94849417506475e-02 + 14 3.22129314152384e+00 0.00000000000000e+00 1.94849417506475e-02 + 15 3.22129314152384e+00 0.00000000000000e+00 1.94849417506475e-02 + 16 3.22320461245070e+00 -4.99712737992112e-02 1.95088141024666e-02 + 17 3.22320461245070e+00 0.00000000000000e+00 1.95088141024666e-02 + 18 3.22320461245070e+00 0.00000000000000e+00 1.95088141024666e-02 + 19 3.22320461245070e+00 0.00000000000000e+00 1.95088141024666e-02 + 20 3.21685416874363e+00 -4.98696666998981e-02 1.94295598184291e-02 diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out index ca317540a..6f4f440d6 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -91,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 0 colvars: # width = 0.5 colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0.5 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -119,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -130,32 +125,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21685 colvars: Restarting harmonic bias "hp_one" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped index c5c46002b..566d795a4 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21397142146894e+00 + x 3.21397142195016e+00 } restraint { diff --git a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj index 25e47276b..e5c68ffe3 100644 --- a/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/016_mts_bias/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_hp_one - 20 3.21685416853788e+00 -4.98696666966061e-02 1.94295598158639e-02 - 21 3.21685416853788e+00 0.00000000000000e+00 1.94295598158639e-02 - 22 3.21685416853788e+00 0.00000000000000e+00 1.94295598158639e-02 - 23 3.21685416853788e+00 0.00000000000000e+00 1.94295598158639e-02 - 24 3.20781524498993e+00 -4.97250439198388e-02 1.93170311939836e-02 - 25 3.20781524498993e+00 0.00000000000000e+00 1.93170311939836e-02 - 26 3.20781524498993e+00 0.00000000000000e+00 1.93170311939836e-02 - 27 3.20781524498993e+00 0.00000000000000e+00 1.93170311939836e-02 - 28 3.20267947244878e+00 -4.96428715591806e-02 1.92532398175101e-02 - 29 3.20267947244878e+00 0.00000000000000e+00 1.92532398175101e-02 - 30 3.20267947244878e+00 0.00000000000000e+00 1.92532398175101e-02 - 31 3.20267947244878e+00 0.00000000000000e+00 1.92532398175101e-02 - 32 3.20367252455682e+00 -4.96587603929091e-02 1.92655662793778e-02 - 33 3.20367252455682e+00 0.00000000000000e+00 1.92655662793778e-02 - 34 3.20367252455682e+00 0.00000000000000e+00 1.92655662793778e-02 - 35 3.20367252455682e+00 0.00000000000000e+00 1.92655662793778e-02 - 36 3.20851202025206e+00 -4.97361923240330e-02 1.93256939601031e-02 - 37 3.20851202025206e+00 0.00000000000000e+00 1.93256939601031e-02 - 38 3.20851202025206e+00 0.00000000000000e+00 1.93256939601031e-02 - 39 3.20851202025206e+00 0.00000000000000e+00 1.93256939601031e-02 - 40 3.21397142146894e+00 -4.98235427435031e-02 1.93936360274506e-02 + 20 3.21685416874363e+00 -4.98696666998981e-02 1.94295598184291e-02 + 21 3.21685416874363e+00 0.00000000000000e+00 1.94295598184291e-02 + 22 3.21685416874363e+00 0.00000000000000e+00 1.94295598184291e-02 + 23 3.21685416874363e+00 0.00000000000000e+00 1.94295598184291e-02 + 24 3.20781524526346e+00 -4.97250439242154e-02 1.93170311973840e-02 + 25 3.20781524526346e+00 0.00000000000000e+00 1.93170311973840e-02 + 26 3.20781524526346e+00 0.00000000000000e+00 1.93170311973840e-02 + 27 3.20781524526346e+00 0.00000000000000e+00 1.93170311973840e-02 + 28 3.20267947278925e+00 -4.96428715646280e-02 1.92532398217355e-02 + 29 3.20267947278925e+00 0.00000000000000e+00 1.92532398217355e-02 + 30 3.20267947278925e+00 0.00000000000000e+00 1.92532398217355e-02 + 31 3.20267947278925e+00 0.00000000000000e+00 1.92532398217355e-02 + 32 3.20367252495752e+00 -4.96587603993203e-02 1.92655662843524e-02 + 33 3.20367252495752e+00 0.00000000000000e+00 1.92655662843524e-02 + 34 3.20367252495752e+00 0.00000000000000e+00 1.92655662843524e-02 + 35 3.20367252495752e+00 0.00000000000000e+00 1.92655662843524e-02 + 36 3.20851202070242e+00 -4.97361923312387e-02 1.93256939657028e-02 + 37 3.20851202070242e+00 0.00000000000000e+00 1.93256939657028e-02 + 38 3.20851202070242e+00 0.00000000000000e+00 1.93256939657028e-02 + 39 3.20851202070242e+00 0.00000000000000e+00 1.93256939657028e-02 + 40 3.21397142195016e+00 -4.98235427512026e-02 1.93936360334447e-02 diff --git a/namd/tests/library/016_mts_bias/namd-version.txt b/namd/tests/library/016_mts_bias/namd-version.txt index 157cac038..08ab1004b 100644 --- a/namd/tests/library/016_mts_bias/namd-version.txt +++ b/namd/tests/library/016_mts_bias/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.11 for Linux-x86_64-multicore diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out index e9eb1b9a5..90ba327a0 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out +++ b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -15,7 +12,6 @@ colvars: # colvarsTrajFrequency = 10 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "c" @@ -29,28 +25,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -67,28 +63,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = 0.51. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -101,6 +97,37 @@ colvars: Warning: Variable r1 is absent from expression "x". colvars: Warning: Variable r2 is absent from expression "x". colvars: Warning: Variable r3 is absent from expression "x". colvars: Warning: Variable r2 is absent from expression "cos(x) + r1 + r3". +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt x. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r1. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r2. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable x is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r1 is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r2 is absent from derivative of "cos(x) + r1 + r3" wrt r3. +colvars: Warning: Variable r3 is absent from derivative of "cos(x) + r1 + r3" wrt r3. colvars: Expecting colvar value of type n-dimensional vector of size 2. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] @@ -131,7 +158,6 @@ colvars: # centers = { ( 20 , -5 ) } colvars: # targetCenters = { ( 20 , -5 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 100 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "c" will be rescaled to 100 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -142,31 +168,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. +colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. +colvars: Re-initialized atom group for variable "c":1/0. 1 atoms: total mass = 12.011, total charge = 0.51. +colvars: Re-initialized atom group for variable "c":1/1. 1 atoms: total mass = 12.011, total charge = 0.51. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 4 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 12.011, total charge = -0.1. colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = 0.07. colvars: Re-initialized atom group for variable "c":1/0. 1 atoms: total mass = 12.011, total charge = 0.51. diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped index aff97d707..cb77abf4e 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name c - x ( 1.65450803779147e+01 , -2.58120974399207e+00 ) + x ( 1.65450803775141e+01 , -2.58120974253005e+00 ) } restraint { diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj index bfd90c361..d7ab641d2 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj +++ b/namd/tests/library/017_custom_function/AutoDiff/test.colvars.traj @@ -1,4 +1,4 @@ # step c 0 ( 1.47736880982107e+01 , 5.47598531906441e-01 ) - 10 ( 1.64732268956376e+01 , -1.86635727005636e+00 ) - 20 ( 1.65450803779147e+01 , -2.58120974399207e+00 ) + 10 ( 1.64732268956053e+01 , -1.86635726975950e+00 ) + 20 ( 1.65450803775141e+01 , -2.58120974253006e+00 ) diff --git a/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped index e7fddb9d1..5b04314b5 100644 --- a/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/017_custom_function/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name c - x ( 1.75996935761212e+01 , -3.48707549970946e+00 ) + x ( 1.75996935759052e+01 , -3.48707550156878e+00 ) } restraint { diff --git a/namd/tests/library/017_custom_function/namd-version.txt b/namd/tests/library/017_custom_function/namd-version.txt index 157cac038..04e884681 100644 --- a/namd/tests/library/017_custom_function/namd-version.txt +++ b/namd/tests/library/017_custom_function/namd-version.txt @@ -1,3 +1 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.12 for Linux-x86_64-multicore diff --git a/namd/tests/library/018_pathCV/namd-version.txt b/namd/tests/library/018_pathCV/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/018_pathCV/namd-version.txt +++ b/namd/tests/library/018_pathCV/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out index 8f6da7076..4d96ba271 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_dihed" @@ -34,56 +32,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -99,56 +97,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -164,56 +162,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -455,7 +453,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -487,53 +485,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -548,53 +546,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -609,53 +607,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -898,7 +896,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -919,25 +917,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - gspathCV colvar component: -colvars: - gzpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -964,11 +943,11 @@ colvars: Re-initialized atom group for variable "gpath_z_dihed":0/10. 1 atoms: t colvars: Re-initialized atom group for variable "gpath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped index d940cb619..0a6f34748 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.state.stripped @@ -10,6 +10,6 @@ colvar { colvar { name gpath_z_dihed - x 9.55645131452191e+01 + x 9.55645131452184e+01 } diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj index ddaf3721c..5fac76756 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step gpath_s_dihed gpath_z_dihed 0 7.83123228264734e-01 3.83533978043175e+01 - 1 7.82945678970628e-01 4.29689076394212e+01 - 2 7.82818444070286e-01 4.79082192050887e+01 - 3 7.82680619902823e-01 5.32968526519466e+01 - 4 7.82481029251750e-01 5.95665170545919e+01 - 5 7.82394193117627e-01 6.58557656139231e+01 - 6 7.82260880668904e-01 7.22764122107677e+01 - 7 7.82016364258954e-01 7.87726707676510e+01 - 8 7.81934087543136e-01 8.51257353163676e+01 - 9 7.81821580461319e-01 8.98923615763005e+01 - 10 7.81811987245692e-01 9.36566870572311e+01 + 1 7.82945678970628e-01 4.29689076394209e+01 + 2 7.82818444070286e-01 4.79082192050889e+01 + 3 7.82680619902823e-01 5.32968526519463e+01 + 4 7.82481029251750e-01 5.95665170545922e+01 + 5 7.82394193117627e-01 6.58557656139234e+01 + 6 7.82260880668904e-01 7.22764122107678e+01 + 7 7.82016364258954e-01 7.87726707676512e+01 + 8 7.81934087543136e-01 8.51257353163675e+01 + 9 7.81821580461319e-01 8.98923615763004e+01 + 10 7.81811987245692e-01 9.36566870572305e+01 11 7.81676091324908e-01 9.70906581768438e+01 12 7.81497401408420e-01 1.00284195800025e+02 13 7.81382447528542e-01 1.01730136329478e+02 - 14 7.81310203934944e-01 1.02632785559219e+02 + 14 7.81310203934944e-01 1.02632785559218e+02 15 7.81107670050000e-01 1.02580995635213e+02 16 7.81000240562519e-01 1.01690738350632e+02 17 7.81032069099019e-01 1.00431749174877e+02 - 18 7.81089334289029e-01 9.86347657918943e+01 + 18 7.81089334289029e-01 9.86347657918941e+01 19 7.81314767005367e-01 9.68745522484514e+01 - 20 7.81476379939767e-01 9.55645131452191e+01 + 20 7.81476379939767e-01 9.55645131452184e+01 diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out index 591e79589..ac4527f9d 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_dihed" @@ -34,56 +32,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -99,56 +97,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -164,56 +162,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -455,7 +453,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -487,53 +485,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -548,53 +546,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -609,53 +607,53 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = off colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. @@ -898,7 +896,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -919,25 +917,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - gspathCV colvar component: -colvars: - gzpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -963,17 +942,17 @@ colvars: Re-initialized atom group for variable "gpath_z_dihed":0/9. 1 atoms: to colvars: Re-initialized atom group for variable "gpath_z_dihed":0/10. 1 atoms: total mass = 12.01, total charge = 0.0337. colvars: Re-initialized atom group for variable "gpath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "gpath_s_dihed" from value: 0.781476 colvars: Restarting collective variable "gpath_z_dihed" from value: 95.5645 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (10 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "gpath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj index d5ec83feb..5b9068d9b 100644 --- a/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/019_gpathCV/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step gpath_s_dihed gpath_z_dihed - 20 7.81476379939767e-01 9.55645131452191e+01 - 21 7.81240698201971e-01 1.06229693509577e+02 + 20 7.81476379939767e-01 9.55645131452184e+01 + 21 7.81240698201971e-01 1.06229693509576e+02 22 7.81005545091406e-01 1.17334167235362e+02 - 23 7.80723779014191e-01 1.28845704977404e+02 + 23 7.80723779014191e-01 1.28845704977403e+02 24 7.80348823600053e-01 1.41207832230497e+02 - 25 7.80052868542975e-01 1.53573472293347e+02 + 25 7.80052868542975e-01 1.53573472293346e+02 26 7.79695411661275e-01 1.65225530758384e+02 27 7.79227129868925e-01 1.75833882118768e+02 28 7.78924791555966e-01 1.85072740224480e+02 - 29 7.78616822792614e-01 1.91408513274007e+02 - 30 7.78445744037639e-01 1.96072266414115e+02 + 29 7.78616822792614e-01 1.91408513274006e+02 + 30 7.78445744037639e-01 1.96072266414114e+02 31 7.78198587511674e-01 1.99830728112820e+02 - 32 7.77969198638703e-01 2.02348834208334e+02 - 33 7.77870454975722e-01 2.01925240313579e+02 + 32 7.77969198638703e-01 2.02348834208335e+02 + 33 7.77870454975722e-01 2.01925240313578e+02 34 7.77892445039517e-01 2.00152956848502e+02 - 35 7.77861620836214e-01 1.96872674617573e+02 - 36 7.78012144635351e-01 1.92375777763847e+02 + 35 7.77861620836214e-01 1.96872674617572e+02 + 36 7.78012144635351e-01 1.92375777763846e+02 37 7.78402492011077e-01 1.87024840666577e+02 38 7.78909881410184e-01 1.81082923676999e+02 - 39 7.79681670070840e-01 1.75290823442271e+02 + 39 7.79681670070840e-01 1.75290823442270e+02 40 7.80475723743606e-01 1.69997870041256e+02 diff --git a/namd/tests/library/019_gpathCV/namd-version.txt b/namd/tests/library/019_gpathCV/namd-version.txt index 157cac038..90b3a010a 100644 --- a/namd/tests/library/019_gpathCV/namd-version.txt +++ b/namd/tests/library/019_gpathCV/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA +colvars: Initializing the collective variables module, version "2019-10-21". +colvars: Using NAMD interface, version "2019-10-21". diff --git a/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj b/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj index f4d864ba8..a2d265a65 100644 --- a/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj +++ b/namd/tests/library/020_gpath/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step gpath_s_cartesian gpath_z_cartesian 0 5.30720368611864e-01 8.61059914994141e-02 - 1 5.30717690590865e-01 8.54273375358692e-02 - 2 5.30714251957229e-01 8.51458403558880e-02 - 3 5.30710055975446e-01 8.51321853522883e-02 - 4 5.30704973571852e-01 8.52949333585580e-02 - 5 5.30697460621445e-01 8.55508921045213e-02 - 6 5.30685286827787e-01 8.56177474112287e-02 - 7 5.30670902617345e-01 8.57812083900462e-02 - 8 5.30652367951073e-01 8.59993861857884e-02 - 9 5.30632081382459e-01 8.62909912963241e-02 - 10 5.30606987319570e-01 8.66946366005643e-02 + 1 5.30717690590865e-01 8.54273375358691e-02 + 2 5.30714251957229e-01 8.51458403558881e-02 + 3 5.30710055975446e-01 8.51321853522884e-02 + 4 5.30704973571852e-01 8.52949333585581e-02 + 5 5.30697460621445e-01 8.55508921045210e-02 + 6 5.30685286827787e-01 8.56177474112286e-02 + 7 5.30670902617345e-01 8.57812083900463e-02 + 8 5.30652367951073e-01 8.59993861857883e-02 + 9 5.30632081382459e-01 8.62909912963239e-02 + 10 5.30606987319570e-01 8.66946366005642e-02 11 5.30579540524640e-01 8.73047828339237e-02 - 12 5.30552631793952e-01 8.81730152476006e-02 - 13 5.30524058862923e-01 8.91926063197971e-02 + 12 5.30552631793952e-01 8.81730152476007e-02 + 13 5.30524058862923e-01 8.91926063197970e-02 14 5.30493980557183e-01 9.03283581585283e-02 15 5.30463117047670e-01 9.15212996991972e-02 16 5.30431734419221e-01 9.30006426174987e-02 - 17 5.30399413235259e-01 9.44575442040143e-02 - 18 5.30368252449657e-01 9.62800980538578e-02 + 17 5.30399413235259e-01 9.44575442040145e-02 + 18 5.30368252449657e-01 9.62800980538579e-02 19 5.30333234090156e-01 9.82010258065717e-02 20 5.30301765703773e-01 1.00592004206710e-01 diff --git a/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj b/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj index 44c3cc8ee..0b4049f9a 100644 --- a/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/020_gpath/AutoDiff/test.restart.colvars.traj @@ -1,6 +1,6 @@ # step gpath_s_cartesian gpath_z_cartesian 20 5.30301765703773e-01 1.00592004206710e-01 - 21 5.30299068311154e-01 1.01776105919982e-01 + 21 5.30299068311154e-01 1.01776105919981e-01 22 5.30296225733479e-01 1.02913020025282e-01 23 5.30293151382629e-01 1.03888660431483e-01 24 5.30289871026115e-01 1.04670153673202e-01 @@ -10,9 +10,9 @@ 28 5.30250537018860e-01 1.05411857890215e-01 29 5.30235512500134e-01 1.05013013758426e-01 30 5.30216395990587e-01 1.04566807352862e-01 - 31 5.30195586650359e-01 1.04225738170003e-01 + 31 5.30195586650359e-01 1.04225738170004e-01 32 5.30176202069296e-01 1.03881270572137e-01 - 33 5.30155909450721e-01 1.03435901761179e-01 + 33 5.30155909450721e-01 1.03435901761180e-01 34 5.30134759237002e-01 1.02902765055984e-01 35 5.30113387291624e-01 1.02318158639028e-01 36 5.30092042017102e-01 1.01828820799264e-01 diff --git a/namd/tests/library/020_gpath/namd-version.txt b/namd/tests/library/020_gpath/namd-version.txt index 157cac038..355758d76 100644 --- a/namd/tests/library/020_gpath/namd-version.txt +++ b/namd/tests/library/020_gpath/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +Info: NAMD 3.0b3 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-07-18. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out index 8b007336e..2825984f5 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_distanceVec" @@ -34,9 +32,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -47,14 +44,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -70,9 +67,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -83,14 +79,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -106,9 +102,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -119,14 +114,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -142,9 +137,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -155,14 +149,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -178,9 +172,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -191,14 +184,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -214,9 +207,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -227,14 +219,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -250,9 +242,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -263,14 +254,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -286,9 +277,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -299,14 +289,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -322,9 +312,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -335,14 +324,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -358,9 +347,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -371,14 +359,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -394,9 +382,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -407,14 +394,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -430,9 +417,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -443,14 +429,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -466,9 +452,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -479,14 +464,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -502,9 +487,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -515,14 +499,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -538,9 +522,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -551,14 +534,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -574,9 +557,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -587,14 +569,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -610,9 +592,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -623,14 +604,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -646,9 +627,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -659,14 +639,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -682,9 +662,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -695,14 +674,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -718,9 +697,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -731,14 +709,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3182,11 +3160,12 @@ colvars: # useSecondClosestFrame = on [default] colvars: Geometric path s(σ) will use the second closest frame to compute s_(m-1) colvars: # useThirdClosestFrame = off [default] colvars: Geometric path s(σ) will use the neighbouring frame to compute s_(m+1) +colvars: Geometric path s(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3218,9 +3197,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3231,14 +3209,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3254,9 +3232,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3267,14 +3244,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3290,9 +3267,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3303,14 +3279,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3326,9 +3302,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3339,14 +3314,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3362,9 +3337,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3375,14 +3349,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3398,9 +3372,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3411,14 +3384,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3434,9 +3407,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3447,14 +3419,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3470,9 +3442,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3483,14 +3454,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3506,9 +3477,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3519,14 +3489,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3542,9 +3512,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3555,14 +3524,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3578,9 +3547,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3591,14 +3559,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3614,9 +3582,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3627,14 +3594,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3650,9 +3617,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3663,14 +3629,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3686,9 +3652,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3699,14 +3664,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3722,9 +3687,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3735,14 +3699,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3758,9 +3722,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3771,14 +3734,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3794,9 +3757,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3807,14 +3769,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3830,9 +3792,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3843,14 +3804,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3866,9 +3827,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3879,14 +3839,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3902,9 +3862,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3915,14 +3874,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6368,11 +6327,12 @@ colvars: # useThirdClosestFrame = off [default] colvars: Geometric path z(σ) will use the neighbouring frame to compute s_(m+1) colvars: # useZsquare = on colvars: Geometric path z(σ) will use the square of distance from current frame to path compute z +colvars: Geometric path z(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6393,26 +6353,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - gspathCV colvar component: -colvars: - gzpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6495,11 +6435,11 @@ colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/38. 0 at colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj index e5d0bb3cf..8e7ee67dd 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.colvars.traj @@ -2,15 +2,15 @@ 0 3.77171678533515e-02 6.76736838399185e+02 1 3.77408160662234e-02 6.76814886658536e+02 2 3.77652902052649e-02 6.76904118559529e+02 - 3 3.77885901836011e-02 6.77002173338060e+02 + 3 3.77885901836011e-02 6.77002173338061e+02 4 3.78148176804083e-02 6.77104722272709e+02 5 3.78372534576845e-02 6.77211769234532e+02 - 6 3.78552413890631e-02 6.77324430169634e+02 + 6 3.78552413890631e-02 6.77324430169633e+02 7 3.78833685463047e-02 6.77427790438348e+02 - 8 3.79119516235524e-02 6.77529691393681e+02 + 8 3.79119516235519e-02 6.77529691393681e+02 9 3.79430521380542e-02 6.77636436765019e+02 - 10 3.79763962901917e-02 6.77753499558135e+02 - 11 3.80148985287524e-02 6.77879781194716e+02 + 10 3.79763962901923e-02 6.77753499558135e+02 + 11 3.80148985287519e-02 6.77879781194716e+02 12 3.80574676219839e-02 6.77995499164433e+02 13 3.80958506694046e-02 6.78083025670623e+02 14 3.81395612603290e-02 6.78153378635457e+02 diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out index 1d14cbe04..e11c82e21 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "gpath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "gpath_s_distanceVec" @@ -34,9 +32,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -47,14 +44,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -70,9 +67,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -83,14 +79,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -106,9 +102,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -119,14 +114,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -142,9 +137,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -155,14 +149,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -178,9 +172,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -191,14 +184,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -214,9 +207,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -227,14 +219,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -250,9 +242,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -263,14 +254,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -286,9 +277,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -299,14 +289,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -322,9 +312,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -335,14 +324,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -358,9 +347,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -371,14 +359,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -394,9 +382,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -407,14 +394,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -430,9 +417,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -443,14 +429,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -466,9 +452,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -479,14 +464,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -502,9 +487,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -515,14 +499,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -538,9 +522,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -551,14 +534,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -574,9 +557,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -587,14 +569,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -610,9 +592,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -623,14 +604,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -646,9 +627,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -659,14 +639,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -682,9 +662,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -695,14 +674,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -718,9 +697,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -731,14 +709,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3182,11 +3160,12 @@ colvars: # useSecondClosestFrame = on [default] colvars: Geometric path s(σ) will use the second closest frame to compute s_(m-1) colvars: # useThirdClosestFrame = off [default] colvars: Geometric path s(σ) will use the neighbouring frame to compute s_(m+1) +colvars: Geometric path s(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3218,9 +3197,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3231,14 +3209,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3254,9 +3232,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3267,14 +3244,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3290,9 +3267,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3303,14 +3279,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3326,9 +3302,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3339,14 +3314,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3362,9 +3337,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3375,14 +3349,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3398,9 +3372,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3411,14 +3384,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3434,9 +3407,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3447,14 +3419,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3470,9 +3442,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3483,14 +3454,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3506,9 +3477,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3519,14 +3489,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3542,9 +3512,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3555,14 +3524,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3578,9 +3547,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3591,14 +3559,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3614,9 +3582,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3627,14 +3594,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3650,9 +3617,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3663,14 +3629,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3686,9 +3652,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3699,14 +3664,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3722,9 +3687,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3735,14 +3699,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3758,9 +3722,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3771,14 +3734,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3794,9 +3757,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3807,14 +3769,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3830,9 +3792,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3843,14 +3804,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3866,9 +3827,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3879,14 +3839,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3902,9 +3862,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3915,14 +3874,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6368,11 +6327,12 @@ colvars: # useThirdClosestFrame = off [default] colvars: Geometric path z(σ) will use the neighbouring frame to compute s_(m+1) colvars: # useZsquare = on colvars: Geometric path z(σ) will use the square of distance from current frame to path compute z +colvars: Geometric path z(σ) will use implicit gradients. colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6393,26 +6353,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - gspathCV colvar component: -colvars: - gzpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6494,17 +6434,17 @@ colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/37. 1 at colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/38. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "gpath_s_distanceVec" from value: 0.0384565 colvars: Restarting collective variable "gpath_z_distanceVec" from value: 678.131 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "gpath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj index 81de6b0bc..defbf6a45 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/021_gpathCV_distanceVec/AutoDiff/test.restart.colvars.traj @@ -10,10 +10,10 @@ 28 3.86084059020791e-02 6.78925279191111e+02 29 3.86298828548808e-02 6.79025716470530e+02 30 3.86527796201097e-02 6.79134948406694e+02 - 31 3.86798568836978e-02 6.79251839399435e+02 + 31 3.86798568836977e-02 6.79251839399435e+02 32 3.87098949985802e-02 6.79356485630484e+02 33 3.87343129795344e-02 6.79430860596411e+02 - 34 3.87624579979551e-02 6.79485989524982e+02 + 34 3.87624579979557e-02 6.79485989524982e+02 35 3.87892874098554e-02 6.79502594982682e+02 36 3.88193203791849e-02 6.79495678267542e+02 37 3.88506047395243e-02 6.79480901306783e+02 diff --git a/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt b/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt index 157cac038..90b3a010a 100644 --- a/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt +++ b/namd/tests/library/021_gpathCV_distanceVec/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA +colvars: Initializing the collective variables module, version "2019-10-21". +colvars: Using NAMD interface, version "2019-10-21". diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out index 4dbd24972..27624c699 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_distanceVec" @@ -34,9 +32,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -47,14 +44,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -70,9 +67,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -83,14 +79,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -106,9 +102,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -119,14 +114,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -142,9 +137,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -155,14 +149,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -178,9 +172,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -191,14 +184,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -214,9 +207,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -227,14 +219,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -250,9 +242,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -263,14 +254,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -286,9 +277,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -299,14 +289,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -322,9 +312,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -335,14 +324,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -358,9 +347,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -371,14 +359,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -394,9 +382,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -407,14 +394,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -430,9 +417,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -443,14 +429,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -466,9 +452,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -479,14 +464,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -502,9 +487,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -515,14 +499,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -538,9 +522,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -551,14 +534,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -574,9 +557,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -587,14 +569,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -610,9 +592,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -623,14 +604,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -646,9 +627,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -659,14 +639,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -682,9 +662,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -695,14 +674,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -718,9 +697,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -731,14 +709,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3179,6 +3157,35 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 1.24993 +colvars: Distance between frame 2 and 3 is 1.22263 +colvars: Distance between frame 3 and 4 is 1.15797 +colvars: Distance between frame 4 and 5 is 1.20671 +colvars: Distance between frame 5 and 6 is 1.22068 +colvars: Distance between frame 6 and 7 is 1.27376 +colvars: Distance between frame 7 and 8 is 1.16679 +colvars: Distance between frame 8 and 9 is 1.23641 +colvars: Distance between frame 9 and 10 is 1.23647 +colvars: Distance between frame 10 and 11 is 1.24224 +colvars: Distance between frame 11 and 12 is 1.21755 +colvars: Distance between frame 12 and 13 is 1.2113 +colvars: Distance between frame 13 and 14 is 1.25829 +colvars: Distance between frame 14 and 15 is 1.14361 +colvars: Distance between frame 15 and 16 is 1.25482 +colvars: Distance between frame 16 and 17 is 1.19127 +colvars: Distance between frame 17 and 18 is 1.21515 +colvars: Distance between frame 18 and 19 is 1.28854 +colvars: Distance between frame 19 and 20 is 1.21558 +colvars: Distance between frame 20 and 21 is 1.18825 +colvars: Distance between frame 21 and 22 is 1.29888 +colvars: Distance between frame 22 and 23 is 1.23365 +colvars: Distance between frame 23 and 24 is 1.17305 +colvars: Distance between frame 24 and 25 is 1.32493 +colvars: Distance between frame 25 and 26 is 1.21926 +colvars: Distance between frame 26 and 27 is 1.1941 +colvars: Distance between frame 27 and 28 is 1.28306 +colvars: Distance between frame 28 and 29 is 1.24978 +colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -3205,7 +3212,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3237,9 +3244,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3250,14 +3256,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3273,9 +3279,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3286,14 +3291,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3309,9 +3314,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3322,14 +3326,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3345,9 +3349,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3358,14 +3361,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3381,9 +3384,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3394,14 +3396,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3417,9 +3419,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3430,14 +3431,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3453,9 +3454,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3466,14 +3466,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3489,9 +3489,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3502,14 +3501,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3525,9 +3524,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3538,14 +3536,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3561,9 +3559,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3574,14 +3571,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3597,9 +3594,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3610,14 +3606,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3633,9 +3629,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3646,14 +3641,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3669,9 +3664,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3682,14 +3676,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3705,9 +3699,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3718,14 +3711,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3741,9 +3734,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3754,14 +3746,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3777,9 +3769,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3790,14 +3781,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3813,9 +3804,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3826,14 +3816,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3849,9 +3839,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3862,14 +3851,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3885,9 +3874,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3898,14 +3886,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3921,9 +3909,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3934,14 +3921,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6382,6 +6369,35 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 1.24993 +colvars: Distance between frame 2 and 3 is 1.22263 +colvars: Distance between frame 3 and 4 is 1.15797 +colvars: Distance between frame 4 and 5 is 1.20671 +colvars: Distance between frame 5 and 6 is 1.22068 +colvars: Distance between frame 6 and 7 is 1.27376 +colvars: Distance between frame 7 and 8 is 1.16679 +colvars: Distance between frame 8 and 9 is 1.23641 +colvars: Distance between frame 9 and 10 is 1.23647 +colvars: Distance between frame 10 and 11 is 1.24224 +colvars: Distance between frame 11 and 12 is 1.21755 +colvars: Distance between frame 12 and 13 is 1.2113 +colvars: Distance between frame 13 and 14 is 1.25829 +colvars: Distance between frame 14 and 15 is 1.14361 +colvars: Distance between frame 15 and 16 is 1.25482 +colvars: Distance between frame 16 and 17 is 1.19127 +colvars: Distance between frame 17 and 18 is 1.21515 +colvars: Distance between frame 18 and 19 is 1.28854 +colvars: Distance between frame 19 and 20 is 1.21558 +colvars: Distance between frame 20 and 21 is 1.18825 +colvars: Distance between frame 21 and 22 is 1.29888 +colvars: Distance between frame 22 and 23 is 1.23365 +colvars: Distance between frame 23 and 24 is 1.17305 +colvars: Distance between frame 24 and 25 is 1.32493 +colvars: Distance between frame 25 and 26 is 1.21926 +colvars: Distance between frame 26 and 27 is 1.1941 +colvars: Distance between frame 27 and 28 is 1.28306 +colvars: Distance between frame 28 and 29 is 1.24978 +colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -6408,7 +6424,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6429,26 +6445,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - aspathCV colvar component: -colvars: - azpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6531,11 +6527,11 @@ colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/38. 0 at colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj index 358b06848..8c3fd2f17 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.colvars.traj @@ -7,10 +7,10 @@ 5 3.71951763458571e-02 6.76437235131064e+02 6 3.72110087084931e-02 6.76548721440867e+02 7 3.72351763642007e-02 6.76650733895917e+02 - 8 3.72595960457660e-02 6.76751383624712e+02 + 8 3.72595960457659e-02 6.76751383624712e+02 9 3.72860044867264e-02 6.76856908644382e+02 - 10 3.73141938916311e-02 6.76972778630392e+02 - 11 3.73465707477626e-02 6.77097844460360e+02 + 10 3.73141938916315e-02 6.76972778630392e+02 + 11 3.73465707477625e-02 6.77097844460360e+02 12 3.73823307193035e-02 6.77212255632268e+02 13 3.74145603254307e-02 6.77298631416326e+02 14 3.74510510199529e-02 6.77367872060677e+02 diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out index 81cb87adf..a31a3d332 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_distanceVec" @@ -34,9 +32,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -47,14 +44,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -70,9 +67,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -83,14 +79,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -106,9 +102,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -119,14 +114,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -142,9 +137,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -155,14 +149,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -178,9 +172,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -191,14 +184,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -214,9 +207,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -227,14 +219,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -250,9 +242,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -263,14 +254,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -286,9 +277,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -299,14 +289,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -322,9 +312,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -335,14 +324,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -358,9 +347,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -371,14 +359,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -394,9 +382,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -407,14 +394,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -430,9 +417,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -443,14 +429,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -466,9 +452,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -479,14 +464,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -502,9 +487,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -515,14 +499,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -538,9 +522,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -551,14 +534,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -574,9 +557,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -587,14 +569,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -610,9 +592,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -623,14 +604,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -646,9 +627,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -659,14 +639,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -682,9 +662,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -695,14 +674,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -718,9 +697,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -731,14 +709,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3179,6 +3157,35 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 1.24993 +colvars: Distance between frame 2 and 3 is 1.22263 +colvars: Distance between frame 3 and 4 is 1.15797 +colvars: Distance between frame 4 and 5 is 1.20671 +colvars: Distance between frame 5 and 6 is 1.22068 +colvars: Distance between frame 6 and 7 is 1.27376 +colvars: Distance between frame 7 and 8 is 1.16679 +colvars: Distance between frame 8 and 9 is 1.23641 +colvars: Distance between frame 9 and 10 is 1.23647 +colvars: Distance between frame 10 and 11 is 1.24224 +colvars: Distance between frame 11 and 12 is 1.21755 +colvars: Distance between frame 12 and 13 is 1.2113 +colvars: Distance between frame 13 and 14 is 1.25829 +colvars: Distance between frame 14 and 15 is 1.14361 +colvars: Distance between frame 15 and 16 is 1.25482 +colvars: Distance between frame 16 and 17 is 1.19127 +colvars: Distance between frame 17 and 18 is 1.21515 +colvars: Distance between frame 18 and 19 is 1.28854 +colvars: Distance between frame 19 and 20 is 1.21558 +colvars: Distance between frame 20 and 21 is 1.18825 +colvars: Distance between frame 21 and 22 is 1.29888 +colvars: Distance between frame 22 and 23 is 1.23365 +colvars: Distance between frame 23 and 24 is 1.17305 +colvars: Distance between frame 24 and 25 is 1.32493 +colvars: Distance between frame 25 and 26 is 1.21926 +colvars: Distance between frame 26 and 27 is 1.1941 +colvars: Distance between frame 27 and 28 is 1.28306 +colvars: Distance between frame 28 and 29 is 1.24978 +colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -3205,7 +3212,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -3237,9 +3244,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3250,14 +3256,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3273,9 +3279,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3286,14 +3291,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3309,9 +3314,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3322,14 +3326,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3345,9 +3349,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3358,14 +3361,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3381,9 +3384,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3394,14 +3396,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3417,9 +3419,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3430,14 +3431,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3453,9 +3454,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3466,14 +3466,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3489,9 +3489,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3502,14 +3501,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3525,9 +3524,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3538,14 +3536,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3561,9 +3559,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3574,14 +3571,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3597,9 +3594,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3610,14 +3606,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3633,9 +3629,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3646,14 +3641,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3669,9 +3664,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3682,14 +3676,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3705,9 +3699,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3718,14 +3711,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3741,9 +3734,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3754,14 +3746,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3777,9 +3769,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3790,14 +3781,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3813,9 +3804,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3826,14 +3816,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3849,9 +3839,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3862,14 +3851,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3885,9 +3874,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3898,14 +3886,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -3921,9 +3909,8 @@ colvars: # forceNoPBC = on colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] @@ -3934,14 +3921,14 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 0 atoms requested: total mass = 1, total charge = 0. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -6382,6 +6369,35 @@ colvars: -5.2304 colvars: -0.9828 colvars: Total number of frames: 30 colvars: # weights = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 1.24993 +colvars: Distance between frame 2 and 3 is 1.22263 +colvars: Distance between frame 3 and 4 is 1.15797 +colvars: Distance between frame 4 and 5 is 1.20671 +colvars: Distance between frame 5 and 6 is 1.22068 +colvars: Distance between frame 6 and 7 is 1.27376 +colvars: Distance between frame 7 and 8 is 1.16679 +colvars: Distance between frame 8 and 9 is 1.23641 +colvars: Distance between frame 9 and 10 is 1.23647 +colvars: Distance between frame 10 and 11 is 1.24224 +colvars: Distance between frame 11 and 12 is 1.21755 +colvars: Distance between frame 12 and 13 is 1.2113 +colvars: Distance between frame 13 and 14 is 1.25829 +colvars: Distance between frame 14 and 15 is 1.14361 +colvars: Distance between frame 15 and 16 is 1.25482 +colvars: Distance between frame 16 and 17 is 1.19127 +colvars: Distance between frame 17 and 18 is 1.21515 +colvars: Distance between frame 18 and 19 is 1.28854 +colvars: Distance between frame 19 and 20 is 1.21558 +colvars: Distance between frame 20 and 21 is 1.18825 +colvars: Distance between frame 21 and 22 is 1.29888 +colvars: Distance between frame 22 and 23 is 1.23365 +colvars: Distance between frame 23 and 24 is 1.17305 +colvars: Distance between frame 24 and 25 is 1.32493 +colvars: Distance between frame 25 and 26 is 1.21926 +colvars: Distance between frame 26 and 27 is 1.1941 +colvars: Distance between frame 27 and 28 is 1.28306 +colvars: Distance between frame 28 and 29 is 1.24978 +colvars: Distance between frame 29 and 30 is 1.16053 colvars: # lambda = 0.6 colvars: Lambda is 0.6 colvars: The weight of CV 0 is 1 @@ -6408,7 +6424,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -6429,26 +6445,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceVec colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - aspathCV colvar component: -colvars: - azpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. @@ -6530,17 +6526,17 @@ colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/37. 1 at colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/38. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_z_distanceVec":0/39. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "apath_s_distanceVec" from value: 0.0377147 colvars: Restarting collective variable "apath_z_distanceVec" from value: 677.339 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (20 scalable groups, 20 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/0. 0 atoms: total mass = 1, total charge = 0. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/1. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "apath_s_distanceVec":0/2. 0 atoms: total mass = 1, total charge = 0. diff --git a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj index 2a0e6503c..9306d59e6 100644 --- a/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/022_apathCV_distanceVec/AutoDiff/test.restart.colvars.traj @@ -13,10 +13,10 @@ 31 3.79086164652580e-02 6.78450434800659e+02 32 3.79338795931516e-02 6.78554453096444e+02 33 3.79543432866692e-02 6.78628383973525e+02 - 34 3.79777414197508e-02 6.78683148858527e+02 + 34 3.79777414197512e-02 6.78683148858527e+02 35 3.79999682058412e-02 6.78699467676242e+02 36 3.80248319961822e-02 6.78692254801370e+02 - 37 3.80506503259602e-02 6.78677248372969e+02 + 37 3.80506503259599e-02 6.78677248372969e+02 38 3.80831517398857e-02 6.78640840179385e+02 39 3.81094518561156e-02 6.78584570499380e+02 40 3.81323012651889e-02 6.78535020169896e+02 diff --git a/namd/tests/library/022_apathCV_distanceVec/namd-version.txt b/namd/tests/library/022_apathCV_distanceVec/namd-version.txt index 157cac038..90b3a010a 100644 --- a/namd/tests/library/022_apathCV_distanceVec/namd-version.txt +++ b/namd/tests/library/022_apathCV_distanceVec/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA +colvars: Initializing the collective variables module, version "2019-10-21". +colvars: Using NAMD interface, version "2019-10-21". diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out index e7178f688..833f3b0c7 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out +++ b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_dihed" @@ -34,56 +32,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -99,56 +97,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -164,56 +162,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -448,6 +446,37 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 13.3844 +colvars: Distance between frame 2 and 3 is 13.3844 +colvars: Distance between frame 3 and 4 is 13.4029 +colvars: Distance between frame 4 and 5 is 13.4142 +colvars: Distance between frame 5 and 6 is 13.4056 +colvars: Distance between frame 6 and 7 is 13.42 +colvars: Distance between frame 7 and 8 is 13.3375 +colvars: Distance between frame 8 and 9 is 13.4007 +colvars: Distance between frame 9 and 10 is 13.0106 +colvars: Distance between frame 10 and 11 is 13.3842 +colvars: Distance between frame 11 and 12 is 11.9956 +colvars: Distance between frame 12 and 13 is 13.2179 +colvars: Distance between frame 13 and 14 is 13.2532 +colvars: Distance between frame 14 and 15 is 13.4171 +colvars: Distance between frame 15 and 16 is 13.4199 +colvars: Distance between frame 16 and 17 is 13.4188 +colvars: Distance between frame 17 and 18 is 13.3433 +colvars: Distance between frame 18 and 19 is 13.2697 +colvars: Distance between frame 19 and 20 is 13.0715 +colvars: Distance between frame 20 and 21 is 13.3511 +colvars: Distance between frame 21 and 22 is 12.7202 +colvars: Distance between frame 22 and 23 is 13.2064 +colvars: Distance between frame 23 and 24 is 13.3364 +colvars: Distance between frame 24 and 25 is 13.3914 +colvars: Distance between frame 25 and 26 is 13.4199 +colvars: Distance between frame 26 and 27 is 13.4148 +colvars: Distance between frame 27 and 28 is 13.3844 +colvars: Distance between frame 28 and 29 is 13.3858 +colvars: Distance between frame 29 and 30 is 13.204 +colvars: Distance between frame 30 and 31 is 13.2614 +colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -457,7 +486,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -489,56 +518,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -554,56 +583,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -619,56 +648,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -903,6 +932,37 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 13.3844 +colvars: Distance between frame 2 and 3 is 13.3844 +colvars: Distance between frame 3 and 4 is 13.4029 +colvars: Distance between frame 4 and 5 is 13.4142 +colvars: Distance between frame 5 and 6 is 13.4056 +colvars: Distance between frame 6 and 7 is 13.42 +colvars: Distance between frame 7 and 8 is 13.3375 +colvars: Distance between frame 8 and 9 is 13.4007 +colvars: Distance between frame 9 and 10 is 13.0106 +colvars: Distance between frame 10 and 11 is 13.3842 +colvars: Distance between frame 11 and 12 is 11.9956 +colvars: Distance between frame 12 and 13 is 13.2179 +colvars: Distance between frame 13 and 14 is 13.2532 +colvars: Distance between frame 14 and 15 is 13.4171 +colvars: Distance between frame 15 and 16 is 13.4199 +colvars: Distance between frame 16 and 17 is 13.4188 +colvars: Distance between frame 17 and 18 is 13.3433 +colvars: Distance between frame 18 and 19 is 13.2697 +colvars: Distance between frame 19 and 20 is 13.0715 +colvars: Distance between frame 20 and 21 is 13.3511 +colvars: Distance between frame 21 and 22 is 12.7202 +colvars: Distance between frame 22 and 23 is 13.2064 +colvars: Distance between frame 23 and 24 is 13.3364 +colvars: Distance between frame 24 and 25 is 13.3914 +colvars: Distance between frame 25 and 26 is 13.4199 +colvars: Distance between frame 26 and 27 is 13.4148 +colvars: Distance between frame 27 and 28 is 13.3844 +colvars: Distance between frame 28 and 29 is 13.3858 +colvars: Distance between frame 29 and 30 is 13.204 +colvars: Distance between frame 30 and 31 is 13.2614 +colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -912,7 +972,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -933,25 +993,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - aspathCV colvar component: -colvars: - azpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -978,11 +1019,11 @@ colvars: Re-initialized atom group for variable "apath_z_dihed":0/10. 1 atoms: t colvars: Re-initialized atom group for variable "apath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: The restart output state file will be "test.restart.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped index 36fd4bb55..2279fe2bc 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.state.stripped @@ -10,6 +10,6 @@ colvar { colvar { name apath_z_dihed - x 4.37232316380885e+00 + x 4.37232316380883e+00 } diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj index 815ea7a8e..f2cfedfcc 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj +++ b/namd/tests/library/023_apathCV/AutoDiff/test.colvars.traj @@ -9,14 +9,14 @@ 7 7.81951384906762e-01 -1.12708542497330e+01 8 7.81862402327513e-01 -5.04973060370784e+00 9 7.81744790117315e-01 -4.11017372635214e-01 - 10 7.81727932105477e-01 3.23713799393060e+00 - 11 7.81587394970700e-01 6.52501229704586e+00 + 10 7.81727932105477e-01 3.23713799393062e+00 + 11 7.81587394970700e-01 6.52501229704612e+00 12 7.81406177092293e-01 9.56998059334305e+00 - 13 7.81288506120401e-01 1.08957744034999e+01 + 13 7.81288506120401e-01 1.08957744035001e+01 14 7.81213577479822e-01 1.17023277179725e+01 15 7.81012363824849e-01 1.15317460999164e+01 - 16 7.80904107517137e-01 1.05479253244908e+01 - 17 7.80932778795886e-01 9.25509175496143e+00 - 18 7.80986172825268e-01 7.43274003628036e+00 + 16 7.80904107517137e-01 1.05479253244909e+01 + 17 7.80932778795886e-01 9.25509175496145e+00 + 18 7.80986172825268e-01 7.43274003628034e+00 19 7.81202292537037e-01 5.68220000516656e+00 - 20 7.81356397470272e-01 4.37232316380885e+00 + 20 7.81356397470272e-01 4.37232316380883e+00 diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out index 9828f21a4..813a12275 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "apath.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 500000 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "apath_s_dihed" @@ -34,56 +32,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -99,56 +97,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -164,56 +162,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -448,6 +446,37 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 13.3844 +colvars: Distance between frame 2 and 3 is 13.3844 +colvars: Distance between frame 3 and 4 is 13.4029 +colvars: Distance between frame 4 and 5 is 13.4142 +colvars: Distance between frame 5 and 6 is 13.4056 +colvars: Distance between frame 6 and 7 is 13.42 +colvars: Distance between frame 7 and 8 is 13.3375 +colvars: Distance between frame 8 and 9 is 13.4007 +colvars: Distance between frame 9 and 10 is 13.0106 +colvars: Distance between frame 10 and 11 is 13.3842 +colvars: Distance between frame 11 and 12 is 11.9956 +colvars: Distance between frame 12 and 13 is 13.2179 +colvars: Distance between frame 13 and 14 is 13.2532 +colvars: Distance between frame 14 and 15 is 13.4171 +colvars: Distance between frame 15 and 16 is 13.4199 +colvars: Distance between frame 16 and 17 is 13.4188 +colvars: Distance between frame 17 and 18 is 13.3433 +colvars: Distance between frame 18 and 19 is 13.2697 +colvars: Distance between frame 19 and 20 is 13.0715 +colvars: Distance between frame 20 and 21 is 13.3511 +colvars: Distance between frame 21 and 22 is 12.7202 +colvars: Distance between frame 22 and 23 is 13.2064 +colvars: Distance between frame 23 and 24 is 13.3364 +colvars: Distance between frame 24 and 25 is 13.3914 +colvars: Distance between frame 25 and 26 is 13.4199 +colvars: Distance between frame 26 and 27 is 13.4148 +colvars: Distance between frame 27 and 28 is 13.3844 +colvars: Distance between frame 28 and 29 is 13.3858 +colvars: Distance between frame 29 and 30 is 13.204 +colvars: Distance between frame 30 and 31 is 13.2614 +colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -457,7 +486,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -489,56 +518,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5972. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -554,56 +583,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -619,56 +648,56 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.01, total charge = 0.5973. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 1 atoms requested: total mass = 14.01, total charge = -0.4157. colvars: Initializing atom group "group3". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group3". colvars: # printAtomIDs = off [default] colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.01, total charge = 0.0337. colvars: Initializing atom group "group4". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group4". colvars: # printAtomIDs = off [default] @@ -903,6 +932,37 @@ colvars: Reading CV 003 with 1 value(s) colvars: -68.2498 colvars: Total number of frames: 32 colvars: # weights = { 1, 1, 1 } [default] +colvars: Distance between frame 1 and 2 is 13.3844 +colvars: Distance between frame 2 and 3 is 13.3844 +colvars: Distance between frame 3 and 4 is 13.4029 +colvars: Distance between frame 4 and 5 is 13.4142 +colvars: Distance between frame 5 and 6 is 13.4056 +colvars: Distance between frame 6 and 7 is 13.42 +colvars: Distance between frame 7 and 8 is 13.3375 +colvars: Distance between frame 8 and 9 is 13.4007 +colvars: Distance between frame 9 and 10 is 13.0106 +colvars: Distance between frame 10 and 11 is 13.3842 +colvars: Distance between frame 11 and 12 is 11.9956 +colvars: Distance between frame 12 and 13 is 13.2179 +colvars: Distance between frame 13 and 14 is 13.2532 +colvars: Distance between frame 14 and 15 is 13.4171 +colvars: Distance between frame 15 and 16 is 13.4199 +colvars: Distance between frame 16 and 17 is 13.4188 +colvars: Distance between frame 17 and 18 is 13.3433 +colvars: Distance between frame 18 and 19 is 13.2697 +colvars: Distance between frame 19 and 20 is 13.0715 +colvars: Distance between frame 20 and 21 is 13.3511 +colvars: Distance between frame 21 and 22 is 12.7202 +colvars: Distance between frame 22 and 23 is 13.2064 +colvars: Distance between frame 23 and 24 is 13.3364 +colvars: Distance between frame 24 and 25 is 13.3914 +colvars: Distance between frame 25 and 26 is 13.4199 +colvars: Distance between frame 26 and 27 is 13.4148 +colvars: Distance between frame 27 and 28 is 13.3844 +colvars: Distance between frame 28 and 29 is 13.3858 +colvars: Distance between frame 29 and 30 is 13.204 +colvars: Distance between frame 30 and 31 is 13.2614 +colvars: Distance between frame 31 and 32 is 13.2614 colvars: # lambda = 0.006 colvars: Lambda is 0.006 colvars: The weight of CV 0 is 1 @@ -912,7 +972,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -933,25 +993,6 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - dihedral colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - aspathCV colvar component: -colvars: - azpathCV colvar component: -colvars: n/a -colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. @@ -977,17 +1018,17 @@ colvars: Re-initialized atom group for variable "apath_z_dihed":0/9. 1 atoms: to colvars: Re-initialized atom group for variable "apath_z_dihed":0/10. 1 atoms: total mass = 12.01, total charge = 0.0337. colvars: Re-initialized atom group for variable "apath_z_dihed":0/11. 1 atoms: total mass = 12.01, total charge = 0.5973. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "apath_s_dihed" from value: 0.781356 colvars: Restarting collective variable "apath_z_dihed" from value: 4.37232 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.restart.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (10 scalable groups, 10 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "apath_s_dihed":0/0. 1 atoms: total mass = 12.01, total charge = 0.5972. colvars: Re-initialized atom group for variable "apath_s_dihed":0/1. 1 atoms: total mass = 14.01, total charge = -0.4157. colvars: Re-initialized atom group for variable "apath_s_dihed":0/2. 1 atoms: total mass = 12.01, total charge = 0.0337. diff --git a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj index c7068744f..5c831af6c 100644 --- a/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/023_apathCV/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step apath_s_dihed apath_z_dihed - 20 7.81356397470272e-01 4.37232316380885e+00 + 20 7.81356397470272e-01 4.37232316380883e+00 21 7.81121297977296e-01 1.48408014536711e+01 22 7.80887161764356e-01 2.57385064204216e+01 - 23 7.80608432401527e-01 3.70202491380729e+01 - 24 7.80239933131218e-01 4.91093814693695e+01 - 25 7.79948040898093e-01 6.12096791457022e+01 + 23 7.80608432401527e-01 3.70202491380727e+01 + 24 7.80239933131218e-01 4.91093814693698e+01 + 25 7.79948040898093e-01 6.12096791457024e+01 26 7.79597382762391e-01 7.25781789569762e+01 - 27 7.79139962688763e-01 8.28720619927340e+01 - 28 7.78844243269635e-01 9.18816600988179e+01 - 29 7.78543385360186e-01 9.80096734023500e+01 + 27 7.79139962688763e-01 8.28720619927337e+01 + 28 7.78844243269635e-01 9.18816600988182e+01 + 29 7.78543385360186e-01 9.80096734023498e+01 30 7.78375612820579e-01 1.02527289564776e+02 31 7.78133685857404e-01 1.06109051968502e+02 32 7.77909386932695e-01 1.08483291935737e+02 - 33 7.77812868144173e-01 1.08011291253484e+02 - 34 7.77834700404172e-01 1.06277606048478e+02 - 35 7.77805205280960e-01 1.03033626610267e+02 - 36 7.77952856594698e-01 9.86638072614039e+01 + 33 7.77812868144174e-01 1.08011291253484e+02 + 34 7.77834700404172e-01 1.06277606048477e+02 + 35 7.77805205280961e-01 1.03033626610267e+02 + 36 7.77952856594698e-01 9.86638072614035e+01 37 7.78335111156798e-01 9.35772864178580e+01 38 7.78830800008326e-01 8.79413506004191e+01 - 39 7.79581636252493e-01 8.25355761517521e+01 + 39 7.79581636252493e-01 8.25355761517518e+01 40 7.80351655557853e-01 7.76247569132204e+01 diff --git a/namd/tests/library/023_apathCV/namd-version.txt b/namd/tests/library/023_apathCV/namd-version.txt index 157cac038..90b3a010a 100644 --- a/namd/tests/library/023_apathCV/namd-version.txt +++ b/namd/tests/library/023_apathCV/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore-CUDA +colvars: Initializing the collective variables module, version "2019-10-21". +colvars: Using NAMD interface, version "2019-10-21". diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out index 054d4b4fb..584abb889 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -89,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -114,28 +112,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -146,7 +144,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -174,7 +172,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.001 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -185,33 +182,17 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped index dc898032e..1500d4fef 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name one - x 3.21687540035845e+00 + x 3.21687540056419e+00 } colvar { name two - x 3.24433796460560e+00 + x 3.24433796455973e+00 } restraint { diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj index 6a7d2b487..b7cc76f65 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one two 0 3.20554673468334e+00 -3.10554673468334e-03 3.24960869251665e+00 - 1 3.20437145934513e+00 -3.10437145934513e-03 3.24790015328133e+00 - 2 3.20384019096481e+00 -3.10384019096481e-03 3.24647131781550e+00 - 3 3.20396699951790e+00 -3.10396699951790e-03 3.24540254818910e+00 - 4 3.20472779827294e+00 -3.10472779827294e-03 3.24474238729463e+00 - 5 3.20606250099130e+00 -3.10606250099130e-03 3.24450566312591e+00 - 6 3.20787906478401e+00 -3.10787906478401e-03 3.24467445124469e+00 - 7 3.21005887073584e+00 -3.11005887073584e-03 3.24520146026858e+00 - 8 3.21246317927417e+00 -3.11246317927417e-03 3.24601517487763e+00 - 9 3.21494069574114e+00 -3.11494069574114e-03 3.24702593004012e+00 - 10 3.21733635383034e+00 -3.11733635383034e-03 3.24813222863437e+00 - 11 3.21950110803244e+00 -3.11950110803244e-03 3.24922682020241e+00 - 12 3.22130200104731e+00 -3.12130200104731e-03 3.25020238852994e+00 - 13 3.22263134337672e+00 -3.12263134337672e-03 3.25095680349705e+00 - 14 3.22341377052897e+00 -3.12341377052897e-03 3.25139789468993e+00 - 15 3.22361031714383e+00 -3.12361031714383e-03 3.25144752038385e+00 - 16 3.22321924431675e+00 -3.12321924431675e-03 3.25104461582539e+00 - 17 3.22227396694008e+00 -3.12227396694008e-03 3.25014689320737e+00 - 18 3.22083879561905e+00 -3.12083879561905e-03 3.24873103007473e+00 - 19 3.21900323728982e+00 -3.11900323728982e-03 3.24679144034112e+00 - 20 3.21687540035845e+00 -3.11687540035845e-03 3.24433796460560e+00 + 1 3.20437145934575e+00 -3.10437145934575e-03 3.24790015328139e+00 + 2 3.20384019096733e+00 -3.10384019096733e-03 3.24647131781566e+00 + 3 3.20396699952362e+00 -3.10396699952362e-03 3.24540254818933e+00 + 4 3.20472779828314e+00 -3.10472779828314e-03 3.24474238729480e+00 + 5 3.20606250100725e+00 -3.10606250100725e-03 3.24450566312581e+00 + 6 3.20787906480694e+00 -3.10787906480694e-03 3.24467445124404e+00 + 7 3.21005887076690e+00 -3.11005887076690e-03 3.24520146026706e+00 + 8 3.21246317931445e+00 -3.11246317931445e-03 3.24601517487488e+00 + 9 3.21494069579163e+00 -3.11494069579163e-03 3.24702593003580e+00 + 10 3.21733635389196e+00 -3.11733635389196e-03 3.24813222862814e+00 + 11 3.21950110810599e+00 -3.11950110810599e-03 3.24922682019398e+00 + 12 3.22130200113352e+00 -3.12130200113352e-03 3.25020238851898e+00 + 13 3.22263134347621e+00 -3.12263134347621e-03 3.25095680348327e+00 + 14 3.22341377064230e+00 -3.12341377064230e-03 3.25139789467301e+00 + 15 3.22361031727151e+00 -3.12361031727151e-03 3.25144752036343e+00 + 16 3.22321924445923e+00 -3.12321924445923e-03 3.25104461580106e+00 + 17 3.22227396709780e+00 -3.12227396709780e-03 3.25014689317864e+00 + 18 3.22083879579240e+00 -3.12083879579240e-03 3.24873103004102e+00 + 19 3.21900323747919e+00 -3.11900323747919e-03 3.24679144030174e+00 + 20 3.21687540056419e+00 -3.11687540056419e-03 3.24433796455973e+00 diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out index 924e11490..4ef6865a5 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.new.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "two" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group3" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group4" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -89,7 +87,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -117,7 +115,6 @@ colvars: # centers = { 0.1 } colvars: # targetCenters = { 0.1 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "two" will be rescaled to 0.001 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -128,35 +125,19 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "two" from value: 3.24434 colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "two":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped index fdc8f77c4..e7f40a07f 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name two - x 3.14862665177989e+00 + x 3.14862665152884e+00 } restraint { diff --git a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj index 105050dcc..7ce7af5cf 100644 --- a/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/024_flexible_restart/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step two - 20 3.24433796460560e+00 - 21 3.24139291207264e+00 - 22 3.23798801582996e+00 - 23 3.23416154810177e+00 - 24 3.22995568096637e+00 - 25 3.22541422333673e+00 - 26 3.22058076826608e+00 - 27 3.21549743768062e+00 - 28 3.21020446914023e+00 - 29 3.20474085873977e+00 - 30 3.19914608370685e+00 - 31 3.19346261304852e+00 - 32 3.18773858987485e+00 - 33 3.18202996232668e+00 - 34 3.17640140687287e+00 - 35 3.17092573613846e+00 - 36 3.16568187395172e+00 - 37 3.16075175422443e+00 - 38 3.15621655979123e+00 - 39 3.15215255867285e+00 - 40 3.14862665177989e+00 + 20 3.24433796455973e+00 + 21 3.24139291201932e+00 + 22 3.23798801576814e+00 + 23 3.23416154803027e+00 + 24 3.22995568088397e+00 + 25 3.22541422324222e+00 + 26 3.22058076815832e+00 + 27 3.21549743755863e+00 + 28 3.21020446900326e+00 + 29 3.20474085858739e+00 + 30 3.19914608353898e+00 + 31 3.19346261286550e+00 + 32 3.18773858967743e+00 + 33 3.18202996211599e+00 + 34 3.17640140665043e+00 + 35 3.17092573590606e+00 + 36 3.16568187371138e+00 + 37 3.16075175397829e+00 + 38 3.15621655954144e+00 + 39 3.15215255842149e+00 + 40 3.14862665152884e+00 diff --git a/namd/tests/library/024_flexible_restart/namd-version.txt b/namd/tests/library/024_flexible_restart/namd-version.txt index 157cac038..47e185902 100644 --- a/namd/tests/library/024_flexible_restart/namd-version.txt +++ b/namd/tests/library/024_flexible_restart/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.13 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-01-27". +colvars: Using NAMD interface, version "2019-12-04". diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out index 622c1934d..c7ba00d0a 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -15,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -29,25 +25,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -67,7 +63,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -92,25 +88,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -132,7 +128,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -157,25 +153,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -201,25 +197,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -245,25 +241,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -286,7 +282,7 @@ colvars: # period = 0 [default] colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -304,7 +300,6 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { rmsd_sym } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] @@ -314,7 +309,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 100 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd_sym" will be rescaled to 100 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -325,33 +319,18 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Symmetry-adapted RMSD: -colvars: Ebrahimi2022 https://doi.org/10.1021/acs.jctc.1c01235 -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":1/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":2/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped index 0067e4445..993abc8ee 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.state.stripped @@ -5,17 +5,17 @@ configuration { colvar { name rmsd - x 1.67010101996502e+00 + x 1.67010101996501e+00 } colvar { name rmsd_sym - x 1.06269628600355e+00 + x 1.06269628600354e+00 } colvar { name rmsd_min - x 1.06269628600355e+00 + x 1.06269628600354e+00 } restraint { diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj index 652bfe40b..6974d2232 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.colvars.traj @@ -3,20 +3,20 @@ 1 2.65583548116796e+00 2.49357076354985e+00 2.49357076354985e+00 2 1.74533483223524e+00 1.47077556782424e+00 1.47077556782424e+00 3 1.40555434624453e+00 1.03079831602729e+00 1.03079831602729e+00 - 4 2.06648653553549e+00 1.82627061136782e+00 1.82627061136782e+00 - 5 2.54017219029395e+00 2.33735720111240e+00 2.33735720111240e+00 - 6 2.44511763951317e+00 2.20810814129125e+00 2.20810814129125e+00 + 4 2.06648653553550e+00 1.82627061136782e+00 1.82627061136782e+00 + 5 2.54017219029394e+00 2.33735720111240e+00 2.33735720111240e+00 + 6 2.44511763951316e+00 2.20810814129124e+00 2.20810814129124e+00 7 1.90917369343023e+00 1.54370117101215e+00 1.54370117101215e+00 - 8 1.46846059624425e+00 8.57092838197608e-01 8.57092838197608e-01 + 8 1.46846059624425e+00 8.57092838197605e-01 8.57092838197605e-01 9 1.73306101411381e+00 1.20805207461003e+00 1.20805207461003e+00 10 2.23122614737732e+00 1.83168666851452e+00 1.83168666851452e+00 11 2.40879160755837e+00 2.03136190092487e+00 2.03136190092487e+00 - 12 2.16660397964881e+00 1.72654978561156e+00 1.72654978561156e+00 - 13 1.72124086387257e+00 1.10943093382589e+00 1.10943093382589e+00 - 14 1.54507113594669e+00 8.13315046570523e-01 8.13315046570523e-01 - 15 1.84201976466438e+00 1.30057662388300e+00 1.30057662388300e+00 - 16 2.18866124657310e+00 1.76429607011378e+00 1.76429607011378e+00 + 12 2.16660397964880e+00 1.72654978561155e+00 1.72654978561155e+00 + 13 1.72124086387256e+00 1.10943093382589e+00 1.10943093382589e+00 + 14 1.54507113594670e+00 8.13315046570531e-01 8.13315046570531e-01 + 15 1.84201976466439e+00 1.30057662388302e+00 1.30057662388302e+00 + 16 2.18866124657311e+00 1.76429607011380e+00 1.76429607011380e+00 17 2.26240711868798e+00 1.85743190829637e+00 1.85743190829637e+00 18 1.99090416866217e+00 1.51280845285182e+00 1.51280845285182e+00 - 19 1.59604958772557e+00 9.31109046188018e-01 9.31109046188018e-01 - 20 1.67010101996502e+00 1.06269628600355e+00 1.06269628600355e+00 + 19 1.59604958772556e+00 9.31109046188012e-01 9.31109046188012e-01 + 20 1.67010101996501e+00 1.06269628600354e+00 1.06269628600354e+00 diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out index 0b153b893..8b384c5c1 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -15,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "rmsd" @@ -29,25 +25,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -67,7 +63,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -92,25 +88,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -132,7 +128,7 @@ colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = on [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -157,25 +153,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -201,25 +197,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -245,25 +241,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "atoms". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = on -colvars: # rotateToReference = on +colvars: # centerReference = on +colvars: # rotateReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: Within atom group "atoms": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 9 atoms requested: total mass = 70.071, total charge = -0.09. @@ -286,7 +282,7 @@ colvars: # period = 0 [default] colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -304,7 +300,6 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { rmsd_sym } -colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] @@ -314,7 +309,6 @@ colvars: # centers = { 0 } colvars: # targetCenters = { 0 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 100 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "rmsd_sym" will be rescaled to 100 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -325,40 +319,25 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Symmetry-adapted RMSD: -colvars: Ebrahimi2022 https://doi.org/10.1021/acs.jctc.1c01235 -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Moving frame of reference: -colvars: - Optimal rotation via flexible fitting: -colvars: - rmsd colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":1/0. 4 atoms: total mass = 15.035, total charge = 0. +colvars: Re-initialized atom group for variable "rmsd_min":2/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Restarting from file "test.colvars.state". colvars: Restarting collective variable "rmsd" from value: 1.6701 colvars: Restarting collective variable "rmsd_sym" from value: 1.0627 colvars: Restarting collective variable "rmsd_min" from value: 1.0627 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (13 atoms). colvars: updating group data (0 scalable groups, 0 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "rmsd":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_sym":0/0. 4 atoms: total mass = 15.035, total charge = 0. colvars: Re-initialized atom group for variable "rmsd_min":0/0. 4 atoms: total mass = 15.035, total charge = 0. diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped index 512353c31..fdae84add 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.state.stripped @@ -10,12 +10,12 @@ colvar { colvar { name rmsd_sym - x 7.26619298562140e-01 + x 7.26619298562136e-01 } colvar { name rmsd_min - x 7.26619298562140e-01 + x 7.26619298562136e-01 } restraint { diff --git a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj index c1832014e..b66d34d1e 100644 --- a/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/025_sym_rmsd/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step rmsd rmsd_sym rmsd_min - 20 1.67010101996502e+00 1.06269628600355e+00 1.06269628600355e+00 - 21 2.04433892429580e+00 1.60292722878384e+00 1.60292722878384e+00 - 22 2.06240612835231e+00 1.64334625236225e+00 1.64334625236225e+00 - 23 1.72479860434135e+00 1.21752251761604e+00 1.21752251761604e+00 - 24 1.45281664722968e+00 8.31805423263470e-01 8.31805423263470e-01 - 25 1.62193082908379e+00 1.13819710156541e+00 1.13819710156541e+00 - 26 1.91428771037452e+00 1.54849490838443e+00 1.54849490838443e+00 - 27 1.93241576009646e+00 1.57970290898645e+00 1.57970290898645e+00 - 28 1.64032456570088e+00 1.19887684608300e+00 1.19887684608300e+00 - 29 1.42831104802460e+00 8.67878207872016e-01 8.67878207872016e-01 - 30 1.71179394524437e+00 1.27004409838276e+00 1.27004409838276e+00 - 31 2.10204997402061e+00 1.75291645597029e+00 1.75291645597029e+00 - 32 2.16523333046788e+00 1.81717671975523e+00 1.81717671975523e+00 - 33 1.85227206897976e+00 1.41097165384594e+00 1.41097165384594e+00 - 34 1.51283191580260e+00 8.90242598276090e-01 8.90242598276090e-01 - 35 1.65809367768181e+00 1.09671669300780e+00 1.09671669300780e+00 - 36 2.03497663158024e+00 1.59379893021682e+00 1.59379893021682e+00 - 37 2.17858401892652e+00 1.75248645511792e+00 1.75248645511792e+00 - 38 1.99046986313611e+00 1.48057223445696e+00 1.48057223445696e+00 - 39 1.64708037387981e+00 9.18991758873730e-01 9.18991758873730e-01 - 40 1.57261614568718e+00 7.26619298562140e-01 7.26619298562140e-01 + 20 1.67010101996501e+00 1.06269628600354e+00 1.06269628600354e+00 + 21 2.04433892429578e+00 1.60292722878381e+00 1.60292722878381e+00 + 22 2.06240612835228e+00 1.64334625236222e+00 1.64334625236222e+00 + 23 1.72479860434134e+00 1.21752251761603e+00 1.21752251761603e+00 + 24 1.45281664722968e+00 8.31805423263468e-01 8.31805423263468e-01 + 25 1.62193082908377e+00 1.13819710156539e+00 1.13819710156539e+00 + 26 1.91428771037449e+00 1.54849490838439e+00 1.54849490838439e+00 + 27 1.93241576009644e+00 1.57970290898642e+00 1.57970290898642e+00 + 28 1.64032456570087e+00 1.19887684608299e+00 1.19887684608299e+00 + 29 1.42831104802460e+00 8.67878207872020e-01 8.67878207872020e-01 + 30 1.71179394524434e+00 1.27004409838273e+00 1.27004409838273e+00 + 31 2.10204997402056e+00 1.75291645597024e+00 1.75291645597024e+00 + 32 2.16523333046785e+00 1.81717671975520e+00 1.81717671975520e+00 + 33 1.85227206897975e+00 1.41097165384593e+00 1.41097165384593e+00 + 34 1.51283191580260e+00 8.90242598276096e-01 8.90242598276096e-01 + 35 1.65809367768181e+00 1.09671669300779e+00 1.09671669300779e+00 + 36 2.03497663158023e+00 1.59379893021680e+00 1.59379893021680e+00 + 37 2.17858401892649e+00 1.75248645511788e+00 1.75248645511788e+00 + 38 1.99046986313608e+00 1.48057223445693e+00 1.48057223445693e+00 + 39 1.64708037387980e+00 9.18991758873705e-01 9.18991758873705e-01 + 40 1.57261614568718e+00 7.26619298562136e-01 7.26619298562136e-01 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out b/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out index 75a651d7a..d6f4b9ad4 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -134,29 +130,16 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.grad b/namd/tests/library/026_ABF_energy/AutoDiff/test.grad index 46dea61eb..16cf7fcda 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.grad +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -1.17682469793588e+01 + 3.25000000000000e+00 -1.17682470708695e+01 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf b/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf index 665e2643f..d27977925 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 5.88412348967941e+00 - 5.00000000000000e-01 5.88412348967941e+00 - 1.00000000000000e+00 5.88412348967941e+00 - 1.50000000000000e+00 5.88412348967941e+00 - 2.00000000000000e+00 5.88412348967941e+00 - 2.50000000000000e+00 5.88412348967941e+00 - 3.00000000000000e+00 5.88412348967941e+00 + 0.00000000000000e+00 5.88412353543475e+00 + 5.00000000000000e-01 5.88412353543475e+00 + 1.00000000000000e+00 5.88412353543475e+00 + 1.50000000000000e+00 5.88412353543475e+00 + 2.00000000000000e+00 5.88412353543475e+00 + 2.50000000000000e+00 5.88412353543475e+00 + 3.00000000000000e+00 5.88412353543475e+00 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out index 865f10f4c..8def9ee51 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.colvars.out @@ -1,12 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -45,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -59,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -134,34 +130,21 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - ABF colvar bias implementation: -colvars: - Internal-forces free energy estimator: -colvars: Henin2010 https://doi.org/10.1021/ct9004432 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.14228 colvars: Restarting abf bias "abf1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad index d348c12f2..8b57bb739 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.grad @@ -7,7 +7,7 @@ 1.75000000000000e+00 0.00000000000000e+00 2.25000000000000e+00 0.00000000000000e+00 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -2.34801644956595e+01 + 3.25000000000000e+00 -2.34801645799521e+01 3.75000000000000e+00 0.00000000000000e+00 4.25000000000000e+00 0.00000000000000e+00 4.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf index 08a4d3d5b..d2eb54957 100644 --- a/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf +++ b/namd/tests/library/026_ABF_energy/AutoDiff/test.restart.pmf @@ -1,13 +1,13 @@ # 1 # -2.50000000000000e-01 5.00000000000000e-01 21 0 - 0.00000000000000e+00 1.17400822478297e+01 - 5.00000000000000e-01 1.17400822478297e+01 - 1.00000000000000e+00 1.17400822478297e+01 - 1.50000000000000e+00 1.17400822478297e+01 - 2.00000000000000e+00 1.17400822478297e+01 - 2.50000000000000e+00 1.17400822478297e+01 - 3.00000000000000e+00 1.17400822478297e+01 + 0.00000000000000e+00 1.17400822899760e+01 + 5.00000000000000e-01 1.17400822899760e+01 + 1.00000000000000e+00 1.17400822899760e+01 + 1.50000000000000e+00 1.17400822899760e+01 + 2.00000000000000e+00 1.17400822899760e+01 + 2.50000000000000e+00 1.17400822899760e+01 + 3.00000000000000e+00 1.17400822899760e+01 3.50000000000000e+00 0.00000000000000e+00 4.00000000000000e+00 0.00000000000000e+00 4.50000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/026_ABF_energy/namd-version.txt b/namd/tests/library/026_ABF_energy/namd-version.txt index 157cac038..402dbcc14 100644 --- a/namd/tests/library/026_ABF_energy/namd-version.txt +++ b/namd/tests/library/026_ABF_energy/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-06-02". +colvars: Using NAMD interface, version "2020-05-04". diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state index ac87bdbc5..ad2a42cd1 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state +++ b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-0.colvars.state @@ -11,10 +11,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 8.70939574046587e-05 - 2.70056900312946e-03 3.08054911230446e-02 1.29272634625682e-01 - 1.99567890849616e-01 1.13339251307472e-01 2.36796683760721e-02 - 1.82002141052347e-03 5.14615641849260e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 8.70939573129658e-05 + 2.70056900100952e-03 3.08054911071083e-02 1.29272634593393e-01 + 1.99567890853138e-01 1.13339251339767e-01 2.36796683891457e-02 + 1.82002141201432e-03 5.14615642408155e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -26,10 +26,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 6.85295349016874e-04 - 1.58481831440929e-02 1.19169844943943e-01 2.41540944181510e-01 - -2.62507763713641e-02 -2.41586884549233e-01 -9.78334326726952e-02 - -1.11595284046322e-02 -4.18461586694560e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 6.85295348342052e-04 + 1.58481831330982e-02 1.19169844898782e-01 2.41540944190337e-01 + -2.62507762651161e-02 -2.41586884557496e-01 -9.78334327140598e-02 + -1.11595284128016e-02 -4.18461587121564e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state index ac87bdbc5..ad2a42cd1 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state +++ b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-1.colvars.state @@ -11,10 +11,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 8.70939574046587e-05 - 2.70056900312946e-03 3.08054911230446e-02 1.29272634625682e-01 - 1.99567890849616e-01 1.13339251307472e-01 2.36796683760721e-02 - 1.82002141052347e-03 5.14615641849260e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 8.70939573129658e-05 + 2.70056900100952e-03 3.08054911071083e-02 1.29272634593393e-01 + 1.99567890853138e-01 1.13339251339767e-01 2.36796683891457e-02 + 1.82002141201432e-03 5.14615642408155e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -26,10 +26,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 6.85295349016874e-04 - 1.58481831440929e-02 1.19169844943943e-01 2.41540944181510e-01 - -2.62507763713641e-02 -2.41586884549233e-01 -9.78334326726952e-02 - -1.11595284046322e-02 -4.18461586694560e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 6.85295348342052e-04 + 1.58481831330982e-02 1.19169844898782e-01 2.41540944190337e-01 + -2.62507762651161e-02 -2.41586884557496e-01 -9.78334327140598e-02 + -1.11595284128016e-02 -4.18461587121564e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state index 30f1b680a..8dcab87f9 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state +++ b/namd/tests/library/027_multiple_runs/AutoDiff/mtd-2.colvars.state @@ -11,10 +11,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.80472755097040e-04 - 5.54447036223268e-03 6.26727288407827e-02 2.60655276117922e-01 - 3.98862365610485e-01 2.24567790690383e-01 4.65199212276517e-02 - 3.54565765284328e-03 9.94306268035517e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.80472754695334e-04 + 5.54447035307032e-03 6.26727287728974e-02 2.60655275982959e-01 + 3.98862365627901e-01 2.24567790825392e-01 4.65199212813745e-02 + 3.54565765888724e-03 9.94306270273247e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -26,10 +26,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.41667561487056e-03 - 3.24357195248848e-02 2.41314964024310e-01 4.82392264917098e-01 - -5.94386861724842e-02 -4.82536712977343e-01 -1.92985724018794e-01 - -2.17993242036534e-02 -8.10150852681438e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.41667561192491e-03 + 3.24357194776196e-02 2.41314963834041e-01 4.82392264961036e-01 + -5.94386857287638e-02 -4.82536713017911e-01 -1.92985724190331e-01 + -2.17993242369277e-02 -8.10150854396533e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out index 5a868114a..93db4f3a8 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.out @@ -1,10 +1,9 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -43,7 +42,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -57,28 +55,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerToOrigin = off [default] -colvars: # centerToReference = off [default] -colvars: # rotateToReference = off [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -115,34 +113,7 @@ colvars: # outputFile = "" [default] colvars: # outputFileDX = "none" [default] colvars: # gatherVectorColvars = off [default] colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "metadynamics" instance. -colvars: # name = "metadynamics1" [default] -colvars: # colvars = { one } -colvars: # stepZeroData = off [default] -colvars: # outputEnergy = off [default] -colvars: # outputFreq = 10 [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] -colvars: # hillWeight = 0.1 -colvars: # newHillFrequency = 10 -colvars: # gaussianSigmas = [default] -colvars: # hillWidth = 2 -colvars: Half-widths of the Gaussian hills (sigma's): -colvars: one: 0.5 -colvars: # multipleReplicas = off [default] -colvars: # useGrids = on [default] -colvars: # gridsUpdateFrequency = 10 [default] -colvars: # rebinGrids = off [default] -colvars: # writeFreeEnergyFile = on [default] -colvars: # keepHills = off [default] -colvars: # keepFreeEnergyFiles = off [default] -colvars: # writeHillsTrajectory = off [default] -colvars: # wellTempered = off [default] -colvars: # biasTemperature = -1 [default] -colvars: # ebMeta = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 2 in total. +colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- @@ -150,31 +121,16 @@ colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Histogram colvar bias implementation: -colvars: - Metadynamics colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". @@ -191,6 +147,12 @@ colvars: Saving collective variables state to "test.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". colvars: Writing the histogram file "test.histogram1.dat". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Writing the histogram file "test.histogram1.dat". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Writing the histogram file "test.histogram1.dat". colvars: Saving collective variables state to "test.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped index eb8fb4fb7..b62b4fcd0 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21415030858830e+00 + x 3.21415030906913e+00 } histogram { @@ -32,10 +32,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.80472755097040e-04 - 5.54447036223268e-03 6.26727288407827e-02 2.60655276117922e-01 - 3.98862365610485e-01 2.24567790690383e-01 4.65199212276517e-02 - 3.54565765284328e-03 9.94306268035517e-05 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.80472754695334e-04 + 5.54447035307032e-03 6.26727287728974e-02 2.60655275982959e-01 + 3.98862365627901e-01 2.24567790825392e-01 4.65199212813745e-02 + 3.54565765888724e-03 9.94306270273247e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -47,10 +47,10 @@ grid_parameters { widths 5.00000000000000e-01 sizes 20 } - 0.00000000000000e+00 0.00000000000000e+00 1.41667561487056e-03 - 3.24357195248848e-02 2.41314964024310e-01 4.82392264917098e-01 - -5.94386861724842e-02 -4.82536712977343e-01 -1.92985724018794e-01 - -2.17993242036534e-02 -8.10150852681438e-04 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 1.41667561192491e-03 + 3.24357194776196e-02 2.41314963834041e-01 4.82392264961036e-01 + -5.94386857287638e-02 -4.82536713017911e-01 -1.92985724190331e-01 + -2.17993242369277e-02 -8.10150854396533e-04 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj index 31091a629..e04394664 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.colvars.traj @@ -1,44 +1,44 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316484e+00 0.00000000000000e+00 - 2 3.20384028588952e+00 0.00000000000000e+00 - 3 3.20396721186862e+00 0.00000000000000e+00 - 4 3.20472817286016e+00 0.00000000000000e+00 - 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 - 7 3.21005997940810e+00 0.00000000000000e+00 - 8 3.21246460651160e+00 0.00000000000000e+00 - 9 3.21494247383722e+00 0.00000000000000e+00 - 10 3.21733851230199e+00 1.30367508844061e-02 - 11 3.21950387395255e+00 1.30367508844061e-02 - 12 3.22130559658681e+00 1.30367508844061e-02 - 13 3.22263598353165e+00 1.30367508844061e-02 - 14 3.22341966109109e+00 1.30367508844061e-02 - 15 3.22361765299886e+00 1.30367508844061e-02 - 16 3.22322820813411e+00 1.30367508844061e-02 - 17 3.22228472829020e+00 1.30367508844061e-02 - 18 3.22085151053088e+00 1.30367508844061e-02 - 19 3.21901804823901e+00 1.30367508844061e-02 - 20 3.21689243666711e+00 2.62507763713641e-02 - 20 3.21689243666711e+00 2.62507763713641e-02 - 20 3.21689243666711e+00 2.62507763713641e-02 - 21 3.21459439240045e+00 2.62507763713641e-02 - 22 3.21224726535912e+00 2.62507763713641e-02 - 23 3.20997056365207e+00 2.62507763713641e-02 - 24 3.20787270637879e+00 2.62507763713641e-02 - 25 3.20604492520325e+00 2.62507763713641e-02 - 26 3.20455694842083e+00 2.62507763713641e-02 - 27 3.20345479563379e+00 2.62507763713641e-02 - 28 3.20276061061291e+00 2.62507763713641e-02 - 29 3.20247408259157e+00 2.62507763713641e-02 - 30 3.20257503670478e+00 4.51356215063288e-02 - 31 3.20302710728970e+00 4.51356215063288e-02 - 32 3.20378117591190e+00 4.51356215063288e-02 - 33 3.20478014892865e+00 4.51356215063288e-02 - 34 3.20596369561551e+00 4.51356215063288e-02 - 35 3.20727281779169e+00 4.51356215063288e-02 - 36 3.20865380534294e+00 4.51356215063288e-02 - 37 3.21006125723226e+00 4.51356215063288e-02 - 38 3.21146012394088e+00 4.51356215063288e-02 - 39 3.21282692105120e+00 4.51356215063288e-02 - 40 3.21415030858830e+00 5.94386861724842e-02 + 1 3.20437148316546e+00 0.00000000000000e+00 + 2 3.20384028589204e+00 0.00000000000000e+00 + 3 3.20396721187433e+00 0.00000000000000e+00 + 4 3.20472817287036e+00 0.00000000000000e+00 + 5 3.20606308066645e+00 0.00000000000000e+00 + 6 3.20787989003051e+00 0.00000000000000e+00 + 7 3.21005997943917e+00 0.00000000000000e+00 + 8 3.21246460655188e+00 0.00000000000000e+00 + 9 3.21494247388772e+00 0.00000000000000e+00 + 10 3.21733851236362e+00 1.30367508599117e-02 + 11 3.21950387402611e+00 1.30367508599117e-02 + 12 3.22130559667303e+00 1.30367508599117e-02 + 13 3.22263598363115e+00 1.30367508599117e-02 + 14 3.22341966120443e+00 1.30367508599117e-02 + 15 3.22361765312655e+00 1.30367508599117e-02 + 16 3.22322820827659e+00 1.30367508599117e-02 + 17 3.22228472844791e+00 1.30367508599117e-02 + 18 3.22085151070423e+00 1.30367508599117e-02 + 19 3.21901804842838e+00 1.30367508599117e-02 + 20 3.21689243687284e+00 2.62507762651161e-02 + 20 3.21689243687284e+00 2.62507762651161e-02 + 20 3.21689243687284e+00 2.62507762651161e-02 + 21 3.21459439262285e+00 2.62507762651161e-02 + 22 3.21224726559843e+00 2.62507762651161e-02 + 23 3.20997056390844e+00 2.62507762651161e-02 + 24 3.20787270665228e+00 2.62507762651161e-02 + 25 3.20604492549381e+00 2.62507762651161e-02 + 26 3.20455694872830e+00 2.62507762651161e-02 + 27 3.20345479595789e+00 2.62507762651161e-02 + 28 3.20276061095329e+00 2.62507762651161e-02 + 29 3.20247408294778e+00 2.62507762651161e-02 + 30 3.20257503707633e+00 4.51356212534586e-02 + 31 3.20302710767604e+00 4.51356212534586e-02 + 32 3.20378117631245e+00 4.51356212534586e-02 + 33 3.20478014934277e+00 4.51356212534586e-02 + 34 3.20596369604249e+00 4.51356212534586e-02 + 35 3.20727281823071e+00 4.51356212534586e-02 + 36 3.20865380579304e+00 4.51356212534586e-02 + 37 3.21006125769230e+00 4.51356212534586e-02 + 38 3.21146012440951e+00 4.51356212534586e-02 + 39 3.21282692152683e+00 4.51356212534586e-02 + 40 3.21415030906913e+00 5.94386857287638e-02 diff --git a/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf b/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf index af5f3fa27..d85393c4f 100644 --- a/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf +++ b/namd/tests/library/027_multiple_runs/AutoDiff/test.pmf @@ -1,23 +1,23 @@ # 1 # 0.00000000000000e+00 5.00000000000000e-01 20 0 - 2.50000000000000e-01 3.98862365610485e-01 - 7.50000000000000e-01 3.98862365610485e-01 - 1.25000000000000e+00 3.98681892855388e-01 - 1.75000000000000e+00 3.93317895248252e-01 - 2.25000000000000e+00 3.36189636769702e-01 - 2.75000000000000e+00 1.38207089492563e-01 + 2.50000000000000e-01 3.98862365627901e-01 + 7.50000000000000e-01 3.98862365627901e-01 + 1.25000000000000e+00 3.98681892873206e-01 + 1.75000000000000e+00 3.93317895274831e-01 + 2.25000000000000e+00 3.36189636855004e-01 + 2.75000000000000e+00 1.38207089644942e-01 3.25000000000000e+00 -0.00000000000000e+00 - 3.75000000000000e+00 1.74294574920103e-01 - 4.25000000000000e+00 3.52342444382833e-01 - 4.75000000000000e+00 3.95316707957642e-01 - 5.25000000000000e+00 3.98762934983682e-01 - 5.75000000000000e+00 3.98862365610485e-01 - 6.25000000000000e+00 3.98862365610485e-01 - 6.75000000000000e+00 3.98862365610485e-01 - 7.25000000000000e+00 3.98862365610485e-01 - 7.75000000000000e+00 3.98862365610485e-01 - 8.25000000000000e+00 3.98862365610485e-01 - 8.75000000000000e+00 3.98862365610485e-01 - 9.25000000000000e+00 3.98862365610485e-01 - 9.75000000000000e+00 3.98862365610485e-01 + 3.75000000000000e+00 1.74294574802509e-01 + 4.25000000000000e+00 3.52342444346527e-01 + 4.75000000000000e+00 3.95316707969014e-01 + 5.25000000000000e+00 3.98762935000874e-01 + 5.75000000000000e+00 3.98862365627901e-01 + 6.25000000000000e+00 3.98862365627901e-01 + 6.75000000000000e+00 3.98862365627901e-01 + 7.25000000000000e+00 3.98862365627901e-01 + 7.75000000000000e+00 3.98862365627901e-01 + 8.25000000000000e+00 3.98862365627901e-01 + 8.75000000000000e+00 3.98862365627901e-01 + 9.25000000000000e+00 3.98862365627901e-01 + 9.75000000000000e+00 3.98862365627901e-01 diff --git a/namd/tests/library/027_multiple_runs/namd-version.txt b/namd/tests/library/027_multiple_runs/namd-version.txt index 157cac038..402dbcc14 100644 --- a/namd/tests/library/027_multiple_runs/namd-version.txt +++ b/namd/tests/library/027_multiple_runs/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14b1 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2020-06-02". +colvars: Using NAMD interface, version "2020-05-04". diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out index 9a80820be..f8931d8a7 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out @@ -1,21 +1,17 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "test.in": +colvars: Reading new configuration from file "test.legacy.in": colvars: # units = "" [default] colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 10 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "c" @@ -60,13 +56,18 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. colvars: Warning: Variable r2 is absent from expression "atan2(r3, r1) * 180 / 3.1415926". +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r1. +colvars: Warning: Variable r1 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r3 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r3. colvars: Expecting colvar value of type scalar number. colvars: # period = 360 colvars: # wrapAround = 0 colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -94,7 +95,6 @@ colvars: # centers = { -179 } colvars: # targetCenters = { -179 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.01 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "c" will be rescaled to 0.01 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -105,31 +105,15 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. +colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. colvars: The restart output state file will be "test.tmp.colvars.state". diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out index b5c095d75..fc34e52ef 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out @@ -1,21 +1,17 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: as well as all other papers listed below for individual features used. +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "test.in": +colvars: Reading new configuration from file "test.legacy.in": colvars: # units = "" [default] colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 10 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "c" @@ -60,13 +56,18 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. colvars: Warning: Variable r2 is absent from expression "atan2(r3, r1) * 180 / 3.1415926". +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r1. +colvars: Warning: Variable r1 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r3 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. +colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r3. colvars: Expecting colvar value of type scalar number. colvars: # period = 360 colvars: # wrapAround = 0 colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 1 [default] +colvars: # upperBoundary = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -94,7 +95,6 @@ colvars: # centers = { -179 } colvars: # targetCenters = { -179 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.01 -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "c" will be rescaled to 0.01 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -105,36 +105,20 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: -colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: -colvars: -colvars: - Colvars module: -colvars: - Colvars-NAMD interface: -colvars: - Harmonic colvar bias implementation: -colvars: - Optimal rotation via flexible fitting: -colvars: - distance colvar component: -colvars: - distanceDir colvar component (derived from distance): -colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 -colvars: -colvars: - NAMD engine: -colvars: - Scalable center-of-mass computation (NAMD): -colvars: Phillips2020 https://doi.org/10.1063/5.0014475 -colvars: -colvars: - Custom functions (Lepton): -colvars: n/a -colvars: -colvars: updating target temperature (T = 0 K). +colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. +colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. colvars: ---------------------------------------------------------------------- colvars: Loading state from file "test.colvars.state". colvars: Restarting collective variable "c" from value: 157.339 colvars: Restarting harmonic bias "harmonic1" from step number 20. colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Opening trajectory file "test.restart.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 0 K). colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. colvars: The restart output state file will be "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/028_periodic_custom_function/namd-version.txt b/namd/tests/library/028_periodic_custom_function/namd-version.txt index 157cac038..fb5cc08df 100644 --- a/namd/tests/library/028_periodic_custom_function/namd-version.txt +++ b/namd/tests/library/028_periodic_custom_function/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 3.0alpha8 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version "2021-03-09". +colvars: Using NAMD interface, version "2021-03-02". diff --git a/namd/tests/library/029_reweightamd/namd-version.txt b/namd/tests/library/029_reweightamd/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/029_reweightamd/namd-version.txt +++ b/namd/tests/library/029_reweightamd/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". diff --git a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out index e3bbc2221..1152d4a8f 100644 --- a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out +++ b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.out @@ -4,7 +4,6 @@ colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -13,7 +12,6 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "end_to_end_distance" @@ -88,6 +86,7 @@ colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # scaledBiasingForce = on colvars: # scaledBiasingForceFactorsGrid = "factors.grid" +colvars: Reading scaling factors for the forces of bias production_abf from factors.grid colvars: # applyBias = on [default] colvars: # updateBias = on [default] colvars: # hideJacobian = off [default] @@ -109,6 +108,7 @@ colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] colvars: # scaledBiasingForce = on colvars: # scaledBiasingForceFactorsGrid = "factors.grid" +colvars: Reading scaling factors for the forces of bias production_mtd from factors.grid colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # hillWeight = 2 @@ -142,7 +142,6 @@ colvars: # colvarsTrajFrequency = 1 [default] colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] -colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- @@ -156,7 +155,6 @@ colvars: # timeStepFactor = 1 colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # forceConstant = 1 [default] -colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 13 } colvars: # upperWalls = { 15 } @@ -196,17 +194,17 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "end_to_end_distance":0/0. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "end_to_end_distance":0/1. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.colvars.state". colvars: The final output state file will be "test.colvars.state". +colvars: Opening trajectory file "test.colvars.traj". +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: Warning: enabling wrapAll can lead to inconsistent results for Colvars calculations: please disable wrapAll, as is the default option in NAMD. colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). colvars: updating grid object data (0 grid objects in total). -colvars: updating target temperature (T = 300 K). colvars: Re-initialized atom group for variable "end_to_end_distance":0/0. 1 atoms: total mass = 12.01, total charge = -0.3662. colvars: Re-initialized atom group for variable "end_to_end_distance":0/1. 1 atoms: total mass = 12.01, total charge = -0.149. colvars: The restart output state file will be "test.colvars.state". diff --git a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped index aaafe01d2..2983b7392 100644 --- a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.state.stripped @@ -61,9 +61,9 @@ gradient 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 0.00000000000000e+00 -2.46034201565941e+01 -1.71228758550381e+01 -4.35028348233383e+00 8.77100343862926e+00 0.00000000000000e+00 2.41578842132070e+01 - 0.00000000000000e+00 3.67760957979660e+01 0.00000000000000e+00 0.00000000000000e+00 4.03080315984188e+01 0.00000000000000e+00 4.91740802690052e+01 0.00000000000000e+00 - 4.58607749339768e+01 0.00000000000000e+00 5.28741550375003e+01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 + 0.00000000000000e+00 0.00000000000000e+00 -2.46034201565942e+01 -1.71228758550407e+01 -4.35028348233554e+00 8.77100343862862e+00 0.00000000000000e+00 2.41578842131827e+01 + 0.00000000000000e+00 3.67760957979561e+01 0.00000000000000e+00 0.00000000000000e+00 4.03080315983995e+01 0.00000000000000e+00 4.91740802690014e+01 0.00000000000000e+00 + 4.58607749339655e+01 0.00000000000000e+00 5.28741550375132e+01 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -129,20 +129,20 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 2.61587935067117e-05 1.94683970632333e-04 - 1.08251565030012e-03 5.09475130902687e-03 2.04659308796424e-02 - 7.06125286654209e-02 2.09435976415536e-01 5.34918613697524e-01 - 1.17861358817339e+00 2.24504431300101e+00 3.70656454838329e+00 - 5.32145917169711e+00 6.67261938563254e+00 7.35195926071128e+00 - 7.18021399808668e+00 6.29685877472027e+00 5.06102998507674e+00 - 3.86183081585070e+00 2.97265484622017e+00 2.49720984195920e+00 - 2.38143486949621e+00 2.47333896395547e+00 2.62156486038421e+00 - 2.76069831296951e+00 2.91199826509797e+00 3.10017196004795e+00 - 3.27504048000548e+00 3.31818588496202e+00 3.12189683918950e+00 - 2.66602374122956e+00 2.03536975844399e+00 1.37396310594800e+00 - 8.12936839978680e-01 4.18576183807702e-01 1.86468431860140e-01 - 7.15657207976055e-02 2.35824489722632e-02 6.65642098671754e-03 - 1.60673261084200e-03 3.28034119054257e-04 5.79178127981109e-05 + 0.00000000000000e+00 2.61587935066948e-05 1.94683970632219e-04 + 1.08251565029956e-03 5.09475130902452e-03 2.04659308796341e-02 + 7.06125286653960e-02 2.09435976415474e-01 5.34918613697393e-01 + 1.17861358817316e+00 2.24504431300069e+00 3.70656454838293e+00 + 5.32145917169682e+00 6.67261938563242e+00 7.35195926071138e+00 + 7.18021399808696e+00 6.29685877472059e+00 5.06102998507698e+00 + 3.86183081585080e+00 2.97265484622012e+00 2.49720984195906e+00 + 2.38143486949602e+00 2.47333896395524e+00 2.62156486038390e+00 + 2.76069831296907e+00 2.91199826509736e+00 3.10017196004723e+00 + 3.27504048000479e+00 3.31818588496156e+00 3.12189683918944e+00 + 2.66602374122993e+00 2.03536975844466e+00 1.37396310594875e+00 + 8.12936839979314e-01 4.18576183808133e-01 1.86468431860379e-01 + 7.15657207977159e-02 2.35824489723058e-02 6.65642098673127e-03 + 1.60673261084573e-03 3.28034119055107e-04 5.79178127982759e-05 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 @@ -204,20 +204,20 @@ grid_parameters { 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 - 0.00000000000000e+00 4.98572553752462e-03 3.44543416760259e-02 - 1.75326645541183e-01 7.47482721295256e-01 2.68947029660910e+00 - 8.20870614494615e+00 2.11986301747035e+01 4.61909880344223e+01 - 8.44826248580398e+01 1.28506873925876e+02 1.59712391231044e+02 - 1.55977235774206e+02 1.07039391871361e+02 2.56744580180974e+01 - -5.75055838168977e+01 -1.12829758918543e+02 -1.27599236648709e+02 - -1.07606408348117e+02 -6.85243194218725e+01 -2.75641170223360e+01 - 1.69829679656285e+00 1.39955997855656e+01 1.45571151643531e+01 - 1.37895289828742e+01 1.70425441756613e+01 1.97475224737415e+01 - 1.31056573124731e+01 -6.41279019649712e+00 -3.32095989551511e+01 - -5.64631191592674e+01 -6.71337049514181e+01 -6.28686158484828e+01 - -4.82254030908254e+01 -3.07787466326868e+01 -1.64540466072889e+01 - -7.39576145057542e+00 -2.79968734690709e+00 -8.93905835951089e-01 - -2.41013764581217e-01 -5.42598821858858e-02 -1.05068277897643e-02 + 0.00000000000000e+00 4.98572553752153e-03 3.44543416760067e-02 + 1.75326645541099e-01 7.47482721294938e-01 2.68947029660812e+00 + 8.20870614494365e+00 2.11986301746983e+01 4.61909880344138e+01 + 8.44826248580294e+01 1.28506873925868e+02 1.59712391231045e+02 + 1.55977235774219e+02 1.07039391871382e+02 2.56744580181185e+01 + -5.75055838168864e+01 -1.12829758918545e+02 -1.27599236648721e+02 + -1.07606408348132e+02 -6.85243194218847e+01 -2.75641170223432e+01 + 1.69829679655862e+00 1.39955997855602e+01 1.45571151643426e+01 + 1.37895289828585e+01 1.70425441756459e+01 1.97475224737359e+01 + 1.31056573124861e+01 -6.41279019646412e+00 -3.32095989551069e+01 + -5.64631191592285e+01 -6.71337049513984e+01 -6.28686158484858e+01 + -4.82254030908433e+01 -3.07787466327079e+01 -1.64540466073052e+01 + -7.39576145058497e+00 -2.79968734691153e+00 -8.93905835952760e-01 + -2.41013764581735e-01 -5.42598821860181e-02 -1.05068277897928e-02 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj index d76c74714..90721e014 100644 --- a/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj +++ b/namd/tests/library/030_scaledBiasingForce/AutoDiff/test.colvars.traj @@ -3,20 +3,20 @@ 1 1.45695261014138e+01 0.00000000000000e+00 2 1.45635632664853e+01 0.00000000000000e+00 3 1.45582489261713e+01 -2.58411685289576e+01 - 4 1.45527923170544e+01 -2.07125939557695e+01 + 4 1.45527923170544e+01 -2.07125939557735e+01 5 1.45473541901844e+01 0.00000000000000e+00 6 1.45442591718140e+01 0.00000000000000e+00 7 1.45431535519741e+01 0.00000000000000e+00 8 1.45439619694008e+01 0.00000000000000e+00 9 1.45475029536962e+01 0.00000000000000e+00 - 10 1.45537536789397e+01 1.61692398556099e+01 - 11 1.45592642275934e+01 1.61692398556099e+01 + 10 1.45537536789397e+01 1.61692398555902e+01 + 11 1.45592642275934e+01 1.61692398555902e+01 12 1.45670515013898e+01 0.00000000000000e+00 - 13 1.45744569915016e+01 1.47925560209934e+02 - 14 1.45916606161846e+01 1.32015920190288e+02 - 15 1.46158023047859e+01 7.80198886000781e+01 + 13 1.45744569915016e+01 1.47925560209933e+02 + 14 1.45916606161846e+01 1.32015920190301e+02 + 15 1.46158023047859e+01 7.80198886000819e+01 16 1.46427017872138e+01 0.00000000000000e+00 - 17 1.46664306062949e+01 0.00000000000000e+00 + 17 1.46664306062950e+01 0.00000000000000e+00 18 1.46862961461938e+01 0.00000000000000e+00 19 1.47010927350238e+01 0.00000000000000e+00 - 20 1.47116192100262e+01 5.64631191592674e+01 + 20 1.47116192100262e+01 5.64631191592285e+01 diff --git a/namd/tests/library/030_scaledBiasingForce/namd-version.txt b/namd/tests/library/030_scaledBiasingForce/namd-version.txt index 157cac038..a8b4c8892 100644 --- a/namd/tests/library/030_scaledBiasingForce/namd-version.txt +++ b/namd/tests/library/030_scaledBiasingForce/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. -colvars: Using NAMD interface, version "2023-07-06". +Info: NAMD 2.14 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2022-01-19. +colvars: Using NAMD interface, version "2021-10-13". diff --git a/namd/tests/library/031_neuralnetwork/namd-version.txt b/namd/tests/library/031_neuralnetwork/namd-version.txt index 157cac038..0c1e6111b 100644 --- a/namd/tests/library/031_neuralnetwork/namd-version.txt +++ b/namd/tests/library/031_neuralnetwork/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2023-07-21. +colvars: Initializing the collective variables module, version 2023-09-05. colvars: Using NAMD interface, version "2023-07-06". From 025b390b7437634876c5d7486b1f302237f67649 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Thu, 7 Sep 2023 15:46:59 +0200 Subject: [PATCH 011/162] Change parameter in finicky test --- .../AutoDiff/test.colvars.out | 2 +- .../AutoDiff/test.colvars.state.stripped | 8 ++-- .../AutoDiff/test.colvars.traj | 42 +++++++++---------- .../AutoDiff/test.restart.colvars.out | 2 +- .../test.restart.colvars.state.stripped | 8 ++-- .../AutoDiff/test.restart.colvars.traj | 42 +++++++++---------- .../test.in | 2 +- 7 files changed, 53 insertions(+), 53 deletions(-) diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out index 5b1c03881..ec75406ef 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.out @@ -130,7 +130,7 @@ colvars: # forceConstant = 0.001 colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } -colvars: # upperWalls = { 0.2 } +colvars: # upperWalls = { 0.3 } colvars: # lowerWallConstant = 0.001 [default] colvars: # upperWallConstant = 0.001 [default] colvars: The lower wall force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped index 83b0d62b7..868eb59c6 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21549617587205e+00 - v 1.63765399419808e-04 - extended_x 3.20653014354441e+00 - extended_v 1.63765399419808e-04 + x 3.21549621301549e+00 + v 1.63839888121770e-04 + extended_x 3.20653095017852e+00 + extended_v 1.63839888121770e-04 } restraint { diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj index ea3cb4584..64538e290 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 -1.20221869387334e-02 - 1 3.20437148316484e+00 3.20554661526430e+00 -1.17525151850328e-03 -1.19419048416827e-07 -1.20221864610572e-02 - 2 3.20384207658198e+00 3.20554521661731e+00 -5.29406582859160e-04 -1.39864698615333e-06 -1.20221808664692e-02 - 3 3.20397336372329e+00 3.20554201761950e+00 1.31287141313052e-04 -3.19899781308815e-06 -1.20221680704780e-02 - 4 3.20474099372294e+00 3.20553715100348e+00 7.67629999647745e-04 -4.86661601385684e-06 -1.20221486040139e-02 - 5 3.20608361725515e+00 3.20553137919306e+00 1.34262353221182e-03 -5.77181042148448e-06 -1.20221255167722e-02 - 6 3.20790704366680e+00 3.20552603300132e+00 1.82342641164146e-03 -5.34619173897510e-06 -1.20221041320053e-02 - 7 3.21008979708265e+00 3.20552291735469e+00 2.18275341585361e-03 -3.11564663055446e-06 -1.20220916694188e-02 - 8 3.21248979691190e+00 3.20552418961958e+00 2.39999982925276e-03 1.27226489358961e-06 -1.20220967584783e-02 - 9 3.21495218466242e+00 3.20553221724516e+00 2.46238775052099e-03 8.02762557980444e-06 -1.20221288689807e-02 - 10 3.21731838884401e+00 3.20554942258746e+00 2.36620418158973e-03 1.72053422961567e-05 -1.20221976903498e-02 - 11 3.21943620052261e+00 3.20557812401472e+00 2.11781167860092e-03 2.87014272571360e-05 -1.20223124960589e-02 - 12 3.22117010488210e+00 3.20562038339497e+00 1.73390435948928e-03 4.22593802508272e-05 -1.20224815335799e-02 - 13 3.22241068502092e+00 3.20567787031321e+00 1.24058013882022e-03 5.74869182386481e-05 -1.20227114812528e-02 - 14 3.22308184564051e+00 3.20575175243336e+00 6.71160619590605e-04 7.38821201480224e-05 -1.20230070097334e-02 - 15 3.22314498293928e+00 3.20584261924273e+00 6.31372987673906e-05 9.08668093725243e-05 -1.20233704769709e-02 - 16 3.22259983048180e+00 3.20595044336978e+00 -5.45152457477549e-04 1.07824127056634e-04 -1.20238017734791e-02 - 17 3.22148232853223e+00 3.20607458034818e+00 -1.11750194957105e-03 1.24136978399328e-04 -1.20242983213927e-02 - 18 3.21986023795765e+00 3.20621380472449e+00 -1.62209057458140e-03 1.39224376306895e-04 -1.20248552188980e-02 - 19 3.21782725344634e+00 3.20636637814499e+00 -2.03298451131184e-03 1.52573420503577e-04 -1.20254655125800e-02 - 20 3.21549617587205e+00 3.20653014354441e+00 -2.33107757428819e-03 1.63765399419808e-04 -1.20261205741777e-02 + 0 3.20554673468334e+00 3.20554673468334e+00 0.00000000000000e+00 0.00000000000000e+00 -1.16221869387334e-02 + 1 3.20437148316484e+00 3.20554661923758e+00 -1.17525151850328e-03 -1.15445759728991e-07 -1.16221864769503e-02 + 2 3.20384207658804e+00 3.20554522853325e+00 -5.29406576805336e-04 -1.39070433041396e-06 -1.16221809141330e-02 + 3 3.20397336375347e+00 3.20554204143963e+00 1.31287165431537e-04 -3.18709362372464e-06 -1.16221681657585e-02 + 4 3.20474099381307e+00 3.20553719067761e+00 7.67630059602453e-04 -4.85076201650243e-06 -1.16221487627105e-02 + 5 3.20608361746435e+00 3.20553143865541e+00 1.34262365128279e-03 -5.75202220486511e-06 -1.16221257546216e-02 + 6 3.20790704408264e+00 3.20552611616669e+00 1.82342661828994e-03 -5.32248871654545e-06 -1.16221044646668e-02 + 7 3.21008979782599e+00 3.20552302811470e+00 2.18275374334675e-03 -3.08805199324812e-06 -1.16220921124588e-02 + 8 3.21248979814124e+00 3.20552433183893e+00 2.40000031525378e-03 1.30372423308412e-06 -1.16220973273557e-02 + 9 3.21495218657788e+00 3.20553239475798e+00 2.46238843663571e-03 8.06291905077686e-06 -1.16221295790319e-02 + 10 3.21731839169077e+00 3.20554963919372e+00 2.36620511289365e-03 1.72444357411129e-05 -1.16221985567749e-02 + 11 3.21943620459394e+00 3.20557838347673e+00 2.11781290316582e-03 2.87442830099992e-05 -1.16223135339069e-02 + 12 3.22117011052185e+00 3.20562068943396e+00 1.73390592791511e-03 4.23059572215591e-05 -1.16224827577358e-02 + 13 3.22241069262564e+00 3.20567822660596e+00 1.24058210378664e-03 5.75371720037448e-05 -1.16227129064238e-02 + 14 3.22308185566108e+00 3.20575216260901e+00 6.71163035445232e-04 7.39360030463537e-05 -1.16230086504360e-02 + 15 3.22314499588221e+00 3.20584308687961e+00 6.31402211261900e-05 9.09242706060132e-05 -1.16233723475184e-02 + 16 3.22259984691011e+00 3.20595097199241e+00 -5.45148972103338e-04 1.07885112795286e-04 -1.16238038879696e-02 + 17 3.22148234906601e+00 3.20607517342430e+00 -1.11749784410220e-03 1.24201431890135e-04 -1.16243006936972e-02 + 18 3.21986026327429e+00 3.20621446566228e+00 -1.62208579171264e-03 1.39292237986185e-04 -1.16248578626491e-02 + 19 3.21782728428053e+00 3.20636711029040e+00 -2.03297899376365e-03 1.52644628112363e-04 -1.16254684411616e-02 + 20 3.21549621301549e+00 3.20653095017852e+00 -2.33107126504306e-03 1.63839888121770e-04 -1.16261238007141e-02 diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out index fd298f3cd..c94a47cb7 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.out @@ -130,7 +130,7 @@ colvars: # forceConstant = 0.001 colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: # lowerWalls = { 0.1 } -colvars: # upperWalls = { 0.2 } +colvars: # upperWalls = { 0.3 } colvars: # lowerWallConstant = 0.001 [default] colvars: # upperWallConstant = 0.001 [default] colvars: The lower wall force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped index 740730ef2..67e9debbf 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.state.stripped @@ -5,10 +5,10 @@ configuration { colvar { name one - x 3.21130917292044e+00 - v 1.00951348854985e-04 - extended_x 3.20938126631322e+00 - extended_v 1.00951348854985e-04 + x 3.21130958093225e+00 + v 1.01074979342738e-04 + extended_x 3.20938413437057e+00 + extended_v 1.01074979342738e-04 } restraint { diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj index e35e1b0ba..457fcb155 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one r_one v_one vr_one fa_one - 20 3.21549617587205e+00 3.20653014354441e+00 0.00000000000000e+00 1.63765399419808e-04 -1.20261205741776e-02 - 21 3.21299146691002e+00 3.20670263860492e+00 -2.50470896202648e-03 1.72495060509838e-04 -1.20268105544197e-02 - 22 3.21044140002284e+00 3.20688122102521e+00 -2.55006688718051e-03 1.78582420285797e-04 -1.20275248841008e-02 - 23 3.20797012436086e+00 3.20706319772925e+00 -2.47127566198468e-03 1.81976704044760e-04 -1.20282527909170e-02 - 24 3.20569018980129e+00 3.20724595005470e+00 -2.27993455957121e-03 1.82752325450367e-04 -1.20289838002188e-02 - 25 3.20369626842688e+00 3.20742704741977e+00 -1.99392137440801e-03 1.81097365062805e-04 -1.20297081896791e-02 - 26 3.20206071195224e+00 3.20760434315979e+00 -1.63555647464264e-03 1.77295740027368e-04 -1.20304173726392e-02 - 27 3.20083128306446e+00 3.20777604805432e+00 -1.22942888777944e-03 1.71704894527817e-04 -1.20311041922173e-02 - 28 3.20003097897692e+00 3.20794077923291e+00 -8.00304087535064e-04 1.64731178591497e-04 -1.20317631169316e-02 - 29 3.19965949808046e+00 3.20809758423739e+00 -3.71480896461218e-04 1.56805004478955e-04 -1.20323903369496e-02 - 30 3.19969592066247e+00 3.20824594166424e+00 3.64225820090880e-05 1.48357426850803e-04 -1.20329837666570e-02 - 31 3.20010221754926e+00 3.20838574103230e+00 4.06296886787061e-04 1.39799368064253e-04 -1.20335429641292e-02 - 32 3.20082741979556e+00 3.20851724535854e+00 7.25202246302015e-04 1.31504326231438e-04 -1.20340689814341e-02 - 33 3.20181227110765e+00 3.20864104059407e+00 9.84851312094914e-04 1.23795235534061e-04 -1.20345641623763e-02 - 34 3.20299412053733e+00 3.20875797656227e+00 1.18184942967092e-03 1.16935968202223e-04 -1.20350319062491e-02 - 35 3.20431162261699e+00 3.20886910428595e+00 1.31750207966386e-03 1.11127723682791e-04 -1.20354764171438e-02 - 36 3.20570880302891e+00 3.20897561440447e+00 1.39718041191950e-03 1.06510118513249e-04 -1.20359024576179e-02 - 37 3.20713815036053e+00 3.20907878075410e+00 1.42934733162248e-03 1.03166349632568e-04 -1.20363151230164e-02 - 38 3.20856270818102e+00 3.20917991221892e+00 1.42455782049122e-03 1.01131464818439e-04 -1.20367196488757e-02 - 39 3.20995731353255e+00 3.20928031496436e+00 1.39460535153013e-03 1.00402745444511e-04 -1.20371212598575e-02 - 40 3.21130917292044e+00 3.20938126631322e+00 1.35185938788940e-03 1.00951348854985e-04 -1.20375250652529e-02 + 20 3.21549621301549e+00 3.20653095017852e+00 0.00000000000000e+00 1.63839888121770e-04 -1.16261238007141e-02 + 21 3.21299151121102e+00 3.20670352294153e+00 -2.50470180446749e-03 1.72572763011582e-04 -1.16268140917661e-02 + 22 3.21044145238583e+00 3.20688218620849e+00 -2.55005882518766e-03 1.78663266959169e-04 -1.16275287448340e-02 + 23 3.20797018574579e+00 3.20706424683154e+00 -2.47126664004549e-03 1.82060623050948e-04 -1.16282569873262e-02 + 24 3.20569026122289e+00 3.20724708607441e+00 -2.27992452289572e-03 1.82839242865593e-04 -1.16289883442976e-02 + 25 3.20369635095381e+00 3.20742827327941e+00 -1.99391026908335e-03 1.81187205005368e-04 -1.16297130931177e-02 + 26 3.20206080670596e+00 3.20760566170420e+00 -1.63554424784840e-03 1.77388424785744e-04 -1.16304226468168e-02 + 27 3.20083139121777e+00 3.20777746204889e+00 -1.22941548818822e-03 1.71800344689496e-04 -1.16311098481956e-02 + 28 3.20003110175216e+00 3.20794229136206e+00 -8.00289465613613e-04 1.64829313172020e-04 -1.16317691654482e-02 + 29 3.19965963674732e+00 3.20809919710311e+00 -3.71465004831428e-04 1.56905741050733e-04 -1.16323967884124e-02 + 30 3.19969607653556e+00 3.20824765778478e+00 3.64397882326450e-05 1.48460681671230e-04 -1.16329906311391e-02 + 31 3.20010239198518e+00 3.20838756284098e+00 4.06315449623662e-04 1.39905056202667e-04 -1.16335502513639e-02 + 32 3.20082761419017e+00 3.20851917520268e+00 7.25222204989162e-04 1.31612361694413e-04 -1.16340767008107e-02 + 33 3.20181248689262e+00 3.20864308073407e+00 9.84872702445738e-04 1.23905531389011e-04 -1.16345723229363e-02 + 34 3.20299435917704e+00 3.20876012917077e+00 1.18187228442679e-03 1.17048436698551e-04 -1.16350405166831e-02 + 35 3.20431188560568e+00 3.20887137144714e+00 1.31752642863958e-03 1.11242276370810e-04 -1.16354854857885e-02 + 36 3.20570909188769e+00 3.20897799811350e+00 1.39720628201090e-03 1.06626666360912e-04 -1.16359119924540e-02 + 37 3.20713846663531e+00 3.20908128291664e+00 1.42937474761640e-03 1.03284803139886e-04 -1.16363251316666e-02 + 38 3.20856305344034e+00 3.20918253465077e+00 1.42458680502822e-03 1.01251734130282e-04 -1.16367301386031e-02 + 39 3.20995768936497e+00 3.20928305939123e+00 1.39463592463418e-03 1.00524740461639e-04 -1.16371322375649e-02 + 40 3.21130958093225e+00 3.20938413437057e+00 1.35189156727877e-03 1.01074979342738e-04 -1.16375365374823e-02 diff --git a/namd/tests/library/000_distance-wall-bypassExtended-off/test.in b/namd/tests/library/000_distance-wall-bypassExtended-off/test.in index 5a5def555..770d32a5b 100644 --- a/namd/tests/library/000_distance-wall-bypassExtended-off/test.in +++ b/namd/tests/library/000_distance-wall-bypassExtended-off/test.in @@ -30,7 +30,7 @@ colvar { harmonicWalls { colvars one lowerWalls 0.1 - upperWalls 0.2 + upperWalls 0.3 forceConstant 0.001 bypassExtendedLagrangian off } From 51bebbf84333ba32128d70485297f986f1c0818e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Fri, 8 Sep 2023 15:12:21 +0200 Subject: [PATCH 012/162] Do not track test output files --- .../test.harmonic1.ti.force | 23 ------------------- .../test.restart.harmonic1.ti.force | 23 ------------------- .../test.harmonic1.ti.force | 23 ------------------- .../test.restart.harmonic1.ti.force | 23 ------------------- .../test.metadynamics1.ti.force | 23 ------------------- .../test.restart.metadynamics1.ti.force | 23 ------------------- 6 files changed, 138 deletions(-) delete mode 100644 lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/test.harmonic1.ti.force delete mode 100644 lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/test.restart.harmonic1.ti.force delete mode 100644 lammps/tests/library/000_distance-grid_harmonic-fixed-ti/test.harmonic1.ti.force delete mode 100644 lammps/tests/library/000_distance-grid_harmonic-fixed-ti/test.restart.harmonic1.ti.force delete mode 100644 lammps/tests/library/000_distance-grid_metadynamics-ti/test.metadynamics1.ti.force delete mode 100644 lammps/tests/library/000_distance-grid_metadynamics-ti/test.restart.metadynamics1.ti.force diff --git a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/test.harmonic1.ti.force b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/test.harmonic1.ti.force deleted file mode 100644 index 41cb0281e..000000000 --- a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/test.harmonic1.ti.force +++ /dev/null @@ -1,23 +0,0 @@ -# 1 -# 0.00000000000000e+00 5.00000000000000e-01 20 0 - - 2.50000000000000e-01 0.00000000000000e+00 - 7.50000000000000e-01 0.00000000000000e+00 - 1.25000000000000e+00 0.00000000000000e+00 - 1.75000000000000e+00 0.00000000000000e+00 - 2.25000000000000e+00 0.00000000000000e+00 - 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -2.90562076256881e+00 - 3.75000000000000e+00 0.00000000000000e+00 - 4.25000000000000e+00 0.00000000000000e+00 - 4.75000000000000e+00 0.00000000000000e+00 - 5.25000000000000e+00 0.00000000000000e+00 - 5.75000000000000e+00 0.00000000000000e+00 - 6.25000000000000e+00 0.00000000000000e+00 - 6.75000000000000e+00 0.00000000000000e+00 - 7.25000000000000e+00 0.00000000000000e+00 - 7.75000000000000e+00 0.00000000000000e+00 - 8.25000000000000e+00 0.00000000000000e+00 - 8.75000000000000e+00 0.00000000000000e+00 - 9.25000000000000e+00 0.00000000000000e+00 - 9.75000000000000e+00 0.00000000000000e+00 diff --git a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/test.restart.harmonic1.ti.force b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/test.restart.harmonic1.ti.force deleted file mode 100644 index 2dd4b82ed..000000000 --- a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/test.restart.harmonic1.ti.force +++ /dev/null @@ -1,23 +0,0 @@ -# 1 -# 0.00000000000000e+00 5.00000000000000e-01 20 0 - - 2.50000000000000e-01 0.00000000000000e+00 - 7.50000000000000e-01 0.00000000000000e+00 - 1.25000000000000e+00 0.00000000000000e+00 - 1.75000000000000e+00 0.00000000000000e+00 - 2.25000000000000e+00 0.00000000000000e+00 - 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 4.14032182279625e+00 - 3.75000000000000e+00 0.00000000000000e+00 - 4.25000000000000e+00 0.00000000000000e+00 - 4.75000000000000e+00 0.00000000000000e+00 - 5.25000000000000e+00 0.00000000000000e+00 - 5.75000000000000e+00 0.00000000000000e+00 - 6.25000000000000e+00 0.00000000000000e+00 - 6.75000000000000e+00 0.00000000000000e+00 - 7.25000000000000e+00 0.00000000000000e+00 - 7.75000000000000e+00 0.00000000000000e+00 - 8.25000000000000e+00 0.00000000000000e+00 - 8.75000000000000e+00 0.00000000000000e+00 - 9.25000000000000e+00 0.00000000000000e+00 - 9.75000000000000e+00 0.00000000000000e+00 diff --git a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/test.harmonic1.ti.force b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/test.harmonic1.ti.force deleted file mode 100644 index 369453b97..000000000 --- a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/test.harmonic1.ti.force +++ /dev/null @@ -1,23 +0,0 @@ -# 1 -# 0.00000000000000e+00 5.00000000000000e-01 20 0 - - 2.50000000000000e-01 0.00000000000000e+00 - 7.50000000000000e-01 0.00000000000000e+00 - 1.25000000000000e+00 0.00000000000000e+00 - 1.75000000000000e+00 0.00000000000000e+00 - 2.25000000000000e+00 0.00000000000000e+00 - 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -2.90553316335429e+00 - 3.75000000000000e+00 0.00000000000000e+00 - 4.25000000000000e+00 0.00000000000000e+00 - 4.75000000000000e+00 0.00000000000000e+00 - 5.25000000000000e+00 0.00000000000000e+00 - 5.75000000000000e+00 0.00000000000000e+00 - 6.25000000000000e+00 0.00000000000000e+00 - 6.75000000000000e+00 0.00000000000000e+00 - 7.25000000000000e+00 0.00000000000000e+00 - 7.75000000000000e+00 0.00000000000000e+00 - 8.25000000000000e+00 0.00000000000000e+00 - 8.75000000000000e+00 0.00000000000000e+00 - 9.25000000000000e+00 0.00000000000000e+00 - 9.75000000000000e+00 0.00000000000000e+00 diff --git a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/test.restart.harmonic1.ti.force b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/test.restart.harmonic1.ti.force deleted file mode 100644 index 969743f75..000000000 --- a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/test.restart.harmonic1.ti.force +++ /dev/null @@ -1,23 +0,0 @@ -# 1 -# 0.00000000000000e+00 5.00000000000000e-01 20 0 - - 2.50000000000000e-01 0.00000000000000e+00 - 7.50000000000000e-01 0.00000000000000e+00 - 1.25000000000000e+00 0.00000000000000e+00 - 1.75000000000000e+00 0.00000000000000e+00 - 2.25000000000000e+00 0.00000000000000e+00 - 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 4.14054595271415e+00 - 3.75000000000000e+00 0.00000000000000e+00 - 4.25000000000000e+00 0.00000000000000e+00 - 4.75000000000000e+00 0.00000000000000e+00 - 5.25000000000000e+00 0.00000000000000e+00 - 5.75000000000000e+00 0.00000000000000e+00 - 6.25000000000000e+00 0.00000000000000e+00 - 6.75000000000000e+00 0.00000000000000e+00 - 7.25000000000000e+00 0.00000000000000e+00 - 7.75000000000000e+00 0.00000000000000e+00 - 8.25000000000000e+00 0.00000000000000e+00 - 8.75000000000000e+00 0.00000000000000e+00 - 9.25000000000000e+00 0.00000000000000e+00 - 9.75000000000000e+00 0.00000000000000e+00 diff --git a/lammps/tests/library/000_distance-grid_metadynamics-ti/test.metadynamics1.ti.force b/lammps/tests/library/000_distance-grid_metadynamics-ti/test.metadynamics1.ti.force deleted file mode 100644 index 3edb75d55..000000000 --- a/lammps/tests/library/000_distance-grid_metadynamics-ti/test.metadynamics1.ti.force +++ /dev/null @@ -1,23 +0,0 @@ -# 1 -# 0.00000000000000e+00 5.00000000000000e-01 20 0 - - 2.50000000000000e-01 0.00000000000000e+00 - 7.50000000000000e-01 0.00000000000000e+00 - 1.25000000000000e+00 0.00000000000000e+00 - 1.75000000000000e+00 0.00000000000000e+00 - 2.25000000000000e+00 0.00000000000000e+00 - 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 -2.91090719796635e+00 - 3.75000000000000e+00 0.00000000000000e+00 - 4.25000000000000e+00 0.00000000000000e+00 - 4.75000000000000e+00 0.00000000000000e+00 - 5.25000000000000e+00 0.00000000000000e+00 - 5.75000000000000e+00 0.00000000000000e+00 - 6.25000000000000e+00 0.00000000000000e+00 - 6.75000000000000e+00 0.00000000000000e+00 - 7.25000000000000e+00 0.00000000000000e+00 - 7.75000000000000e+00 0.00000000000000e+00 - 8.25000000000000e+00 0.00000000000000e+00 - 8.75000000000000e+00 0.00000000000000e+00 - 9.25000000000000e+00 0.00000000000000e+00 - 9.75000000000000e+00 0.00000000000000e+00 diff --git a/lammps/tests/library/000_distance-grid_metadynamics-ti/test.restart.metadynamics1.ti.force b/lammps/tests/library/000_distance-grid_metadynamics-ti/test.restart.metadynamics1.ti.force deleted file mode 100644 index ced5d2875..000000000 --- a/lammps/tests/library/000_distance-grid_metadynamics-ti/test.restart.metadynamics1.ti.force +++ /dev/null @@ -1,23 +0,0 @@ -# 1 -# 0.00000000000000e+00 5.00000000000000e-01 20 0 - - 2.50000000000000e-01 0.00000000000000e+00 - 7.50000000000000e-01 0.00000000000000e+00 - 1.25000000000000e+00 0.00000000000000e+00 - 1.75000000000000e+00 0.00000000000000e+00 - 2.25000000000000e+00 0.00000000000000e+00 - 2.75000000000000e+00 0.00000000000000e+00 - 3.25000000000000e+00 4.13122374770902e+00 - 3.75000000000000e+00 0.00000000000000e+00 - 4.25000000000000e+00 0.00000000000000e+00 - 4.75000000000000e+00 0.00000000000000e+00 - 5.25000000000000e+00 0.00000000000000e+00 - 5.75000000000000e+00 0.00000000000000e+00 - 6.25000000000000e+00 0.00000000000000e+00 - 6.75000000000000e+00 0.00000000000000e+00 - 7.25000000000000e+00 0.00000000000000e+00 - 7.75000000000000e+00 0.00000000000000e+00 - 8.25000000000000e+00 0.00000000000000e+00 - 8.75000000000000e+00 0.00000000000000e+00 - 9.25000000000000e+00 0.00000000000000e+00 - 9.75000000000000e+00 0.00000000000000e+00 From 06557c0cf29efa5de5267867c43672e7b08565fd Mon Sep 17 00:00:00 2001 From: HanatoK Date: Tue, 19 Sep 2023 11:37:05 -0500 Subject: [PATCH 013/162] Optimize the matrix multiplication in NeuralNetwork --- src/colvar_neuralnetworkcompute.cpp | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/colvar_neuralnetworkcompute.cpp b/src/colvar_neuralnetworkcompute.cpp index b0b5e2941..e5916eaa6 100644 --- a/src/colvar_neuralnetworkcompute.cpp +++ b/src/colvar_neuralnetworkcompute.cpp @@ -267,13 +267,17 @@ std::vector> neuralNetworkCompute::multiply_matrix(const std const size_t n = B.size(); if (A[0].size() != n) { std::cerr << "Error on multiplying matrices!\n"; + // std::cerr << fmt::format("Error on multiplying matrices ({}, {}) and ({}, {})!\n", m, A[0].size(), n, B[0].size()); } const size_t t = B[0].size(); std::vector> C(m, std::vector(t, 0.0)); for (size_t i = 0; i < m; ++i) { - for (size_t j = 0; j < t; ++j) { - for (size_t k = 0; k < n; ++k) { - C[i][j] += A[i][k] * B[k][j]; + for (size_t k = 0; k < n; ++k) { + const auto tmp = A[i][k]; + auto& C_i = C[i]; + auto& B_k = B[k]; + for (size_t j = 0; j < t; ++j) { + C_i[j] += tmp * B_k[j]; } } } From 1a6cef55c60719f07c732b9f298b18ad3c8eb355 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Tue, 19 Sep 2023 13:20:16 -0500 Subject: [PATCH 014/162] Remove unused comment --- src/colvar_neuralnetworkcompute.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/colvar_neuralnetworkcompute.cpp b/src/colvar_neuralnetworkcompute.cpp index e5916eaa6..b77db0cfa 100644 --- a/src/colvar_neuralnetworkcompute.cpp +++ b/src/colvar_neuralnetworkcompute.cpp @@ -267,7 +267,6 @@ std::vector> neuralNetworkCompute::multiply_matrix(const std const size_t n = B.size(); if (A[0].size() != n) { std::cerr << "Error on multiplying matrices!\n"; - // std::cerr << fmt::format("Error on multiplying matrices ({}, {}) and ({}, {})!\n", m, A[0].size(), n, B[0].size()); } const size_t t = B[0].size(); std::vector> C(m, std::vector(t, 0.0)); From a0b4314bd6b1180b4a94d5183671a7cb4c94c2fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Mon, 18 Sep 2023 11:09:28 +0200 Subject: [PATCH 015/162] Track date-based CV dashboard versions and remove all hard-coded version strings --- devel-tools/version_functions.sh | 37 ++++++++++++++++++++++++++++--- vmd/cv_dashboard/Makefile | 3 ++- vmd/cv_dashboard/Makefile.local | 4 +++- vmd/cv_dashboard/VERSION | 1 + vmd/cv_dashboard/cv_dashboard.tcl | 8 ++++++- vmd/cv_dashboard/pkgIndex.tcl | 12 ++++++++-- 6 files changed, 57 insertions(+), 8 deletions(-) create mode 100644 vmd/cv_dashboard/VERSION diff --git a/devel-tools/version_functions.sh b/devel-tools/version_functions.sh index 40077c215..d1f85266b 100644 --- a/devel-tools/version_functions.sh +++ b/devel-tools/version_functions.sh @@ -52,6 +52,22 @@ get_colvarproxy_vmd_version() { vmd/src/colvarproxy_vmd.h } +get_cv_dashboard_version() { + local commit="${1}:" + if [ "${commit}" = ":" ] ; then + # Use work tree + commit="HEAD:" + fi + local file1="vmd/cv_dashboard/VERSION" + local file2="vmd/cv_dashboard/cv_dashboard.tcl" + local version=$(git cat-file -p ${commit}${file1} 2> /dev/null) + if [ "x${version}" = "x" ] ; then + version=$(git grep "package provide cv_dashboard" ${commit}${file2} 2> /dev/null) + version=$(echo ${version} | awk '{ print $4 }' | tr -d '"') + fi + echo ${version} +} + get_last_master_commit() { local grep_pattern=${1} local commit @@ -89,9 +105,13 @@ write_version_string() { local macro=${1} local file=${2} local version_str=${3} - echo -e "#ifndef ${macro}\n\ -#define ${macro} \"${version_str}\"\n\ -#endif" > ${file} + if [ "${macro}" = "none" ] ; then + echo -e "${version_str}" > ${file} + else + echo -e "#ifndef ${macro}\n\ + #define ${macro} \"${version_str}\"\n\ + #endif" > ${file} + fi if [ "${file}" = "src/colvars_version.h" ] ; then local version_str_tex=$(version_str_for_tex ${version_str}) echo -E "\newcommand{\cvversion}{${version_str_tex}}" \ @@ -196,6 +216,13 @@ update_all_versions() { vmd/src/colvarproxy_vmd_version.h \ ${branch} \ && \ + update_version_string "Colvars Dashboard" \ + '^vmd/cv_dashboard' \ + get_cv_dashboard_version \ + none \ + vmd/cv_dashboard/VERSION \ + ${branch} \ + && \ git commit -m "Update version strings" } @@ -226,4 +253,8 @@ write_all_versions_branch() { COLVARPROXY_VERSION \ gromacs/src/colvarproxy_gromacs_version.h \ ${branch} + write_version_branch get_cv_dashboard_version \ + none \ + vmd/cv_dashboard/VERSION \ + ${branch} } diff --git a/vmd/cv_dashboard/Makefile b/vmd/cv_dashboard/Makefile index 09d880d58..93af75f0d 100644 --- a/vmd/cv_dashboard/Makefile +++ b/vmd/cv_dashboard/Makefile @@ -1,7 +1,8 @@ .SILENT: VMFILES := $(wildcard *.tcl) templates -VMVERSION = 1.5 +cat := $(if $(filter $(OS),Windows_NT),type,cat) +VMVERSION := $(shell $(cat) VERSION) DIR = $(PLUGINDIR)/noarch/tcl/cv_dashboard$(VMVERSION) bins: diff --git a/vmd/cv_dashboard/Makefile.local b/vmd/cv_dashboard/Makefile.local index 1b0cbaa37..ce84a5e25 100644 --- a/vmd/cv_dashboard/Makefile.local +++ b/vmd/cv_dashboard/Makefile.local @@ -1,6 +1,8 @@ # -*- makefile -*- -VERSION = 1.5 +cat := $(if $(filter $(OS),Windows_NT),type,cat) +VERSION := $(shell $(cat) VERSION) + ifeq (${DESTINATION},) DESTINATION = ${HOME}/lib/vmd/plugins/noarch/tcl/cv_dashboard${VERSION} endif diff --git a/vmd/cv_dashboard/VERSION b/vmd/cv_dashboard/VERSION new file mode 100644 index 000000000..b3f3232ae --- /dev/null +++ b/vmd/cv_dashboard/VERSION @@ -0,0 +1 @@ +2023-01-11 diff --git a/vmd/cv_dashboard/cv_dashboard.tcl b/vmd/cv_dashboard/cv_dashboard.tcl index 90c72a097..7d64ee82b 100644 --- a/vmd/cv_dashboard/cv_dashboard.tcl +++ b/vmd/cv_dashboard/cv_dashboard.tcl @@ -23,7 +23,13 @@ # TODO maybe: # - index group builder -package provide cv_dashboard 1.5 +set dir [file dirname [info script]] +set version_file [open "${dir}/VERSION"] +gets $version_file CV_DASHBOARD_VERSION +close $version_file +# Convert to Tcl-style package version number +set CV_DASHBOARD_TCL_VERSION [string map { "-" "." } $CV_DASHBOARD_VERSION] +package provide cv_dashboard $CV_DASHBOARD_TCL_VERSION namespace eval ::cv_dashboard { # General UI state diff --git a/vmd/cv_dashboard/pkgIndex.tcl b/vmd/cv_dashboard/pkgIndex.tcl index d3bada8cf..d546adde1 100644 --- a/vmd/cv_dashboard/pkgIndex.tcl +++ b/vmd/cv_dashboard/pkgIndex.tcl @@ -1,5 +1,6 @@ # Tcl package index file, version 1.1 -# This file is generated by the "pkg_mkIndex" command + +# This file is generated manually # and sourced either when an application starts up or # by a "package unknown" script. It invokes the # "package ifneeded" command to set up package-related @@ -8,4 +9,11 @@ # script is sourced, the variable $dir must contain the # full path name of this file's directory. -package ifneeded cv_dashboard 1.5 "set env(CV_DASHBOARD_DIR) [list $dir]; [list source [file join $dir cv_dashboard.tcl]]" +set dir [file dirname [info script]] +set version_file [open "${dir}/VERSION"] +gets $version_file CV_DASHBOARD_VERSION +close $version_file +# Convert to Tcl-style package version number +set CV_DASHBOARD_TCL_VERSION [string map { "-" "." } $CV_DASHBOARD_VERSION] + +package ifneeded cv_dashboard $CV_DASHBOARD_TCL_VERSION "set env(CV_DASHBOARD_DIR) [list $dir]; [list source [file join $dir cv_dashboard.tcl]]" From 6902942532954cac31fa69d9b999e3a6ff303352 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Tue, 29 Aug 2023 13:34:34 +0200 Subject: [PATCH 016/162] Add default check_only = false to set_unit_system --- lammps/src/COLVARS/colvarproxy_lammps.h | 2 +- misc_interfaces/C_fortran/colvarproxy_C.h | 2 +- misc_interfaces/stubs/colvarproxy_stub.h | 2 +- namd/src/colvarproxy_namd.h | 2 +- src/colvarproxy_system.h | 2 +- tests/functional/run_colvars_test.cpp | 2 +- tests/unittests/read_xyz_traj.cpp | 2 +- vmd/src/colvarproxy_vmd.C | 2 +- vmd/src/colvarproxy_vmd.h | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/lammps/src/COLVARS/colvarproxy_lammps.h b/lammps/src/COLVARS/colvarproxy_lammps.h index 6d85a378e..df624960a 100644 --- a/lammps/src/COLVARS/colvarproxy_lammps.h +++ b/lammps/src/COLVARS/colvarproxy_lammps.h @@ -83,7 +83,7 @@ class colvarproxy_lammps : public colvarproxy { bool deserialize_status(std::string &); // Request to set the units used internally by Colvars - int set_unit_system(std::string const &units_in, bool check_only) override; + int set_unit_system(std::string const &units_in, bool check_only = false) override; /// Convert a command-line argument to string char const *script_obj_to_str(unsigned char *obj); diff --git a/misc_interfaces/C_fortran/colvarproxy_C.h b/misc_interfaces/C_fortran/colvarproxy_C.h index 8babb0c42..b2e203cf9 100644 --- a/misc_interfaces/C_fortran/colvarproxy_C.h +++ b/misc_interfaces/C_fortran/colvarproxy_C.h @@ -12,7 +12,7 @@ class colvarproxy_C : public colvarproxy { ~colvarproxy_C(); private: - int set_unit_system(std::string const &units, bool check_only) { return 0.; } + int set_unit_system(std::string const &units, bool check_only = false) { return 0.; } /// \brief Boltzmann constant cvm::real boltzmann() { return 0.; } diff --git a/misc_interfaces/stubs/colvarproxy_stub.h b/misc_interfaces/stubs/colvarproxy_stub.h index ec2ffdd56..ca97d9d6e 100644 --- a/misc_interfaces/stubs/colvarproxy_stub.h +++ b/misc_interfaces/stubs/colvarproxy_stub.h @@ -35,7 +35,7 @@ class colvarproxy_stub : public colvarproxy { void error(std::string const &message) override; - int set_unit_system(std::string const &units_in, bool check_only) override; + int set_unit_system(std::string const &units_in, bool check_only = false) override; int init_atom(int atom_number) override; diff --git a/namd/src/colvarproxy_namd.h b/namd/src/colvarproxy_namd.h index afbfbcb52..4fea9a613 100644 --- a/namd/src/colvarproxy_namd.h +++ b/namd/src/colvarproxy_namd.h @@ -82,7 +82,7 @@ class colvarproxy_namd : public colvarproxy, public GlobalMaster { void log(std::string const &message) override; void error(std::string const &message) override; - int set_unit_system(std::string const &units_in, bool check_only) override; + int set_unit_system(std::string const &units_in, bool check_only = false) override; void add_energy(cvm::real energy) override; void request_total_force(bool yesno) override; diff --git a/src/colvarproxy_system.h b/src/colvarproxy_system.h index 67d0938e5..6e117eccd 100644 --- a/src/colvarproxy_system.h +++ b/src/colvarproxy_system.h @@ -32,7 +32,7 @@ class colvarproxy_system { std::string units; /// \brief Request to set the units used internally by Colvars - virtual int set_unit_system(std::string const &units, bool check_only); + virtual int set_unit_system(std::string const &units, bool check_only = false); /// \brief Convert a length from Angstrom to internal inline cvm::real angstrom_to_internal(cvm::real l) const diff --git a/tests/functional/run_colvars_test.cpp b/tests/functional/run_colvars_test.cpp index 5ddf4ebb2..b10dd5ac5 100644 --- a/tests/functional/run_colvars_test.cpp +++ b/tests/functional/run_colvars_test.cpp @@ -18,7 +18,7 @@ extern "C" int main(int argc, char *argv[]) { colvarproxy_stub *proxy = new colvarproxy_stub(); // Initialize simple unit system to test file input - err |= proxy->set_unit_system("real", false); + err |= proxy->set_unit_system("real"); if (argc > 3) { err |= proxy->set_output_prefix(argv[3]); diff --git a/tests/unittests/read_xyz_traj.cpp b/tests/unittests/read_xyz_traj.cpp index 9a8751ad0..80b54cb3f 100644 --- a/tests/unittests/read_xyz_traj.cpp +++ b/tests/unittests/read_xyz_traj.cpp @@ -9,7 +9,7 @@ extern "C" int main(int argc, char *argv[]) { colvarproxy_stub *proxy = new colvarproxy_stub(); - proxy->set_unit_system("real", false); + proxy->set_unit_system("real"); proxy->set_output_prefix("test.out"); proxy->colvars->setup_input(); proxy->colvars->setup_output(); diff --git a/vmd/src/colvarproxy_vmd.C b/vmd/src/colvarproxy_vmd.C index 4cd448112..53cd003ea 100644 --- a/vmd/src/colvarproxy_vmd.C +++ b/vmd/src/colvarproxy_vmd.C @@ -155,7 +155,7 @@ cvm::real colvarproxy_vmd::rand_gaussian() int colvarproxy_vmd::set_unit_system(std::string const &units_in, bool check_only) { // if check_only is specified, just test for compatibility - // cvolvarmodule does that if new units are requested while colvars are already defined + // colvarmodule sets this flag if new units are requested while colvars are already defined if (check_only) { if ((units != "" && units_in != units) || (units == "" && units_in != "real")) { cvm::error("Specified unit system \"" + units_in + "\" is incompatible with previous setting \"" diff --git a/vmd/src/colvarproxy_vmd.h b/vmd/src/colvarproxy_vmd.h index 539bc31cb..fb08beb59 100644 --- a/vmd/src/colvarproxy_vmd.h +++ b/vmd/src/colvarproxy_vmd.h @@ -68,7 +68,7 @@ class colvarproxy_vmd : public colvarproxy { virtual void error(std::string const &message); - virtual int set_unit_system(std::string const &units_in, bool check_only); + virtual int set_unit_system(std::string const &units_in, bool check_only = false); virtual int run_force_callback(); From dcb7c6b514b89648ee152a394bc4ff465f409b55 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 19 Sep 2023 17:52:19 -0400 Subject: [PATCH 017/162] Update version strings --- doc/cv_version.tex | 2 +- gromacs/src/colvarproxy_gromacs_version.h | 4 ++-- lammps/src/COLVARS/colvarproxy_lammps_version.h | 4 ++-- namd/src/colvarproxy_namd_version.h | 4 ++-- src/colvars_version.h | 4 ++-- vmd/src/colvarproxy_vmd_version.h | 4 ++-- 6 files changed, 11 insertions(+), 11 deletions(-) diff --git a/doc/cv_version.tex b/doc/cv_version.tex index b6e6fcfa9..d8416deef 100644 --- a/doc/cv_version.tex +++ b/doc/cv_version.tex @@ -1 +1 @@ -\newcommand{\cvversion}{2023-09-07} +\newcommand{\cvversion}{2023-09-19} diff --git a/gromacs/src/colvarproxy_gromacs_version.h b/gromacs/src/colvarproxy_gromacs_version.h index 53c2d8efc..b013b2eac 100644 --- a/gromacs/src/colvarproxy_gromacs_version.h +++ b/gromacs/src/colvarproxy_gromacs_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2023-07-06" -#endif + #define COLVARPROXY_VERSION "2023-09-19" + #endif diff --git a/lammps/src/COLVARS/colvarproxy_lammps_version.h b/lammps/src/COLVARS/colvarproxy_lammps_version.h index 53c2d8efc..b013b2eac 100644 --- a/lammps/src/COLVARS/colvarproxy_lammps_version.h +++ b/lammps/src/COLVARS/colvarproxy_lammps_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2023-07-06" -#endif + #define COLVARPROXY_VERSION "2023-09-19" + #endif diff --git a/namd/src/colvarproxy_namd_version.h b/namd/src/colvarproxy_namd_version.h index 53c2d8efc..b013b2eac 100644 --- a/namd/src/colvarproxy_namd_version.h +++ b/namd/src/colvarproxy_namd_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2023-07-06" -#endif + #define COLVARPROXY_VERSION "2023-09-19" + #endif diff --git a/src/colvars_version.h b/src/colvars_version.h index 7d6b181ee..17aa3ce67 100644 --- a/src/colvars_version.h +++ b/src/colvars_version.h @@ -1,3 +1,3 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2023-09-07" -#endif + #define COLVARS_VERSION "2023-09-19" + #endif diff --git a/vmd/src/colvarproxy_vmd_version.h b/vmd/src/colvarproxy_vmd_version.h index 53c2d8efc..b013b2eac 100644 --- a/vmd/src/colvarproxy_vmd_version.h +++ b/vmd/src/colvarproxy_vmd_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2023-07-06" -#endif + #define COLVARPROXY_VERSION "2023-09-19" + #endif From 23b9411929907a5db633993fa3eacde7d1f958bd Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 20 Sep 2023 20:12:36 -0400 Subject: [PATCH 018/162] Fix indentation issue --- devel-tools/version_functions.sh | 4 ++-- gromacs/src/colvarproxy_gromacs_version.h | 4 ++-- lammps/src/COLVARS/colvarproxy_lammps_version.h | 4 ++-- namd/src/colvarproxy_namd_version.h | 4 ++-- src/colvars_version.h | 4 ++-- vmd/src/colvarproxy_vmd_version.h | 4 ++-- 6 files changed, 12 insertions(+), 12 deletions(-) diff --git a/devel-tools/version_functions.sh b/devel-tools/version_functions.sh index d1f85266b..f6f94adc0 100644 --- a/devel-tools/version_functions.sh +++ b/devel-tools/version_functions.sh @@ -109,8 +109,8 @@ write_version_string() { echo -e "${version_str}" > ${file} else echo -e "#ifndef ${macro}\n\ - #define ${macro} \"${version_str}\"\n\ - #endif" > ${file} +#define ${macro} \"${version_str}\"\n\ +#endif" > ${file} fi if [ "${file}" = "src/colvars_version.h" ] ; then local version_str_tex=$(version_str_for_tex ${version_str}) diff --git a/gromacs/src/colvarproxy_gromacs_version.h b/gromacs/src/colvarproxy_gromacs_version.h index b013b2eac..cf70c1d84 100644 --- a/gromacs/src/colvarproxy_gromacs_version.h +++ b/gromacs/src/colvarproxy_gromacs_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION - #define COLVARPROXY_VERSION "2023-09-19" - #endif +#define COLVARPROXY_VERSION "2023-09-19" +#endif diff --git a/lammps/src/COLVARS/colvarproxy_lammps_version.h b/lammps/src/COLVARS/colvarproxy_lammps_version.h index b013b2eac..cf70c1d84 100644 --- a/lammps/src/COLVARS/colvarproxy_lammps_version.h +++ b/lammps/src/COLVARS/colvarproxy_lammps_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION - #define COLVARPROXY_VERSION "2023-09-19" - #endif +#define COLVARPROXY_VERSION "2023-09-19" +#endif diff --git a/namd/src/colvarproxy_namd_version.h b/namd/src/colvarproxy_namd_version.h index b013b2eac..cf70c1d84 100644 --- a/namd/src/colvarproxy_namd_version.h +++ b/namd/src/colvarproxy_namd_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION - #define COLVARPROXY_VERSION "2023-09-19" - #endif +#define COLVARPROXY_VERSION "2023-09-19" +#endif diff --git a/src/colvars_version.h b/src/colvars_version.h index 17aa3ce67..ee9f36675 100644 --- a/src/colvars_version.h +++ b/src/colvars_version.h @@ -1,3 +1,3 @@ #ifndef COLVARS_VERSION - #define COLVARS_VERSION "2023-09-19" - #endif +#define COLVARS_VERSION "2023-09-19" +#endif diff --git a/vmd/src/colvarproxy_vmd_version.h b/vmd/src/colvarproxy_vmd_version.h index b013b2eac..cf70c1d84 100644 --- a/vmd/src/colvarproxy_vmd_version.h +++ b/vmd/src/colvarproxy_vmd_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION - #define COLVARPROXY_VERSION "2023-09-19" - #endif +#define COLVARPROXY_VERSION "2023-09-19" +#endif From e376fcf5516baaafbcb5b71f0f737019b012a40f Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 20 Sep 2023 22:30:44 -0400 Subject: [PATCH 019/162] Enforce intra-node communication on recent OpenMPI versions --- devel-tools/load-openmpi.sh | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/devel-tools/load-openmpi.sh b/devel-tools/load-openmpi.sh index e2109f9c6..1e6623d9d 100644 --- a/devel-tools/load-openmpi.sh +++ b/devel-tools/load-openmpi.sh @@ -1,6 +1,12 @@ if declare -f module >& /dev/null ; then + # Ensure that Lmod is properly initialized + source /etc/profile # Default modulefile in OpenMPI RPM package if module load mpi/openmpi-x86_64 >& /dev/null ; then echo "Loaded OpenMPI version $(mpirun --version | head -n 1 | rev | cut -d' ' -f1 | rev)" + if ompi_info --param btl vader | grep -q vader ; then + # Enforce intra-node communication on recent OpenMPI versions + export OMPI_MCA_btl="vader,self" + fi fi fi From 78dd9b7c702d51b365c4b2ff39a9e7c63a23f761 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 20 Sep 2023 22:31:12 -0400 Subject: [PATCH 020/162] More robust MPI loading in LAMMPS test-lammps --- lammps/tests/library/run_tests.sh | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/lammps/tests/library/run_tests.sh b/lammps/tests/library/run_tests.sh index 25b9e0895..499b06b26 100755 --- a/lammps/tests/library/run_tests.sh +++ b/lammps/tests/library/run_tests.sh @@ -40,13 +40,14 @@ if [ ${NUM_TASKS} -gt ${NUM_CPUS} ] ; then NUM_TASKS=${NUM_CPUS} fi -if $BINARY -h > /dev/null ; then - if $BINARY -h | grep ^MPI | grep -q STUBS ; then +if $BINARY -h >& /dev/null ; then + if $BINARY -h 2> /dev/null | grep ^MPI | grep -q STUBS ; then MPI_BUILD=no else - MPI_BUILD=yes - source ${TOPDIR}/devel-tools/load-openmpi.sh - BINARY="mpirun -n ${NUM_TASKS} $BINARY" + if source ${TOPDIR}/devel-tools/load-openmpi.sh ; then + MPI_BUILD=yes + BINARY="mpirun -n ${NUM_TASKS} $BINARY" + fi fi else echo "Error: executable $BINARY did not return a help screen" >& 2 From 9a1f7e9ccdcf5ce16c9c7a09c21a5f9b730c1894 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 20 Sep 2023 18:12:23 -0400 Subject: [PATCH 021/162] Reset error code when invoking colvarmodule::reset() --- src/colvarmodule.cpp | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 5281be29a..40d75b883 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -1279,7 +1279,9 @@ int colvarmodule::reset() proxy->flush_output_streams(); proxy->reset(); - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + clear_error(); + + return COLVARS_OK; } From 8a152fc46e1652ec8e9136dc8261afc35f93e859 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 21 Sep 2023 09:07:11 -0400 Subject: [PATCH 022/162] Initialize integer and floating point members of colvar class --- src/colvar.h | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/src/colvar.h b/src/colvar.h index f04bd8c9d..7150cf03d 100644 --- a/src/colvar.h +++ b/src/colvar.h @@ -88,7 +88,7 @@ class colvar : public colvarparse, public colvardeps { /// calculations, \link colvarbias_abf \endlink, it is used to /// calculate the grid spacing in the direction of this collective /// variable. - cvm::real width; + cvm::real width = 1.0; /// \brief Implementation of the feature list for colvar static std::vector cv_features; @@ -181,13 +181,13 @@ class colvar : public colvarparse, public colvardeps { /// Previous velocity of the restraint center colvarvalue prev_v_ext; /// Mass of the restraint center - cvm::real ext_mass; + cvm::real ext_mass = 0.0; /// Restraint force constant - cvm::real ext_force_k; + cvm::real ext_force_k = 0.0; /// Friction coefficient for Langevin extended dynamics - cvm::real ext_gamma; + cvm::real ext_gamma = 0.0; /// Amplitude of Gaussian white noise for Langevin extended dynamics - cvm::real ext_sigma; + cvm::real ext_sigma = 0.0; /// \brief Applied force on extended DOF, for output (unscaled if using MTS) colvarvalue fr; @@ -221,14 +221,14 @@ class colvar : public colvarparse, public colvardeps { colvarvalue ft; /// Period, if this variable is periodic - cvm::real period; + cvm::real period = 0.0; /// Center of wrapping, if this variable is periodic - cvm::real wrap_center; + cvm::real wrap_center = 0.0; /// \brief Expand the boundaries of multiples of width, to keep the /// value always within range - bool expand_boundaries; + bool expand_boundaries = false; /// \brief Location of the lower boundary colvarvalue lower_boundary; @@ -383,10 +383,10 @@ class colvar : public colvarparse, public colvardeps { protected: /// \brief Number of CVC objects with an active flag - size_t n_active_cvcs; + size_t n_active_cvcs = 0; /// Sum of square coefficients for active cvcs - cvm::real active_cvc_square_norm; + cvm::real active_cvc_square_norm = 0.0; /// Update the sum of square coefficients for active cvcs void update_active_cvc_square_norm(); @@ -550,15 +550,15 @@ class colvar : public colvarparse, public colvardeps { /// Current value of the running average colvarvalue runave; /// Current value of the square deviation from the running average - cvm::real runave_variance; + cvm::real runave_variance = 0.0; /// Calculate the running average and its standard deviation int calc_runave(); /// If extended Lagrangian active: colvar kinetic energy - cvm::real kinetic_energy; + cvm::real kinetic_energy = 0.0; /// If extended Lagrangian active: colvar harmonic potential - cvm::real potential_energy; + cvm::real potential_energy = 0.0; public: From c72ed0469fb05f1b95cbfcc10116aa594711e555 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 21 Sep 2023 10:00:25 -0400 Subject: [PATCH 023/162] Update version strings --- doc/cv_version.tex | 2 +- src/colvars_version.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/cv_version.tex b/doc/cv_version.tex index d8416deef..654ab903f 100644 --- a/doc/cv_version.tex +++ b/doc/cv_version.tex @@ -1 +1 @@ -\newcommand{\cvversion}{2023-09-19} +\newcommand{\cvversion}{2023-09-21} diff --git a/src/colvars_version.h b/src/colvars_version.h index ee9f36675..b4b482933 100644 --- a/src/colvars_version.h +++ b/src/colvars_version.h @@ -1,3 +1,3 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2023-09-19" +#define COLVARS_VERSION "2023-09-21" #endif From f6e543eb90719c31134dc734ae3aa625b9a3e4a5 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Wed, 26 Jul 2023 09:24:34 -0500 Subject: [PATCH 024/162] Use rotation matrix instead of rotate() --- src/colvaratoms.cpp | 25 ++++++++++++++----------- src/colvarcomp.cpp | 12 ++++++------ src/colvarcomp_distances.cpp | 3 ++- src/colvarcomp_gpath.cpp | 12 ++++++++---- 4 files changed, 30 insertions(+), 22 deletions(-) diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index 4fe1b6936..534ca967b 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -1062,14 +1062,15 @@ void cvm::atom_group::calc_apply_roto_translation() fitting_group->atoms: this->atoms, ref_pos); + const auto rot_mat = rot.matrix(); cvm::atom_iter ai; for (ai = this->begin(); ai != this->end(); ai++) { - ai->pos = rot.rotate(ai->pos); + ai->pos = rot_mat * ai->pos; } if (fitting_group) { for (ai = fitting_group->begin(); ai != fitting_group->end(); ai++) { - ai->pos = rot.rotate(ai->pos); + ai->pos = rot_mat * ai->pos; } } } @@ -1109,9 +1110,10 @@ void cvm::atom_group::read_velocities() if (is_enabled(f_ag_rotate)) { + const auto rot_mat = rot.matrix(); for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->read_velocity(); - ai->vel = rot.rotate(ai->vel); + ai->vel = rot_mat * ai->vel; } } else { @@ -1130,9 +1132,10 @@ void cvm::atom_group::read_total_forces() if (is_enabled(f_ag_rotate)) { + const auto rot_mat = rot.matrix(); for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->read_total_force(); - ai->total_force = rot.rotate(ai->total_force); + ai->total_force = rot_mat * ai->total_force; } } else { @@ -1234,7 +1237,7 @@ void cvm::atom_group::calc_fit_gradients_impl() { // the center of geometry contribution to the gradients cvm::rvector atom_grad; // the rotation matrix contribution to the gradients - cvm::rotation const rot_inv = rot.inverse(); + const auto rot_inv = rot.inverse().matrix(); // temporary variables for computing and summing derivatives cvm::real sum_dxdq[4] = {0, 0, 0, 0}; cvm::vector1d dq0_1(4); @@ -1243,7 +1246,7 @@ void cvm::atom_group::calc_fit_gradients_impl() { cvm::atom_pos pos_orig; if (B_ag_center) { atom_grad += atoms[i].grad; - if (B_ag_rotate) pos_orig = rot_inv.rotate(atoms[i].pos - ref_pos_cog); + if (B_ag_rotate) pos_orig = rot_inv * (atoms[i].pos - ref_pos_cog); } else { if (B_ag_rotate) pos_orig = atoms[i].pos; } @@ -1258,7 +1261,7 @@ void cvm::atom_group::calc_fit_gradients_impl() { } } if (B_ag_center) { - if (B_ag_rotate) atom_grad = (rot.inverse()).rotate(atom_grad); + if (B_ag_rotate) atom_grad = rot.inverse().matrix() * atom_grad; atom_grad *= (-1.0)/(cvm::real(group_for_fit->size())); } // loop 2: iterate over the fitting group @@ -1406,9 +1409,9 @@ void cvm::atom_group::apply_colvar_force(cvm::real const &force) if (is_enabled(f_ag_rotate)) { // rotate forces back to the original frame - cvm::rotation const rot_inv = rot.inverse(); + const auto rot_inv = rot.inverse().matrix(); for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { - ai->apply_force(rot_inv.rotate(force * ai->grad)); + ai->apply_force(rot_inv * (force * ai->grad)); } } else { @@ -1451,9 +1454,9 @@ void cvm::atom_group::apply_force(cvm::rvector const &force) if (is_enabled(f_ag_rotate)) { - cvm::rotation const rot_inv = rot.inverse(); + const auto rot_inv = rot.inverse().matrix(); for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { - ai->apply_force(rot_inv.rotate((ai->mass/total_mass) * force)); + ai->apply_force(rot_inv * ((ai->mass/total_mass) * force)); } } else { diff --git a/src/colvarcomp.cpp b/src/colvarcomp.cpp index 151a25569..a5327bb42 100644 --- a/src/colvarcomp.cpp +++ b/src/colvarcomp.cpp @@ -476,12 +476,12 @@ void colvar::cvc::collect_gradients(std::vector const &atom_ids, std::vecto // If necessary, apply inverse rotation to get atomic // gradient in the laboratory frame if (ag.is_enabled(f_ag_rotate)) { - cvm::rotation const rot_inv = ag.rot.inverse(); + const auto rot_inv = ag.rot.inverse().matrix(); for (size_t k = 0; k < ag.size(); k++) { size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(), ag[k].id) - atom_ids.begin(); - atomic_gradients[a] += coeff * rot_inv.rotate(ag[k].grad); + atomic_gradients[a] += coeff * (rot_inv * ag[k].grad); } } else { @@ -542,8 +542,8 @@ void colvar::cvc::debug_gradients() cvm::atom_group *group = atom_groups[ig]; if (group->b_dummy) continue; - cvm::rotation const rot_0 = group->rot; - cvm::rotation const rot_inv = group->rot.inverse(); + const auto rot_0 = group->rot.matrix(); + const auto rot_inv = group->rot.inverse().matrix(); cvm::real x_0 = x.real_value; if ((x.type() == colvarvalue::type_vector) && (x.size() == 1)) x_0 = x[0]; @@ -564,7 +564,7 @@ void colvar::cvc::debug_gradients() cvm::log((group->fitting_group ? std::string("refPosGroup") : group->key) + "[" + cvm::to_str(j) + "] = " + (group->is_enabled(f_ag_rotate) ? - cvm::to_str(rot_0.rotate(group_for_fit->fit_gradients[j])) : + cvm::to_str(rot_0 * (group_for_fit->fit_gradients[j])) : cvm::to_str(group_for_fit->fit_gradients[j]))); } } @@ -575,7 +575,7 @@ void colvar::cvc::debug_gradients() // tests are best conducted in the unrotated (simulation) frame cvm::rvector const atom_grad = (group->is_enabled(f_ag_rotate) ? - rot_inv.rotate((*group)[ia].grad) : + rot_inv * ((*group)[ia].grad) : (*group)[ia].grad); gradient_sum += atom_grad; diff --git a/src/colvarcomp_distances.cpp b/src/colvarcomp_distances.cpp index f051dc497..fbf54704d 100644 --- a/src/colvarcomp_distances.cpp +++ b/src/colvarcomp_distances.cpp @@ -1359,8 +1359,9 @@ colvar::eigenvector::eigenvector(std::string const &conf) } if (atoms->is_enabled(f_ag_rotate)) { atoms->rot.calc_optimal_rotation(eigenvec, ref_pos); + const auto rot_mat = atoms->rot.matrix(); for (size_t i = 0; i < atoms->size(); i++) { - eigenvec[i] = atoms->rot.rotate(eigenvec[i]); + eigenvec[i] = rot_mat * eigenvec[i]; } } cvm::log("\"differenceVector\" is on: subtracting the reference positions from the provided vector: v = x_vec - x_ref.\n"); diff --git a/src/colvarcomp_gpath.cpp b/src/colvarcomp_gpath.cpp index 9297eb323..ba7b11f92 100644 --- a/src/colvarcomp_gpath.cpp +++ b/src/colvarcomp_gpath.cpp @@ -222,8 +222,9 @@ void colvar::gspath::prepareVectors() { } else { rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_2); } + const auto rot_mat_v3 = rot_v3.matrix(); for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { - v3[i_atom] = rot_v3.q.rotate(tmp_reference_frame_1[i_atom]) - tmp_reference_frame_2[i_atom]; + v3[i_atom] = rot_mat_v3 * tmp_reference_frame_1[i_atom] - tmp_reference_frame_2[i_atom]; } } else { cvm::atom_pos reference_cog_1, reference_cog_3; @@ -257,9 +258,10 @@ void colvar::gspath::prepareVectors() { } else { rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_3); } + const auto rot_mat_v3 = rot_v3.matrix(); for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { // v3 = s_(m+1) - s_m - v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_v3.q.rotate(tmp_reference_frame_1[i_atom]); + v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_mat_v3 * tmp_reference_frame_1[i_atom]; } } } @@ -365,12 +367,13 @@ void colvar::gzpath::prepareVectors() { } else { rot_v4.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_2); } + const auto rot_mat_v4 = rot_v4.matrix(); for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { v1[i_atom] = reference_frames[min_frame_index_1][i_atom] - (*(comp_atoms[min_frame_index_1]))[i_atom].pos; v2[i_atom] = (*(comp_atoms[min_frame_index_2]))[i_atom].pos - reference_frames[min_frame_index_2][i_atom]; // v4 only computes in gzpath // v4 = s_m - s_(m-1) - v4[i_atom] = rot_v4.q.rotate(tmp_reference_frame_1[i_atom]) - tmp_reference_frame_2[i_atom]; + v4[i_atom] = rot_mat_v4 * tmp_reference_frame_1[i_atom] - tmp_reference_frame_2[i_atom]; } if (min_frame_index_3 < 0 || min_frame_index_3 > M) { v3 = v4; @@ -398,9 +401,10 @@ void colvar::gzpath::prepareVectors() { } else { rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_3); } + const auto rot_mat_v3 = rot_v3.matrix(); for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { // v3 = s_(m+1) - s_m - v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_v3.q.rotate(tmp_reference_frame_1[i_atom]); + v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_mat_v3 * tmp_reference_frame_1[i_atom]; } } } From ee9a2ba4387cfb904ab41bc73977d544620ef7d6 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Wed, 26 Jul 2023 10:54:30 -0500 Subject: [PATCH 025/162] Use fixed-size array for diagonlization --- src/colvar_rotation_derivative.h | 33 +++++++++++++----------- src/colvartypes.cpp | 44 ++++++++++++++++---------------- src/colvartypes.h | 15 ++++++----- src/nr_jacobi.cpp | 10 ++++---- src/nr_jacobi.h | 6 ++--- 5 files changed, 56 insertions(+), 52 deletions(-) diff --git a/src/colvar_rotation_derivative.h b/src/colvar_rotation_derivative.h index 162067536..7050537d9 100644 --- a/src/colvar_rotation_derivative.h +++ b/src/colvar_rotation_derivative.h @@ -3,6 +3,7 @@ #include "colvartypes.h" #include +#include /// \brief Helper function for loading the ia-th atom in the vector pos to x, y and z (C++11 SFINAE is used) template ::value, bool>::type = true> @@ -80,7 +81,7 @@ struct rotation_derivative { */ void prepare_derivative(rotation_derivative_dldq require_dl_dq) { if (require_dl_dq & rotation_derivative_dldq::use_dl) { - const auto &Q0 = m_rot.S_eigvec[0].data; + const auto &Q0 = m_rot.S_eigvec[0]; tmp_Q0Q0[0][0] = Q0[0] * Q0[0]; tmp_Q0Q0[0][1] = Q0[0] * Q0[1]; tmp_Q0Q0[0][2] = Q0[0] * Q0[2]; @@ -99,10 +100,10 @@ struct rotation_derivative { tmp_Q0Q0[3][3] = Q0[3] * Q0[3]; } if (require_dl_dq & rotation_derivative_dldq::use_dq) { - const auto &Q0 = m_rot.S_eigvec[0].data; - const auto &Q1 = m_rot.S_eigvec[1].data; - const auto &Q2 = m_rot.S_eigvec[2].data; - const auto &Q3 = m_rot.S_eigvec[3].data; + const auto &Q0 = m_rot.S_eigvec[0]; + const auto &Q1 = m_rot.S_eigvec[1]; + const auto &Q2 = m_rot.S_eigvec[2]; + const auto &Q3 = m_rot.S_eigvec[3]; cvm::real const L0 = m_rot.S_eigval[0]; cvm::real const L1 = m_rot.S_eigval[1]; cvm::real const L2 = m_rot.S_eigval[2]; @@ -572,14 +573,17 @@ void debug_gradients( cvm::vector1d dq0_2(4); cvm::matrix2d ds_2; #ifdef COLVARS_LAMMPS - MathEigen::Jacobi &, - cvm::matrix2d &> *ecalc = - reinterpret_cast &, - cvm::matrix2d &> *>(rot.jacobi); + MathEigen::Jacobi *ecalc = + reinterpret_cast *>(jacobi); #endif deriv.prepare_derivative(rotation_derivative_dldq::use_dl | rotation_derivative_dldq::use_dq); + cvm::real S_new[4][4]; + cvm::real S_new_eigval[4]; + cvm::real S_new_eigvec[4][4]; for (size_t ia = 0; ia < pos2.size(); ++ia) { // cvm::real const &a1x = pos1[ia].x; // cvm::real const &a1y = pos1[ia].y; @@ -588,10 +592,9 @@ void debug_gradients( // make an infitesimal move along each cartesian coordinate of // this atom, and solve again the eigenvector problem for (size_t comp = 0; comp < 3; comp++) { - cvm::matrix2d S_new(4, 4); - cvm::vector1d S_new_eigval(4); - cvm::matrix2d S_new_eigvec(4, 4); - S_new = rot.S_backup; + std::memcpy(S_new, rot.S_backup, sizeof(cvm::real) * 4 * 4); + std::memset(S_new_eigval, 0, sizeof(cvm::real) * 4); + std::memset(S_new_eigvec, 0, sizeof(cvm::real) * 4 * 4); for (size_t i = 0; i < 4; i++) { for (size_t j = 0; j < 4; j++) { S_new[i][j] += diff --git a/src/colvartypes.cpp b/src/colvartypes.cpp index 5a13e2323..b75bef8ea 100644 --- a/src/colvartypes.cpp +++ b/src/colvartypes.cpp @@ -340,26 +340,24 @@ void colvarmodule::rotation::compute_overlap_matrix() #ifndef COLVARS_LAMMPS namespace NR { -void diagonalize_matrix(cvm::matrix2d &m, - cvm::vector1d &eigval, - cvm::matrix2d &eigvec) +void diagonalize_matrix(cvm::real m[4][4], + cvm::real eigval[4], + cvm::real eigvec[4][4]) { - eigval.resize(4); - eigval.reset(); - eigvec.resize(4, 4); - eigvec.reset(); + std::memset(eigval, 0, sizeof(cvm::real) * 4); + std::memset(eigvec, 0, sizeof(cvm::real) * 4 * 4); // diagonalize int jac_nrot = 0; - if (NR_Jacobi::jacobi(m.c_array(), eigval.c_array(), eigvec.c_array(), &jac_nrot) != + if (NR_Jacobi::jacobi(m, eigval, eigvec, &jac_nrot) != COLVARS_OK) { cvm::error("Too many iterations in jacobi diagonalization.\n" "This is usually the result of an ill-defined set of atoms for " "rotational alignment (RMSD, rotateReference, etc).\n"); } - NR_Jacobi::eigsrt(eigval.c_array(), eigvec.c_array()); + NR_Jacobi::eigsrt(eigval, eigvec); // jacobi saves eigenvectors by columns - NR_Jacobi::transpose(eigvec.c_array()); + NR_Jacobi::transpose(eigvec); // normalize eigenvectors for (size_t ie = 0; ie < 4; ie++) { @@ -410,27 +408,29 @@ void colvarmodule::rotation::calc_optimal_rotation( // Seok C, Dill KA. Using quaternions to calculate RMSD. J Comput // Chem. 25(15):1849-57 (2004) DOI: 10.1002/jcc.20110 PubMed: 15376254 void colvarmodule::rotation::calc_optimal_rotation_impl() { - S.resize(4, 4); - S.reset(); compute_overlap_matrix(); - S_backup.resize(4, 4); - S_backup = S; + // S_backup = S; + std::memcpy(&S_backup[0][0], &S, 4*4*sizeof(cvm::real)); if (b_debug_gradients) { - cvm::log("S = "+cvm::to_str(S_backup, cvm::cv_width, cvm::cv_prec)+"\n"); + cvm::matrix2d S_backup_out(4, 4); + for (size_t i = 0; i < 4; ++i) { + for (size_t j = 0; j < 4; ++j) { + S_backup_out[i][j] = S_backup[i][j]; + } + } + cvm::log("S = "+cvm::to_str(S_backup_out, cvm::cv_width, cvm::cv_prec)+"\n"); } - S_eigval.resize(4); - S_eigvec.resize(4, 4); #ifdef COLVARS_LAMMPS MathEigen::Jacobi &, - cvm::matrix2d &> *ecalc = + cvm::real[4], + cvm::real[4][4]> *ecalc = reinterpret_cast &, - cvm::matrix2d &> *>(jacobi); + cvm::real[4], + cvm::real[4][4]> *>(jacobi); int ierror = ecalc->Diagonalize(S, S_eigval, S_eigvec); if (ierror) { @@ -441,7 +441,7 @@ void colvarmodule::rotation::calc_optimal_rotation_impl() { #else NR::diagonalize_matrix(S, S_eigval, S_eigvec); #endif - q = cvm::quaternion(S_eigvec[0]); + q = cvm::quaternion{S_eigvec[0][0], S_eigvec[0][1], S_eigvec[0][2], S_eigvec[0][3]}; if (cvm::rotation::monitor_crossings) { if (q_old.norm2() > 0.0) { diff --git a/src/colvartypes.h b/src/colvartypes.h index 2630fa99a..3502b8f6c 100644 --- a/src/colvartypes.h +++ b/src/colvartypes.h @@ -11,6 +11,7 @@ #define COLVARTYPES_H #include +#include #ifdef COLVARS_LAMMPS // Use open-source Jacobi implementation @@ -1288,9 +1289,9 @@ class colvarmodule::quaternion { #ifndef COLVARS_LAMMPS namespace NR { -void diagonalize_matrix(cvm::matrix2d &m, - cvm::vector1d &eigval, - cvm::matrix2d &eigvec); +void diagonalize_matrix(cvm::real m[4][4], + cvm::real eigval[4], + cvm::real eigvec[4][4]); } #endif @@ -1304,16 +1305,16 @@ class colvarmodule::rotation cvm::rmatrix C; /// Overlap matrix S (4, 4) - cvm::matrix2d S; + cvm::real S[4][4]; /// Eigenvalues of S - cvm::vector1d S_eigval; + cvm::real S_eigval[4]; /// Eigenvectors of S - cvm::matrix2d S_eigvec; + cvm::real S_eigvec[4][4]; /// Used for debugging gradients - cvm::matrix2d S_backup; + cvm::real S_backup[4][4]; public: /// \brief Perform gradient tests diff --git a/src/nr_jacobi.cpp b/src/nr_jacobi.cpp index 58ff6d1dc..51c24e86c 100644 --- a/src/nr_jacobi.cpp +++ b/src/nr_jacobi.cpp @@ -14,13 +14,13 @@ namespace NR_Jacobi { -int jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot) +int jacobi(cvm::real a[4][4], cvm::real d[4], cvm::real v[4][4], int *nrot) { int j,iq,ip,i; cvm::real tresh,theta,tau,t,sm,s,h,g,c; - cvm::vector1d b(n); - cvm::vector1d z(n); + cvm::real b[n]; + cvm::real z[n]; for (ip=0;ip Date: Sat, 16 Sep 2023 09:33:48 -0500 Subject: [PATCH 026/162] Fix LAMMPS build. --- src/colvar_rotation_derivative.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/colvar_rotation_derivative.h b/src/colvar_rotation_derivative.h index 7050537d9..50f4f1aa9 100644 --- a/src/colvar_rotation_derivative.h +++ b/src/colvar_rotation_derivative.h @@ -578,7 +578,7 @@ void debug_gradients( cvm::real[4][4]> *ecalc = reinterpret_cast *>(jacobi); + cvm::real[4][4]> *>(rot.jacobi); #endif deriv.prepare_derivative(rotation_derivative_dldq::use_dl | rotation_derivative_dldq::use_dq); cvm::real S_new[4][4]; From c0d472da29e9a79046d66a6c8f5928925816155a Mon Sep 17 00:00:00 2001 From: HanatoK Date: Wed, 20 Sep 2023 16:13:35 -0500 Subject: [PATCH 027/162] Remove unused header file --- src/colvartypes.h | 1 - 1 file changed, 1 deletion(-) diff --git a/src/colvartypes.h b/src/colvartypes.h index 3502b8f6c..aa0c388af 100644 --- a/src/colvartypes.h +++ b/src/colvartypes.h @@ -11,7 +11,6 @@ #define COLVARTYPES_H #include -#include #ifdef COLVARS_LAMMPS // Use open-source Jacobi implementation From 1034fd1aa6978ed2d9170118d79252149ef99aad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Mon, 24 Jul 2023 20:19:29 +0200 Subject: [PATCH 028/162] Option to run NAMD regtests in GPU-resident mode using the option CUDASOAintegrate in NAMD3 This is controlled by the new script option -gpu, via the environment variable NAMD_CUDASOA. This required disabling zeroMomentum and tclForces. --- namd/tests/library/Common/common.namd | 3 ++- namd/tests/library/Common/test.namd | 9 ++++++++- namd/tests/library/README.md | 1 + namd/tests/library/run_tests.sh | 9 +++++++-- 4 files changed, 18 insertions(+), 4 deletions(-) diff --git a/namd/tests/library/Common/common.namd b/namd/tests/library/Common/common.namd index cfd9ac352..6e729f0b4 100644 --- a/namd/tests/library/Common/common.namd +++ b/namd/tests/library/Common/common.namd @@ -70,7 +70,8 @@ if { [info exists xsc_file] > 0 } { } COMmotion no -zeroMomentum yes +# incompatible with TclForces as of 07/2023 +#zeroMomentum yes timestep 1.0 diff --git a/namd/tests/library/Common/test.namd b/namd/tests/library/Common/test.namd index 0672c2767..77643f701 100644 --- a/namd/tests/library/Common/test.namd +++ b/namd/tests/library/Common/test.namd @@ -3,7 +3,14 @@ # Note: see also test.restart.namd, test.legacy.namd, test.restart.legacy.namd source ../Common/common.namd -source ../Common/measure_net_force_torque.tcl + +if { [info exists env(NAMD_CUDASOA)] && $env(NAMD_CUDASOA) } { + CUDASOAIntegrate on + # incompatible with TclForces as of 07/2023 +} else { + source ../Common/measure_net_force_torque.tcl +} + colvars on diff --git a/namd/tests/library/README.md b/namd/tests/library/README.md index 43056eab5..b0074997f 100644 --- a/namd/tests/library/README.md +++ b/namd/tests/library/README.md @@ -12,6 +12,7 @@ This is the usage information for `run_tests.sh`: ``` Usage: ./run_tests.sh [-h] [-g] [path_to_namd2] [testdir1 [testdir2 ...]] The -g option (re)generates reference outputs in the given directories + The -gpu option enables the GPU-resident NAMD3 code path (CUDASOAIntegrate) If no executable is given, "namd2" is used If no directories are given, all matches of [0-9][0-9][0-9]_* are used ``` diff --git a/namd/tests/library/run_tests.sh b/namd/tests/library/run_tests.sh index fe4362409..c2bdd179b 100755 --- a/namd/tests/library/run_tests.sh +++ b/namd/tests/library/run_tests.sh @@ -14,6 +14,8 @@ export TMPDIR=${TMPDIR:-/tmp} DIRLIST='' BINARY=namd2 +CUDASOA=0 + while [ $# -ge 1 ]; do if { echo $1 | grep -q namd ; }; then echo "Using NAMD executable from $1" @@ -22,13 +24,16 @@ while [ $# -ge 1 ]; do gen_ref_output='yes' echo "Generating reference output" elif [ "x$1" = 'x-h' ]; then - echo "Usage: ./run_tests.sh [-h] [-g] [path_to_namd2] [testdir1 [testdir2 ...]]" >& 2 + echo "Usage: ./run_tests.sh [-h] [-g] [-gpu] [path_to_namd2] [testdir1 [testdir2 ...]]" >& 2 echo " The -g option (re)generates reference outputs in the given directories" >& 2 + echo " The -gpu option enables the GPU-resident NAMD3 code path (CUDASOAIntegrate)" >& 2 echo " If no executable is given, \"namd2\" is used" >& 2 echo " If no directories are given, all matches of [0-9][0-9][0-9]_* are used" >& 2 echo " This script relies on the executable spiff to be available, and will try to " >& 2 echo " download and build it into $TMPDIR if needed." >& 2 exit 0 + elif [ "x$1" = 'x-gpu' ]; then + CUDASOA=1 else DIRLIST=`echo ${DIRLIST} $1` fi @@ -164,7 +169,7 @@ for dir in ${DIRLIST} ; do # Run the test (use a subshell to avoid cluttering stdout) # Use multiple threads to test SMP code (TODO: move SMP tests to interface?) - $BINARY +p ${NUM_THREADS_THIS} $script > ${basename}.out + NAMD_CUDASOA=$CUDASOA $BINARY +p ${NUM_THREADS_THIS} $script > ${basename}.out # Output of Colvars module, minus the version numbers grep "^colvars:" ${basename}.out | grep -v 'Initializing the collective variables module' \ From b3d515ff3b607349dda1de059c807afee7c764db Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 25 Jul 2023 14:11:39 -0400 Subject: [PATCH 029/162] Do not repeat tests when multiple files fail --- namd/tests/library/run_tests.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/namd/tests/library/run_tests.sh b/namd/tests/library/run_tests.sh index c2bdd179b..eb8ba1c53 100755 --- a/namd/tests/library/run_tests.sh +++ b/namd/tests/library/run_tests.sh @@ -299,11 +299,11 @@ else echo "$(${TPUT_RED})There were failed tests.$(${TPUT_CLEAR})" if [ ${#failed_tests[@]} -gt 0 ]; then echo "The following tests are failed:" - printf "%s\n" "${failed_tests[@]}" + printf "%s\n" "${failed_tests[@]}" | sort -u fi if [ ${#failed_tests_low_prec[@]} -gt 0 ]; then echo "The following tests are failed, but passed at low precisions:" - printf "%s\n" "${failed_tests_low_prec[@]}" + printf "%s\n" "${failed_tests_low_prec[@]}" | sort -u fi exit 1 fi From 6e63279084d31c6625e2c897272a150fa2c80e55 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Thu, 21 Sep 2023 18:22:55 +0200 Subject: [PATCH 030/162] Change test option to -cudasoa also, fix small mixup in comment --- namd/tests/library/Common/common.namd | 2 +- namd/tests/library/README.md | 2 +- namd/tests/library/run_tests.sh | 6 +++--- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/namd/tests/library/Common/common.namd b/namd/tests/library/Common/common.namd index 6e729f0b4..846f52d08 100644 --- a/namd/tests/library/Common/common.namd +++ b/namd/tests/library/Common/common.namd @@ -70,7 +70,7 @@ if { [info exists xsc_file] > 0 } { } COMmotion no -# incompatible with TclForces as of 07/2023 +# incompatible with CUDASOAIntegrate as of 09/2023 #zeroMomentum yes timestep 1.0 diff --git a/namd/tests/library/README.md b/namd/tests/library/README.md index b0074997f..2f0b32c79 100644 --- a/namd/tests/library/README.md +++ b/namd/tests/library/README.md @@ -12,7 +12,7 @@ This is the usage information for `run_tests.sh`: ``` Usage: ./run_tests.sh [-h] [-g] [path_to_namd2] [testdir1 [testdir2 ...]] The -g option (re)generates reference outputs in the given directories - The -gpu option enables the GPU-resident NAMD3 code path (CUDASOAIntegrate) + The -cudasoa option enables the GPU-resident NAMD3 code path (CUDASOAIntegrate) If no executable is given, "namd2" is used If no directories are given, all matches of [0-9][0-9][0-9]_* are used ``` diff --git a/namd/tests/library/run_tests.sh b/namd/tests/library/run_tests.sh index eb8ba1c53..8342d4aed 100755 --- a/namd/tests/library/run_tests.sh +++ b/namd/tests/library/run_tests.sh @@ -24,15 +24,15 @@ while [ $# -ge 1 ]; do gen_ref_output='yes' echo "Generating reference output" elif [ "x$1" = 'x-h' ]; then - echo "Usage: ./run_tests.sh [-h] [-g] [-gpu] [path_to_namd2] [testdir1 [testdir2 ...]]" >& 2 + echo "Usage: ./run_tests.sh [-h] [-g] [-cudasoa] [path_to_namd2] [testdir1 [testdir2 ...]]" >& 2 echo " The -g option (re)generates reference outputs in the given directories" >& 2 - echo " The -gpu option enables the GPU-resident NAMD3 code path (CUDASOAIntegrate)" >& 2 + echo " The -cudasoa option enables the GPU-resident NAMD3 code path (CUDASOAIntegrate)" >& 2 echo " If no executable is given, \"namd2\" is used" >& 2 echo " If no directories are given, all matches of [0-9][0-9][0-9]_* are used" >& 2 echo " This script relies on the executable spiff to be available, and will try to " >& 2 echo " download and build it into $TMPDIR if needed." >& 2 exit 0 - elif [ "x$1" = 'x-gpu' ]; then + elif [ "x$1" = 'x-cudasoa' ]; then CUDASOA=1 else DIRLIST=`echo ${DIRLIST} $1` From a56127095044d632d66a34e6c91a9ae6befc06a8 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 21 Sep 2023 16:03:16 -0400 Subject: [PATCH 031/162] Simplify loader scripts for GCC and Git --- devel-tools/load-recent-gcc.sh | 9 +++------ devel-tools/load-recent-git.sh | 9 +++------ 2 files changed, 6 insertions(+), 12 deletions(-) diff --git a/devel-tools/load-recent-gcc.sh b/devel-tools/load-recent-gcc.sh index e0cfe24b2..98deb5656 100644 --- a/devel-tools/load-recent-gcc.sh +++ b/devel-tools/load-recent-gcc.sh @@ -1,7 +1,4 @@ -# Load Software Collections packages on a RedHat-style distribution -if hash scl >& /dev/null ; then - if scl -l | grep -q ^devtoolset-10 ; then - source /opt/rh/devtoolset-10/enable && \ - echo "Loaded: $(gcc --version)" - fi +# Load Software Collections package for RHEL/CentOS 7 +if [ -s /etc/redhat-release ] && [ -s /opt/rh/devtoolset-10/enable ] ; then + source /opt/rh/devtoolset-10/enable && echo "Loaded: $(gcc --version)" | head -n 1 fi diff --git a/devel-tools/load-recent-git.sh b/devel-tools/load-recent-git.sh index 58431b2dc..3a1da9550 100644 --- a/devel-tools/load-recent-git.sh +++ b/devel-tools/load-recent-git.sh @@ -1,7 +1,4 @@ -# Load Software Collections packages on a RedHat-style distribution -if hash scl >& /dev/null ; then - if scl -l | grep -q ^rh-git227 ; then - source /opt/rh/rh-git227/enable && \ - echo "Loaded: $(git --version)" - fi +# Load Software Collections package for RHEL/CentOS 7 +if [ -s /etc/redhat-release ] && [ -s /opt/rh/rh-git227/enable ] ; then + source /opt/rh/rh-git227/enable && echo "Loaded: $(git --version)" fi From a61083e2166ef3a5cba6c15e39e2b523247dd4e4 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 14 Sep 2023 15:36:16 -0400 Subject: [PATCH 032/162] Simplify and make more portable the GROMACS build script --- devel-tools/compile-gromacs.sh | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/devel-tools/compile-gromacs.sh b/devel-tools/compile-gromacs.sh index 788a345ae..e0afccf78 100755 --- a/devel-tools/compile-gromacs.sh +++ b/devel-tools/compile-gromacs.sh @@ -9,6 +9,10 @@ source $(dirname $0)/set-ccache.sh compile_gromacs_target() { + if [ -n "${GROMACS_REGRESSION_TESTS}" ] ; then + export GROMACS_BUILD_TESTS=1 + fi + local CMAKE=cmake CTEST=ctest if hash cmake3 >& /dev/null ; then CMAKE=cmake3 @@ -68,8 +72,9 @@ compile_gromacs_target() { fi fi - # When on GitHub Actions, download the tests as well + # When on GitHub Actions, build the tests as well if [ -n "${GITHUB_ACTION}" ] ; then + export GROMACS_BUILD_TESTS=1 GMX_BUILD_OPTS+=(-DREGRESSIONTEST_DOWNLOAD=ON) fi @@ -98,25 +103,22 @@ compile_gromacs_target() { ${CMAKE} --build "${GMX_BUILD_DIR}" --parallel $(nproc --all) ret_code=$? - if [ -n "${GROMACS_REGRESSION_TESTS}" ] ; then + if [ -n "${GROMACS_BUILD_TESTS}" ] ; then # Build the tests as well ${CMAKE} --build "${GMX_BUILD_DIR}" --target tests --parallel $(nproc --all) ret_code=$((${ret_code} || $?)) fi if [ ${ret_code} = 0 ] ; then - pushd "${GMX_BUILD_DIR}" - ${CTEST} --output-on-failure - retcode=$? - if [ -n "${GMX_INSTALL_DIR}" ] ; then - if hash ninja >& /dev/null ; then - ninja install - else - make install - fi - ret_code=$((${ret_code} || $?)) + if [ -n "${GROMACS_BUILD_TESTS}" ] && [ -z "${GITHUB_ACTION}" ] ; then + # Some GROMACS tests are extremely long, we run them only offline + pushd "${GMX_BUILD_DIR}" + ${CTEST} --output-on-failure + retcode=$((${ret_code} || $?)) + popd fi - popd + ${CMAKE} --install "${GMX_BUILD_DIR}" + ret_code=$((${ret_code} || $?)) fi popd From 8d2a58c5d0400706f77718b237b09129036de7de Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 22 Aug 2023 15:56:25 +0200 Subject: [PATCH 033/162] Simplify formatted state writing --- src/colvarbias.cpp | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp index 653804a4b..c961a96f4 100644 --- a/src/colvarbias.cpp +++ b/src/colvarbias.cpp @@ -504,13 +504,9 @@ std::ostream & colvarbias::write_state(std::ostream &os) os.setf(std::ios::scientific, std::ios::floatfield); os.precision(cvm::cv_prec); os << state_keyword << " {\n" - << " configuration {\n"; - std::istringstream is(get_state_params()); - std::string line; - while (std::getline(is, line)) { - os << " " << line << "\n"; - } - os << " }\n"; + << " configuration {\n" + << get_state_params() + << " }\n"; write_state_data(os); os << "}\n\n"; return os; From c28fba6a6e88ed59041b4ab28443097161b5e54b Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 20 Jul 2023 17:39:04 -0400 Subject: [PATCH 034/162] Remove trivial derivations of base-class functions --- src/colvarbias_restraint.cpp | 36 ------------------------------------ src/colvarbias_restraint.h | 8 -------- 2 files changed, 44 deletions(-) diff --git a/src/colvarbias_restraint.cpp b/src/colvarbias_restraint.cpp index 0a66a2999..56200198d 100644 --- a/src/colvarbias_restraint.cpp +++ b/src/colvarbias_restraint.cpp @@ -844,18 +844,6 @@ int colvarbias_restraint_harmonic::set_state_params(std::string const &conf) } -std::ostream & colvarbias_restraint_harmonic::write_state_data(std::ostream &os) -{ - return colvarbias_ti::write_state_data(os); -} - - -std::istream & colvarbias_restraint_harmonic::read_state_data(std::istream &is) -{ - return colvarbias_ti::read_state_data(is); -} - - std::ostream & colvarbias_restraint_harmonic::write_traj_label(std::ostream &os) { colvarbias_restraint::write_traj_label(os); @@ -1143,18 +1131,6 @@ int colvarbias_restraint_harmonic_walls::set_state_params(std::string const &con } -std::ostream & colvarbias_restraint_harmonic_walls::write_state_data(std::ostream &os) -{ - return colvarbias_ti::write_state_data(os); -} - - -std::istream & colvarbias_restraint_harmonic_walls::read_state_data(std::istream &is) -{ - return colvarbias_ti::read_state_data(is); -} - - std::ostream & colvarbias_restraint_harmonic_walls::write_traj_label(std::ostream &os) { colvarbias_restraint::write_traj_label(os); @@ -1300,18 +1276,6 @@ int colvarbias_restraint_linear::set_state_params(std::string const &conf) } -std::ostream & colvarbias_restraint_linear::write_state_data(std::ostream &os) -{ - return colvarbias_ti::write_state_data(os); -} - - -std::istream & colvarbias_restraint_linear::read_state_data(std::istream &is) -{ - return colvarbias_ti::read_state_data(is); -} - - std::ostream & colvarbias_restraint_linear::write_traj_label(std::ostream &os) { colvarbias_restraint::write_traj_label(os); diff --git a/src/colvarbias_restraint.h b/src/colvarbias_restraint.h index 45a96d14f..c19132ede 100644 --- a/src/colvarbias_restraint.h +++ b/src/colvarbias_restraint.h @@ -38,8 +38,6 @@ class colvarbias_restraint virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); - // virtual std::ostream & write_state_data(std::ostream &os); - // virtual std::istream & read_state_data(std::istream &os); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); @@ -242,8 +240,6 @@ class colvarbias_restraint_harmonic virtual int update(); virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); - virtual std::ostream & write_state_data(std::ostream &os); - virtual std::istream & read_state_data(std::istream &os); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); virtual int change_configuration(std::string const &conf); @@ -269,8 +265,6 @@ class colvarbias_restraint_harmonic_walls virtual int update(); virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); - virtual std::ostream & write_state_data(std::ostream &os); - virtual std::istream & read_state_data(std::istream &os); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); @@ -311,8 +305,6 @@ class colvarbias_restraint_linear virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); - virtual std::ostream & write_state_data(std::ostream &os); - virtual std::istream & read_state_data(std::istream &os); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); From 332857b0bedb9109449f0e6a5a8b6b90c6b59986 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 23 Jun 2023 16:29:15 -0400 Subject: [PATCH 035/162] Initial implementation of memory_stream class --- src/colvarmodule.h | 2 + src/colvars_memstream.h | 278 +++++++++++++++++++++++++++++++++++++++ vmd/src/colvars_files.pl | 1 + 3 files changed, 281 insertions(+) create mode 100644 src/colvars_memstream.h diff --git a/src/colvarmodule.h b/src/colvarmodule.h index 236d432a9..f14c9ecdb 100644 --- a/src/colvarmodule.h +++ b/src/colvarmodule.h @@ -190,7 +190,9 @@ class colvarmodule { template class matrix2d; class quaternion; class rotation; + class usage; + class memory_stream; /// Residue identifier typedef int residue_id; diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h new file mode 100644 index 000000000..61125b68c --- /dev/null +++ b/src/colvars_memstream.h @@ -0,0 +1,278 @@ +// -*- c++ -*- + +#ifndef MEMORY_STREAM_H +#define MEMORY_STREAM_H + +#include +#include +#include +#include + +class cvm::memory_stream { + +public: + + /// Set up an empty stream with an internal buffer, suitable for writing to + /// \param max_length Maximum allowed capacity (default is 64 GiB) + memory_stream(size_t max_length = (1L << 36)) : max_length_(max_length) {} + + /// Set up a stream based on an external input buffer + memory_stream(size_t n, unsigned char const *buf) + : external_input_buffer_(buf), internal_buffer_(), data_length_(n), max_length_(data_length_) + { + } + + /// Length of the buffer + inline size_t length() const { return data_length_; } + + /// Output buffer + inline unsigned char *output_buffer() + { + return (external_output_buffer_ ? external_output_buffer_ : internal_buffer_.data()); + } + + /// Next location to write to + inline unsigned char *output_location() { return output_buffer() + data_length_; } + + /// Input buffer + inline unsigned char const *input_buffer() const + { + return (external_input_buffer_ ? external_input_buffer_ : internal_buffer_.data()); + } + + /// Next location to read from + inline unsigned char const *input_location() const { return input_buffer() + read_pos_; } + + /// Cast operator to be used to test for errors + inline explicit operator bool() const { return error_code_ == 0; } + + /// Write a simple object to the output buffer + template void write_object(T const &t); + + /// Wrapper to write_object() + template friend memory_stream &operator<<(memory_stream &os, T const &t); + + /// Write a vector of simple objects to the output buffer + template void write_vector(std::vector const &t); + + /// Wrapper to write_vector() + template + friend memory_stream &operator<<(memory_stream &os, std::vector const &t); + + /// Read a simple object from the buffer + template void read_object(T &t); + + /// Wrapper to read_object() + template friend memory_stream &operator>>(memory_stream &is, T &t); + + /// Read a vector of simple objects from the buffer + template void read_vector(std::vector &t); + + /// Wrapper to read_vector() + template friend memory_stream &operator>>(memory_stream &is, std::vector &t); + +protected: + + /// External output buffer + unsigned char *external_output_buffer_ = nullptr; + + /// External input buffer + unsigned char const *external_input_buffer_ = nullptr; + + /// Internal buffer (may server for both input and output) + std::vector internal_buffer_; + + /// Length of the data buffer (either internal or external) + size_t data_length_ = 0L; + + /// Largest allowed capacity of the data buffer + size_t const max_length_; + + /// Error status + int error_code_ = 0; + + /// Add the requester number of bytes to the array capacity; return false if buffer is external + inline bool expand_ouput_buffer(size_t add_bytes) + { + if (external_output_buffer_) { + // Cannot resize an external buffer + error_code_ = 1; + } else { + if ((internal_buffer_.size() + add_bytes) <= max_length_) { + internal_buffer_.resize((internal_buffer_.size() + add_bytes)); + } else { + error_code_ = 1; + } + } + return (error_code_ == 0); + } + + /// Move the buffer position past the data just written + inline void incr_write_pos(size_t c) { data_length_ += c; } + + /// Input buffer (may be the same as output, apart from const-ness) + unsigned char const *input_buffer_ = nullptr; + + /// Current position when reading from the buffer + size_t read_pos_ = 0L; + + /// Begin an attempt to read an object + inline void begin_reading() { error_code_ = -1; } + + /// Mark the reading attempt succesful + inline void done_reading() { error_code_ = 0; } + + /// Move the buffer position past the data just read + inline void incr_read_pos(size_t c) { read_pos_ += c; } + + /// Check that the buffer contains enough bytes to read as the argument says, set error otherwise + inline bool has_remaining(size_t c) { return c <= (data_length_ - read_pos_); } +}; + +template void cvm::memory_stream::write_object(T const &t) +{ + static_assert(std::is_trivially_copyable::value, "Cannot use write_object() on complex type"); + size_t const new_data_size = sizeof(T); + if (expand_ouput_buffer(new_data_size)) { + std::memcpy(output_location(), &t, sizeof(T)); + incr_write_pos(new_data_size); + } +} + +template cvm::memory_stream &operator<<(cvm::memory_stream &os, T const &t) +{ + os.write_object(t); + return os; +} + +template <> void cvm::memory_stream::write_object(std::string const &t) +{ + size_t const string_length = t.size(); + size_t const new_data_size = sizeof(size_t) + sizeof(char) * string_length; + if (expand_ouput_buffer(new_data_size)) { + std::memcpy(output_location(), &string_length, sizeof(size_t)); + incr_write_pos(sizeof(size_t)); + std::memcpy(output_location(), t.c_str(), t.size() * sizeof(char)); + incr_write_pos(t.size() * sizeof(char)); + } +} + +template <> cvm::memory_stream &operator<<(cvm::memory_stream &os, std::string const &t) +{ + os.write_object(t); + return os; +} + +template <> void cvm::memory_stream::write_object(cvm::vector1d const &t) +{ + return write_vector(t.data_array()); +} + +template <> +cvm::memory_stream &operator<<(cvm::memory_stream &os, cvm::vector1d const &t) +{ + os.write_vector(t.data_array()); + return os; +} + +template <> void cvm::memory_stream::write_object(colvarvalue const &t) {} + +template <> cvm::memory_stream &operator<<(cvm::memory_stream &os, colvarvalue const &t) +{ + os.write_object(t); + return os; +} + +template void cvm::memory_stream::write_vector(std::vector const &t) +{ + static_assert(std::is_trivially_copyable::value, "Cannot use write_vector() on complex type"); + size_t const vector_length = t.size(); + size_t const new_data_size = sizeof(size_t) + sizeof(T) * vector_length; + if (expand_ouput_buffer(new_data_size)) { + std::memcpy(output_location(), &vector_length, sizeof(size_t)); + incr_write_pos(sizeof(T)); + std::memcpy(output_location(), t.data(), t.size() * sizeof(T)); + incr_write_pos(t.size() * sizeof(T)); + } +} + +template +cvm::memory_stream &operator<<(cvm::memory_stream &os, std::vector const &t) +{ + os.write_vector(t); + return os; +} + +template void cvm::memory_stream::read_object(T &t) +{ + static_assert(std::is_trivially_copyable::value, "Cannot use read_object() on complex type"); + begin_reading(); + if (has_remaining(sizeof(T))) { + std::memcpy(&t, input_location(), sizeof(T)); + incr_read_pos(sizeof(T)); + done_reading(); + } +} + +template cvm::memory_stream &operator>>(cvm::memory_stream &is, T &t) +{ + is.read_object(t); + return is; +} + +template <> void cvm::memory_stream::read_object(std::string &t) +{ + begin_reading(); + size_t string_length = 0; + if (has_remaining(sizeof(size_t))) { + std::memcpy(&string_length, input_location(), sizeof(size_t)); + incr_read_pos(sizeof(size_t)); + if (has_remaining(string_length * sizeof(char))) { + t.assign(reinterpret_cast(input_location()), string_length); + incr_read_pos(string_length * sizeof(char)); + done_reading(); + } + } +} + +template <> cvm::memory_stream &operator>>(cvm::memory_stream &is, std::string &t) +{ + is.read_object(t); + return is; +} + +template <> void cvm::memory_stream::read_object(cvm::vector1d &t) +{ + return read_vector(t.data_array()); +} + +template <> cvm::memory_stream &operator>>(cvm::memory_stream &is, cvm::vector1d &t) +{ + is.read_vector(t.data_array()); + return is; +} + +template void cvm::memory_stream::read_vector(std::vector &t) +{ + static_assert(std::is_trivially_copyable::value, "Cannot use read_vector() on complex type"); + begin_reading(); + size_t vector_length = 0; + if (has_remaining(sizeof(size_t))) { + std::memcpy(&vector_length, input_location(), sizeof(size_t)); + incr_read_pos(sizeof(size_t)); + if (has_remaining(vector_length * sizeof(T))) { + t.resize(vector_length); + std::memcpy(t.data(), input_location(), vector_length * sizeof(T)); + incr_read_pos(vector_length * sizeof(T)); + done_reading(); + } + } +} + +template cvm::memory_stream &operator>>(cvm::memory_stream &is, std::vector &t) +{ + is.read_vector(t); + return is; +} + +#endif diff --git a/vmd/src/colvars_files.pl b/vmd/src/colvars_files.pl index ec2c0f6f9..3575b99ab 100644 --- a/vmd/src/colvars_files.pl +++ b/vmd/src/colvars_files.pl @@ -85,6 +85,7 @@ 'colvarscript_commands.h', 'colvarscript_commands_bias.h', 'colvarscript_commands_colvar.h', + 'colvars_memstream.h', 'colvars_version.h', 'colvartypes.h', 'colvarvalue.h', From 61bd189e0454c21503a84f92a8c38cae2a9de217 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 23 Jun 2023 16:29:31 -0400 Subject: [PATCH 036/162] Add missing const accessors --- src/colvartypes.h | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/colvartypes.h b/src/colvartypes.h index aa0c388af..765166fd7 100644 --- a/src/colvartypes.h +++ b/src/colvartypes.h @@ -80,6 +80,12 @@ template class colvarmodule::vector1d return data; } + /// Return a reference to the data + inline std::vector const &data_array() const + { + return data; + } + inline ~vector1d() { data.clear(); @@ -504,6 +510,12 @@ template class colvarmodule::matrix2d return data; } + /// Return a reference to the data + inline std::vector const &data_array() const + { + return data; + } + inline row & operator [] (size_t const i) { return rows[i]; From d77a99fecb72f099787e0ed04421b2f8a23bf9bf Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 23 Jun 2023 16:31:54 -0400 Subject: [PATCH 037/162] Abstract the stream operators for colvarvalue --- src/colvarvalue.cpp | 64 +++++++++++++++++++++++++++++++-------------- src/colvarvalue.h | 20 +++++++++++--- 2 files changed, 61 insertions(+), 23 deletions(-) diff --git a/src/colvarvalue.cpp b/src/colvarvalue.cpp index e57859dfa..8d0f63212 100644 --- a/src/colvarvalue.cpp +++ b/src/colvarvalue.cpp @@ -13,6 +13,7 @@ #include "colvarmodule.h" #include "colvarvalue.h" +#include "colvars_memstream.h" @@ -721,29 +722,43 @@ int colvarvalue::from_simple_string(std::string const &s) return COLVARS_ERROR; } -std::ostream & operator << (std::ostream &os, colvarvalue const &x) + +template void colvarvalue::write_to_stream(OST &os) const { - switch (x.type()) { + switch (type()) { case colvarvalue::type_scalar: - os << x.real_value; + os << real_value; break; case colvarvalue::type_3vector: case colvarvalue::type_unit3vector: case colvarvalue::type_unit3vectorderiv: - os << x.rvector_value; + os << rvector_value; break; case colvarvalue::type_quaternion: case colvarvalue::type_quaternionderiv: - os << x.quaternion_value; + os << quaternion_value; break; case colvarvalue::type_vector: - os << x.vector1d_value; + os << vector1d_value; break; case colvarvalue::type_notset: default: os << "not set"; break; } +} + + +std::ostream & operator << (std::ostream &os, colvarvalue const &x) +{ + x.write_to_stream(os); + return os; +} + + +cvm::memory_stream & operator << (cvm::memory_stream &os, colvarvalue const &x) +{ + x.write_to_stream(os); return os; } @@ -758,44 +773,55 @@ std::ostream & operator << (std::ostream &os, std::vector const &v) } -std::istream & operator >> (std::istream &is, colvarvalue &x) +template void colvarvalue::read_from_stream(IST &is) { - if (x.type() == colvarvalue::type_notset) { + if (type() == colvarvalue::type_notset) { cvm::error("Trying to read from a stream a colvarvalue, " "which has not yet been assigned a data type.\n"); - return is; } - switch (x.type()) { + switch (type()) { case colvarvalue::type_scalar: - is >> x.real_value; + is >> real_value; break; case colvarvalue::type_3vector: case colvarvalue::type_unit3vectorderiv: - is >> x.rvector_value; + is >> rvector_value; break; case colvarvalue::type_unit3vector: - is >> x.rvector_value; - x.apply_constraints(); + is >> rvector_value; + apply_constraints(); break; case colvarvalue::type_quaternion: - is >> x.quaternion_value; - x.apply_constraints(); + is >> quaternion_value; + apply_constraints(); break; case colvarvalue::type_quaternionderiv: - is >> x.quaternion_value; + is >> quaternion_value; break; case colvarvalue::type_vector: - is >> x.vector1d_value; + is >> vector1d_value; break; case colvarvalue::type_notset: default: - x.undef_op(); + undef_op(); } +} + + +std::istream & operator >> (std::istream &is, colvarvalue &x) +{ + x.read_from_stream(is); return is; } +cvm::memory_stream & operator >> (cvm::memory_stream &is, colvarvalue &x) +{ + x.read_from_stream(is); + return is; +} + size_t colvarvalue::output_width(size_t const &real_width) const { switch (this->value_type) { diff --git a/src/colvarvalue.h b/src/colvarvalue.h index 6bc7a57c7..b2edaa5a5 100644 --- a/src/colvarvalue.h +++ b/src/colvarvalue.h @@ -299,11 +299,23 @@ class colvarvalue { void undef_op() const; - /// \brief Formatted output operator - friend std::ostream & operator << (std::ostream &os, colvarvalue const &q); + /// Generic stream writing function (formatted and not) + template void write_to_stream(OST &os) const; - /// \brief Formatted input operator - friend std::istream & operator >> (std::istream &is, colvarvalue &q); + /// Formatted output operator + friend std::ostream & operator << (std::ostream &os, colvarvalue const &x); + + /// Unformatted output operator + friend cvm::memory_stream & operator << (cvm::memory_stream &os, colvarvalue const &x); + + /// Generic stream reading function (formatted and not) + template void read_from_stream(IST &is); + + /// Formatted input operator + friend std::istream & operator >> (std::istream &is, colvarvalue &x); + + /// Unformatted input operator + friend cvm::memory_stream & operator >> (cvm::memory_stream &is, colvarvalue &x); /// Give the number of characters required to output this /// colvarvalue, given the current type assigned and the number of From e8bc153349c391ac74fcfbd03fb0e042e97b2044 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 23 Jun 2023 16:32:16 -0400 Subject: [PATCH 038/162] Formatting tweaks --- src/.clang-format | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/.clang-format b/src/.clang-format index e05242256..66e78c8b5 100644 --- a/src/.clang-format +++ b/src/.clang-format @@ -8,4 +8,7 @@ ObjCBlockIndentWidth: 2 PenaltyBreakAssignment: 2 AccessModifierOffset: -2 BreakBeforeBraces: WebKit +EmptyLineAfterAccessModifier: Leave +NamespaceIndentation: None +MaxEmptyLinesToKeep: 2 ... From 256dc6d0c769a16c03f586ac684a338267a4c0df Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 23 Jun 2023 22:42:08 -0400 Subject: [PATCH 039/162] Add unit test for memory stream --- tests/unittests/CMakeLists.txt | 29 +++++------ tests/unittests/memory_stream.cpp | 86 +++++++++++++++++++++++++++++++ 2 files changed, 100 insertions(+), 15 deletions(-) create mode 100644 tests/unittests/memory_stream.cpp diff --git a/tests/unittests/CMakeLists.txt b/tests/unittests/CMakeLists.txt index e2804ae75..84d3160f8 100644 --- a/tests/unittests/CMakeLists.txt +++ b/tests/unittests/CMakeLists.txt @@ -1,12 +1,18 @@ -add_executable(colvarvalue_unit3vector colvarvalue_unit3vector.cpp) -target_link_libraries(colvarvalue_unit3vector PRIVATE colvars) -target_include_directories(colvarvalue_unit3vector PRIVATE ${COLVARS_SOURCE_DIR}/src) -add_test(NAME colvarvalue_unit3vector COMMAND colvarvalue_unit3vector) +set(COLVARS_STUBS_DIR ${COLVARS_SOURCE_DIR}/misc_interfaces/stubs/) -add_executable(file_io file_io.cpp) -target_link_libraries(file_io PRIVATE colvars) -target_include_directories(file_io PRIVATE ${COLVARS_SOURCE_DIR}/src) -add_test(NAME file_io COMMAND file_io) +foreach(CMD + colvarvalue_unit3vector + file_io + memory_stream + read_xyz_traj + ) + add_executable(${CMD} ${CMD}.cpp) + target_link_libraries(${CMD} PRIVATE colvars) + target_include_directories(${CMD} PRIVATE ${COLVARS_SOURCE_DIR}/src) + target_include_directories(${CMD} PRIVATE ${COLVARS_STUBS_DIR}) + target_link_libraries(${CMD} PRIVATE colvars colvars_stubs) + add_test(NAME ${CMD} COMMAND ${CMD}) +endforeach() if(COLVARS_TCL) add_executable(embedded_tcl embedded_tcl.cpp) @@ -15,13 +21,6 @@ if(COLVARS_TCL) add_test(NAME embedded_tcl COMMAND embedded_tcl) endif() -# Last test requires the stubs proxy -add_executable(read_xyz_traj read_xyz_traj.cpp) -set(COLVARS_STUBS_DIR ${COLVARS_SOURCE_DIR}/misc_interfaces/stubs/) -target_link_libraries(read_xyz_traj PRIVATE colvars colvars_stubs) -target_include_directories(read_xyz_traj PRIVATE ${COLVARS_SOURCE_DIR}/src) -target_include_directories(read_xyz_traj PRIVATE ${COLVARS_STUBS_DIR}) -add_test(NAME read_xyz_traj COMMAND read_xyz_traj) add_custom_command( TARGET read_xyz_traj POST_BUILD COMMAND ${CMAKE_COMMAND} -E create_symlink diff --git a/tests/unittests/memory_stream.cpp b/tests/unittests/memory_stream.cpp new file mode 100644 index 000000000..107784746 --- /dev/null +++ b/tests/unittests/memory_stream.cpp @@ -0,0 +1,86 @@ +#include + +#include "colvarmodule.h" +#include "colvartypes.h" +#include "colvarvalue.h" +#include "colvars_memstream.h" + + +template std::ostream &operator<<(std::ostream &os, std::vector const &v) +{ + os << "{"; + for (auto &vi : v) + os << " " << vi; + os << " }"; + return os; +} + +template void read_and_print(cvm::memory_stream &is, T &t) +{ + if (is >> t) { + std::cout << typeid(T).name() << ": " << t << std::endl; + } +} + + +int main(int argc, char const *argv[]) +{ + cvm::real x = -101.0; + size_t count = 1240566; + std::vector const a{1, 2, 3, 4, 5, 6, 7, 8}; + cvm::rvector const v = (cvm::rvector(-1.0, 1.0, 0.5)).unit(); + std::string const text("Vabbé / Está bien / Ça va / 好吧"); + std::vector> const a2(1, a); + + cvm::vector1d v_from_a(a.size(), a.data()); + + colvarvalue cv(v, colvarvalue::type_unit3vector); + + size_t n = (1L << 26); + if (argc > 1) { + n = atoi(argv[1]); + } + + cvm::memory_stream buf(n); + + // Use standard functions and operators interchangeably + buf.write_object(x); + buf.write_object(count); + buf.write_object(v); + buf << text; + buf << a; + + buf << v_from_a; + + buf << cv; + + // // The following will raise a compile error + // buf << a2; + + if (buf) { + + cvm::real new_x = 0.0; + read_and_print(buf, new_x); + + size_t new_count = 0; + read_and_print(buf, new_count); + + cvm::rvector new_v; + read_and_print(buf, new_v); + + std::string new_text; + read_and_print(buf, new_text); + + std::vector new_a; + read_and_print(buf, new_a); + + cvm::vector1d new_v_from_a; + read_and_print(buf, new_v_from_a); + + colvarvalue new_cv(colvarvalue::type_unit3vector); + read_and_print(buf, new_cv); + + } + + return buf ? 0 : 1; +} From e7762942cd22d0054ea5a81746c7b4234204e7b1 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sun, 25 Jun 2023 18:25:45 -0400 Subject: [PATCH 040/162] Work around incomplete C++11 compliance for old GCC --- src/colvars_memstream.h | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index 61125b68c..7da6bbad5 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -8,6 +8,14 @@ #include #include +// Work around missing std::is_trivially_copyable in old GCC versions +// TODO remove this after CentOS 7 has been beyond EOL for a while +#if __GNUG__ && (__GNUC__ < 5) +#define IS_TRIVIALLY_COPYABLE(T) __has_trivial_copy(T) +#else +#define IS_TRIVIALLY_COPYABLE(T) std::is_trivially_copyable::value +#endif + class cvm::memory_stream { public: @@ -131,7 +139,7 @@ class cvm::memory_stream { template void cvm::memory_stream::write_object(T const &t) { - static_assert(std::is_trivially_copyable::value, "Cannot use write_object() on complex type"); + static_assert(IS_TRIVIALLY_COPYABLE(T), "Cannot use write_object() on complex type"); size_t const new_data_size = sizeof(T); if (expand_ouput_buffer(new_data_size)) { std::memcpy(output_location(), &t, sizeof(T)); @@ -185,7 +193,7 @@ template <> cvm::memory_stream &operator<<(cvm::memory_stream &os, colvarvalue c template void cvm::memory_stream::write_vector(std::vector const &t) { - static_assert(std::is_trivially_copyable::value, "Cannot use write_vector() on complex type"); + static_assert(IS_TRIVIALLY_COPYABLE(T), "Cannot use write_vector() on complex type"); size_t const vector_length = t.size(); size_t const new_data_size = sizeof(size_t) + sizeof(T) * vector_length; if (expand_ouput_buffer(new_data_size)) { @@ -205,7 +213,7 @@ cvm::memory_stream &operator<<(cvm::memory_stream &os, std::vector const &t) template void cvm::memory_stream::read_object(T &t) { - static_assert(std::is_trivially_copyable::value, "Cannot use read_object() on complex type"); + static_assert(IS_TRIVIALLY_COPYABLE(T), "Cannot use read_object() on complex type"); begin_reading(); if (has_remaining(sizeof(T))) { std::memcpy(&t, input_location(), sizeof(T)); @@ -254,7 +262,7 @@ template <> cvm::memory_stream &operator>>(cvm::memory_stream &is, cvm::vector1d template void cvm::memory_stream::read_vector(std::vector &t) { - static_assert(std::is_trivially_copyable::value, "Cannot use read_vector() on complex type"); + static_assert(IS_TRIVIALLY_COPYABLE(T), "Cannot use read_vector() on complex type"); begin_reading(); size_t vector_length = 0; if (has_remaining(sizeof(size_t))) { From d0db47ace22dfc73ae1da50c78f7c563d401f105 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 21 Jul 2023 11:22:30 -0400 Subject: [PATCH 041/162] Refine compiler selection to address overlap between Clang and GCC macros 1. Clang defines __GNUC__ 2. Older Clang versions do not support std::trivially_copyable yet, but the most recent ones deprecate __has_trivial_copy --- src/colvars_memstream.h | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index 7da6bbad5..25859b1f6 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -8,14 +8,17 @@ #include #include -// Work around missing std::is_trivially_copyable in old GCC versions + +// Work around missing std::is_trivially_copyable in old GCC and Clang versions // TODO remove this after CentOS 7 has been beyond EOL for a while -#if __GNUG__ && (__GNUC__ < 5) +#if (defined(__GNUC__) && (__GNUC__ < 5) && !defined(__clang__)) || (defined(__clang__) && (__clang_major__ < 7)) +// Clang needs an exception, because it defines __GNUC__ as well #define IS_TRIVIALLY_COPYABLE(T) __has_trivial_copy(T) #else #define IS_TRIVIALLY_COPYABLE(T) std::is_trivially_copyable::value #endif + class cvm::memory_stream { public: From bd37e812c6206bc7b8463da340164267a057034f Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sun, 25 Jun 2023 18:34:15 -0400 Subject: [PATCH 042/162] MSVC fixes --- cmake/CMakeLists.txt | 2 +- src/colvars_memstream.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index d3e87459c..2c548ea6a 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -142,7 +142,7 @@ if(COLVARS_DEBUG) endif() option(ENABLE_COVERAGE "Enable code coverage reporting" ON) -if(ENABLE_COVERAGE AND (NOT CMAKE_CXX_COMPILER_ID STREQUAL "SunPro")) +if(ENABLE_COVERAGE AND (NOT CMAKE_CXX_COMPILER_ID STREQUAL "SunPro") AND (NOT CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")) target_compile_options(colvars PUBLIC --coverage) target_link_options(colvars PUBLIC --coverage) endif() diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index 25859b1f6..80e31a020 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -25,7 +25,7 @@ class cvm::memory_stream { /// Set up an empty stream with an internal buffer, suitable for writing to /// \param max_length Maximum allowed capacity (default is 64 GiB) - memory_stream(size_t max_length = (1L << 36)) : max_length_(max_length) {} + memory_stream(size_t max_length = (static_cast(1L) << 36)) : max_length_(max_length) {} /// Set up a stream based on an external input buffer memory_stream(size_t n, unsigned char const *buf) From d00da58f84312c0d3e4f854323c6feafd88cbd27 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 19 Jul 2023 16:12:57 -0400 Subject: [PATCH 043/162] Add template specializations to ignore formatting operators --- src/colvars_memstream.h | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index 80e31a020..f90214a76 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -7,6 +7,7 @@ #include #include #include +#include // Work around missing std::is_trivially_copyable in old GCC and Clang versions @@ -82,6 +83,9 @@ class cvm::memory_stream { /// Wrapper to read_vector() template friend memory_stream &operator>>(memory_stream &is, std::vector &t); + /// No-op function to ignore formatting operators + inline void setf(decltype(std::ios::fmtflags(0)), decltype(std::ios::floatfield)) {} + protected: /// External output buffer @@ -286,4 +290,16 @@ template cvm::memory_stream &operator>>(cvm::memory_stream &is, std return is; } +template cvm::memory_stream &operator<<(cvm::memory_stream &os, + decltype(std::setprecision(10)) const &) +{ + return os; +} + +template cvm::memory_stream &operator<<(cvm::memory_stream &os, + decltype(std::setw(10)) const &) +{ + return os; +} + #endif From f0b2376b0e7124b450a6be37c3ffaea625ed8f52 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 19 Jul 2023 16:41:03 -0400 Subject: [PATCH 044/162] Do not specify the starting point if not needed --- src/colvar.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/colvar.cpp b/src/colvar.cpp index efa7242e2..01dfd4891 100644 --- a/src/colvar.cpp +++ b/src/colvar.cpp @@ -2281,7 +2281,7 @@ std::istream & colvar::read_state(std::istream &is) if ( !(is >> colvarparse::read_block("colvar", &conf)) ) { // this is not a colvar block is.clear(); - is.seekg(start_pos, std::ios::beg); + is.seekg(start_pos); is.setstate(std::ios::failbit); return is; } @@ -2294,7 +2294,7 @@ std::istream & colvar::read_state(std::istream &is) cvm::error("Error: Collective variable in the " "restart file without any identifier.\n", COLVARS_INPUT_ERROR); is.clear(); - is.seekg(start_pos, std::ios::beg); + is.seekg(start_pos); is.setstate(std::ios::failbit); return is; } @@ -2304,7 +2304,7 @@ std::istream & colvar::read_state(std::istream &is) cvm::log("Ignoring state of colvar \""+check_name+ "\": this colvar is named \""+name+"\".\n"); } - is.seekg(start_pos, std::ios::beg); + is.seekg(start_pos); return is; } } @@ -2364,7 +2364,7 @@ std::istream & colvar::read_traj(std::istream &is) cvm::log("Error: in reading the value of colvar \""+ this->name+"\" from trajectory.\n"); is.clear(); - is.seekg(start_pos, std::ios::beg); + is.seekg(start_pos); is.setstate(std::ios::failbit); return is; } From 541c2a0b0e58ac2d5907a13f9d8d8389d0550e6d Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 19 Jul 2023 17:24:49 -0400 Subject: [PATCH 045/162] Move specializations to source file --- lammps/lib/colvars/Makefile.common | 1 + lammps/lib/colvars/Makefile.deps | 294 ++++++++++++++++------------- namd/colvars/Make.depends | 70 ++++--- namd/colvars/src/Makefile.namd | 1 + src/colvars_memstream.cpp | 104 ++++++++++ src/colvars_memstream.h | 119 ++++-------- vmd/src/colvars_files.pl | 1 + 7 files changed, 351 insertions(+), 239 deletions(-) create mode 100644 src/colvars_memstream.cpp diff --git a/lammps/lib/colvars/Makefile.common b/lammps/lib/colvars/Makefile.common index 9e7be1295..e645d8457 100644 --- a/lammps/lib/colvars/Makefile.common +++ b/lammps/lib/colvars/Makefile.common @@ -59,6 +59,7 @@ COLVARS_SRCS = \ colvarscript_commands.cpp \ colvarscript_commands_bias.cpp \ colvarscript_commands_colvar.cpp \ + colvars_memstream.cpp \ colvartypes.cpp \ colvarvalue.cpp \ colvar_neuralnetworkcompute.cpp diff --git a/lammps/lib/colvars/Makefile.deps b/lammps/lib/colvars/Makefile.deps index 3ed21bba8..dee9cbca6 100644 --- a/lammps/lib/colvars/Makefile.deps +++ b/lammps/lib/colvars/Makefile.deps @@ -1,201 +1,231 @@ -$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \ +$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvardeps.h \ + colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \ + colvartypes.h ../../src/math_eigen_impl.h colvarparams.h colvarproxy.h \ colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvarparse.h colvarparams.h colvaratoms.h \ - colvardeps.h colvar_rotation_derivative.h + colvarproxy_volmaps.h colvaratoms.h colvar_rotation_derivative.h $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \ - colvars_version.h colvar.h colvarvalue.h colvartypes.h colvarparse.h \ - colvarparams.h colvardeps.h colvarbias_abf.h colvarproxy.h \ - colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvarbias.h colvargrid.h colvar_UIestimator.h + colvars_version.h colvar.h colvarvalue.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvardeps.h \ + colvarbias_abf.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \ + colvarproxy_tcl.h colvarproxy_volmaps.h colvarbias.h colvargrid.h \ + colvar_UIestimator.h $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \ - colvars_version.h colvarbias.h colvar.h colvarvalue.h colvartypes.h \ - colvarparse.h colvarparams.h colvardeps.h colvarbias_alb.h + colvars_version.h colvarproxy.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarvalue.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvarbias.h colvar.h colvarparse.h colvarparams.h colvardeps.h \ + colvarbias_alb.h $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \ - colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvarbias.h colvar.h colvarparse.h colvarparams.h \ - colvardeps.h colvargrid.h + colvars_version.h colvarproxy.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarvalue.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvarbias.h colvar.h colvarparse.h colvarparams.h colvardeps.h \ + colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \ colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \ - colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvar.h colvarparse.h colvarparams.h colvardeps.h \ - colvarbias_histogram.h colvarbias.h colvargrid.h + ../../src/math_eigen_impl.h colvarvalue.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h \ + colvarparse.h colvarparams.h colvardeps.h colvarbias_histogram.h \ + colvarbias.h colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_histogram_reweight_amd.o: \ colvarbias_histogram_reweight_amd.cpp \ colvarbias_histogram_reweight_amd.h colvarbias_histogram.h colvarbias.h \ colvar.h colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \ - colvarparse.h colvarparams.h colvardeps.h colvargrid.h colvarproxy.h \ - colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvardeps.h \ + colvargrid.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \ + colvarproxy_tcl.h colvarproxy_volmaps.h $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \ - colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvar.h colvarparse.h colvarparams.h colvardeps.h \ - colvarbias_meta.h colvarbias.h colvargrid.h + colvars_version.h colvarproxy.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarvalue.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h \ + colvarparse.h colvarparams.h colvardeps.h colvarbias_meta.h colvarbias.h \ + colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \ colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \ - colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvarbias_restraint.h colvarbias.h colvar.h \ - colvarparse.h colvarparams.h colvardeps.h + ../../src/math_eigen_impl.h colvarvalue.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \ + colvarparams.h colvardeps.h $(COLVARS_OBJ_DIR)colvarcomp_alchlambda.o: colvarcomp_alchlambda.cpp \ colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \ - colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \ - colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \ - colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \ - colvar_geometricpath.h + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvar.h \ + colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvar_arithmeticpath.h colvar_geometricpath.h $(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \ colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \ - colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \ - colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvardeps.h \ + colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvar_arithmeticpath.h colvar_geometricpath.h $(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp colvarmodule.h \ - colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \ - colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \ - colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h + colvars_version.h colvarvalue.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvar.h \ + colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvar_arithmeticpath.h colvar_geometricpath.h $(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \ colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \ - colvartypes.h colvarparams.h colvaratoms.h colvarproxy.h \ - colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ + colvartypes.h ../../src/math_eigen_impl.h colvarparams.h colvaratoms.h \ + colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ colvarproxy_volmaps.h colvardeps.h colvar.h colvarcomp.h \ colvar_arithmeticpath.h colvar_geometricpath.h $(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \ - colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \ - colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \ - colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h + colvars_version.h colvarvalue.h colvartypes.h \ + ../../src/math_eigen_impl.h colvar.h colvarparse.h colvarparams.h \ + colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvar_arithmeticpath.h colvar_geometricpath.h $(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \ colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \ - colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \ - colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \ - colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \ - colvar_geometricpath.h colvar_rotation_derivative.h -$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp colvarmodule.h \ - colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \ - colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \ - colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h -$(COLVARS_OBJ_DIR)colvarcomp_neuralnetwork.o: \ - colvarcomp_neuralnetwork.cpp colvarmodule.h colvars_version.h \ - colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \ + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvar.h \ colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \ colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ colvar_arithmeticpath.h colvar_geometricpath.h \ + colvar_rotation_derivative.h +$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp colvarmodule.h \ + colvars_version.h colvarvalue.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvar.h \ + colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvar_arithmeticpath.h colvar_geometricpath.h +$(COLVARS_OBJ_DIR)colvarcomp_neuralnetwork.o: \ + colvarcomp_neuralnetwork.cpp colvarmodule.h colvars_version.h \ + colvarvalue.h colvartypes.h ../../src/math_eigen_impl.h colvarparse.h \ + colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \ + colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ + colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h \ colvar_neuralnetworkcompute.h $(COLVARS_OBJ_DIR)colvarcomp_combination.o: colvarcomp_combination.cpp \ - colvarcomp.h colvarmodule.h colvars_version.h colvar.h colvarvalue.h \ - colvartypes.h colvarparse.h colvarparams.h colvardeps.h colvaratoms.h \ - colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h + colvarcomp.h colvarmodule.h colvars_version.h colvaratoms.h \ + colvarproxy.h colvartypes.h ../../src/math_eigen_impl.h colvarvalue.h \ + colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ + colvarproxy_volmaps.h colvarparse.h colvarparams.h colvardeps.h colvar.h \ + colvar_arithmeticpath.h colvar_geometricpath.h $(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \ colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \ - colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \ - colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \ - colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \ - colvar_geometricpath.h + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvar.h \ + colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvar_arithmeticpath.h colvar_geometricpath.h $(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \ colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \ - colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \ - colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \ - colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \ - colvar_geometricpath.h colvar_rotation_derivative.h + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvar.h \ + colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvar_arithmeticpath.h colvar_geometricpath.h \ + colvar_rotation_derivative.h $(COLVARS_OBJ_DIR)colvarcomp_volmaps.o: colvarcomp_volmaps.cpp \ colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \ - colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \ - colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \ - colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \ - colvar_geometricpath.h -$(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \ - colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \ + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvar.h \ colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \ colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ - colvar_arithmeticpath.h colvar_geometricpath.h colvarscript.h \ - colvarbias.h colvarscript_commands.h colvarscript_commands_colvar.h \ - colvarscript_commands_bias.h + colvar_arithmeticpath.h colvar_geometricpath.h +$(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \ + colvarvalue.h colvartypes.h ../../src/math_eigen_impl.h colvarparse.h \ + colvarparams.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvardeps.h colvar.h colvar_arithmeticpath.h colvar_geometricpath.h \ + colvarscript.h colvarbias.h colvarscript_commands.h \ + colvarscript_commands_colvar.h colvarscript_commands_bias.h \ + colvars_memstream.h $(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \ - colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h + colvars_version.h colvarproxy.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarvalue.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvardeps.h colvarparse.h colvarparams.h $(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \ - colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \ - colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \ - colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h \ - colvargrid.h colvargrid_def.h + colvars_version.h colvarvalue.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h colvar.h \ + colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvar_arithmeticpath.h colvar_geometricpath.h colvargrid.h \ + colvargrid_def.h $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \ colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \ - colvarparams.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \ - colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvardeps.h \ - colvarbias.h colvarbias_abf.h colvargrid.h colvar_UIestimator.h \ - colvarbias_alb.h colvarbias_histogram.h \ - colvarbias_histogram_reweight_amd.h colvarbias_meta.h \ - colvarbias_restraint.h colvarscript.h colvarscript_commands.h \ - colvarscript_commands_colvar.h colvarscript_commands_bias.h \ - colvaratoms.h colvarcomp.h colvar_arithmeticpath.h \ - colvar_geometricpath.h colvarmodule_refs.h + ../../src/math_eigen_impl.h colvarparams.h colvarproxy.h \ + colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ + colvarproxy_volmaps.h colvar.h colvardeps.h colvarbias.h \ + colvarbias_abf.h colvargrid.h colvar_UIestimator.h colvarbias_alb.h \ + colvarbias_histogram.h colvarbias_histogram_reweight_amd.h \ + colvarbias_meta.h colvarbias_restraint.h colvarscript.h \ + colvarscript_commands.h colvarscript_commands_colvar.h \ + colvarscript_commands_bias.h colvaratoms.h colvarcomp.h \ + colvar_arithmeticpath.h colvar_geometricpath.h colvarmodule_refs.h $(COLVARS_OBJ_DIR)colvarparams.o: colvarparams.cpp colvarmodule.h \ - colvars_version.h colvarvalue.h colvartypes.h colvarparams.h + colvars_version.h colvarvalue.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarparams.h $(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \ - colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \ - colvarparams.h + colvars_version.h colvarvalue.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarparse.h colvarparams.h \ + colvars_memstream.h $(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \ - colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvarscript.h colvarbias.h colvar.h colvarparse.h \ - colvarparams.h colvardeps.h colvarscript_commands.h \ - colvarscript_commands_colvar.h colvarscript_commands_bias.h \ - colvaratoms.h colvarmodule_utils.h + colvars_version.h colvarproxy.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarvalue.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvarscript.h colvarbias.h colvar.h colvarparse.h colvarparams.h \ + colvardeps.h colvarscript_commands.h colvarscript_commands_colvar.h \ + colvarscript_commands_bias.h colvaratoms.h colvarmodule_utils.h $(COLVARS_OBJ_DIR)colvarproxy_io.o: colvarproxy_io.cpp colvarmodule.h \ colvars_version.h colvarproxy_io.h $(COLVARS_OBJ_DIR)colvarproxy_replicas.o: colvarproxy_replicas.cpp \ colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \ - colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h + ../../src/math_eigen_impl.h colvarvalue.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h $(COLVARS_OBJ_DIR)colvarproxy_system.o: colvarproxy_system.cpp \ - colvarmodule.h colvars_version.h colvartypes.h colvarproxy_system.h + colvarmodule.h colvars_version.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarproxy_system.h $(COLVARS_OBJ_DIR)colvarproxy_tcl.o: colvarproxy_tcl.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \ - colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvaratoms.h colvarparse.h colvarparams.h \ - colvardeps.h + colvars_version.h colvarproxy.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarvalue.h colvarproxy_io.h \ + colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ + colvaratoms.h colvarparse.h colvarparams.h colvardeps.h $(COLVARS_OBJ_DIR)colvarproxy_volmaps.o: colvarproxy_volmaps.cpp \ colvarmodule.h colvars_version.h colvarproxy_volmaps.h \ colvarmodule_utils.h $(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarproxy.h \ - colvarmodule.h colvars_version.h colvartypes.h colvarvalue.h \ - colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \ - colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \ - colvarscript_commands_colvar.h colvarscript_commands_bias.h -$(COLVARS_OBJ_DIR)colvarscript_commands.o: colvarscript_commands.cpp \ - colvarproxy.h colvarmodule.h colvars_version.h colvartypes.h \ - colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ - colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \ - colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \ - colvarscript_commands_colvar.h colvarscript_commands_bias.h -$(COLVARS_OBJ_DIR)colvarscript_commands_bias.o: \ - colvarscript_commands_bias.cpp colvarproxy.h colvarmodule.h \ - colvars_version.h colvartypes.h colvarvalue.h colvarproxy_io.h \ + colvarmodule.h colvars_version.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarvalue.h colvarproxy_io.h \ colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ colvardeps.h colvarparse.h colvarparams.h colvarscript.h colvarbias.h \ colvar.h colvarscript_commands.h colvarscript_commands_colvar.h \ colvarscript_commands_bias.h -$(COLVARS_OBJ_DIR)colvarscript_commands_colvar.o: \ - colvarscript_commands_colvar.cpp colvarproxy.h colvarmodule.h \ - colvars_version.h colvartypes.h colvarvalue.h colvarproxy_io.h \ +$(COLVARS_OBJ_DIR)colvarscript_commands.o: colvarscript_commands.cpp \ + colvarproxy.h colvarmodule.h colvars_version.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarvalue.h colvarproxy_io.h \ colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \ colvardeps.h colvarparse.h colvarparams.h colvarscript.h colvarbias.h \ colvar.h colvarscript_commands.h colvarscript_commands_colvar.h \ colvarscript_commands_bias.h +$(COLVARS_OBJ_DIR)colvarscript_commands_bias.o: \ + colvarscript_commands_bias.cpp colvarproxy.h colvarmodule.h \ + colvars_version.h colvartypes.h ../../src/math_eigen_impl.h \ + colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ + colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \ + colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \ + colvarscript_commands_colvar.h colvarscript_commands_bias.h +$(COLVARS_OBJ_DIR)colvarscript_commands_colvar.o: \ + colvarscript_commands_colvar.cpp colvarproxy.h colvarmodule.h \ + colvars_version.h colvartypes.h ../../src/math_eigen_impl.h \ + colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ + colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \ + colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \ + colvarscript_commands_colvar.h colvarscript_commands_bias.h +$(COLVARS_OBJ_DIR)colvars_memstream.o: colvars_memstream.cpp \ + colvarmodule.h colvars_version.h colvartypes.h \ + ../../src/math_eigen_impl.h colvarvalue.h colvars_memstream.h $(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarparse.h colvarvalue.h \ - colvarparams.h colvar_rotation_derivative.h ../../src/math_eigen_impl.h + colvars_version.h colvartypes.h ../../src/math_eigen_impl.h \ + colvarparse.h colvarvalue.h colvarparams.h colvaratoms.h colvarproxy.h \ + colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ + colvarproxy_volmaps.h colvardeps.h colvar_rotation_derivative.h $(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \ - colvars_version.h colvarvalue.h colvartypes.h + colvars_version.h colvarvalue.h colvartypes.h \ + ../../src/math_eigen_impl.h colvars_memstream.h $(COLVARS_OBJ_DIR)colvar_neuralnetworkcompute.o: \ colvar_neuralnetworkcompute.cpp colvar_neuralnetworkcompute.h \ colvarparse.h colvarmodule.h colvars_version.h colvarvalue.h \ - colvartypes.h colvarparams.h colvarproxy.h colvarproxy_io.h \ - colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h + colvartypes.h ../../src/math_eigen_impl.h colvarparams.h colvarproxy.h \ + colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \ + colvarproxy_volmaps.h diff --git a/namd/colvars/Make.depends b/namd/colvars/Make.depends index 54b99dc92..af0333e7b 100644 --- a/namd/colvars/Make.depends +++ b/namd/colvars/Make.depends @@ -7,8 +7,6 @@ obj/colvar.o: \ colvars/src/colvartypes.h \ colvars/src/colvarparse.h \ colvars/src/colvarparams.h \ - colvars/src/colvar.h \ - colvars/src/colvardeps.h \ colvars/src/colvarcomp.h \ colvars/src/colvaratoms.h \ colvars/src/colvarproxy.h \ @@ -16,31 +14,34 @@ obj/colvar.o: \ colvars/src/colvarproxy_system.h \ colvars/src/colvarproxy_tcl.h \ colvars/src/colvarproxy_volmaps.h \ + colvars/src/colvardeps.h \ + colvars/src/colvar.h \ colvars/src/colvar_arithmeticpath.h \ colvars/src/colvar_geometricpath.h \ colvars/src/colvarscript.h \ colvars/src/colvarbias.h \ colvars/src/colvarscript_commands.h \ colvars/src/colvarscript_commands_colvar.h \ - colvars/src/colvarscript_commands_bias.h + colvars/src/colvarscript_commands_bias.h \ + colvars/src/colvars_memstream.h $(CXX) $(COLVARSCXXFLAGS) $(COPTO)obj/colvar.o $(COPTC) colvars/src/colvar.cpp obj/colvaratoms.o: \ obj/.exists \ colvars/src/colvaratoms.cpp \ + colvars/src/colvardeps.h \ colvars/src/colvarmodule.h \ colvars/src/colvars_version.h \ - colvars/src/colvarproxy.h \ - colvars/src/colvartypes.h \ + colvars/src/colvarparse.h \ colvars/src/colvarvalue.h \ + colvars/src/colvartypes.h \ + colvars/src/colvarparams.h \ + colvars/src/colvarproxy.h \ colvars/src/colvarproxy_io.h \ colvars/src/colvarproxy_system.h \ colvars/src/colvarproxy_tcl.h \ colvars/src/colvarproxy_volmaps.h \ - colvars/src/colvarparse.h \ - colvars/src/colvarparams.h \ colvars/src/colvaratoms.h \ - colvars/src/colvardeps.h \ - colvars/src/colvar_rotation_derivative.h + colvars/src/colvar_rotation_derivative.h $(CXX) $(COLVARSCXXFLAGS) $(COPTO)obj/colvaratoms.o $(COPTC) colvars/src/colvaratoms.cpp obj/colvarbias.o: \ obj/.exists \ @@ -87,10 +88,15 @@ obj/colvarbias_alb.o: \ colvars/src/colvarbias_alb.cpp \ colvars/src/colvarmodule.h \ colvars/src/colvars_version.h \ + colvars/src/colvarproxy.h \ + colvars/src/colvartypes.h \ + colvars/src/colvarvalue.h \ + colvars/src/colvarproxy_io.h \ + colvars/src/colvarproxy_system.h \ + colvars/src/colvarproxy_tcl.h \ + colvars/src/colvarproxy_volmaps.h \ colvars/src/colvarbias.h \ colvars/src/colvar.h \ - colvars/src/colvarvalue.h \ - colvars/src/colvartypes.h \ colvars/src/colvarparse.h \ colvars/src/colvarparams.h \ colvars/src/colvardeps.h \ @@ -301,7 +307,7 @@ obj/colvarcomp_distances.o: \ colvars/src/colvarproxy_volmaps.h \ colvars/src/colvar_arithmeticpath.h \ colvars/src/colvar_geometricpath.h \ - colvars/src/colvar_rotation_derivative.h + colvars/src/colvar_rotation_derivative.h $(CXX) $(COLVARSCXXFLAGS) $(COPTO)obj/colvarcomp_distances.o $(COPTC) colvars/src/colvarcomp_distances.cpp obj/colvarcomp_gpath.o: \ obj/.exists \ @@ -365,7 +371,7 @@ obj/colvarcomp_rotations.o: \ colvars/src/colvarproxy_volmaps.h \ colvars/src/colvar_arithmeticpath.h \ colvars/src/colvar_geometricpath.h \ - colvars/src/colvar_rotation_derivative.h + colvars/src/colvar_rotation_derivative.h $(CXX) $(COLVARSCXXFLAGS) $(COPTO)obj/colvarcomp_rotations.o $(COPTC) colvars/src/colvarcomp_rotations.cpp obj/colvarcomp_volmaps.o: \ obj/.exists \ @@ -394,18 +400,18 @@ obj/colvarcomp_combination.o: \ colvars/src/colvarcomp.h \ colvars/src/colvarmodule.h \ colvars/src/colvars_version.h \ - colvars/src/colvar.h \ - colvars/src/colvarvalue.h \ - colvars/src/colvartypes.h \ - colvars/src/colvarparse.h \ - colvars/src/colvarparams.h \ - colvars/src/colvardeps.h \ colvars/src/colvaratoms.h \ colvars/src/colvarproxy.h \ + colvars/src/colvartypes.h \ + colvars/src/colvarvalue.h \ colvars/src/colvarproxy_io.h \ colvars/src/colvarproxy_system.h \ colvars/src/colvarproxy_tcl.h \ colvars/src/colvarproxy_volmaps.h \ + colvars/src/colvarparse.h \ + colvars/src/colvarparams.h \ + colvars/src/colvardeps.h \ + colvars/src/colvar.h \ colvars/src/colvar_arithmeticpath.h \ colvars/src/colvar_geometricpath.h $(CXX) $(COLVARSCXXFLAGS) $(COPTO)obj/colvarcomp_combination.o $(COPTC) colvars/src/colvarcomp_combination.cpp @@ -538,7 +544,8 @@ obj/colvarparse.o: \ colvars/src/colvarvalue.h \ colvars/src/colvartypes.h \ colvars/src/colvarparse.h \ - colvars/src/colvarparams.h + colvars/src/colvarparams.h \ + colvars/src/colvars_memstream.h $(CXX) $(COLVARSCXXFLAGS) $(COPTO)obj/colvarparse.o $(COPTC) colvars/src/colvarparse.cpp obj/colvarproxy.o: \ obj/.exists \ @@ -705,6 +712,15 @@ obj/colvarscript_commands_colvar.o: \ colvars/src/colvarscript_commands_colvar.h \ colvars/src/colvarscript_commands_bias.h $(CXX) $(COLVARSCXXFLAGS) $(COPTO)obj/colvarscript_commands_colvar.o $(COPTC) colvars/src/colvarscript_commands_colvar.cpp +obj/colvars_memstream.o: \ + obj/.exists \ + colvars/src/colvars_memstream.cpp \ + colvars/src/colvarmodule.h \ + colvars/src/colvars_version.h \ + colvars/src/colvartypes.h \ + colvars/src/colvarvalue.h \ + colvars/src/colvars_memstream.h + $(CXX) $(COLVARSCXXFLAGS) $(COPTO)obj/colvars_memstream.o $(COPTC) colvars/src/colvars_memstream.cpp obj/colvartypes.o: \ obj/.exists \ colvars/src/colvartypes.cpp \ @@ -714,8 +730,15 @@ obj/colvartypes.o: \ colvars/src/colvarparse.h \ colvars/src/colvarvalue.h \ colvars/src/colvarparams.h \ - colvars/src/nr_jacobi.h \ - colvars/src/colvar_rotation_derivative.h + colvars/src/colvaratoms.h \ + colvars/src/colvarproxy.h \ + colvars/src/colvarproxy_io.h \ + colvars/src/colvarproxy_system.h \ + colvars/src/colvarproxy_tcl.h \ + colvars/src/colvarproxy_volmaps.h \ + colvars/src/colvardeps.h \ + colvars/src/colvar_rotation_derivative.h \ + colvars/src/nr_jacobi.h $(CXX) $(COLVARSCXXFLAGS) $(COPTO)obj/colvartypes.o $(COPTC) colvars/src/colvartypes.cpp obj/colvarvalue.o: \ obj/.exists \ @@ -723,7 +746,8 @@ obj/colvarvalue.o: \ colvars/src/colvarmodule.h \ colvars/src/colvars_version.h \ colvars/src/colvarvalue.h \ - colvars/src/colvartypes.h + colvars/src/colvartypes.h \ + colvars/src/colvars_memstream.h $(CXX) $(COLVARSCXXFLAGS) $(COPTO)obj/colvarvalue.o $(COPTC) colvars/src/colvarvalue.cpp obj/nr_jacobi.o: \ obj/.exists \ diff --git a/namd/colvars/src/Makefile.namd b/namd/colvars/src/Makefile.namd index 93a993c7e..636f29681 100644 --- a/namd/colvars/src/Makefile.namd +++ b/namd/colvars/src/Makefile.namd @@ -36,6 +36,7 @@ COLVARSLIB = \ $(DSTDIR)/colvarscript_commands.o \ $(DSTDIR)/colvarscript_commands_bias.o \ $(DSTDIR)/colvarscript_commands_colvar.o \ + $(DSTDIR)/colvars_memstream.o \ $(DSTDIR)/colvartypes.o \ $(DSTDIR)/colvarvalue.o \ $(DSTDIR)/nr_jacobi.o diff --git a/src/colvars_memstream.cpp b/src/colvars_memstream.cpp new file mode 100644 index 000000000..b6544e945 --- /dev/null +++ b/src/colvars_memstream.cpp @@ -0,0 +1,104 @@ +// -*- c++ -*- + +// This file is part of the Collective Variables module (Colvars). +// The original version of Colvars and its updates are located at: +// https://github.com/Colvars/colvars +// Please update all Colvars source files before making any changes. +// If you wish to distribute your changes, please submit them to the +// Colvars repository at GitHub. + + +#include "colvarmodule.h" +#include "colvartypes.h" +#include "colvarvalue.h" +#include "colvars_memstream.h" + + +bool cvm::memory_stream::expand_ouput_buffer(size_t add_bytes) +{ + if (external_output_buffer_) { + // Cannot resize an external buffer + setstate(std::ios::badbit); + } else { + if ((internal_buffer_.size() + add_bytes) <= max_length_) { + internal_buffer_.resize((internal_buffer_.size() + add_bytes)); + } else { + setstate(std::ios::badbit); + } + } + return bool(*this); +} + + +template <> void cvm::memory_stream::write_object(std::string const &t) +{ + size_t const string_length = t.size(); + size_t const new_data_size = sizeof(size_t) + sizeof(char) * string_length; + if (expand_ouput_buffer(new_data_size)) { + std::memcpy(output_location(), &string_length, sizeof(size_t)); + incr_write_pos(sizeof(size_t)); + std::memcpy(output_location(), t.c_str(), t.size() * sizeof(char)); + incr_write_pos(t.size() * sizeof(char)); + } +} + +template <> cvm::memory_stream &operator<<(cvm::memory_stream &os, std::string const &t) +{ + os.write_object(t); + return os; +} + +template <> void cvm::memory_stream::write_object(colvarvalue const &t) +{ + *this << t; +} + +template <> void cvm::memory_stream::write_object(cvm::vector1d const &t) +{ + return write_vector(t.data_array()); +} + +template <> +cvm::memory_stream &operator<<(cvm::memory_stream &os, cvm::vector1d const &t) +{ + os.write_vector(t.data_array()); + return os; +} + + +template <> void cvm::memory_stream::read_object(std::string &t) +{ + begin_reading(); + size_t string_length = 0; + if (has_remaining(sizeof(size_t))) { + std::memcpy(&string_length, input_location(), sizeof(size_t)); + incr_read_pos(sizeof(size_t)); + if (has_remaining(string_length * sizeof(char))) { + t.assign(reinterpret_cast(input_location()), string_length); + incr_read_pos(string_length * sizeof(char)); + done_reading(); + } + } +} + +template <> cvm::memory_stream &operator>>(cvm::memory_stream &is, std::string &t) +{ + is.read_object(t); + return is; +} + +template <> void cvm::memory_stream::read_object(colvarvalue &t) +{ + *this >> t; +} + +template <> void cvm::memory_stream::read_object(cvm::vector1d &t) +{ + return read_vector(t.data_array()); +} + +template <> cvm::memory_stream &operator>>(cvm::memory_stream &is, cvm::vector1d &t) +{ + is.read_vector(t.data_array()); + return is; +} diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index f90214a76..88048e2a2 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -1,5 +1,12 @@ // -*- c++ -*- +// This file is part of the Collective Variables module (Colvars). +// The original version of Colvars and its updates are located at: +// https://github.com/Colvars/colvars +// Please update all Colvars source files before making any changes. +// If you wish to distribute your changes, please submit them to the +// Colvars repository at GitHub. + #ifndef MEMORY_STREAM_H #define MEMORY_STREAM_H @@ -107,20 +114,7 @@ class cvm::memory_stream { int error_code_ = 0; /// Add the requester number of bytes to the array capacity; return false if buffer is external - inline bool expand_ouput_buffer(size_t add_bytes) - { - if (external_output_buffer_) { - // Cannot resize an external buffer - error_code_ = 1; - } else { - if ((internal_buffer_.size() + add_bytes) <= max_length_) { - internal_buffer_.resize((internal_buffer_.size() + add_bytes)); - } else { - error_code_ = 1; - } - } - return (error_code_ == 0); - } + bool expand_ouput_buffer(size_t add_bytes); /// Move the buffer position past the data just written inline void incr_write_pos(size_t c) { data_length_ += c; } @@ -160,44 +154,6 @@ template cvm::memory_stream &operator<<(cvm::memory_stream &os, T c return os; } -template <> void cvm::memory_stream::write_object(std::string const &t) -{ - size_t const string_length = t.size(); - size_t const new_data_size = sizeof(size_t) + sizeof(char) * string_length; - if (expand_ouput_buffer(new_data_size)) { - std::memcpy(output_location(), &string_length, sizeof(size_t)); - incr_write_pos(sizeof(size_t)); - std::memcpy(output_location(), t.c_str(), t.size() * sizeof(char)); - incr_write_pos(t.size() * sizeof(char)); - } -} - -template <> cvm::memory_stream &operator<<(cvm::memory_stream &os, std::string const &t) -{ - os.write_object(t); - return os; -} - -template <> void cvm::memory_stream::write_object(cvm::vector1d const &t) -{ - return write_vector(t.data_array()); -} - -template <> -cvm::memory_stream &operator<<(cvm::memory_stream &os, cvm::vector1d const &t) -{ - os.write_vector(t.data_array()); - return os; -} - -template <> void cvm::memory_stream::write_object(colvarvalue const &t) {} - -template <> cvm::memory_stream &operator<<(cvm::memory_stream &os, colvarvalue const &t) -{ - os.write_object(t); - return os; -} - template void cvm::memory_stream::write_vector(std::vector const &t) { static_assert(IS_TRIVIALLY_COPYABLE(T), "Cannot use write_vector() on complex type"); @@ -235,38 +191,6 @@ template cvm::memory_stream &operator>>(cvm::memory_stream &is, T & return is; } -template <> void cvm::memory_stream::read_object(std::string &t) -{ - begin_reading(); - size_t string_length = 0; - if (has_remaining(sizeof(size_t))) { - std::memcpy(&string_length, input_location(), sizeof(size_t)); - incr_read_pos(sizeof(size_t)); - if (has_remaining(string_length * sizeof(char))) { - t.assign(reinterpret_cast(input_location()), string_length); - incr_read_pos(string_length * sizeof(char)); - done_reading(); - } - } -} - -template <> cvm::memory_stream &operator>>(cvm::memory_stream &is, std::string &t) -{ - is.read_object(t); - return is; -} - -template <> void cvm::memory_stream::read_object(cvm::vector1d &t) -{ - return read_vector(t.data_array()); -} - -template <> cvm::memory_stream &operator>>(cvm::memory_stream &is, cvm::vector1d &t) -{ - is.read_vector(t.data_array()); - return is; -} - template void cvm::memory_stream::read_vector(std::vector &t) { static_assert(IS_TRIVIALLY_COPYABLE(T), "Cannot use read_vector() on complex type"); @@ -302,4 +226,31 @@ template cvm::memory_stream &operator<<(cvm::memory_stream &os, return os; } +// Declare specializations + +template <> void cvm::memory_stream::write_object(std::string const &t); + +template <> cvm::memory_stream &operator<<(cvm::memory_stream &os, std::string const &t); + +template <> void cvm::memory_stream::write_object(colvarvalue const &t); + +template <> cvm::memory_stream &operator<<(cvm::memory_stream &os, colvarvalue const &x); + +template <> void cvm::memory_stream::write_object(cvm::vector1d const &t); + +template <> +cvm::memory_stream &operator<<(cvm::memory_stream &os, cvm::vector1d const &t); + +template <> void cvm::memory_stream::read_object(std::string &t); + +template <> cvm::memory_stream &operator>>(cvm::memory_stream &is, std::string &t); + +template <> void cvm::memory_stream::read_object(colvarvalue &t); + +template <> cvm::memory_stream &operator>>(cvm::memory_stream &is, colvarvalue &t); + +template <> void cvm::memory_stream::read_object(cvm::vector1d &t); + +template <> cvm::memory_stream &operator>>(cvm::memory_stream &is, cvm::vector1d &t); + #endif diff --git a/vmd/src/colvars_files.pl b/vmd/src/colvars_files.pl index 3575b99ab..b6bfdbf2a 100644 --- a/vmd/src/colvars_files.pl +++ b/vmd/src/colvars_files.pl @@ -49,6 +49,7 @@ 'colvarscript_commands.C', 'colvarscript_commands_bias.C', 'colvarscript_commands_colvar.C', + 'colvars_memstream.C', 'colvartypes.C', 'colvarvalue.C', 'nr_jacobi.C'); From 8190e6f83cf71f4bdb83fc71de4b267973a74349 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 19 Jul 2023 17:25:25 -0400 Subject: [PATCH 046/162] Make memory_stream compatible with STL streams in templates --- src/colvars_memstream.cpp | 2 ++ src/colvars_memstream.h | 35 ++++++++++++++++++++++++++--------- 2 files changed, 28 insertions(+), 9 deletions(-) diff --git a/src/colvars_memstream.cpp b/src/colvars_memstream.cpp index b6544e945..2243dc96a 100644 --- a/src/colvars_memstream.cpp +++ b/src/colvars_memstream.cpp @@ -77,6 +77,8 @@ template <> void cvm::memory_stream::read_object(std::string &t) t.assign(reinterpret_cast(input_location()), string_length); incr_read_pos(string_length * sizeof(char)); done_reading(); + } else { + setstate(std::ios::failbit); } } } diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index 88048e2a2..482bf1ed6 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -63,7 +63,7 @@ class cvm::memory_stream { inline unsigned char const *input_location() const { return input_buffer() + read_pos_; } /// Cast operator to be used to test for errors - inline explicit operator bool() const { return error_code_ == 0; } + inline explicit operator bool() const { return state_ == std::ios::goodbit; } /// Write a simple object to the output buffer template void write_object(T const &t); @@ -90,9 +90,27 @@ class cvm::memory_stream { /// Wrapper to read_vector() template friend memory_stream &operator>>(memory_stream &is, std::vector &t); - /// No-op function to ignore formatting operators + + // Compatibility with STL stream functions + + /// Report the current position in the buffer + inline size_t const tellg() const { return read_pos_; } + + /// Report the current position in the buffer + inline memory_stream & seekg(size_t pos) { if (bool()) read_pos_ = pos; return *this; } + + /// Ignore formatting operators inline void setf(decltype(std::ios::fmtflags(0)), decltype(std::ios::floatfield)) {} + /// Get the error code + inline std::ios::iostate rdstate() const { return state_; } + + /// Set the error code + inline void setstate(std::ios::iostate new_state) { state_ |= new_state; } + + /// Clear the error code + inline void clear() { state_ = std::ios::goodbit; } + protected: /// External output buffer @@ -111,7 +129,7 @@ class cvm::memory_stream { size_t const max_length_; /// Error status - int error_code_ = 0; + std::ios::iostate state_ = std::ios::goodbit; /// Add the requester number of bytes to the array capacity; return false if buffer is external bool expand_ouput_buffer(size_t add_bytes); @@ -119,17 +137,14 @@ class cvm::memory_stream { /// Move the buffer position past the data just written inline void incr_write_pos(size_t c) { data_length_ += c; } - /// Input buffer (may be the same as output, apart from const-ness) - unsigned char const *input_buffer_ = nullptr; - /// Current position when reading from the buffer size_t read_pos_ = 0L; - /// Begin an attempt to read an object - inline void begin_reading() { error_code_ = -1; } + /// Begin an attempt to read an object; assume EOF unless there is space remaining + inline void begin_reading() { setstate(std::ios::eofbit); } /// Mark the reading attempt succesful - inline void done_reading() { error_code_ = 0; } + inline void done_reading() { clear(); } /// Move the buffer position past the data just read inline void incr_read_pos(size_t c) { read_pos_ += c; } @@ -204,6 +219,8 @@ template void cvm::memory_stream::read_vector(std::vector &t) std::memcpy(t.data(), input_location(), vector_length * sizeof(T)); incr_read_pos(vector_length * sizeof(T)); done_reading(); + } else { + setstate(std::ios::failbit); } } } From 9811c499d6635b89529b2d5486ef36a43398bd03 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 19 Jul 2023 18:16:38 -0400 Subject: [PATCH 047/162] Unformatted I/O for colvar objects --- src/colvar.cpp | 53 ++++++++++++++++++++++++++++++++++++++++++++++---- src/colvar.h | 23 ++++++++++++++++++---- 2 files changed, 68 insertions(+), 8 deletions(-) diff --git a/src/colvar.cpp b/src/colvar.cpp index 01dfd4891..c81e43bfd 100644 --- a/src/colvar.cpp +++ b/src/colvar.cpp @@ -19,6 +19,7 @@ #include "colvarcomp.h" #include "colvar.h" #include "colvarscript.h" +#include "colvars_memstream.h" std::map> @@ -2354,6 +2355,31 @@ std::istream & colvar::read_state(std::istream &is) } +cvm::memory_stream & colvar::read_state(cvm::memory_stream &is) +{ + auto const start_pos = is.tellg(); + std::string key; + if (is >> key) { + if (key != "colvar") { + is.seekg(start_pos); + return is; + } + // Read parameters as a formatted string, then use the formatted I/O + std::string data; + if (is >> data) { + std::istringstream iss(data); + if (read_state(iss)) { + return is; + } + } + } + is.clear(); + is.seekg(start_pos); + is.setstate(std::ios::failbit); + return is; +} + + std::istream & colvar::read_traj(std::istream &is) { std::streampos const start_pos = is.tellg(); @@ -2404,10 +2430,23 @@ std::istream & colvar::read_traj(std::istream &is) // ******************** OUTPUT FUNCTIONS ******************** -std::ostream & colvar::write_state(std::ostream &os) { +std::ostream & colvar::write_state(std::ostream &os) const +{ + os << "colvar {\n" << get_state_params() << "}\n\n"; + + if (runave_outfile.size() > 0) { + cvm::main()->proxy->flush_output_stream(runave_outfile); + } + + return os; +} + - os << "colvar {\n" - << " name " << name << "\n" +std::string const colvar::get_state_params() const +{ + std::ostringstream os; + + os << " name " << name << "\n" << " x " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) @@ -2431,7 +2470,13 @@ std::ostream & colvar::write_state(std::ostream &os) { << v_reported << "\n"; } - os << "}\n\n"; + return os.str(); +} + + +cvm::memory_stream & colvar::write_state(cvm::memory_stream &os) const +{ + os << "colvar" << get_state_params(); if (runave_outfile.size() > 0) { cvm::main()->proxy->flush_output_stream(runave_outfile); diff --git a/src/colvar.h b/src/colvar.h index 7150cf03d..3959965f2 100644 --- a/src/colvar.h +++ b/src/colvar.h @@ -456,10 +456,26 @@ class colvar : public colvarparse, public colvardeps { /// Write a label to the trajectory file (comment line) std::ostream & write_traj_label(std::ostream &os); - /// Read the collective variable from a restart file + /// Read the colvar's state from a formatted input stream std::istream & read_state(std::istream &is); - /// Write the collective variable to a restart file - std::ostream & write_state(std::ostream &os); + + /// Read the colvar's state from an unformatted input stream + cvm::memory_stream & read_state(cvm::memory_stream &is); + + /// Check the name of the bias vs. the given string, set the matching_state flag accordingly + int check_matching_state(std::string const &state_conf); + + /// Read the values of colvar mutable data from a string (used by both versions of read_state()) + int set_state_params(std::string const &state_conf); + + /// Write the state information of this colvar in a block of text, suitable for later parsing + std::string const get_state_params() const; + + /// Write the colvar's state to a formatted output stream + std::ostream & write_state(std::ostream &os) const; + + /// Write the colvar's state to an unformatted output stream + cvm::memory_stream & write_state(cvm::memory_stream &os) const; /// Write output files (if defined, e.g. in analysis mode) int write_output_files(); @@ -758,4 +774,3 @@ inline void colvar::reset_bias_force() { } #endif - From d6098f50d394f7016c6dc046acbb76dfcdf0e707 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 19 Jul 2023 18:17:36 -0400 Subject: [PATCH 048/162] Implement read_block() for unformatted input streams --- src/colvarparse.cpp | 105 ++++++++++++++++++++++-------- src/colvarparse.h | 36 ++++++---- tests/unittests/memory_stream.cpp | 21 ++++++ 3 files changed, 122 insertions(+), 40 deletions(-) diff --git a/src/colvarparse.cpp b/src/colvarparse.cpp index 4146300c1..c189a9e89 100644 --- a/src/colvarparse.cpp +++ b/src/colvarparse.cpp @@ -14,6 +14,7 @@ #include "colvarmodule.h" #include "colvarvalue.h" #include "colvarparse.h" +#include "colvars_memstream.h" // space & tab @@ -866,55 +867,107 @@ colvarparse::read_block::~read_block() std::istream & operator>> (std::istream &is, colvarparse::read_block const &rb) { - std::streampos start_pos = is.tellg(); - std::string read_key, next; + auto start_pos = is.tellg(); - if ( !(is >> read_key) || !(read_key == rb.key) || - !(is >> next) ) { - // the requested keyword has not been found, or it is not possible - // to read data after it + std::string read_key; + if ( !(is >> read_key) || !(read_key == rb.key) ) { + // the requested keyword has not been found is.clear(); - is.seekg(start_pos, std::ios::beg); + is.seekg(start_pos); is.setstate(std::ios::failbit); return is; } - if (next != "{") { - if (rb.data) { - *(rb.data) = next; + std::string next; + if (is >> next) { + if (next == "{") { + // Parse a formatted brace-delimited block + rb.read_block_contents(is); + } else { + if (rb.data) { + *(rb.data) = next; + } } - return is; + } else { + is.clear(); + is.seekg(start_pos); + is.setstate(std::ios::badbit); } - size_t brace_count = 1; + return is; +} + + +std::istream &colvarparse::read_block::read_block_contents(std::istream &is, + bool block_only) const +{ + int brace_count = block_only ? 0 : 1; + auto const start_pos = is.tellg(); std::string line; while (colvarparse::getline_nocomments(is, line)) { size_t br = 0, br_old = 0; - while ( (br = line.find_first_of("{}", br)) != std::string::npos) { - if (line[br] == '{') brace_count++; - if (line[br] == '}') brace_count--; + while ((br = line.find_first_of("{}", br)) != std::string::npos) { + if (line[br] == '{') + brace_count++; + if (line[br] == '}') + brace_count--; br_old = br; br++; } - if (brace_count) { - if (rb.data) { - (rb.data)->append(line + "\n"); + if (brace_count || block_only) { + // Add whole line if (1) brace are unmatched or (2) we're reading the whole stream anyway + if (data) { + data->append(line + "\n"); } - } - else { - if (rb.data) { - (rb.data)->append(line, 0, br_old); + } else { + // Not reading whole block and braces are matched; add until before the last brace + if (data) { + data->append(line.substr(0, br_old) + "\n"); } break; } } - if (brace_count) { - // end-of-file reached - // restore initial position + + if (block_only) { + if (is.rdstate() & std::ios::eofbit) { + // Clear EOF errors if we were meant to read the whole block + is.clear(); + } + } else { + if (brace_count) { + // Could not match braces, restore initial position and set fail bit + is.clear(); + is.seekg(start_pos); + is.setstate(std::ios::failbit); + } + } + + return is; +} + + +cvm::memory_stream &operator>>(cvm::memory_stream &is, colvarparse::read_block const &rb) +{ + auto const start_pos = is.tellg(); + + std::string read_key; + if ( !(is >> read_key) || !(read_key == rb.key) ) { + // the requested keyword has not been found is.clear(); - is.seekg(start_pos, std::ios::beg); + is.seekg(start_pos); is.setstate(std::ios::failbit); + return is; } + + std::string content; + if (is >> content) { + std::istringstream iss(content); + if (!rb.read_block_contents(iss, true)) { + is.seekg(start_pos); + is.setstate(std::ios::failbit); + } + } + return is; } diff --git a/src/colvarparse.h b/src/colvarparse.h index 447651609..402997a31 100644 --- a/src/colvarparse.h +++ b/src/colvarparse.h @@ -267,28 +267,36 @@ class colvarparse : public colvarparams { return out; } - /// \brief Helper class to read a block of the type "key { ... }" - /// from a stream and store it in a string + /// Helper class to read a block "key { ... }" from a stream and store it in a string /// - /// Useful on restarts, where the file is too big to be loaded in a - /// string by key_lookup; it can only check that the keyword is - /// correct and the block is properly delimited by braces, not - /// skipping other blocks + /// Useful on restarts, where the file is too big to be loaded in a string + /// by key_lookup(); it can only check that the keyword is correct and the + /// block is properly delimited by braces, not skipping other blocks class read_block { - - /// The keyword that identifies the block - std::string const key; - - /// Where to keep the data (may be NULL) - std::string * const data; - public: - read_block(std::string const &key_in, std::string *data_in = nullptr); + read_block(std::string const &key, std::string *data = nullptr); ~read_block(); + /// Read block from stream, first check that key matches, then call read_contents() friend std::istream & operator >> (std::istream &is, read_block const &rb); + + /// Read block from stream, first check that key matches, then call read_contents() + friend cvm::memory_stream & operator >> (cvm::memory_stream &is, read_block const &rb); + + private: + + /// Keyword that identifies the block + std::string const key; + + /// Where to keep the data + std::string * const data; + + /// Read the contents of a formatted block after checking that the keyword matches + /// \param[in] is Stream object + /// \param[in] block_only If true, stream is assumed to contain only the block without braces + std::istream & read_block_contents(std::istream &is, bool block_only = false) const; }; diff --git a/tests/unittests/memory_stream.cpp b/tests/unittests/memory_stream.cpp index 107784746..915c2142b 100644 --- a/tests/unittests/memory_stream.cpp +++ b/tests/unittests/memory_stream.cpp @@ -1,8 +1,11 @@ +// -*- c++ -*- + #include #include "colvarmodule.h" #include "colvartypes.h" #include "colvarvalue.h" +#include "colvarparse.h" #include "colvars_memstream.h" @@ -54,6 +57,11 @@ int main(int argc, char const *argv[]) buf << cv; + std::string const block_key("colvar"); + std::string const block(" name a_colvar\n" + " x 1.0\n"); + buf << block_key << block; + // // The following will raise a compile error // buf << a2; @@ -80,7 +88,20 @@ int main(int argc, char const *argv[]) colvarvalue new_cv(colvarvalue::type_unit3vector); read_and_print(buf, new_cv); + std::string block; + buf >> colvarparse::read_block("colvar", &block); + if (block.size()) { + std::cout << "block: \"\n" << block << "\"" << std::endl; + } } + std::cout << "buf.tellg() = " << buf.tellg() << std::endl; + std::cout << "buf.length() = " << buf.length() << std::endl; + std::cout << "buf.rdstate() = " << buf.rdstate() << std::endl; + std::cout << "goodbit = " << std::ios::goodbit << std::endl; + std::cout << "eofbit = " << std::ios::eofbit << std::endl; + std::cout << "badbit = " << std::ios::badbit << std::endl; + std::cout << "failbit = " << std::ios::failbit << std::endl; + return buf ? 0 : 1; } From 92102189dc2259470c6e4895e430e49f25991e51 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 20 Jul 2023 16:49:37 -0400 Subject: [PATCH 049/162] Separate checking the name of the colvar from reading its state data --- src/colvar.cpp | 87 ++++++++++++++++++++++++++++++++------------------ src/colvar.h | 3 ++ 2 files changed, 59 insertions(+), 31 deletions(-) diff --git a/src/colvar.cpp b/src/colvar.cpp index c81e43bfd..b7177186b 100644 --- a/src/colvar.cpp +++ b/src/colvar.cpp @@ -38,6 +38,8 @@ colvar::colvar() dev_null = 0.0; #endif + matching_state = false; + expand_boundaries = false; description = "uninitialized colvar"; @@ -2276,10 +2278,11 @@ void colvar::wrap(colvarvalue &x_unwrapped) const std::istream & colvar::read_state(std::istream &is) { - std::streampos const start_pos = is.tellg(); + auto const start_pos = is.tellg(); std::string conf; - if ( !(is >> colvarparse::read_block("colvar", &conf)) ) { + if ( !(is >> colvarparse::read_block("colvar", &conf)) || + (check_matching_state(conf) != COLVARS_OK) ) { // this is not a colvar block is.clear(); is.seekg(start_pos); @@ -2287,33 +2290,53 @@ std::istream & colvar::read_state(std::istream &is) return is; } - { - std::string check_name = ""; - get_keyval(conf, "name", check_name, - std::string(""), colvarparse::parse_silent); - if (check_name.size() == 0) { - cvm::error("Error: Collective variable in the " - "restart file without any identifier.\n", COLVARS_INPUT_ERROR); - is.clear(); - is.seekg(start_pos); - is.setstate(std::ios::failbit); - return is; - } + if (!matching_state) { + // No errors reading, but this state is not for this colvar; rewind + is.seekg(start_pos); + return is; + } - if (check_name != name) { - if (cvm::debug()) { - cvm::log("Ignoring state of colvar \""+check_name+ - "\": this colvar is named \""+name+"\".\n"); - } - is.seekg(start_pos); - return is; + if (set_state_params(conf) != COLVARS_OK) { + is.clear(); + is.seekg(start_pos); + is.setstate(std::ios::failbit); + } + + return is; +} + + +int colvar::check_matching_state(std::string const &conf) +{ + std::string check_name = ""; + get_keyval(conf, "name", check_name, std::string(""), colvarparse::parse_silent); + + if (check_name.size() == 0) { + return cvm::error("Error: Collective variable in the " + "state file without any identifier.\n", COLVARS_INPUT_ERROR); + } + + if (check_name != name) { + if (cvm::debug()) { + cvm::log("Ignoring state of colvar \""+check_name+ + "\": this colvar is named \""+name+"\".\n"); } + matching_state = false; + } else { + matching_state = true; } + return COLVARS_OK; +} + + +int colvar::set_state_params(std::string const &conf) +{ + int error_code = COLVARS_OK; if ( !(get_keyval(conf, "x", x, x, colvarparse::parse_silent)) ) { - cvm::log("Error: restart file does not contain " - "the value of the colvar \""+ - name+"\" .\n"); + error_code |= cvm::error("Error: restart file does not contain " + "the value of the colvar \""+ + name+"\" .\n", COLVARS_INPUT_ERROR); } else { cvm::log("Restarting collective variable \""+name+"\" from value: "+ cvm::to_str(x)+"\n"); @@ -2326,9 +2349,10 @@ std::istream & colvar::read_state(std::istream &is) colvarvalue(x.type()), colvarparse::parse_silent)) || !(get_keyval(conf, "extended_v", v_ext, colvarvalue(x.type()), colvarparse::parse_silent)) ) { - cvm::log("Error: restart file does not contain " - "\"extended_x\" or \"extended_v\" for the colvar \""+ - name+"\", but you requested \"extendedLagrangian\".\n"); + error_code |= cvm::error("Error: restart file does not contain " + "\"extended_x\" or \"extended_v\" for the colvar \""+ + name+"\", but you requested \"extendedLagrangian\".\n", + COLVARS_INPUT_ERROR); } x_reported = x_ext; } else { @@ -2339,9 +2363,10 @@ std::istream & colvar::read_state(std::istream &is) if ( !(get_keyval(conf, "v", v_fdiff, colvarvalue(x.type()), colvarparse::parse_silent)) ) { - cvm::log("Error: restart file does not contain " - "the velocity for the colvar \""+ - name+"\", but you requested \"outputVelocity\".\n"); + error_code |= cvm::error("Error: restart file does not contain " + "the velocity for the colvar \""+ + name+"\", but you requested \"outputVelocity\".\n", + COLVARS_INPUT_ERROR); } if (is_enabled(f_cv_extended_Lagrangian)) { @@ -2351,7 +2376,7 @@ std::istream & colvar::read_state(std::istream &is) } } - return is; + return error_code; } diff --git a/src/colvar.h b/src/colvar.h index 3959965f2..19b863468 100644 --- a/src/colvar.h +++ b/src/colvar.h @@ -482,6 +482,9 @@ class colvar : public colvarparse, public colvardeps { protected: + /// Flag used to tell if the state string being read is for this colvar + bool matching_state; + /// Previous value (to calculate velocities during analysis) colvarvalue x_old; From d413cacafa5dc0c462c19422d47c3744ee1791fb Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 20 Jul 2023 19:41:29 -0400 Subject: [PATCH 050/162] Unformatted I/O for grid objects --- src/colvargrid.cpp | 123 ++++++++++++++++++++++++++++++ src/colvargrid.h | 175 +++++++++++++++++++++++++------------------ src/colvargrid_def.h | 123 ++++++++++++++++++++++++++++++ 3 files changed, 350 insertions(+), 71 deletions(-) diff --git a/src/colvargrid.cpp b/src/colvargrid.cpp index 2fd385cce..59bceb265 100644 --- a/src/colvargrid.cpp +++ b/src/colvargrid.cpp @@ -37,6 +37,47 @@ colvar_grid_count::colvar_grid_count(std::vector &colvars, : colvar_grid(colvars, def_count, 1, margin) {} +std::istream & colvar_grid_count::read_restart(std::istream &is) +{ + return colvar_grid::read_restart(is); +} + +cvm::memory_stream & colvar_grid_count::read_restart(cvm::memory_stream &is) +{ + return colvar_grid::read_restart(is); +} + +std::ostream & colvar_grid_count::write_restart(std::ostream &os) +{ + return colvar_grid::write_restart(os); +} + +cvm::memory_stream & colvar_grid_count::write_restart(cvm::memory_stream &os) +{ + return colvar_grid::write_restart(os); +} + +std::istream &colvar_grid_count::read_raw(std::istream &is) +{ + return colvar_grid::read_raw(is); +} + +cvm::memory_stream &colvar_grid_count::read_raw(cvm::memory_stream &is) +{ + return colvar_grid::read_raw(is); +} + +std::ostream &colvar_grid_count::write_raw(std::ostream &os, size_t const buf_size) const +{ + return colvar_grid::write_raw(os, buf_size); +} + +cvm::memory_stream &colvar_grid_count::write_raw(cvm::memory_stream &os, + size_t const buf_size) const +{ + return colvar_grid::write_raw(os, buf_size); +} + std::istream & colvar_grid_count::read_multicol(std::istream &is, bool add) { return colvar_grid::read_multicol(is, add); @@ -96,6 +137,48 @@ colvar_grid_scalar::~colvar_grid_scalar() { } + +std::istream &colvar_grid_scalar::read_restart(std::istream &is) +{ + return colvar_grid::read_restart(is); +} + +cvm::memory_stream &colvar_grid_scalar::read_restart(cvm::memory_stream &is) +{ + return colvar_grid::read_restart(is); +} + +std::ostream &colvar_grid_scalar::write_restart(std::ostream &os) +{ + return colvar_grid::write_restart(os); +} + +cvm::memory_stream &colvar_grid_scalar::write_restart(cvm::memory_stream &os) +{ + return colvar_grid::write_restart(os); +} + +std::istream &colvar_grid_scalar::read_raw(std::istream &is) +{ + return colvar_grid::read_raw(is); +} + +cvm::memory_stream &colvar_grid_scalar::read_raw(cvm::memory_stream &is) +{ + return colvar_grid::read_raw(is); +} + +std::ostream &colvar_grid_scalar::write_raw(std::ostream &os, size_t const buf_size) const +{ + return colvar_grid::write_raw(os, buf_size); +} + +cvm::memory_stream &colvar_grid_scalar::write_raw(cvm::memory_stream &os, + size_t const buf_size) const +{ + return colvar_grid::write_raw(os, buf_size); +} + std::istream & colvar_grid_scalar::read_multicol(std::istream &is, bool add) { return colvar_grid::read_multicol(is, add); @@ -280,6 +363,46 @@ colvar_grid_gradient::colvar_grid_gradient(std::string &filename) cvm::main()->proxy->close_input_stream(filename); } +std::istream &colvar_grid_gradient::read_restart(std::istream &is) +{ + return colvar_grid::read_restart(is); +} + +cvm::memory_stream &colvar_grid_gradient::read_restart(cvm::memory_stream &is) +{ + return colvar_grid::read_restart(is); +} + +std::ostream &colvar_grid_gradient::write_restart(std::ostream &os) +{ + return colvar_grid::write_restart(os); +} + +cvm::memory_stream &colvar_grid_gradient::write_restart(cvm::memory_stream &os) +{ + return colvar_grid::write_restart(os); +} + +std::istream &colvar_grid_gradient::read_raw(std::istream &is) +{ + return colvar_grid::read_raw(is); +} + +cvm::memory_stream &colvar_grid_gradient::read_raw(cvm::memory_stream &is) +{ + return colvar_grid::read_raw(is); +} + +std::ostream &colvar_grid_gradient::write_raw(std::ostream &os, size_t const buf_size) const +{ + return colvar_grid::write_raw(os, buf_size); +} + +cvm::memory_stream &colvar_grid_gradient::write_raw(cvm::memory_stream &os, + size_t const buf_size) const +{ + return colvar_grid::write_raw(os, buf_size); +} std::istream & colvar_grid_gradient::read_multicol(std::istream &is, bool add) { diff --git a/src/colvargrid.h b/src/colvargrid.h index e2fc1e0fe..08b9fb04a 100644 --- a/src/colvargrid.h +++ b/src/colvargrid.h @@ -24,7 +24,8 @@ /// Only scalar colvars supported so far: vector colvars are treated as arrays template class colvar_grid : public colvarparse { -protected: + //protected: +public: // TODO create accessors for these after all instantiations work /// Number of dimensions size_t nd; @@ -950,83 +951,33 @@ template class colvar_grid : public colvarparse { } } + /// Read all grid parameters and data from a formatted stream + std::istream & read_restart(std::istream &is); - /// \brief Read grid entry in restart file - std::istream & read_restart(std::istream &is) - { - std::streampos const start_pos = is.tellg(); - std::string key, conf; - if ((is >> key) && (key == std::string("grid_parameters"))) { - is.seekg(start_pos, std::ios::beg); - is >> colvarparse::read_block("grid_parameters", &conf); - parse_params(conf, colvarparse::parse_silent); - } else { - cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n"); - is.seekg(start_pos, std::ios::beg); - } - read_raw(is); - return is; - } - - /// \brief Write grid entry in restart file - std::ostream & write_restart(std::ostream &os) - { - write_params(os); - write_raw(os); - return os; - } + /// Read all grid parameters and data from an unformatted stream + cvm::memory_stream & read_restart(cvm::memory_stream &is); + /// Write all grid parameters and data to a formatted stream + std::ostream & write_restart(std::ostream &os); - /// \brief Write the grid data without labels, as they are - /// represented in memory - /// \param buf_size Number of values per line - std::ostream & write_raw(std::ostream &os, - size_t const buf_size = 3) const - { - std::streamsize const w = os.width(); - std::streamsize const p = os.precision(); - - std::vector ix = new_index(); - size_t count = 0; - for ( ; index_ok(ix); incr(ix)) { - for (size_t imult = 0; imult < mult; imult++) { - os << " " - << std::setw(w) << std::setprecision(p) - << value_output(ix, imult); - if (((++count) % buf_size) == 0) - os << "\n"; - } - } - // write a final newline only if buffer is not empty - if ((count % buf_size) != 0) - os << "\n"; + /// Write all grid parameters and data to an unformatted stream + cvm::memory_stream & write_restart(cvm::memory_stream &os); - return os; - } + /// Read all grid parameters and data from a formatted stream + std::istream &read_raw(std::istream &is); - /// \brief Read data written by colvar_grid::write_raw() - std::istream & read_raw(std::istream &is) - { - std::streampos const start_pos = is.tellg(); + /// Read all grid parameters and data from an unformatted stream + cvm::memory_stream &read_raw(cvm::memory_stream &is); - for (std::vector ix = new_index(); index_ok(ix); incr(ix)) { - for (size_t imult = 0; imult < mult; imult++) { - T new_value; - if (is >> new_value) { - value_input(ix, new_value, imult); - } else { - is.clear(); - is.seekg(start_pos, std::ios::beg); - is.setstate(std::ios::failbit); - cvm::error("Error: failed to read all of the grid points from file. Possible explanations: grid parameters in the configuration (lowerBoundary, upperBoundary, width) are different from those in the file, or the file is corrupt/incomplete.\n"); - return is; - } - } - } + /// Write all grid data to a formatted stream (without labels, as they are represented in memory) + /// \param[in,out] os Stream object + /// \param[in] buf_size Number of values per line + std::ostream &write_raw(std::ostream &os, size_t const buf_size = 3) const; - has_data = true; - return is; - } + /// Write all grid data to an unformatted stream + /// \param[in,out] os Stream object + /// \param[in] buf_size Number of values per line (note: ignored because there is no formatting) + cvm::memory_stream &write_raw(cvm::memory_stream &os, size_t const buf_size = 3) const; /// Read a grid written by write_multicol(), incrementing if add is true std::istream & read_multicol(std::istream &is, bool add = false); @@ -1088,6 +1039,34 @@ class colvar_grid_count : public colvar_grid return new_data[address(ix) + imult]; } + /// Read all grid parameters and data from a formatted stream + std::istream & read_restart(std::istream &is); + + /// Read all grid parameters and data from an unformatted stream + cvm::memory_stream & read_restart(cvm::memory_stream &is); + + /// Write all grid parameters and data to a formatted stream + std::ostream & write_restart(std::ostream &os); + + /// Write all grid parameters and data to an unformatted stream + cvm::memory_stream & write_restart(cvm::memory_stream &os); + + /// Read all grid parameters and data from a formatted stream + std::istream &read_raw(std::istream &is); + + /// Read all grid parameters and data from an unformatted stream + cvm::memory_stream &read_raw(cvm::memory_stream &is); + + /// Write all grid data to a formatted stream (without labels, as they are represented in memory) + /// \param[in,out] os Stream object + /// \param[in] buf_size Number of values per line + std::ostream &write_raw(std::ostream &os, size_t const buf_size = 3) const; + + /// Write all grid data to an unformatted stream + /// \param[in,out] os Stream object + /// \param[in] buf_size Number of values per line (note: ignored because there is no formatting) + cvm::memory_stream &write_raw(cvm::memory_stream &os, size_t const buf_size = 3) const; + /// Read a grid written by write_multicol(), incrementin if data is true std::istream & read_multicol(std::istream &is, bool add = false); @@ -1260,6 +1239,33 @@ class colvar_grid_scalar : public colvar_grid samples->incr_count(ix); has_data = true; } + /// Read all grid parameters and data from a formatted stream + std::istream & read_restart(std::istream &is); + + /// Read all grid parameters and data from an unformatted stream + cvm::memory_stream & read_restart(cvm::memory_stream &is); + + /// Write all grid parameters and data to a formatted stream + std::ostream & write_restart(std::ostream &os); + + /// Write all grid parameters and data to an unformatted stream + cvm::memory_stream & write_restart(cvm::memory_stream &os); + + /// Read all grid parameters and data from a formatted stream + std::istream &read_raw(std::istream &is); + + /// Read all grid parameters and data from an unformatted stream + cvm::memory_stream &read_raw(cvm::memory_stream &is); + + /// Write all grid data to a formatted stream (without labels, as they are represented in memory) + /// \param[in,out] os Stream object + /// \param[in] buf_size Number of values per line + std::ostream &write_raw(std::ostream &os, size_t const buf_size = 3) const; + + /// Write all grid data to an unformatted stream + /// \param[in,out] os Stream object + /// \param[in] buf_size Number of values per line (note: ignored because there is no formatting) + cvm::memory_stream &write_raw(cvm::memory_stream &os, size_t const buf_size = 3) const; /// Read a grid written by write_multicol(), incrementin if data is true std::istream & read_multicol(std::istream &is, bool add = false); @@ -1470,6 +1476,33 @@ class colvar_grid_gradient : public colvar_grid /// Constructor from a multicol file colvar_grid_gradient(std::string &filename); + /// Read all grid parameters and data from a formatted stream + std::istream & read_restart(std::istream &is); + + /// Read all grid parameters and data from an unformatted stream + cvm::memory_stream & read_restart(cvm::memory_stream &is); + + /// Write all grid parameters and data to a formatted stream + std::ostream & write_restart(std::ostream &os); + + /// Write all grid parameters and data to an unformatted stream + cvm::memory_stream & write_restart(cvm::memory_stream &os); + + /// Read all grid parameters and data from a formatted stream + std::istream &read_raw(std::istream &is); + + /// Read all grid parameters and data from an unformatted stream + cvm::memory_stream &read_raw(cvm::memory_stream &is); + + /// Write all grid data to a formatted stream (without labels, as they are represented in memory) + /// \param[in,out] os Stream object + /// \param[in] buf_size Number of values per line + std::ostream &write_raw(std::ostream &os, size_t const buf_size = 3) const; + + /// Write all grid data to an unformatted stream + /// \param[in,out] os Stream object + /// \param[in] buf_size Number of values per line (note: ignored because there is no formatting) + cvm::memory_stream &write_raw(cvm::memory_stream &os, size_t const buf_size = 3) const; /// Read a grid written by write_multicol(), incrementin if data is true virtual std::istream & read_multicol(std::istream &is, bool add = false); diff --git a/src/colvargrid_def.h b/src/colvargrid_def.h index f2245f3d8..78e3a4e08 100644 --- a/src/colvargrid_def.h +++ b/src/colvargrid_def.h @@ -19,6 +19,129 @@ #include "colvarproxy.h" #include "colvar.h" #include "colvargrid.h" +#include "colvars_memstream.h" + + +template IST &read_restart_template(colvar_grid &g, IST &is) +{ + auto const start_pos = is.tellg(); + std::string key, conf; + if ((is >> key) && (key == std::string("grid_parameters"))) { + is.seekg(start_pos); + is >> colvarparse::read_block("grid_parameters", &conf); + g.parse_params(conf, colvarparse::parse_silent); + } else { + cvm::log("Grid parameters are missing in the restart file, " + "using those from the configuration.\n"); + is.seekg(start_pos); + } + g.read_raw(is); + return is; +} + + +template std::istream &colvar_grid::read_restart(std::istream &is) +{ + return read_restart_template(*this, is); +} + + +template cvm::memory_stream &colvar_grid::read_restart(cvm::memory_stream &is) +{ + return read_restart_template(*this, is); +} + + +template std::ostream &colvar_grid::write_restart(std::ostream &os) +{ + write_params(os); + write_raw(os); + return os; +} + + +template cvm::memory_stream &colvar_grid::write_restart(cvm::memory_stream &os) +{ + std::ostringstream oss; + write_params(oss); + os << oss.str(); + write_raw(os); + return os; +} + + +template IST &read_raw_template(colvar_grid &g, IST &is) +{ + auto const start_pos = is.tellg(); + + for (std::vector ix = g.new_index(); g.index_ok(ix); g.incr(ix)) { + for (size_t imult = 0; imult < g.mult; imult++) { + T new_value; + if (is >> new_value) { + g.value_input(ix, new_value, imult); + } else { + is.clear(); + is.seekg(start_pos); + is.setstate(std::ios::failbit); + cvm::error( + "Error: failed to read all of the grid points from file. Possible explanations: grid " + "parameters in the configuration (lowerBoundary, upperBoundary, width) are different " + "from those in the file, or the file is corrupt/incomplete.\n", + COLVARS_INPUT_ERROR); + return is; + } + } + } + + g.has_data = true; + return is; +} + + +template std::istream &colvar_grid::read_raw(std::istream &is) +{ + return read_raw_template(*this, is); +} + + +template cvm::memory_stream &colvar_grid::read_raw(cvm::memory_stream &is) +{ + return read_raw_template(*this, is); +} + + +template +std::ostream &colvar_grid::write_raw(std::ostream &os, size_t const buf_size) const +{ + auto const w = os.width(); + auto const p = os.precision(); + + size_t count = 0; + for (auto ix = new_index(); index_ok(ix); incr(ix)) { + for (size_t imult = 0; imult < mult; imult++) { + os << " " << std::setw(w) << std::setprecision(p) << value_output(ix, imult); + if (((++count) % buf_size) == 0) + os << "\n"; + } + } + // write a final newline only if buffer is not empty + if ((count % buf_size) != 0) + os << "\n"; + + return os; +} + + +template +cvm::memory_stream &colvar_grid::write_raw(cvm::memory_stream &os, size_t const buf_size) const +{ + for (auto ix = new_index(); index_ok(ix); incr(ix)) { + for (size_t imult = 0; imult < mult; imult++) { + os << value_output(ix, imult); + } + } + return os; +} template From da197e77bc8a172712f2bf0a8bcf9d6ce6ecc47a Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 21 Jul 2023 10:26:14 -0400 Subject: [PATCH 051/162] Remove duplicate specialization specific to Visual Studio and Sun compiler --- src/colvars_memstream.h | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index 482bf1ed6..fac1a42eb 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -237,11 +237,14 @@ template cvm::memory_stream &operator<<(cvm::memory_stream &os, return os; } +#if !defined(_MSC_VER) && !defined(__SUNPRO_CC) +// Visual Studio and MSVC use the same return type for both modifiers template cvm::memory_stream &operator<<(cvm::memory_stream &os, decltype(std::setw(10)) const &) { return os; } +#endif // Declare specializations From 78671870cf5c57b08fc2c75999885eb39cbef9dc Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 21 Aug 2023 16:34:54 +0200 Subject: [PATCH 052/162] Unformatted I/O for colvarbias base class --- src/colvarbias.cpp | 141 +++++++++++++++++++++++++++++++++++---------- src/colvarbias.h | 58 ++++++++++++++++--- 2 files changed, 159 insertions(+), 40 deletions(-) diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp index c961a96f4..4f8fd9042 100644 --- a/src/colvarbias.cpp +++ b/src/colvarbias.cpp @@ -15,6 +15,7 @@ #include "colvarvalue.h" #include "colvarbias.h" #include "colvargrid.h" +#include "colvars_memstream.h" colvarbias::colvarbias(char const *key) @@ -499,7 +500,7 @@ int colvarbias::set_state_params(std::string const &conf) std::ostream & colvarbias::write_state(std::ostream &os) { if (cvm::debug()) { - cvm::log("Writing state file for bias \""+name+"\"\n"); + cvm::log("Writing formatted state for bias \""+name+"\"\n"); } os.setf(std::ios::scientific, std::ios::floatfield); os.precision(cvm::cv_prec); @@ -513,50 +514,83 @@ std::ostream & colvarbias::write_state(std::ostream &os) } -std::istream & colvarbias::read_state(std::istream &is) +cvm::memory_stream & colvarbias::write_state(cvm::memory_stream &os) +{ + if (cvm::debug()) { + cvm::log("Writing unformatted state for bias \""+name+"\"\n"); + } + os << state_keyword << "configuration" << get_state_params(); + write_state_data(os); + return os; +} + + +template +void raise_error_rewind(IST &is, SPT start_pos, std::string const &bias_type, + std::string const &bias_name) +{ + cvm::error("Error: in reading state for \"" + bias_type + "\" bias \"" + bias_name + + "\" at position " + cvm::to_str(static_cast(is.tellg())) + " in stream.\n", + COLVARS_INPUT_ERROR); + auto state = is.rdstate(); + is.clear(); + is.seekg(start_pos); + is.setstate(state); +} + + +template IST & colvarbias::read_state_from_stream(IST &is) { auto const start_pos = is.tellg(); std::string key, brace, conf; - if ( !(is >> key) || !(key == state_keyword || key == bias_type) || - !(is >> brace) || !(brace == "{") || - !(is >> colvarparse::read_block("configuration", &conf)) || - (check_matching_state(conf) != COLVARS_OK) ) { - cvm::error("Error: in reading state configuration for \""+bias_type+ - "\" bias \""+ - this->name+"\" at position "+ - cvm::to_str(static_cast(is.tellg()))+ - " in stream.\n", COLVARS_INPUT_ERROR); - is.clear(); - is.seekg(start_pos); - is.setstate(std::ios::failbit); + if (is >> key) { + if (key == state_keyword || key == bias_type) { + + if (! std::is_same::value) { + // Formatted input only + if (!(is >> brace) || !(brace == "{") ) { + raise_error_rewind(is, start_pos, bias_type, name); + return is; + } + } + + if (!(is >> colvarparse::read_block("configuration", &conf)) || + (check_matching_state(conf) != COLVARS_OK)) { + raise_error_rewind(is, start_pos, bias_type, name); + return is; + } + + } else { + // Not a match for this bias type, rewind without error + is.seekg(start_pos); + return is; + } + + } else { + raise_error_rewind(is, start_pos, bias_type, name); return is; } if (!matching_state) { - // No errors reading, but this state is not for this bias; rewind + // No errors, but not a match for this bias instance; rewind is.seekg(start_pos); return is; } if ((set_state_params(conf) != COLVARS_OK) || !read_state_data(is)) { - cvm::error("Error: in reading state data for \""+bias_type+"\" bias \""+ - this->name+"\" at position "+ - cvm::to_str(static_cast(is.tellg()))+ - " in stream.\n", COLVARS_INPUT_ERROR); - auto state = is.rdstate(); - is.clear(); - is.seekg(start_pos); - is.setstate(state); + raise_error_rewind(is, start_pos, bias_type, name); } - is >> brace; - if (brace != "}") { - cvm::error("Error: corrupt restart information for \""+bias_type+"\" bias \""+ - this->name+"\": no matching brace at position "+ - cvm::to_str(static_cast(is.tellg()))+ - " in stream.\n"); - is.setstate(std::ios::failbit); + if (! std::is_same::value) { + is >> brace; + if (brace != "}") { + cvm::error("Error: corrupt restart information for \""+bias_type+"\" bias \""+ + this->name+"\": no matching brace at position "+ + cvm::to_str(static_cast(is.tellg()))+ + " in stream.\n"); + raise_error_rewind(is, start_pos, bias_type, name); + } } cvm::log("Restarted " + bias_type + " bias \"" + name + "\" with step number " + @@ -566,6 +600,18 @@ std::istream & colvarbias::read_state(std::istream &is) } +std::istream &colvarbias::read_state(std::istream &is) +{ + return read_state_from_stream(is); +} + + +cvm::memory_stream &colvarbias::read_state(cvm::memory_stream &is) +{ + return read_state_from_stream(is); +} + + int colvarbias::write_state_prefix(std::string const &prefix) { std::string const filename = @@ -636,9 +682,23 @@ int colvarbias::read_state_string(char const *buffer) } +std::ostream & colvarbias::write_state_data_key(std::ostream &os, char const *key) +{ + os << "\n" << key << "\n"; + return os; +} + + +cvm::memory_stream & colvarbias::write_state_data_key(cvm::memory_stream &os, char const *key) +{ + os << key; + return os; +} + + std::istream & colvarbias::read_state_data_key(std::istream &is, char const *key) { - std::streampos const start_pos = is.tellg(); + auto const start_pos = is.tellg(); std::string key_in; if ( !(is >> key_in) || !(to_lower_cppstr(key_in) == to_lower_cppstr(std::string(key))) ) { @@ -647,7 +707,24 @@ std::istream & colvarbias::read_state_data_key(std::istream &is, char const *key cvm::to_str(static_cast(is.tellg()))+ " in stream.\n", COLVARS_INPUT_ERROR); is.clear(); - is.seekg(start_pos, std::ios::beg); + is.seekg(start_pos); + is.setstate(std::ios::failbit); + return is; + } + return is; +} + + +cvm::memory_stream & colvarbias::read_state_data_key(cvm::memory_stream &is, char const *key) +{ + auto const start_pos = is.tellg(); + std::string key_in; + if ( !(is >> key_in) || + !(to_lower_cppstr(key_in) == to_lower_cppstr(std::string(key))) ) { + cvm::error("Error: in reading restart configuration for "+ + bias_type+" bias \""+this->name+"\".\n", COLVARS_INPUT_ERROR); + is.clear(); + is.seekg(start_pos); is.setstate(std::ios::failbit); return is; } diff --git a/src/colvarbias.h b/src/colvarbias.h index de7b04b51..baba27523 100644 --- a/src/colvarbias.h +++ b/src/colvarbias.h @@ -139,29 +139,69 @@ class colvarbias /// Read the values of specific mutable properties from a string virtual int set_state_params(std::string const &state_conf); - /// Write all mutable data not already written by get_state_params() + /// Write all mutable data not already written by get_state_params() to a formatted stream virtual std::ostream & write_state_data(std::ostream &os) { return os; } - /// Read all mutable data not already set by set_state_params() + /// Write all mutable data not already written by get_state_params() to an unformatted stream + virtual cvm::memory_stream & write_state_data(cvm::memory_stream &os) + { + return os; + } + + /// Read all mutable data not already set by set_state_params() from a formatted stream virtual std::istream & read_state_data(std::istream &is) { return is; } - /// Read a keyword from the state data (typically a header) - /// \param Input stream - /// \param Keyword labeling the header block + /// Read all mutable data not already set by set_state_params() from an unformatted stream + virtual cvm::memory_stream & read_state_data(cvm::memory_stream &is) + { + return is; + } + + /// Write a keyword header for a data sequence to a formatted stream + /// \param[in,out] os Output stream + /// \param[in] key Keyword labeling the header block + std::ostream & write_state_data_key(std::ostream &os, char const *key); + + /// Write a keyword header for a data sequence to an unformatted stream + /// \param[in,out] os Output stream + /// \param[in] key Keyword labeling the header block + cvm::memory_stream & write_state_data_key(cvm::memory_stream &os, char const *key); + + /// Read a keyword header for a data sequence from a formatted stream + /// \param[in,out] Input stream + /// \param[in] Keyword labeling the header block; an error will be raised if not matching std::istream & read_state_data_key(std::istream &is, char const *key); - /// Write the bias configuration to a state file or other stream - std::ostream & write_state(std::ostream &os); + /// Read a keyword header for a data sequence from an unformatted stream + /// \param[in,out] Input stream + /// \param[in] Keyword labeling the header block; an error will be raised if not matching + cvm::memory_stream & read_state_data_key(cvm::memory_stream &is, char const *key); + +private: - /// Read the bias configuration from a restart file or other stream + /// Generic stream reading function (formatted and not) + template IST & read_state_from_stream(IST &is); + +public: + + /// Write the bias configuration to a formatted stream + std::ostream &write_state(std::ostream &os); + + /// Write the bias configuration to an unformatted stream + cvm::memory_stream & write_state(cvm::memory_stream &os); + + /// Read the bias configuration from a formatted stream std::istream & read_state(std::istream &is); + /// Read the bias configuration from an unformatted stream + cvm::memory_stream & read_state(cvm::memory_stream &is); + /// Write the bias state to a file with the given prefix int write_state_prefix(std::string const &prefix); @@ -291,7 +331,9 @@ class colvarbias_ti : public virtual colvarbias { virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &state_conf); virtual std::ostream & write_state_data(std::ostream &os); + virtual cvm::memory_stream & write_state_data(cvm::memory_stream &os); virtual std::istream & read_state_data(std::istream &is); + virtual cvm::memory_stream & read_state_data(cvm::memory_stream &is); virtual int write_output_files(); protected: From 79938bbbf3b36f2079d3d9a1dc9342ddbe1c121a Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 21 Aug 2023 18:31:57 +0200 Subject: [PATCH 053/162] Unformatted I/O for colvarbias_abf and colvarbias_histogram --- src/colvarbias_abf.cpp | 39 +++++++++++++++++++++++++++++------- src/colvarbias_abf.h | 22 +++++++++++++++++--- src/colvarbias_histogram.cpp | 28 ++++++++++++++++++++------ src/colvarbias_histogram.h | 8 +++++--- src/colvarbias_restraint.h | 8 ++++++++ 5 files changed, 86 insertions(+), 19 deletions(-) diff --git a/src/colvarbias_abf.cpp b/src/colvarbias_abf.cpp index 7d6b7b7fe..d8927e29a 100644 --- a/src/colvarbias_abf.cpp +++ b/src/colvarbias_abf.cpp @@ -12,6 +12,7 @@ #include "colvarmodule.h" #include "colvar.h" #include "colvarbias_abf.h" +#include "colvars_memstream.h" colvarbias_abf::colvarbias_abf(char const *key) @@ -741,24 +742,24 @@ int colvarbias_abf::read_gradients_samples() } -std::ostream & colvarbias_abf::write_state_data(std::ostream& os) +template OST & colvarbias_abf::write_to_stream(OST &os) { - std::ios::fmtflags flags(os.flags()); + auto flags = os.flags(); os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format - os << "\nsamples\n"; + write_state_data_key(os, "samples"); samples->write_raw(os, 8); os.flags(flags); - os << "\ngradient\n"; + write_state_data_key(os, "gradient"); gradients->write_raw(os, 8); if (b_CZAR_estimator) { os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format - os << "\nz_samples\n"; + write_state_data_key(os, "z_samples"); z_samples->write_raw(os, 8); os.flags(flags); - os << "\nz_gradient\n"; + write_state_data_key(os, "z_gradient"); z_gradients->write_raw(os, 8); } @@ -767,7 +768,19 @@ std::ostream & colvarbias_abf::write_state_data(std::ostream& os) } -std::istream & colvarbias_abf::read_state_data(std::istream& is) +std::ostream & colvarbias_abf::write_state_data(std::ostream& os) +{ + return write_to_stream(os); +} + + +cvm::memory_stream & colvarbias_abf::write_state_data(cvm::memory_stream& os) +{ + return write_to_stream(os); +} + + +template IST &colvarbias_abf::read_from_stream(IST &is) { if ( input_prefix.size() > 0 ) { cvm::error("ERROR: cannot provide both inputPrefix and a colvars state file.\n", COLVARS_INPUT_ERROR); @@ -812,6 +825,18 @@ std::istream & colvarbias_abf::read_state_data(std::istream& is) } +std::istream & colvarbias_abf::read_state_data(std::istream& is) +{ + return read_from_stream(is); +} + + +cvm::memory_stream & colvarbias_abf::read_state_data(cvm::memory_stream& is) +{ + return read_from_stream(is); +} + + int colvarbias_abf::write_output_files() { if (cvm::debug()) { diff --git a/src/colvarbias_abf.h b/src/colvarbias_abf.h index 9eae867a7..17cfba63e 100644 --- a/src/colvarbias_abf.h +++ b/src/colvarbias_abf.h @@ -159,9 +159,25 @@ class colvarbias_abf : public colvarbias { std::string const &name, bool close); - virtual std::istream& read_state_data(std::istream&); - virtual std::ostream& write_state_data(std::ostream&); - virtual int write_output_files(); +private: + + /// Generic stream writing function (formatted and not) + template OST &write_to_stream(OST &os); + + /// Generic stream readingx function (formatted and not) + template IST &read_from_stream(IST &is); + +public: + + std::ostream &write_state_data(std::ostream &os) override; + + cvm::memory_stream &write_state_data(cvm::memory_stream &os) override; + + std::istream &read_state_data(std::istream &is) override; + + cvm::memory_stream &read_state_data(cvm::memory_stream &is) override; + + int write_output_files() override; /// Calculate the bias energy for 1D ABF virtual int calc_energy(std::vector const *values); diff --git a/src/colvarbias_histogram.cpp b/src/colvarbias_histogram.cpp index 84f1a5bde..640bec353 100644 --- a/src/colvarbias_histogram.cpp +++ b/src/colvarbias_histogram.cpp @@ -7,10 +7,13 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#include + #include "colvarmodule.h" #include "colvarproxy.h" #include "colvar.h" #include "colvarbias_histogram.h" +#include "colvars_memstream.h" colvarbias_histogram::colvarbias_histogram(char const *key) @@ -197,13 +200,18 @@ int colvarbias_histogram::write_output_files() std::istream & colvarbias_histogram::read_state_data(std::istream& is) { - if (! read_state_data_key(is, "grid")) { - return is; - } - if (! grid->read_raw(is)) { - return is; + if (read_state_data_key(is, "grid")) { + grid->read_raw(is); } + return is; +} + +cvm::memory_stream & colvarbias_histogram::read_state_data(cvm::memory_stream& is) +{ + if (read_state_data_key(is, "grid")) { + grid->read_raw(is); + } return is; } @@ -212,8 +220,16 @@ std::ostream & colvarbias_histogram::write_state_data(std::ostream& os) { std::ios::fmtflags flags(os.flags()); os.setf(std::ios::fmtflags(0), std::ios::floatfield); - os << "grid\n"; + write_state_data_key(os, "grid"); grid->write_raw(os, 8); os.flags(flags); return os; } + + +cvm::memory_stream & colvarbias_histogram::write_state_data(cvm::memory_stream& os) +{ + write_state_data_key(os, "grid"); + grid->write_raw(os); + return os; +} diff --git a/src/colvarbias_histogram.h b/src/colvarbias_histogram.h index 6044fa189..48b9056f0 100644 --- a/src/colvarbias_histogram.h +++ b/src/colvarbias_histogram.h @@ -29,6 +29,11 @@ class colvarbias_histogram : public colvarbias { virtual int update(); virtual int write_output_files(); + virtual std::ostream & write_state_data(std::ostream &os); + virtual cvm::memory_stream & write_state_data(cvm::memory_stream &os); + virtual std::istream & read_state_data(std::istream &is); + virtual cvm::memory_stream & read_state_data(cvm::memory_stream &is); + protected: /// n-dim histogram @@ -40,9 +45,6 @@ class colvarbias_histogram : public colvarbias { size_t colvar_array_size; /// If colvar_array_size is larger than 1, weigh each one by this number before accumulating the histogram std::vector weights; - - virtual std::istream & read_state_data(std::istream &is); - virtual std::ostream & write_state_data(std::ostream &os); }; #endif diff --git a/src/colvarbias_restraint.h b/src/colvarbias_restraint.h index c19132ede..45a96d14f 100644 --- a/src/colvarbias_restraint.h +++ b/src/colvarbias_restraint.h @@ -38,6 +38,8 @@ class colvarbias_restraint virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); + // virtual std::ostream & write_state_data(std::ostream &os); + // virtual std::istream & read_state_data(std::istream &os); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); @@ -240,6 +242,8 @@ class colvarbias_restraint_harmonic virtual int update(); virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); + virtual std::ostream & write_state_data(std::ostream &os); + virtual std::istream & read_state_data(std::istream &os); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); virtual int change_configuration(std::string const &conf); @@ -265,6 +269,8 @@ class colvarbias_restraint_harmonic_walls virtual int update(); virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); + virtual std::ostream & write_state_data(std::ostream &os); + virtual std::istream & read_state_data(std::istream &os); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); @@ -305,6 +311,8 @@ class colvarbias_restraint_linear virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); + virtual std::ostream & write_state_data(std::ostream &os); + virtual std::istream & read_state_data(std::istream &os); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); From a69b80e3421624c23311590689f7428a604cea6b Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 21 Aug 2023 18:32:51 +0200 Subject: [PATCH 054/162] More formatting functions being ignored --- src/colvars_memstream.h | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index fac1a42eb..9742bfc96 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -102,6 +102,12 @@ class cvm::memory_stream { /// Ignore formatting operators inline void setf(decltype(std::ios::fmtflags(0)), decltype(std::ios::floatfield)) {} + /// Ignore formatting operators + inline void flags(decltype(std::ios::fmtflags(0))) {} + + /// Get the current formatting flags (i.e. none because this stream is unformatted) + inline decltype(std::ios::fmtflags(0)) flags() const { return std::ios::fmtflags(0); } + /// Get the error code inline std::ios::iostate rdstate() const { return state_; } From b018e8cda8dc1e78be69afd018ca7b67f5ede793 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 21 Aug 2023 19:33:12 +0200 Subject: [PATCH 055/162] Unformatted I/O for colvarbias_ti --- src/colvarbias.cpp | 44 ++++++++++++++++++++++++++++++++++++++++++-- src/colvarbias_abf.h | 10 +++++----- 2 files changed, 47 insertions(+), 7 deletions(-) diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp index 4f8fd9042..6d47f9361 100644 --- a/src/colvarbias.cpp +++ b/src/colvarbias.cpp @@ -938,9 +938,22 @@ std::ostream & colvarbias_ti::write_state_data(std::ostream &os) if (! is_enabled(f_cvb_calc_ti_samples)) { return os; } - os << "\nhistogram\n"; + write_state_data_key(os, "histogram"); ti_count->write_raw(os); - os << "\nsystem_forces\n"; + write_state_data_key(os, "system_forces"); + ti_avg_forces->write_raw(os); + return os; +} + + +cvm::memory_stream & colvarbias_ti::write_state_data(cvm::memory_stream &os) +{ + if (! is_enabled(f_cvb_calc_ti_samples)) { + return os; + } + write_state_data_key(os, "histogram"); + ti_count->write_raw(os); + write_state_data_key(os, "system_forces"); ti_avg_forces->write_raw(os); return os; } @@ -973,6 +986,33 @@ std::istream & colvarbias_ti::read_state_data(std::istream &is) } +cvm::memory_stream & colvarbias_ti::read_state_data(cvm::memory_stream &is) +{ + if (! is_enabled(f_cvb_calc_ti_samples)) { + return is; + } + if (cvm::debug()) { + cvm::log("Reading state data for the TI estimator.\n"); + } + if (! read_state_data_key(is, "histogram")) { + return is; + } + if (! ti_count->read_raw(is)) { + return is; + } + if (! read_state_data_key(is, "system_forces")) { + return is; + } + if (! ti_avg_forces->read_raw(is)) { + return is; + } + if (cvm::debug()) { + cvm::log("Done reading state data for the TI estimator.\n"); + } + return is; +} + + int colvarbias_ti::write_output_files() { int error_code = COLVARS_OK; diff --git a/src/colvarbias_abf.h b/src/colvarbias_abf.h index 17cfba63e..e9887562d 100644 --- a/src/colvarbias_abf.h +++ b/src/colvarbias_abf.h @@ -169,15 +169,15 @@ class colvarbias_abf : public colvarbias { public: - std::ostream &write_state_data(std::ostream &os) override; + virtual std::ostream &write_state_data(std::ostream &os); - cvm::memory_stream &write_state_data(cvm::memory_stream &os) override; + virtual cvm::memory_stream &write_state_data(cvm::memory_stream &os); - std::istream &read_state_data(std::istream &is) override; + virtual std::istream &read_state_data(std::istream &is); - cvm::memory_stream &read_state_data(cvm::memory_stream &is) override; + virtual cvm::memory_stream &read_state_data(cvm::memory_stream &is); - int write_output_files() override; + virtual int write_output_files(); /// Calculate the bias energy for 1D ABF virtual int calc_energy(std::vector const *values); From 0f1ccb7baae305fbc11370fc85464a86712c6ef3 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 21 Aug 2023 19:33:38 +0200 Subject: [PATCH 056/162] Remove obsolete code block --- src/colvarbias_meta.cpp | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/src/colvarbias_meta.cpp b/src/colvarbias_meta.cpp index 0d2634533..dc8bd0bb6 100644 --- a/src/colvarbias_meta.cpp +++ b/src/colvarbias_meta.cpp @@ -1302,17 +1302,6 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) { if (use_grids) { - if (expand_grids) { - // the boundaries of the colvars may have been changed; TODO: - // this reallocation is only for backward-compatibility, and may - // be deleted when grid_parameters (i.e. colvargrid's own - // internal reallocation) has kicked in - delete hills_energy; - delete hills_energy_gradients; - hills_energy = new colvar_grid_scalar(colvars); - hills_energy_gradients = new colvar_grid_gradient(colvars); - } - colvar_grid_scalar *hills_energy_backup = NULL; colvar_grid_gradient *hills_energy_gradients_backup = NULL; From 98ded6fe43b9f03ac218c908f8fe132a17791484 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 21 Aug 2023 22:42:00 +0200 Subject: [PATCH 057/162] Forward declare STL streams in colvargrid template --- src/colvarbias_meta.cpp | 4 +- src/colvargrid.cpp | 32 ++++++++++ src/colvargrid.h | 131 +++++++++------------------------------- src/colvargrid_def.h | 112 ++++++++++++++++++++++++++++++++-- 4 files changed, 170 insertions(+), 109 deletions(-) diff --git a/src/colvarbias_meta.cpp b/src/colvarbias_meta.cpp index dc8bd0bb6..eebbcf921 100644 --- a/src/colvarbias_meta.cpp +++ b/src/colvarbias_meta.cpp @@ -1451,9 +1451,9 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) if (cvm::debug()) { std::ostringstream tmp_os; tmp_os << "hills_energy parameters:\n"; - hills_energy->write_params(tmp_os); + tmp_os << hills_energy->get_state_params(); tmp_os << "new_hills_energy parameters:\n"; - new_hills_energy->write_params(tmp_os); + tmp_os << new_hills_energy->get_state_params(); cvm::log(tmp_os.str()); } diff --git a/src/colvargrid.cpp b/src/colvargrid.cpp index 59bceb265..5ab10439c 100644 --- a/src/colvargrid.cpp +++ b/src/colvargrid.cpp @@ -37,6 +37,17 @@ colvar_grid_count::colvar_grid_count(std::vector &colvars, : colvar_grid(colvars, def_count, 1, margin) {} +std::string colvar_grid_count::get_state_params() const +{ + return colvar_grid::get_state_params(); +} + +int colvar_grid_count::parse_params(std::string const &conf, + colvarparse::Parse_Mode const parse_mode) +{ + return colvar_grid::parse_params(conf, parse_mode); +} + std::istream & colvar_grid_count::read_restart(std::istream &is) { return colvar_grid::read_restart(is); @@ -137,6 +148,16 @@ colvar_grid_scalar::~colvar_grid_scalar() { } +std::string colvar_grid_scalar::get_state_params() const +{ + return colvar_grid::get_state_params(); +} + +int colvar_grid_scalar::parse_params(std::string const &conf, + colvarparse::Parse_Mode const parse_mode) +{ + return colvar_grid::parse_params(conf, parse_mode); +} std::istream &colvar_grid_scalar::read_restart(std::istream &is) { @@ -363,6 +384,17 @@ colvar_grid_gradient::colvar_grid_gradient(std::string &filename) cvm::main()->proxy->close_input_stream(filename); } +std::string colvar_grid_gradient::get_state_params() const +{ + return colvar_grid::get_state_params(); +} + +int colvar_grid_gradient::parse_params(std::string const &conf, + colvarparse::Parse_Mode const parse_mode) +{ + return colvar_grid::parse_params(conf, parse_mode); +} + std::istream &colvar_grid_gradient::read_restart(std::istream &is) { return colvar_grid::read_restart(is); diff --git a/src/colvargrid.h b/src/colvargrid.h index 08b9fb04a..ef3d96734 100644 --- a/src/colvargrid.h +++ b/src/colvargrid.h @@ -10,8 +10,7 @@ #ifndef COLVARGRID_H #define COLVARGRID_H -#include -#include +#include #include "colvar.h" #include "colvarmodule.h" @@ -804,109 +803,12 @@ template class colvar_grid : public colvarparse { } } - /// Write the grid parameters (number of colvars, boundaries, width and number of points) - std::ostream & write_params(std::ostream &os) - { - size_t i; - os << "grid_parameters {\n n_colvars " << nd << "\n"; - - os << " lower_boundaries "; - for (i = 0; i < nd; i++) - os << " " << lower_boundaries[i]; - os << "\n"; - - os << " upper_boundaries "; - for (i = 0; i < nd; i++) - os << " " << upper_boundaries[i]; - os << "\n"; - - os << " widths "; - for (i = 0; i < nd; i++) - os << " " << widths[i]; - os << "\n"; + /// Write the current grid parameters to a string + std::string get_state_params() const; - os << " sizes "; - for (i = 0; i < nd; i++) - os << " " << nx[i]; - os << "\n"; - - os << "}\n"; - return os; - } - - /// Read a grid definition from a config string + /// Read new grid parameters from a string int parse_params(std::string const &conf, - colvarparse::Parse_Mode const parse_mode = colvarparse::parse_normal) - { - if (cvm::debug()) cvm::log("Reading grid configuration from string.\n"); - - std::vector old_nx = nx; - std::vector old_lb = lower_boundaries; - std::vector old_ub = upper_boundaries; - std::vector old_w = widths; - - { - size_t nd_in = 0; - // this is only used in state files - colvarparse::get_keyval(conf, "n_colvars", nd_in, nd, colvarparse::parse_silent); - if (nd_in != nd) { - cvm::error("Error: trying to read data for a grid " - "that contains a different number of colvars ("+ - cvm::to_str(nd_in)+") than the grid defined " - "in the configuration file("+cvm::to_str(nd)+ - ").\n"); - return COLVARS_ERROR; - } - } - - // underscore keywords are used in state file - colvarparse::get_keyval(conf, "lower_boundaries", - lower_boundaries, lower_boundaries, colvarparse::parse_silent); - colvarparse::get_keyval(conf, "upper_boundaries", - upper_boundaries, upper_boundaries, colvarparse::parse_silent); - - // camel case keywords are used in config file - colvarparse::get_keyval(conf, "lowerBoundaries", - lower_boundaries, lower_boundaries, parse_mode); - colvarparse::get_keyval(conf, "upperBoundaries", - upper_boundaries, upper_boundaries, parse_mode); - - colvarparse::get_keyval(conf, "widths", widths, widths, parse_mode); - - // only used in state file - colvarparse::get_keyval(conf, "sizes", nx, nx, colvarparse::parse_silent); - - if (nd < lower_boundaries.size()) nd = lower_boundaries.size(); - - if (! use_actual_value.size()) use_actual_value.assign(nd, false); - if (! periodic.size()) periodic.assign(nd, false); - if (! widths.size()) widths.assign(nd, 1.0); - - cvm::real eps = 1.e-10; - - bool new_params = false; - if (old_nx.size()) { - for (size_t i = 0; i < nd; i++) { - if (old_nx[i] != nx[i] || - cvm::sqrt(cv[i]->dist2(old_lb[i], lower_boundaries[i])) > eps || - cvm::sqrt(cv[i]->dist2(old_ub[i], upper_boundaries[i])) > eps || - cvm::fabs(old_w[i] - widths[i]) > eps) { - new_params = true; - } - } - } else { - new_params = true; - } - - // reallocate the array in case the grid params have just changed - if (new_params) { - init_from_boundaries(); - // data.clear(); // no longer needed: setup calls clear() - return this->setup(nx, T(), mult); - } - - return COLVARS_OK; - } + colvarparse::Parse_Mode const parse_mode = colvarparse::parse_normal); /// \brief Check that the grid information inside (boundaries, /// widths, ...) is consistent with the current setting of the @@ -1039,6 +941,13 @@ class colvar_grid_count : public colvar_grid return new_data[address(ix) + imult]; } + /// Write the current grid parameters to a string + std::string get_state_params() const; + + /// Read new grid parameters from a string + int parse_params(std::string const &conf, + colvarparse::Parse_Mode const parse_mode = colvarparse::parse_normal); + /// Read all grid parameters and data from a formatted stream std::istream & read_restart(std::istream &is); @@ -1239,6 +1148,14 @@ class colvar_grid_scalar : public colvar_grid samples->incr_count(ix); has_data = true; } + + /// Write the current grid parameters to a string + std::string get_state_params() const; + + /// Read new grid parameters from a string + int parse_params(std::string const &conf, + colvarparse::Parse_Mode const parse_mode = colvarparse::parse_normal); + /// Read all grid parameters and data from a formatted stream std::istream & read_restart(std::istream &is); @@ -1476,6 +1393,14 @@ class colvar_grid_gradient : public colvar_grid /// Constructor from a multicol file colvar_grid_gradient(std::string &filename); + + /// Write the current grid parameters to a string + std::string get_state_params() const; + + /// Read new grid parameters from a string + int parse_params(std::string const &conf, + colvarparse::Parse_Mode const parse_mode = colvarparse::parse_normal); + /// Read all grid parameters and data from a formatted stream std::istream & read_restart(std::istream &is); diff --git a/src/colvargrid_def.h b/src/colvargrid_def.h index 78e3a4e08..21ead0c5b 100644 --- a/src/colvargrid_def.h +++ b/src/colvargrid_def.h @@ -54,7 +54,7 @@ template cvm::memory_stream &colvar_grid::read_restart(cvm::memory_ template std::ostream &colvar_grid::write_restart(std::ostream &os) { - write_params(os); + os << get_state_params(); write_raw(os); return os; } @@ -62,9 +62,7 @@ template std::ostream &colvar_grid::write_restart(std::ostream &os) template cvm::memory_stream &colvar_grid::write_restart(cvm::memory_stream &os) { - std::ostringstream oss; - write_params(oss); - os << oss.str(); + os << get_state_params(); write_raw(os); return os; } @@ -144,6 +142,112 @@ cvm::memory_stream &colvar_grid::write_raw(cvm::memory_stream &os, size_t con } +template std::string colvar_grid::get_state_params() const +{ + std::ostringstream os; + size_t i; + os << "grid_parameters {\n n_colvars " << nd << "\n"; + + os << " lower_boundaries "; + for (i = 0; i < nd; i++) + os << " " << lower_boundaries[i]; + os << "\n"; + + os << " upper_boundaries "; + for (i = 0; i < nd; i++) + os << " " << upper_boundaries[i]; + os << "\n"; + + os << " widths "; + for (i = 0; i < nd; i++) + os << " " << widths[i]; + os << "\n"; + + os << " sizes "; + for (i = 0; i < nd; i++) + os << " " << nx[i]; + os << "\n"; + + os << "}\n"; + return os.str(); +} + + +template int colvar_grid::parse_params(std::string const &conf, + colvarparse::Parse_Mode const parse_mode) +{ + if (cvm::debug()) + cvm::log("Reading grid configuration from string.\n"); + + std::vector old_nx = nx; + std::vector old_lb = lower_boundaries; + std::vector old_ub = upper_boundaries; + std::vector old_w = widths; + + { + size_t nd_in = 0; + // this is only used in state files + colvarparse::get_keyval(conf, "n_colvars", nd_in, nd, colvarparse::parse_silent); + if (nd_in != nd) { + cvm::error("Error: trying to read data for a grid " + "that contains a different number of colvars ("+ + cvm::to_str(nd_in)+") than the grid defined " + "in the configuration file("+cvm::to_str(nd)+ + ").\n"); + return COLVARS_ERROR; + } + } + + // underscore keywords are used in state file + colvarparse::get_keyval(conf, "lower_boundaries", + lower_boundaries, lower_boundaries, colvarparse::parse_silent); + colvarparse::get_keyval(conf, "upper_boundaries", + upper_boundaries, upper_boundaries, colvarparse::parse_silent); + + // camel case keywords are used in config file + colvarparse::get_keyval(conf, "lowerBoundaries", + lower_boundaries, lower_boundaries, parse_mode); + colvarparse::get_keyval(conf, "upperBoundaries", + upper_boundaries, upper_boundaries, parse_mode); + + colvarparse::get_keyval(conf, "widths", widths, widths, parse_mode); + + // only used in state file + colvarparse::get_keyval(conf, "sizes", nx, nx, colvarparse::parse_silent); + + if (nd < lower_boundaries.size()) nd = lower_boundaries.size(); + + if (! use_actual_value.size()) use_actual_value.assign(nd, false); + if (! periodic.size()) periodic.assign(nd, false); + if (! widths.size()) widths.assign(nd, 1.0); + + cvm::real eps = 1.e-10; + + bool new_params = false; + if (old_nx.size()) { + for (size_t i = 0; i < nd; i++) { + if (old_nx[i] != nx[i] || + cvm::sqrt(cv[i]->dist2(old_lb[i], lower_boundaries[i])) > eps || + cvm::sqrt(cv[i]->dist2(old_ub[i], upper_boundaries[i])) > eps || + cvm::fabs(old_w[i] - widths[i]) > eps) { + new_params = true; + } + } + } else { + new_params = true; + } + + // reallocate the array in case the grid params have just changed + if (new_params) { + init_from_boundaries(); + // data.clear(); // no longer needed: setup calls clear() + return this->setup(nx, T(), mult); + } + + return COLVARS_OK; +} + + template std::istream & colvar_grid::read_multicol(std::istream &is, bool add) { From 1126132c5bd056ee10f4c80ebbbb64c7d58f06cf Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 22 Aug 2023 12:12:21 +0200 Subject: [PATCH 058/162] Small fixes --- src/colvarbias_histogram.h | 2 +- src/colvarbias_meta.h | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/colvarbias_histogram.h b/src/colvarbias_histogram.h index 48b9056f0..2c6ee84d1 100644 --- a/src/colvarbias_histogram.h +++ b/src/colvarbias_histogram.h @@ -24,7 +24,7 @@ class colvarbias_histogram : public colvarbias { public: colvarbias_histogram(char const *key); - ~colvarbias_histogram(); + virtual ~colvarbias_histogram(); virtual int init(std::string const &conf); virtual int update(); virtual int write_output_files(); diff --git a/src/colvarbias_meta.h b/src/colvarbias_meta.h index 59ce6a83f..4b3351486 100644 --- a/src/colvarbias_meta.h +++ b/src/colvarbias_meta.h @@ -17,6 +17,7 @@ #include "colvarbias.h" #include "colvargrid.h" + /// Metadynamics bias (implementation of \link colvarbias \endlink) class colvarbias_meta : public virtual colvarbias, @@ -57,8 +58,8 @@ class colvarbias_meta virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &state_conf); - virtual std::ostream & write_state_data(std::ostream &os); - virtual std::istream & read_state_data(std::istream &os); + virtual std::ostream &write_state_data(std::ostream &os); + virtual std::istream &read_state_data(std::istream &is); virtual int setup_output(); virtual int write_output_files(); From 96b02ddd45c3f838220ce5748617a1641f9d493c Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 23 Aug 2023 09:50:22 +0200 Subject: [PATCH 059/162] Remove declarations of functions that were never defined --- src/colvarbias_restraint.h | 9 --------- 1 file changed, 9 deletions(-) diff --git a/src/colvarbias_restraint.h b/src/colvarbias_restraint.h index 45a96d14f..f030a5cad 100644 --- a/src/colvarbias_restraint.h +++ b/src/colvarbias_restraint.h @@ -38,9 +38,6 @@ class colvarbias_restraint virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); - // virtual std::ostream & write_state_data(std::ostream &os); - // virtual std::istream & read_state_data(std::istream &os); - virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); @@ -242,8 +239,6 @@ class colvarbias_restraint_harmonic virtual int update(); virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); - virtual std::ostream & write_state_data(std::ostream &os); - virtual std::istream & read_state_data(std::istream &os); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); virtual int change_configuration(std::string const &conf); @@ -269,8 +264,6 @@ class colvarbias_restraint_harmonic_walls virtual int update(); virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); - virtual std::ostream & write_state_data(std::ostream &os); - virtual std::istream & read_state_data(std::istream &os); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); @@ -311,8 +304,6 @@ class colvarbias_restraint_linear virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &conf); - virtual std::ostream & write_state_data(std::ostream &os); - virtual std::istream & read_state_data(std::istream &os); virtual std::ostream & write_traj_label(std::ostream &os); virtual std::ostream & write_traj(std::ostream &os); From 51f8b9897bf51d8c58fa05680e4f37f4b9a29cc4 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 23 Aug 2023 10:36:03 +0200 Subject: [PATCH 060/162] Simplify and improve error handling --- src/colvarbias.cpp | 51 ++++++++++++++++++++-------------------------- src/colvarbias.h | 9 ++++++++ 2 files changed, 31 insertions(+), 29 deletions(-) diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp index 6d47f9361..6dc8126f6 100644 --- a/src/colvarbias.cpp +++ b/src/colvarbias.cpp @@ -527,15 +527,16 @@ cvm::memory_stream & colvarbias::write_state(cvm::memory_stream &os) template void raise_error_rewind(IST &is, SPT start_pos, std::string const &bias_type, - std::string const &bias_name) + std::string const &bias_name, std::string const added_msg = "") { - cvm::error("Error: in reading state for \"" + bias_type + "\" bias \"" + bias_name + - "\" at position " + cvm::to_str(static_cast(is.tellg())) + " in stream.\n", - COLVARS_INPUT_ERROR); auto state = is.rdstate(); is.clear(); is.seekg(start_pos); - is.setstate(state); + is.setstate(state | std::ios::failbit); + cvm::error("Error: in reading state for \"" + bias_type + "\" bias \"" + bias_name + + "\" at position " + cvm::to_str(static_cast(is.tellg())) + " in stream." + + added_msg + "\n", + COLVARS_INPUT_ERROR); } @@ -696,42 +697,34 @@ cvm::memory_stream & colvarbias::write_state_data_key(cvm::memory_stream &os, ch } -std::istream & colvarbias::read_state_data_key(std::istream &is, char const *key) +template IST &colvarbias::read_state_data_key_template(IST &is, char const *key) { auto const start_pos = is.tellg(); std::string key_in; - if ( !(is >> key_in) || - !(to_lower_cppstr(key_in) == to_lower_cppstr(std::string(key))) ) { - cvm::error("Error: in reading restart configuration for "+ - bias_type+" bias \""+this->name+"\" at position "+ - cvm::to_str(static_cast(is.tellg()))+ - " in stream.\n", COLVARS_INPUT_ERROR); - is.clear(); - is.seekg(start_pos); - is.setstate(std::ios::failbit); - return is; + if (is >> key_in) { + if (to_lower_cppstr(key_in) != to_lower_cppstr(std::string(key))) { + raise_error_rewind(is, start_pos, bias_type, name, + " Expected keyword \"" + std::string(key) + "\", found \"" + key_in + + "\"."); + } + } else { + raise_error_rewind(is, start_pos, bias_type, name); } return is; } -cvm::memory_stream & colvarbias::read_state_data_key(cvm::memory_stream &is, char const *key) +std::istream & colvarbias::read_state_data_key(std::istream &is, char const *key) { - auto const start_pos = is.tellg(); - std::string key_in; - if ( !(is >> key_in) || - !(to_lower_cppstr(key_in) == to_lower_cppstr(std::string(key))) ) { - cvm::error("Error: in reading restart configuration for "+ - bias_type+" bias \""+this->name+"\".\n", COLVARS_INPUT_ERROR); - is.clear(); - is.seekg(start_pos); - is.setstate(std::ios::failbit); - return is; - } - return is; + return read_state_data_key_template(is, key); } +cvm::memory_stream & colvarbias::read_state_data_key(cvm::memory_stream &is, char const *key) +{ + return read_state_data_key_template(is, key); +} + std::ostream & colvarbias::write_traj_label(std::ostream &os) { diff --git a/src/colvarbias.h b/src/colvarbias.h index baba27523..10494a373 100644 --- a/src/colvarbias.h +++ b/src/colvarbias.h @@ -173,6 +173,15 @@ class colvarbias /// \param[in] key Keyword labeling the header block cvm::memory_stream & write_state_data_key(cvm::memory_stream &os, char const *key); +private: + + /// Read a keyword header for a data sequence from a stream + /// \param[in,out] Input stream + /// \param[in] Keyword labeling the header block; an error will be raised if not matching + template IST &read_state_data_key_template(IST &is, char const *key); + +public: + /// Read a keyword header for a data sequence from a formatted stream /// \param[in,out] Input stream /// \param[in] Keyword labeling the header block; an error will be raised if not matching From 80dd305392d4cc6b60b635d658081abf89805e26 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 23 Aug 2023 10:59:12 +0200 Subject: [PATCH 061/162] More forward declarations of STL streams --- colvartools/poisson_integrator.cpp | 1 + misc_interfaces/stubs/colvarproxy_stub.cpp | 2 ++ src/colvar.h | 4 ++-- src/colvar_geometricpath.h | 1 + src/colvarcomp_apath.cpp | 3 ++- 5 files changed, 8 insertions(+), 3 deletions(-) diff --git a/colvartools/poisson_integrator.cpp b/colvartools/poisson_integrator.cpp index 5e561e29e..01aa220f7 100644 --- a/colvartools/poisson_integrator.cpp +++ b/colvartools/poisson_integrator.cpp @@ -1,3 +1,4 @@ +#include #include #include "colvargrid.h" diff --git a/misc_interfaces/stubs/colvarproxy_stub.cpp b/misc_interfaces/stubs/colvarproxy_stub.cpp index 576d23a0e..f94273557 100644 --- a/misc_interfaces/stubs/colvarproxy_stub.cpp +++ b/misc_interfaces/stubs/colvarproxy_stub.cpp @@ -7,6 +7,8 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#include + #include "colvarmodule.h" #include "colvarscript.h" #include "colvaratoms.h" diff --git a/src/colvar.h b/src/colvar.h index 19b863468..4dee696ce 100644 --- a/src/colvar.h +++ b/src/colvar.h @@ -10,9 +10,9 @@ #ifndef COLVAR_H #define COLVAR_H -#include -#include #include +#include +#include #include "colvarmodule.h" #include "colvarvalue.h" diff --git a/src/colvar_geometricpath.h b/src/colvar_geometricpath.h index 9ff78261f..ae28f6dda 100644 --- a/src/colvar_geometricpath.h +++ b/src/colvar_geometricpath.h @@ -14,6 +14,7 @@ #include #include #include +#include namespace GeometricPathCV { diff --git a/src/colvarcomp_apath.cpp b/src/colvarcomp_apath.cpp index a5535ba40..38c570add 100644 --- a/src/colvarcomp_apath.cpp +++ b/src/colvarcomp_apath.cpp @@ -7,11 +7,12 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. -#include #include #include #include +#include #include +#include #include "colvarvalue.h" #include "colvarparse.h" From f91a861ebfd5402766e3c744b6f03d7ffebdabfb Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 23 Aug 2023 11:32:42 +0200 Subject: [PATCH 062/162] Unformatted I/O for reweightAMD --- src/colvarbias_histogram_reweight_amd.cpp | 39 +++++++++++++++++++---- src/colvarbias_histogram_reweight_amd.h | 5 +++ 2 files changed, 38 insertions(+), 6 deletions(-) diff --git a/src/colvarbias_histogram_reweight_amd.cpp b/src/colvarbias_histogram_reweight_amd.cpp index 85f1bde35..de2f6d9b8 100644 --- a/src/colvarbias_histogram_reweight_amd.cpp +++ b/src/colvarbias_histogram_reweight_amd.cpp @@ -9,6 +9,7 @@ #include "colvarbias_histogram_reweight_amd.h" #include "colvarproxy.h" +#include "colvars_memstream.h" colvarbias_reweightaMD::colvarbias_reweightaMD(char const *key) : colvarbias_histogram(key), grid_count(NULL), grid_dV(NULL), @@ -343,23 +344,37 @@ void colvarbias_reweightaMD::compute_cumulant_expansion_factor( } } -std::ostream & colvarbias_reweightaMD::write_state_data(std::ostream& os) + +template OST & colvarbias_reweightaMD::write_state_data_template_(OST& os) { std::ios::fmtflags flags(os.flags()); os.setf(std::ios::fmtflags(0), std::ios::floatfield); - os << "grid\n"; + write_state_data_key(os, "grid"); grid->write_raw(os, 8); - os << "grid_count\n"; + write_state_data_key(os, "grid_count"); grid_count->write_raw(os, 8); - os << "grid_dV\n"; + write_state_data_key(os, "grid_dV"); grid_dV->write_raw(os, 8); - os << "grid_dV_square\n"; + write_state_data_key(os, "grid_dV_square"); grid_dV_square->write_raw(os, 8); os.flags(flags); return os; } -std::istream & colvarbias_reweightaMD::read_state_data(std::istream& is) + +std::ostream & colvarbias_reweightaMD::write_state_data(std::ostream& os) +{ + return write_state_data_template_(os); +} + + +cvm::memory_stream & colvarbias_reweightaMD::write_state_data(cvm::memory_stream& os) +{ + return write_state_data_template_(os); +} + + +template IST & colvarbias_reweightaMD::read_state_data_template_(IST& is) { if (! read_state_data_key(is, "grid")) { return is; @@ -387,3 +402,15 @@ std::istream & colvarbias_reweightaMD::read_state_data(std::istream& is) } return is; } + + +std::istream & colvarbias_reweightaMD::read_state_data(std::istream& is) +{ + return read_state_data_template_(is); +} + + +cvm::memory_stream & colvarbias_reweightaMD::read_state_data(cvm::memory_stream& is) +{ + return read_state_data_template_(is); +} diff --git a/src/colvarbias_histogram_reweight_amd.h b/src/colvarbias_histogram_reweight_amd.h index 7f50eb0f3..43759b3bd 100644 --- a/src/colvarbias_histogram_reweight_amd.h +++ b/src/colvarbias_histogram_reweight_amd.h @@ -79,9 +79,14 @@ class colvarbias_reweightaMD : public colvarbias_histogram { /// Write gradients of the PMF? bool b_write_gradients; + template OST & write_state_data_template_(OST& os); + template IST & read_state_data_template_(IST& is); + /// save and restore virtual std::istream & read_state_data(std::istream &is) override; + virtual cvm::memory_stream & read_state_data(cvm::memory_stream &is) override; virtual std::ostream & write_state_data(std::ostream &os) override; + virtual cvm::memory_stream & write_state_data(cvm::memory_stream &os) override; private: /// temporary grids for evaluating PMFs From 2bffdc6b61ab3376972ea540b4a6ad0e6bd93393 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 23 Aug 2023 18:36:28 +0200 Subject: [PATCH 063/162] Condense and simplify metadynamics state reading --- src/colvarbias_meta.cpp | 183 +++++++++++++++++----------------------- src/colvarbias_meta.h | 11 +++ 2 files changed, 88 insertions(+), 106 deletions(-) diff --git a/src/colvarbias_meta.cpp b/src/colvarbias_meta.cpp index eebbcf921..672c6ab71 100644 --- a/src/colvarbias_meta.cpp +++ b/src/colvarbias_meta.cpp @@ -1298,6 +1298,36 @@ int colvarbias_meta::set_state_params(std::string const &state_conf) } +template +IST & colvarbias_meta::read_grid_data_template_(IST& is, std::string const &key, + GT *grid, GT *backup_grid) +{ + auto const start_pos = is.tellg(); + std::string key_in; + if (is >> key_in) { + if ((key != key_in) || !(grid->read_restart(is))) { + is.clear(); + is.seekg(start_pos); + is.setstate(std::ios::failbit); + if (!rebin_grids) { + if ((backup_grid == nullptr) || (comm == single_replica)) { + cvm::error("Error: couldn't read grid data for metadynamics bias \""+ + this->name+"\""+ + ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ + "; if useGrids was off when the state file was written, " + "try enabling rebinGrids now to regenerate the grids.\n", COLVARS_INPUT_ERROR); + } + } + } + } else { + is.clear(); + is.seekg(start_pos); + is.setstate(std::ios::failbit); + } + return is; +} + + std::istream & colvarbias_meta::read_state_data(std::istream& is) { if (use_grids) { @@ -1316,95 +1346,26 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) hills_energy_gradients = new colvar_grid_gradient(colvars); } - std::streampos const hills_energy_pos = is.tellg(); - std::string key; - if (!(is >> key)) { - if (hills_energy_backup != NULL) { - delete hills_energy; - delete hills_energy_gradients; - hills_energy = hills_energy_backup; - hills_energy_gradients = hills_energy_gradients_backup; - } - is.clear(); - is.seekg(hills_energy_pos, std::ios::beg); - is.setstate(std::ios::failbit); - return is; - } else if (!(key == std::string("hills_energy")) || - !(hills_energy->read_restart(is))) { - is.clear(); - is.seekg(hills_energy_pos, std::ios::beg); - if (!rebin_grids) { - if ((hills_energy_backup == NULL) || (comm == single_replica)) { - cvm::error("Error: couldn't read the energy grid for metadynamics bias \""+ - this->name+"\""+ - ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ - "; if useGrids was off when the state file was written, " - "enable rebinGrids now to regenerate the grids.\n"); - } else { - delete hills_energy; - delete hills_energy_gradients; - hills_energy = hills_energy_backup; - hills_energy_gradients = hills_energy_gradients_backup; - is.setstate(std::ios::failbit); - return is; - } - } - } + read_grid_data_template_(is, "hills_energy", hills_energy, + hills_energy_backup); - std::streampos const hills_energy_gradients_pos = is.tellg(); - if (!(is >> key)) { - if (hills_energy_backup != NULL) { - delete hills_energy; - delete hills_energy_gradients; - hills_energy = hills_energy_backup; - hills_energy_gradients = hills_energy_gradients_backup; + read_grid_data_template_( + is, "hills_energy_gradients", hills_energy_gradients, hills_energy_gradients_backup); + + if (is) { + cvm::log(" successfully read the biasing potential and its gradients from grids.\n"); + if (hills_energy_backup != nullptr) { + // Now that we have successfully updated the grids, delete the backup copies + delete hills_energy_backup; + delete hills_energy_gradients_backup; } - is.clear(); - is.seekg(hills_energy_gradients_pos, std::ios::beg); - is.setstate(std::ios::failbit); + } else { return is; - } else if (!(key == std::string("hills_energy_gradients")) || - !(hills_energy_gradients->read_restart(is))) { - is.clear(); - is.seekg(hills_energy_gradients_pos, std::ios::beg); - if (!rebin_grids) { - if ((hills_energy_backup == NULL) || (comm == single_replica)) { - cvm::error("Error: couldn't read the gradients grid for metadynamics bias \""+ - this->name+"\""+ - ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ - "; if useGrids was off when the state file was written, " - "enable rebinGrids now to regenerate the grids.\n"); - } else { - delete hills_energy; - delete hills_energy_gradients; - hills_energy = hills_energy_backup; - hills_energy_gradients = hills_energy_gradients_backup; - is.setstate(std::ios::failbit); - return is; - } - } - } - - if (cvm::debug()) - cvm::log("Successfully read new grids for bias \""+ - this->name+"\""+ - ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+"\n"); - - cvm::log(" read biasing energy and forces from grids.\n"); - - if (hills_energy_backup != NULL) { - // now that we have successfully updated the grids, delete the - // backup copies - if (cvm::debug()) - cvm::log("Deallocating the older grids.\n"); - - delete hills_energy_backup; - delete hills_energy_gradients_backup; } } - // Save references to the end of the list of existing hills, so that it can - // be cleared if hills are read successfully state + // Save references to the end of the list of existing hills, so that they can + // be cleared if hills are read successfully from the stream bool const existing_hills = !hills.empty(); size_t const old_hills_size = hills.size(); hill_iter old_hills_end = hills.end(); @@ -1423,12 +1384,15 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) cvm::to_str((hills.back()).it)+".\n"); } } + is.clear(); + new_hills_begin = hills.end(); - cvm::log(" read "+cvm::to_str(hills.size() - old_hills_size)+ - " additional explicit hills.\n"); + cvm::log(" successfully read "+cvm::to_str(hills.size() - old_hills_size)+ + " explicit hills from state.\n"); if (existing_hills) { + // Prune any hills that pre-existed those just read hills.erase(hills.begin(), old_hills_end); hills_off_grid.erase(hills_off_grid.begin(), old_hills_off_grid_end); if (cvm::debug()) { @@ -1437,6 +1401,34 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) } } + // If rebinGrids is set, rebin the grids based on the current information + rebin_grids_after_restart(); + + if (use_grids) { + if (!hills_off_grid.empty()) { + cvm::log(cvm::to_str(hills_off_grid.size())+" hills are near the " + "grid boundaries: they will be computed analytically " + "and saved to the state files.\n"); + } + } + + colvarbias_ti::read_state_data(is); + + if (cvm::debug()) + cvm::log("colvarbias_meta::read_restart() done\n"); + + has_data = true; + + if (comm == multiple_replicas) { + read_replica_files(); + } + + return is; +} + + +void colvarbias_meta::rebin_grids_after_restart() +{ if (rebin_grids) { // allocate new grids (based on the new boundaries and widths just @@ -1483,27 +1475,6 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) if (!hills.empty()) recount_hills_off_grid(hills.begin(), hills.end(), hills_energy); } - - if (use_grids) { - if (!hills_off_grid.empty()) { - cvm::log(cvm::to_str(hills_off_grid.size())+" hills are near the " - "grid boundaries: they will be computed analytically " - "and saved to the state files.\n"); - } - } - - colvarbias_ti::read_state_data(is); - - if (cvm::debug()) - cvm::log("colvarbias_meta::read_restart() done\n"); - - has_data = true; - - if (comm != single_replica) { - read_replica_files(); - } - - return is; } diff --git a/src/colvarbias_meta.h b/src/colvarbias_meta.h index 4b3351486..40b67c311 100644 --- a/src/colvarbias_meta.h +++ b/src/colvarbias_meta.h @@ -58,9 +58,20 @@ class colvarbias_meta virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &state_conf); + virtual std::ostream &write_state_data(std::ostream &os); virtual std::istream &read_state_data(std::istream &is); +private: + + template + IST &read_grid_data_template_(IST &is, std::string const &key, GT *grid, GT *backup_grid); + +public: + + /// Function called by read_state_data() to execute rebinning (if requested) + void rebin_grids_after_restart(); + virtual int setup_output(); virtual int write_output_files(); virtual void write_pmf(); From 8d442f0cb2a636de679c50d9c0ad7dd43be9a487 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 24 Aug 2023 10:13:32 +0200 Subject: [PATCH 064/162] Refactor formatted I/O for metadynamics before adding unformatted version --- src/colvarbias.cpp | 7 +- src/colvarbias.h | 7 +- src/colvarbias_meta.cpp | 230 ++++++++++++++++++++++------------------ src/colvarbias_meta.h | 14 ++- 4 files changed, 144 insertions(+), 114 deletions(-) diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp index 6dc8126f6..6a691fe08 100644 --- a/src/colvarbias.cpp +++ b/src/colvarbias.cpp @@ -683,14 +683,15 @@ int colvarbias::read_state_string(char const *buffer) } -std::ostream & colvarbias::write_state_data_key(std::ostream &os, char const *key) +std::ostream & colvarbias::write_state_data_key(std::ostream &os, char const *key, bool header) { - os << "\n" << key << "\n"; + os << (header ? "\n" : "") << key << (header ? "\n" : " "); return os; } -cvm::memory_stream & colvarbias::write_state_data_key(cvm::memory_stream &os, char const *key) +cvm::memory_stream & colvarbias::write_state_data_key(cvm::memory_stream &os, char const *key, + bool /* header */) { os << key; return os; diff --git a/src/colvarbias.h b/src/colvarbias.h index 10494a373..c080d947d 100644 --- a/src/colvarbias.h +++ b/src/colvarbias.h @@ -166,12 +166,15 @@ class colvarbias /// Write a keyword header for a data sequence to a formatted stream /// \param[in,out] os Output stream /// \param[in] key Keyword labeling the header block - std::ostream & write_state_data_key(std::ostream &os, char const *key); + /// \param[in] header Whether this is the header of a multi-line segment vs a single line + std::ostream & write_state_data_key(std::ostream &os, char const *key, bool header = true); /// Write a keyword header for a data sequence to an unformatted stream /// \param[in,out] os Output stream /// \param[in] key Keyword labeling the header block - cvm::memory_stream & write_state_data_key(cvm::memory_stream &os, char const *key); + /// \param[in] header Ignored + cvm::memory_stream & write_state_data_key(cvm::memory_stream &os, char const *key, + bool header = true); private: diff --git a/src/colvarbias_meta.cpp b/src/colvarbias_meta.cpp index 672c6ab71..05378ab80 100644 --- a/src/colvarbias_meta.cpp +++ b/src/colvarbias_meta.cpp @@ -35,6 +35,7 @@ #include "colvarproxy.h" #include "colvar.h" #include "colvarbias_meta.h" +#include "colvars_memstream.h" colvarbias_meta::colvarbias_meta(char const *key) @@ -625,7 +626,7 @@ int colvarbias_meta::update_bias() std::ostream &replica_hills_os = cvm::proxy->output_stream(replica_hills_file); if (replica_hills_os) { - replica_hills_os << hills.back(); + write_hill(replica_hills_os, hills.back()); } else { return cvm::error("Error: in metadynamics bias \""+this->name+"\""+ ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ @@ -1328,7 +1329,7 @@ IST & colvarbias_meta::read_grid_data_template_(IST& is, std::string const &key, } -std::istream & colvarbias_meta::read_state_data(std::istream& is) +template IST &colvarbias_meta::read_state_data_template_(IST &is) { if (use_grids) { @@ -1427,6 +1428,18 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) } +std::istream & colvarbias_meta::read_state_data(std::istream& is) +{ + return read_state_data_template_(is); +} + + +// cvm::memory_stream &colvarbias_meta::read_state_data(cvm::memory_stream &is) +// { +// return read_state_data_template_(is); +// } + + void colvarbias_meta::rebin_grids_after_restart() { if (rebin_grids) { @@ -1478,25 +1491,70 @@ void colvarbias_meta::rebin_grids_after_restart() } -inline std::istream & reset_istream(std::istream &is, size_t start_pos) +std::ostream &colvarbias_meta::write_hill(std::ostream &os, colvarbias_meta::hill const &h) +{ + os.setf(std::ios::scientific, std::ios::floatfield); + + write_state_data_key(os, "hill", false); + + os << "{\n"; + + write_state_data_key(os, "step", false); + os << std::setw(cvm::it_width) << h.it << "\n"; + + write_state_data_key(os, "weight", false); + os << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << h.W << "\n"; + + if (h.replica.size()) { + write_state_data_key(os, "replicaID", false); + os << h.replica << "\n"; + } + + size_t i; + write_state_data_key(os, "centers", false); + for (i = 0; i < (h.centers).size(); i++) { + os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << h.centers[i]; + } + os << "\n"; + + // For backward compatibility, write the widths instead of the sigmas + write_state_data_key(os, "widths", false); + for (i = 0; i < (h.sigmas).size(); i++) { + os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << 2.0 * h.sigmas[i]; + } + os << "\n"; + + os << "}\n"; + + return os; +} + + +template IST &hill_stream_error(IST &is, size_t start_pos, std::string const &key) { is.clear(); - is.seekg(start_pos, std::ios::beg); + is.seekg(start_pos); is.setstate(std::ios::failbit); + cvm::error("Error: in reading data for keyword \"" + key + "\" from stream.\n", + COLVARS_INPUT_ERROR); return is; } -std::istream & colvarbias_meta::read_hill(std::istream &is) +std::istream &colvarbias_meta::read_hill(std::istream &is) { - if (!is) return is; // do nothing if failbit is set + if (!is) + return is; // do nothing if failbit is set - std::streampos const start_pos = is.tellg(); - size_t i = 0; + auto const start_pos = is.tellg(); std::string data; - if ( !(is >> read_block("hill", &data)) ) { - return reset_istream(is, start_pos); + if (!(is >> read_block("hill", &data))) { + auto state = is.rdstate(); + is.clear(); + is.seekg(start_pos); + is.setstate(state); + return is; } std::istringstream data_is(data); @@ -1504,62 +1562,56 @@ std::istream & colvarbias_meta::read_hill(std::istream &is) cvm::step_number h_it = 0L; cvm::real h_weight = 0.0; std::vector h_centers(num_variables()); - for (i = 0; i < num_variables(); i++) { + for (size_t i = 0; i < num_variables(); i++) { h_centers[i].type(variables(i)->value()); } std::vector h_sigmas(num_variables()); std::string h_replica; - std::string keyword; - while (data_is >> keyword) { + if (!read_state_data_key(data_is, "step") || !(data_is >> h_it)) { + return hill_stream_error(is, start_pos, "step"); + } - if (keyword == "step") { - if ( !(data_is >> h_it)) { - return reset_istream(is, start_pos); - } - if ((h_it <= state_file_step) && !restart_keep_hills) { - if (cvm::debug()) - cvm::log("Skipping a hill older than the state file for metadynamics bias \""+ - this->name+"\""+ - ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+"\n"); - return is; - } - } + if ((h_it <= state_file_step) && !restart_keep_hills) { + if (cvm::debug()) + cvm::log("Skipping a hill older than the state file for metadynamics bias \"" + this->name + + "\"" + ((comm != single_replica) ? ", replica \"" + replica_id + "\"" : "") + "\n"); + return is; + } - if (keyword == "weight") { - if ( !(data_is >> h_weight)) { - return reset_istream(is, start_pos); - } + if (read_state_data_key(data_is, "weight")) { + if (!(data_is >> h_weight)) { + return hill_stream_error(is, start_pos, "weight"); } + } - if (keyword == "centers") { - for (i = 0; i < num_variables(); i++) { - if ( !(data_is >> h_centers[i])) { - return reset_istream(is, start_pos); - } + if (read_state_data_key(data_is, "centers")) { + for (size_t i = 0; i < num_variables(); i++) { + if (!(data_is >> h_centers[i])) { + return hill_stream_error(is, start_pos, "centers"); } } + } - if (keyword == "widths") { - for (i = 0; i < num_variables(); i++) { - if ( !(data_is >> h_sigmas[i])) { - return reset_istream(is, start_pos); - } - // For backward compatibility, read the widths instead of the sigmas - h_sigmas[i] /= 2.0; + if (read_state_data_key(data_is, "widths")) { + for (size_t i = 0; i < num_variables(); i++) { + if (!(data_is >> h_sigmas[i])) { + return hill_stream_error(is, start_pos, "widths"); } + // For backward compatibility, read the widths instead of the sigmas + h_sigmas[i] /= 2.0; } + } - if (comm != single_replica) { - if (keyword == "replicaID") { - if ( !(data_is >> h_replica)) { - return reset_istream(is, start_pos); - } - if (h_replica != replica_id) { - cvm::error("Error: trying to read a hill created by replica \""+ - h_replica+"\" for replica \""+replica_id+ - "\"; did you swap output files?\n", COLVARS_INPUT_ERROR); - } + if (comm != single_replica) { + if (read_state_data_key(data_is, "replicaID")) { + if (!(data_is >> h_replica)) { + return hill_stream_error(is, start_pos, "replicaID"); + } + if (h_replica != replica_id) { + cvm::error("Error: trying to read a hill created by replica \"" + h_replica + + "\" for replica \"" + replica_id + "\"; did you swap output files?\n", + COLVARS_INPUT_ERROR); } } } @@ -1576,7 +1628,7 @@ std::istream & colvarbias_meta::read_hill(std::istream &is) // add this also to the list of hills that are off-grid, which will // be computed analytically cvm::real const min_dist = - hills_energy->bin_distance_from_boundaries((hills.back()).centers, true); + hills_energy->bin_distance_from_boundaries((hills.back()).centers, true); if (min_dist < (3.0 * cvm::floor(hill_width)) + 1.0) { hills_off_grid.push_back(hills.back()); } @@ -1719,36 +1771,32 @@ std::string const colvarbias_meta::get_state_params() const } -std::ostream & colvarbias_meta::write_state_data(std::ostream& os) +template OST &colvarbias_meta::write_state_data_template_(OST &os) { if (use_grids) { // this is a very good time to project hills, if you haven't done // it already! - project_hills(new_hills_begin, hills.end(), - hills_energy, hills_energy_gradients); + project_hills(new_hills_begin, hills.end(), hills_energy, hills_energy_gradients); new_hills_begin = hills.end(); // write down the grids to the restart file - os << " hills_energy\n"; + write_state_data_key(os, "hills_energy"); hills_energy->write_restart(os); - os << " hills_energy_gradients\n"; + write_state_data_key(os, "hills_energy_gradients"); hills_energy_gradients->write_restart(os); } - if ( (!use_grids) || keep_hills ) { + if ((!use_grids) || keep_hills) { // write all hills currently in memory - for (std::list::const_iterator h = this->hills.begin(); - h != this->hills.end(); - h++) { - os << *h; + for (std::list::const_iterator h = this->hills.begin(); h != this->hills.end(); h++) { + write_hill(os, *h); } } else { // write just those that are near the grid boundaries for (std::list::const_iterator h = this->hills_off_grid.begin(); - h != this->hills_off_grid.end(); - h++) { - os << *h; + h != this->hills_off_grid.end(); h++) { + write_hill(os, *h); } } @@ -1757,6 +1805,18 @@ std::ostream & colvarbias_meta::write_state_data(std::ostream& os) } +std::ostream & colvarbias_meta::write_state_data(std::ostream& os) +{ + return write_state_data_template_(os); +} + + +// cvm::memory_stream &colvarbias_meta::write_state_data(cvm::memory_stream &os) +// { +// return write_state_data_template_(os); +// } + + int colvarbias_meta::write_state_to_replicas() { int error_code = COLVARS_OK; @@ -2008,43 +2068,3 @@ colvarbias_meta::hill::operator = (colvarbias_meta::hill const &h) colvarbias_meta::hill::~hill() {} - - -std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h) -{ - os.setf(std::ios::scientific, std::ios::floatfield); - - os << "hill {\n"; - os << " step " << std::setw(cvm::it_width) << h.it << "\n"; - os << " weight " - << std::setprecision(cvm::en_prec) - << std::setw(cvm::en_width) - << h.W << "\n"; - - if (h.replica.size()) - os << " replicaID " << h.replica << "\n"; - - size_t i; - os << " centers "; - for (i = 0; i < (h.centers).size(); i++) { - os << " " - << std::setprecision(cvm::cv_prec) - << std::setw(cvm::cv_width) - << h.centers[i]; - } - os << "\n"; - - // For backward compatibility, write the widths instead of the sigmas - os << " widths "; - for (i = 0; i < (h.sigmas).size(); i++) { - os << " " - << std::setprecision(cvm::cv_prec) - << std::setw(cvm::cv_width) - << 2.0 * h.sigmas[i]; - } - os << "\n"; - - os << "}\n"; - - return os; -} diff --git a/src/colvarbias_meta.h b/src/colvarbias_meta.h index 40b67c311..c6d916b38 100644 --- a/src/colvarbias_meta.h +++ b/src/colvarbias_meta.h @@ -60,13 +60,19 @@ class colvarbias_meta virtual int set_state_params(std::string const &state_conf); virtual std::ostream &write_state_data(std::ostream &os); + // virtual cvm::memory_stream &write_state_data(cvm::memory_stream &os); virtual std::istream &read_state_data(std::istream &is); + // virtual cvm::memory_stream &read_state_data(cvm::memory_stream &is); private: template IST &read_grid_data_template_(IST &is, std::string const &key, GT *grid, GT *backup_grid); + template IST &read_state_data_template_(IST &is); + + template OST &write_state_data_template_(OST &os); + public: /// Function called by read_state_data() to execute rebinning (if requested) @@ -119,7 +125,10 @@ class colvarbias_meta void recount_hills_off_grid(hill_iter h_first, hill_iter h_last, colvar_grid_scalar *ge); - /// Read a hill from a file + /// Write a hill to a stream + std::ostream & write_hill(std::ostream &os, hill const &h); + + /// Read a new hill from a state stream std::istream & read_hill(std::istream &is); /// \brief Add a new hill; if a .hills trajectory is written, @@ -413,9 +422,6 @@ class colvarbias_meta::hill { /// Represent the hill ina string suitable for a trajectory file std::string output_traj(); - /// Write the hill to an output stream - friend std::ostream & operator << (std::ostream &os, hill const &h); - }; From 90e1611094e6334e52dd65c7a67e73a2e4e08835 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 25 Aug 2023 12:06:18 +0200 Subject: [PATCH 065/162] Unformatted state I/O for metadynamics --- src/colvarbias_meta.cpp | 174 +++++++++++++++++++++++++++------------- src/colvarbias_meta.h | 22 +++-- 2 files changed, 134 insertions(+), 62 deletions(-) diff --git a/src/colvarbias_meta.cpp b/src/colvarbias_meta.cpp index 05378ab80..b00b2482c 100644 --- a/src/colvarbias_meta.cpp +++ b/src/colvarbias_meta.cpp @@ -1347,10 +1347,10 @@ template IST &colvarbias_meta::read_state_data_template_(IST &is) hills_energy_gradients = new colvar_grid_gradient(colvars); } - read_grid_data_template_(is, "hills_energy", hills_energy, - hills_energy_backup); + read_grid_data_template_(is, "hills_energy", hills_energy, + hills_energy_backup); - read_grid_data_template_( + read_grid_data_template_( is, "hills_energy_gradients", hills_energy_gradients, hills_energy_gradients_backup); if (is) { @@ -1380,9 +1380,9 @@ template IST &colvarbias_meta::read_state_data_template_(IST &is) while (read_hill(is)) { if (cvm::debug()) { cvm::log("Read a previously saved hill under the " - "metadynamics bias \""+ - this->name+"\", created at step "+ - cvm::to_str((hills.back()).it)+".\n"); + "metadynamics bias \"" + + this->name + "\", created at step " + cvm::to_str((hills.back()).it) + + "; position in stream is " + cvm::to_str(is.tellg()) + ".\n"); } } @@ -1434,10 +1434,10 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is) } -// cvm::memory_stream &colvarbias_meta::read_state_data(cvm::memory_stream &is) -// { -// return read_state_data_template_(is); -// } +cvm::memory_stream &colvarbias_meta::read_state_data(cvm::memory_stream &is) +{ + return read_state_data_template_(is); +} void colvarbias_meta::rebin_grids_after_restart() @@ -1491,45 +1491,81 @@ void colvarbias_meta::rebin_grids_after_restart() } -std::ostream &colvarbias_meta::write_hill(std::ostream &os, colvarbias_meta::hill const &h) +template +OST &colvarbias_meta::write_hill_template_(OST &os, colvarbias_meta::hill const &h) { - os.setf(std::ios::scientific, std::ios::floatfield); + bool const formatted = !std::is_same::value; + + if (formatted) { + os.setf(std::ios::scientific, std::ios::floatfield); + } write_state_data_key(os, "hill", false); - os << "{\n"; + if (formatted) + os << "{\n"; write_state_data_key(os, "step", false); - os << std::setw(cvm::it_width) << h.it << "\n"; + if (formatted) + os << std::setw(cvm::it_width); + os << h.it; + if (formatted) + os << "\n"; write_state_data_key(os, "weight", false); - os << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << h.W << "\n"; - - if (h.replica.size()) { - write_state_data_key(os, "replicaID", false); - os << h.replica << "\n"; - } + if (formatted) + os << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width); + os << h.W; + if (formatted) + os << "\n"; size_t i; write_state_data_key(os, "centers", false); for (i = 0; i < (h.centers).size(); i++) { - os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << h.centers[i]; + if (formatted) + os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width); + os << h.centers[i]; } - os << "\n"; + if (formatted) + os << "\n"; // For backward compatibility, write the widths instead of the sigmas write_state_data_key(os, "widths", false); for (i = 0; i < (h.sigmas).size(); i++) { - os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << 2.0 * h.sigmas[i]; + if (formatted) + os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width); + os << 2.0 * h.sigmas[i]; + } + if (formatted) + os << "\n"; + + if (h.replica.size()) { + write_state_data_key(os, "replicaID", false); + os << h.replica; + if (formatted) + os << "\n"; } - os << "\n"; - os << "}\n"; + if (formatted) + os << "}\n"; return os; } +std::ostream &colvarbias_meta::write_hill(std::ostream &os, colvarbias_meta::hill const &h) +{ + return write_hill_template_(os, h); +} + + +cvm::memory_stream &colvarbias_meta::write_hill(cvm::memory_stream &os, + colvarbias_meta::hill const &h) +{ + return write_hill_template_(os, h); +} + + template IST &hill_stream_error(IST &is, size_t start_pos, std::string const &key) { is.clear(); @@ -1541,23 +1577,29 @@ template IST &hill_stream_error(IST &is, size_t start_pos, std::s } -std::istream &colvarbias_meta::read_hill(std::istream &is) +template IST &colvarbias_meta::read_hill_template_(IST &is) { if (!is) return is; // do nothing if failbit is set + bool const formatted = !std::is_same::value; + auto const start_pos = is.tellg(); - std::string data; - if (!(is >> read_block("hill", &data))) { - auto state = is.rdstate(); + std::string key; + if (!(is >> key) || (key != "hill")) { is.clear(); is.seekg(start_pos); - is.setstate(state); + is.setstate(std::ios::failbit); return is; } - std::istringstream data_is(data); + if (formatted) { + std::string brace; + if (!(is >> brace) || (brace != "{")) { + return hill_stream_error(is, start_pos, "hill"); + } + } cvm::step_number h_it = 0L; cvm::real h_weight = 0.0; @@ -1568,35 +1610,28 @@ std::istream &colvarbias_meta::read_hill(std::istream &is) std::vector h_sigmas(num_variables()); std::string h_replica; - if (!read_state_data_key(data_is, "step") || !(data_is >> h_it)) { - return hill_stream_error(is, start_pos, "step"); + if (!read_state_data_key(is, "step") || !(is >> h_it)) { + return hill_stream_error(is, start_pos, "step"); } - if ((h_it <= state_file_step) && !restart_keep_hills) { - if (cvm::debug()) - cvm::log("Skipping a hill older than the state file for metadynamics bias \"" + this->name + - "\"" + ((comm != single_replica) ? ", replica \"" + replica_id + "\"" : "") + "\n"); - return is; - } - - if (read_state_data_key(data_is, "weight")) { - if (!(data_is >> h_weight)) { - return hill_stream_error(is, start_pos, "weight"); + if (read_state_data_key(is, "weight")) { + if (!(is >> h_weight)) { + return hill_stream_error(is, start_pos, "weight"); } } - if (read_state_data_key(data_is, "centers")) { + if (read_state_data_key(is, "centers")) { for (size_t i = 0; i < num_variables(); i++) { - if (!(data_is >> h_centers[i])) { - return hill_stream_error(is, start_pos, "centers"); + if (!(is >> h_centers[i])) { + return hill_stream_error(is, start_pos, "centers"); } } } - if (read_state_data_key(data_is, "widths")) { + if (read_state_data_key(is, "widths")) { for (size_t i = 0; i < num_variables(); i++) { - if (!(data_is >> h_sigmas[i])) { - return hill_stream_error(is, start_pos, "widths"); + if (!(is >> h_sigmas[i])) { + return hill_stream_error(is, start_pos, "widths"); } // For backward compatibility, read the widths instead of the sigmas h_sigmas[i] /= 2.0; @@ -1604,18 +1639,33 @@ std::istream &colvarbias_meta::read_hill(std::istream &is) } if (comm != single_replica) { - if (read_state_data_key(data_is, "replicaID")) { - if (!(data_is >> h_replica)) { - return hill_stream_error(is, start_pos, "replicaID"); + if (read_state_data_key(is, "replicaID")) { + if (!(is >> h_replica)) { + return hill_stream_error(is, start_pos, "replicaID"); } if (h_replica != replica_id) { cvm::error("Error: trying to read a hill created by replica \"" + h_replica + "\" for replica \"" + replica_id + "\"; did you swap output files?\n", COLVARS_INPUT_ERROR); + return hill_stream_error(is, start_pos, "replicaID"); } } } + if (formatted) { + std::string brace; + if (!(is >> brace) || (brace != "}")) { + return hill_stream_error(is, start_pos, "hill"); + } + } + + if ((h_it <= state_file_step) && !restart_keep_hills) { + if (cvm::debug()) + cvm::log("Skipping a hill older than the state file for metadynamics bias \"" + this->name + + "\"" + ((comm != single_replica) ? ", replica \"" + replica_id + "\"" : "") + "\n"); + return is; + } + hill_iter const hills_end = hills.end(); hills.push_back(hill(h_it, h_weight, h_centers, h_sigmas, h_replica)); if (new_hills_begin == hills_end) { @@ -1639,6 +1689,18 @@ std::istream &colvarbias_meta::read_hill(std::istream &is) } +std::istream &colvarbias_meta::read_hill(std::istream &is) +{ + return read_hill_template_(is); +} + + +cvm::memory_stream &colvarbias_meta::read_hill(cvm::memory_stream &is) +{ + return read_hill_template_(is); +} + + int colvarbias_meta::setup_output() { int error_code = COLVARS_OK; @@ -1811,10 +1873,10 @@ std::ostream & colvarbias_meta::write_state_data(std::ostream& os) } -// cvm::memory_stream &colvarbias_meta::write_state_data(cvm::memory_stream &os) -// { -// return write_state_data_template_(os); -// } +cvm::memory_stream &colvarbias_meta::write_state_data(cvm::memory_stream &os) +{ + return write_state_data_template_(os); +} int colvarbias_meta::write_state_to_replicas() diff --git a/src/colvarbias_meta.h b/src/colvarbias_meta.h index c6d916b38..f85bb0fdc 100644 --- a/src/colvarbias_meta.h +++ b/src/colvarbias_meta.h @@ -60,9 +60,9 @@ class colvarbias_meta virtual int set_state_params(std::string const &state_conf); virtual std::ostream &write_state_data(std::ostream &os); - // virtual cvm::memory_stream &write_state_data(cvm::memory_stream &os); + virtual cvm::memory_stream &write_state_data(cvm::memory_stream &os); virtual std::istream &read_state_data(std::istream &is); - // virtual cvm::memory_stream &read_state_data(cvm::memory_stream &is); + virtual cvm::memory_stream &read_state_data(cvm::memory_stream &is); private: @@ -123,14 +123,24 @@ class colvarbias_meta /// Regenerate the hills_off_grid list void recount_hills_off_grid(hill_iter h_first, hill_iter h_last, - colvar_grid_scalar *ge); + colvar_grid_scalar *ge); - /// Write a hill to a stream - std::ostream & write_hill(std::ostream &os, hill const &h); + template OST &write_hill_template_(OST &os, colvarbias_meta::hill const &h); - /// Read a new hill from a state stream + /// Write a hill to a formatted stream + std::ostream &write_hill(std::ostream &os, hill const &h); + + /// Write a hill to an unformatted stream + cvm::memory_stream &write_hill(cvm::memory_stream &os, hill const &h); + + template IST &read_hill_template_(IST &is); + + /// Read a new hill from a formatted stream std::istream & read_hill(std::istream &is); + /// Read a new hill from an unformatted stream + cvm::memory_stream & read_hill(cvm::memory_stream &is); + /// \brief Add a new hill; if a .hills trajectory is written, /// write it there; if there is more than one replica, communicate /// it to the others From 3e8e9e3c8b301340fcf3e6b5b1677972fcdff4ef Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 31 Aug 2023 10:09:43 -0400 Subject: [PATCH 066/162] Ensure that a string object is written --- src/colvar.cpp | 2 +- src/colvarbias.cpp | 19 ++++++++++--------- src/colvarbias.h | 12 ++++++------ src/colvargrid_def.h | 28 ++++++++++++++-------------- 4 files changed, 31 insertions(+), 30 deletions(-) diff --git a/src/colvar.cpp b/src/colvar.cpp index b7177186b..0e9b28b18 100644 --- a/src/colvar.cpp +++ b/src/colvar.cpp @@ -2501,7 +2501,7 @@ std::string const colvar::get_state_params() const cvm::memory_stream & colvar::write_state(cvm::memory_stream &os) const { - os << "colvar" << get_state_params(); + os << std::string("colvar") << get_state_params(); if (runave_outfile.size() > 0) { cvm::main()->proxy->flush_output_stream(runave_outfile); diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp index 6a691fe08..451d82aac 100644 --- a/src/colvarbias.cpp +++ b/src/colvarbias.cpp @@ -519,7 +519,7 @@ cvm::memory_stream & colvarbias::write_state(cvm::memory_stream &os) if (cvm::debug()) { cvm::log("Writing unformatted state for bias \""+name+"\"\n"); } - os << state_keyword << "configuration" << get_state_params(); + os << state_keyword << std::string("configuration") << get_state_params(); write_state_data(os); return os; } @@ -683,27 +683,28 @@ int colvarbias::read_state_string(char const *buffer) } -std::ostream & colvarbias::write_state_data_key(std::ostream &os, char const *key, bool header) +std::ostream &colvarbias::write_state_data_key(std::ostream &os, std::string const &key, + bool header) { os << (header ? "\n" : "") << key << (header ? "\n" : " "); return os; } -cvm::memory_stream & colvarbias::write_state_data_key(cvm::memory_stream &os, char const *key, - bool /* header */) +cvm::memory_stream &colvarbias::write_state_data_key(cvm::memory_stream &os, std::string const &key, + bool /* header */) { - os << key; + os << std::string(key); return os; } -template IST &colvarbias::read_state_data_key_template(IST &is, char const *key) +template IST &colvarbias::read_state_data_key_template(IST &is, std::string const &key) { auto const start_pos = is.tellg(); std::string key_in; if (is >> key_in) { - if (to_lower_cppstr(key_in) != to_lower_cppstr(std::string(key))) { + if (key_in != key) { raise_error_rewind(is, start_pos, bias_type, name, " Expected keyword \"" + std::string(key) + "\", found \"" + key_in + "\"."); @@ -715,13 +716,13 @@ template IST &colvarbias::read_state_data_key_template(IST &is, c } -std::istream & colvarbias::read_state_data_key(std::istream &is, char const *key) +std::istream & colvarbias::read_state_data_key(std::istream &is, std::string const &key) { return read_state_data_key_template(is, key); } -cvm::memory_stream & colvarbias::read_state_data_key(cvm::memory_stream &is, char const *key) +cvm::memory_stream & colvarbias::read_state_data_key(cvm::memory_stream &is, std::string const &key) { return read_state_data_key_template(is, key); } diff --git a/src/colvarbias.h b/src/colvarbias.h index c080d947d..1217a2b2b 100644 --- a/src/colvarbias.h +++ b/src/colvarbias.h @@ -167,33 +167,33 @@ class colvarbias /// \param[in,out] os Output stream /// \param[in] key Keyword labeling the header block /// \param[in] header Whether this is the header of a multi-line segment vs a single line - std::ostream & write_state_data_key(std::ostream &os, char const *key, bool header = true); + std::ostream &write_state_data_key(std::ostream &os, std::string const &key, bool header = true); /// Write a keyword header for a data sequence to an unformatted stream /// \param[in,out] os Output stream /// \param[in] key Keyword labeling the header block /// \param[in] header Ignored - cvm::memory_stream & write_state_data_key(cvm::memory_stream &os, char const *key, - bool header = true); + cvm::memory_stream &write_state_data_key(cvm::memory_stream &os, std::string const &key, + bool header = true); private: /// Read a keyword header for a data sequence from a stream /// \param[in,out] Input stream /// \param[in] Keyword labeling the header block; an error will be raised if not matching - template IST &read_state_data_key_template(IST &is, char const *key); + template IST &read_state_data_key_template(IST &is, std::string const &key); public: /// Read a keyword header for a data sequence from a formatted stream /// \param[in,out] Input stream /// \param[in] Keyword labeling the header block; an error will be raised if not matching - std::istream & read_state_data_key(std::istream &is, char const *key); + std::istream & read_state_data_key(std::istream &is, std::string const &key); /// Read a keyword header for a data sequence from an unformatted stream /// \param[in,out] Input stream /// \param[in] Keyword labeling the header block; an error will be raised if not matching - cvm::memory_stream & read_state_data_key(cvm::memory_stream &is, char const *key); + cvm::memory_stream & read_state_data_key(cvm::memory_stream &is, std::string const &key); private: diff --git a/src/colvargrid_def.h b/src/colvargrid_def.h index 21ead0c5b..c109ef1bf 100644 --- a/src/colvargrid_def.h +++ b/src/colvargrid_def.h @@ -25,17 +25,18 @@ template IST &read_restart_template(colvar_grid &g, IST &is) { auto const start_pos = is.tellg(); - std::string key, conf; - if ((is >> key) && (key == std::string("grid_parameters"))) { - is.seekg(start_pos); - is >> colvarparse::read_block("grid_parameters", &conf); - g.parse_params(conf, colvarparse::parse_silent); - } else { - cvm::log("Grid parameters are missing in the restart file, " - "using those from the configuration.\n"); - is.seekg(start_pos); + std::string conf; + if ((is >> colvarparse::read_block("grid_parameters", &conf)) && + (g.parse_params(conf, colvarparse::parse_restart) == COLVARS_OK) && g.read_raw(is)) { + return is; } - g.read_raw(is); + auto const error_pos = is.tellg(); + is.clear(); + is.seekg(start_pos); + is.setstate(std::ios::failbit); + cvm::error("Error: in reading grid state from stream at position " + cvm::to_str(error_pos) + + "\n", + COLVARS_INPUT_ERROR); return is; } @@ -54,7 +55,7 @@ template cvm::memory_stream &colvar_grid::read_restart(cvm::memory_ template std::ostream &colvar_grid::write_restart(std::ostream &os) { - os << get_state_params(); + os << "grid_parameters {\n" << get_state_params() << "}\n"; write_raw(os); return os; } @@ -62,7 +63,7 @@ template std::ostream &colvar_grid::write_restart(std::ostream &os) template cvm::memory_stream &colvar_grid::write_restart(cvm::memory_stream &os) { - os << get_state_params(); + os << std::string("grid_parameters") << get_state_params(); write_raw(os); return os; } @@ -146,7 +147,7 @@ template std::string colvar_grid::get_state_params() const { std::ostringstream os; size_t i; - os << "grid_parameters {\n n_colvars " << nd << "\n"; + os << " n_colvars " << nd << "\n"; os << " lower_boundaries "; for (i = 0; i < nd; i++) @@ -168,7 +169,6 @@ template std::string colvar_grid::get_state_params() const os << " " << nx[i]; os << "\n"; - os << "}\n"; return os.str(); } From 3c44fe55cb0047c50bb3af1822e2b4d27401e014 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 25 Aug 2023 14:40:25 +0200 Subject: [PATCH 067/162] Unformatted I/O for colvarmodule --- src/colvar.cpp | 34 +++++--- src/colvarmodule.cpp | 175 ++++++++++++++++++++++++++++++-------- src/colvarmodule.h | 30 ++++++- src/colvars_memstream.cpp | 3 + src/colvars_memstream.h | 3 + 5 files changed, 194 insertions(+), 51 deletions(-) diff --git a/src/colvar.cpp b/src/colvar.cpp index 0e9b28b18..b90350737 100644 --- a/src/colvar.cpp +++ b/src/colvar.cpp @@ -2380,27 +2380,37 @@ int colvar::set_state_params(std::string const &conf) } -cvm::memory_stream & colvar::read_state(cvm::memory_stream &is) +cvm::memory_stream &colvar::read_state(cvm::memory_stream &is) { auto const start_pos = is.tellg(); - std::string key; + std::string key, data; if (is >> key) { - if (key != "colvar") { - is.seekg(start_pos); - return is; - } - // Read parameters as a formatted string, then use the formatted I/O - std::string data; - if (is >> data) { - std::istringstream iss(data); - if (read_state(iss)) { - return is; + if (key == "colvar") { + // Read a formatted config string, then read the state parameters from it + if (is >> data) { + if (set_state_params(data) == COLVARS_OK) { + return is; + } } } } + + auto const error_pos = is.tellg(); + is.clear(); is.seekg(start_pos); is.setstate(std::ios::failbit); + + std::string error_msg("Error: in reading state data for colvar \"" + name + " at position " + + cvm::to_str(error_pos) + " in unformatted stream.\n"); + if (key.size() && key != "colvar") { + error_msg += "; the keyword read was \"" + key + "\", but \"colvar\" was expected"; + } + if (data.size()) { + error_msg += "; the configuration string read was not recognized"; + } + error_msg += ".\n"; + cvm::error(error_msg, COLVARS_INPUT_ERROR); return is; } diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 40d75b883..91eff4142 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -29,7 +29,7 @@ #include "colvarscript.h" #include "colvaratoms.h" #include "colvarcomp.h" - +#include "colvars_memstream.h" /// Track usage of Colvars features @@ -69,6 +69,11 @@ class colvarmodule::usage { }; +namespace { + constexpr uint32_t colvars_magic_number = 2013813594; +} + + colvarmodule::colvarmodule(colvarproxy *proxy_in) { depth_s = 0; @@ -118,6 +123,8 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) // set initial default values + binary_restart = true; + // "it_restart" will be set by the input state file, if any; // "it" should be updated by the proxy colvarmodule::it = colvarmodule::it_restart = 0; @@ -1079,9 +1086,22 @@ int colvarmodule::write_restart_file(std::string const &out_name) cvm::log("Saving collective variables state to \""+out_name+"\".\n"); std::ostream &restart_out_os = proxy->output_stream(out_name, "state file"); if (!restart_out_os) return COLVARS_FILE_ERROR; - if (!write_restart(restart_out_os)) { - return cvm::error("Error: in writing restart file.\n", COLVARS_FILE_ERROR); + + if (binary_restart) { + cvm::memory_stream mem_os; + if (!write_state(mem_os)) { + return cvm::error("Error: in writing binary state information to file.\n", COLVARS_ERROR); + } + if (!restart_out_os.write(reinterpret_cast(mem_os.output_buffer()), + mem_os.length())) { + return cvm::error("Error: in writing restart file.\n", COLVARS_FILE_ERROR); + } + } else { + if (!write_state(restart_out_os)) { + return cvm::error("Error: in writing restart file.\n", COLVARS_FILE_ERROR); + } } + proxy->close_output_stream(out_name); // Take the opportunity to flush colvars.traj @@ -1094,7 +1114,7 @@ int colvarmodule::write_restart_string(std::string &output) { cvm::log("Saving state to output buffer.\n"); std::ostringstream os; - if (!write_restart(os)) { + if (!write_state(os)) { return cvm::error("Error: in writing restart to buffer.\n", COLVARS_FILE_ERROR); } output = os.str(); @@ -1310,8 +1330,30 @@ int colvarmodule::setup_input() proxy->set_input_prefix(""); cvm::log(cvm::line_marker); - cvm::log("Loading state from file \""+restart_in_name+"\".\n"); - read_restart(*input_is); + + if (binary_restart) { + cvm::log("Loading state from binary file \""+restart_in_name+"\".\n"); + input_is->seekg(0, std::ios::end); + auto const file_size = input_is->tellg(); + input_is->seekg(0, std::ios::beg); + // TODO integrate istream.read() into memory_stream to avoid copying + auto *buf = new unsigned char[file_size]; + if (input_is->read(reinterpret_cast(buf), file_size)) { + cvm::memory_stream mem_is(file_size, buf); + if (!read_state(mem_is)) { + input_is->setstate(std::ios::failbit); + cvm::error("Error: cannot interpret contents of binary file \""+restart_in_name+"\".\n", + COLVARS_INPUT_ERROR); + } + } else { + cvm::error("Error: cannot read from binary file \"" + restart_in_name + "\".\n", + COLVARS_INPUT_ERROR); + } + delete [] buf; + } else { + cvm::log("Loading state from text file \"" + restart_in_name + "\".\n"); + read_state(*input_is); + } cvm::log(cvm::line_marker); proxy->delete_input_stream(restart_in_name); @@ -1320,7 +1362,7 @@ int colvarmodule::setup_input() if (proxy->input_stream_exists("input state string")) { cvm::log(cvm::line_marker); cvm::log("Loading state from string.\n"); - read_restart(proxy->input_stream("input state string")); + read_state(proxy->input_stream("input state string")); cvm::log(cvm::line_marker); proxy->delete_input_stream("input state string"); @@ -1385,8 +1427,7 @@ std::string colvarmodule::state_file_prefix(char const *filename) } - -std::istream & colvarmodule::read_restart(std::istream &is) +template IST & colvarmodule::read_state_template_(IST &is) { bool warn_total_forces = false; @@ -1448,35 +1489,58 @@ std::istream & colvarmodule::read_restart(std::istream &is) } +std::istream & colvarmodule::read_state(std::istream &is) +{ + return read_state_template_(is); +} + + +cvm::memory_stream &colvarmodule::read_state(cvm::memory_stream &is) +{ + uint32_t file_magic_number = 0; + if (!(is >> file_magic_number)) { + return is; + } + if (file_magic_number == colvars_magic_number) { + return read_state_template_(is); + } else { + is.setstate(std::ios::failbit); + cvm::error("Error: magic number of binary file (" + + cvm::to_str(static_cast(file_magic_number)) + + ") does not match the expected magic number for a Colvars state file (" + + cvm::to_str(static_cast(colvars_magic_number)) + ").\n", + COLVARS_INPUT_ERROR); + } + return is; +} + std::istream & colvarmodule::read_objects_state(std::istream &is) { - std::streampos pos = 0; + auto pos = is.tellg(); std::string word; - while (is.good()) { + while (is) { pos = is.tellg(); - word.clear(); - is >> word; - if (word.size()) { + if (is >> word) { - is.seekg(pos, std::ios::beg); + is.seekg(pos); if (word == "colvar") { cvm::increase_depth(); - for (std::vector::iterator cvi = colvars.begin(); - cvi != colvars.end(); - cvi++) { - if ( !((*cvi)->read_state(is)) ) { + for (std::vector::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { + if (!((*cvi)->read_state(is))) { // Here an error signals that the variable is a match, but the // state is corrupt; otherwise, the variable rewinds is silently - cvm::error("Error: in reading restart configuration for " - "collective variable \""+(*cvi)->name+"\".\n", + cvm::error("Error: in reading state for collective variable \"" + + (*cvi)->name + "\" at position " + cvm::to_str(is.tellg()) + + " in stream.\n", COLVARS_INPUT_ERROR); } - if (is.tellg() > pos) break; // found it + if (is.tellg() > pos) + break; // found it } cvm::decrease_depth(); @@ -1493,11 +1557,12 @@ std::istream & colvarmodule::read_objects_state(std::istream &is) } if (!((*bi)->read_state(is))) { // Same as above, an error means a match but the state is incorrect - cvm::error("Error: in reading restart configuration for bias \""+ - (*bi)->name+"\".\n", + cvm::error("Error: in reading state for bias \"" + (*bi)->name + "\" at position " + + cvm::to_str(is.tellg()) + " in stream.\n", COLVARS_INPUT_ERROR); } - if (is.tellg() > pos) break; // found it + if (is.tellg() > pos) + break; // found it } cvm::decrease_depth(); } @@ -1516,6 +1581,25 @@ std::istream & colvarmodule::read_objects_state(std::istream &is) } +cvm::memory_stream &colvarmodule::read_objects_state(cvm::memory_stream &is) +{ + // An unformatted stream must match the objects' exact configuration + cvm::increase_depth(); + for (std::vector::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { + if (!(*cvi)->read_state(is)) { + return is; + } + } + for (std::vector::iterator bi = biases.begin(); bi != biases.end(); bi++) { + if (!(*bi)->read_state(is)) { + return is; + } + } + cvm::decrease_depth(); + return is; +} + + int colvarmodule::print_total_forces_errning(bool warn_total_forces) { if (warn_total_forces) { @@ -1638,18 +1722,24 @@ int colvarmodule::read_traj(char const *traj_filename, } -std::ostream & colvarmodule::write_restart(std::ostream &os) +template OST &colvarmodule::write_state_template_(OST &os) { - os.setf(std::ios::scientific, std::ios::floatfield); - os << "configuration {\n" - << " step " << std::setw(it_width) - << it << "\n" - << " dt " << dt() << "\n" - << " version " << std::string(COLVARS_VERSION) << "\n"; + bool const formatted = !std::is_same::value; + + std::ostringstream oss; + oss.setf(std::ios::scientific, std::ios::floatfield); + oss << " step " << std::setw(it_width) + << it << "\n" + << " dt " << dt() << "\n" + << " version " << std::string(COLVARS_VERSION) << "\n"; if (proxy->units.size() > 0) { - os << " units " << proxy->units << "\n"; + oss << " units " << proxy->units << "\n"; } - os << "}\n\n"; + + os << std::string("configuration"); + if (formatted) os << " {\n"; + os << oss.str(); + if (formatted) os << "}\n\n"; int error_code = COLVARS_OK; @@ -1676,7 +1766,22 @@ std::ostream & colvarmodule::write_restart(std::ostream &os) } -std::ostream & colvarmodule::write_traj_label(std::ostream &os) +std::ostream &colvarmodule::write_state(std::ostream &os) +{ + return write_state_template_(os); +} + + +cvm::memory_stream &colvarmodule::write_state(cvm::memory_stream &os) +{ + if (os << colvars_magic_number) { + write_state_template_(os); + } + return os; +} + + +std::ostream &colvarmodule::write_traj_label(std::ostream &os) { os.setf(std::ios::scientific, std::ios::floatfield); diff --git a/src/colvarmodule.h b/src/colvarmodule.h index f14c9ecdb..da98640ab 100644 --- a/src/colvarmodule.h +++ b/src/colvarmodule.h @@ -249,6 +249,8 @@ class colvarmodule { return it; } + bool binary_restart; + /// \brief Finite difference step size (if there is no dynamics, or /// if gradients need to be tested independently from the size of /// dt) @@ -451,17 +453,37 @@ class colvarmodule { /// (Re)initialize the output trajectory and state file (does not write it yet) int setup_output(); - /// Read a restart file - std::istream & read_restart(std::istream &is); +private: + + template IST & read_state_template_(IST &is); + +public: + + /// Read all objects' state fron a formatted (text) stream + std::istream & read_state(std::istream &is); + + /// Read all objects' state fron an unformatted (binary) stream + memory_stream & read_state(memory_stream &is); /// Read the states of individual objects; allows for changes std::istream & read_objects_state(std::istream &is); + /// Read the states of individual objects; allows for changes + memory_stream & read_objects_state(memory_stream &is); + /// If needed (old restart file), print the warning that cannot be ignored int print_total_forces_errning(bool warn_total_forces); - /// Write the output restart file - std::ostream & write_restart(std::ostream &os); +private: + template OST &write_state_template_(OST &os); + +public: + + /// Write the state of the module to a formatted (text) file + std::ostream & write_state(std::ostream &os); + + /// Write the state of the module to an unformatted (binary) file + memory_stream & write_state(memory_stream &os); /// Strips .colvars.state from filename and checks that it is not empty static std::string state_file_prefix(char const *filename); diff --git a/src/colvars_memstream.cpp b/src/colvars_memstream.cpp index 2243dc96a..ed5518d9a 100644 --- a/src/colvars_memstream.cpp +++ b/src/colvars_memstream.cpp @@ -34,6 +34,9 @@ template <> void cvm::memory_stream::write_object(std::string const &t) { size_t const string_length = t.size(); size_t const new_data_size = sizeof(size_t) + sizeof(char) * string_length; + if (cvm::debug()) { + cvm::log("Writing object of type std::string, value = " + cvm::to_str(t)); + } if (expand_ouput_buffer(new_data_size)) { std::memcpy(output_location(), &string_length, sizeof(size_t)); incr_write_pos(sizeof(size_t)); diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index 9742bfc96..ca438ab7a 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -161,6 +161,9 @@ class cvm::memory_stream { template void cvm::memory_stream::write_object(T const &t) { + if (cvm::debug()) { + cvm::log("Writing object of type " + std::string(typeid(T).name()) + "\n"); + } static_assert(IS_TRIVIALLY_COPYABLE(T), "Cannot use write_object() on complex type"); size_t const new_data_size = sizeof(T); if (expand_ouput_buffer(new_data_size)) { From 04aa3dd6caddf2f9ca5d7ca5b51b8947b8cc1b1d Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 31 Aug 2023 10:09:16 -0400 Subject: [PATCH 068/162] Always allow seeking in a memory buffer --- src/colvars_memstream.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index ca438ab7a..a856b5b12 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -97,7 +97,7 @@ class cvm::memory_stream { inline size_t const tellg() const { return read_pos_; } /// Report the current position in the buffer - inline memory_stream & seekg(size_t pos) { if (bool()) read_pos_ = pos; return *this; } + inline memory_stream & seekg(size_t pos) { read_pos_ = pos; return *this; } /// Ignore formatting operators inline void setf(decltype(std::ios::fmtflags(0)), decltype(std::ios::floatfield)) {} From 7a30f4dc7a4482e22e839e7440c93c264904ded0 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 25 Aug 2023 14:56:49 +0200 Subject: [PATCH 069/162] Stop using preprocessor macros for return codes --- src/colvarmodule.cpp | 2 +- src/colvarmodule.h | 24 +++++++++++++----------- 2 files changed, 14 insertions(+), 12 deletions(-) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 91eff4142..4969de9da 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -1910,7 +1910,7 @@ void colvarmodule::clear_error() int colvarmodule::error(std::string const &message, int code) { - set_error_bits(code); + set_error_bits(code >= 0 ? code : COLVARS_ERROR); std::string const trailing_newline = (message.size() > 0) ? (message[message.size()-1] == '\n' ? "" : "\n") : ""; diff --git a/src/colvarmodule.h b/src/colvarmodule.h index da98640ab..393718058 100644 --- a/src/colvarmodule.h +++ b/src/colvarmodule.h @@ -33,15 +33,6 @@ You can browse the class hierarchy or the list of source files. /// shared between all object instances) to be accessed from other /// objects. -#define COLVARS_OK 0 -#define COLVARS_ERROR 1 -#define COLVARS_NOT_IMPLEMENTED (1<<1) -#define COLVARS_INPUT_ERROR (1<<2) // out of bounds or inconsistent input -#define COLVARS_BUG_ERROR (1<<3) // Inconsistent state indicating bug -#define COLVARS_FILE_ERROR (1<<4) -#define COLVARS_MEMORY_ERROR (1<<5) -#define COLVARS_NO_SUCH_FRAME (1<<6) // Cannot load the requested frame - #include #include #include @@ -674,7 +665,7 @@ class colvarmodule { static void log(std::string const &message, int min_log_level = 10); /// Print a message to the main log and set global error code - static int error(std::string const &message, int code = COLVARS_ERROR); + static int error(std::string const &message, int code = -1); private: @@ -862,9 +853,20 @@ class colvarmodule { typedef colvarmodule cvm; - std::ostream & operator << (std::ostream &os, cvm::rvector const &v); std::istream & operator >> (std::istream &is, cvm::rvector &v); +namespace { + constexpr int32_t COLVARS_OK = 0; + constexpr int32_t COLVARS_ERROR = 1; + constexpr int32_t COLVARS_NOT_IMPLEMENTED = (1<<1); + constexpr int32_t COLVARS_INPUT_ERROR = (1<<2); // out of bounds or inconsistent input + constexpr int32_t COLVARS_BUG_ERROR = (1<<3); // Inconsistent state indicating bug + constexpr int32_t COLVARS_FILE_ERROR = (1<<4); + constexpr int32_t COLVARS_MEMORY_ERROR = (1<<5); + constexpr int32_t COLVARS_NO_SUCH_FRAME = (1<<6); // Cannot load the requested frame +} + + #endif From bb0f85fc4db32de2dbf6c4238d795726d83bc76e Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sat, 26 Aug 2023 14:25:23 +0200 Subject: [PATCH 070/162] Open text files in binary mode (we are not using EOL conversion anyway) --- namd/src/colvarproxy_namd.C | 2 +- src/colvarproxy_io.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C index fac6de032..d20bf19dd 100644 --- a/namd/src/colvarproxy_namd.C +++ b/namd/src/colvarproxy_namd.C @@ -1049,7 +1049,7 @@ std::ostream & colvarproxy_namd::output_stream(std::string const &output_name, backup_file(output_name.c_str()); - output_streams_[output_name] = new ofstream_namd(output_name.c_str()); + output_streams_[output_name] = new ofstream_namd(output_name.c_str(), std::ios::binary); if (! output_streams_[output_name]->good()) { cvm::error("Error: cannot write to "+description+" \""+output_name+"\".\n", COLVARS_FILE_ERROR); diff --git a/src/colvarproxy_io.cpp b/src/colvarproxy_io.cpp index 7e7cd3829..e3039afb8 100644 --- a/src/colvarproxy_io.cpp +++ b/src/colvarproxy_io.cpp @@ -358,7 +358,7 @@ std::ostream & colvarproxy_io::output_stream(std::string const &output_name, backup_file(output_name.c_str()); - output_streams_[output_name] = new std::ofstream(output_name.c_str()); + output_streams_[output_name] = new std::ofstream(output_name.c_str(), std::ios::binary); if (!*(output_streams_[output_name])) { cvm::error("Error: cannot write to "+description+" \""+output_name+"\".\n", COLVARS_FILE_ERROR); From 7a4665dc766b1bcbce4e8cd76154547416ec6396 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 1 Sep 2023 17:19:32 -0400 Subject: [PATCH 071/162] Remove check no longer needed after #537 --- namd/tests/library/run_tests.sh | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/namd/tests/library/run_tests.sh b/namd/tests/library/run_tests.sh index 8342d4aed..31a1e2c51 100755 --- a/namd/tests/library/run_tests.sh +++ b/namd/tests/library/run_tests.sh @@ -161,15 +161,9 @@ for dir in ${DIRLIST} ; do script=`basename ${script}` basename=${script%.namd} - # Don't do multithreading for reinitatoms - NUM_THREADS_THIS=${NUM_THREADS} - if [ ${dir} == 003_reinitatoms ] ; then - NUM_THREADS_THIS=1 - fi - # Run the test (use a subshell to avoid cluttering stdout) # Use multiple threads to test SMP code (TODO: move SMP tests to interface?) - NAMD_CUDASOA=$CUDASOA $BINARY +p ${NUM_THREADS_THIS} $script > ${basename}.out + NAMD_CUDASOA=$CUDASOA $BINARY +p ${NUM_THREADS} $script > ${basename}.out # Output of Colvars module, minus the version numbers grep "^colvars:" ${basename}.out | grep -v 'Initializing the collective variables module' \ From 2611a77c6c70560a36c9e793d2d749a921db4187 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 1 Sep 2023 17:28:27 -0400 Subject: [PATCH 072/162] Enable binary restarts from environment variable --- .github/workflows/backend-template.yml | 9 +++++++++ gromacs/tests/library/run_tests.sh | 6 ++++++ lammps/tests/library/run_tests.sh | 4 ++++ namd/tests/library/run_tests.sh | 13 +++++++++++++ src/colvarmodule.cpp | 22 +++++++++++++++------- 5 files changed, 47 insertions(+), 7 deletions(-) diff --git a/.github/workflows/backend-template.yml b/.github/workflows/backend-template.yml index 72259b407..2bb65b736 100644 --- a/.github/workflows/backend-template.yml +++ b/.github/workflows/backend-template.yml @@ -184,3 +184,12 @@ jobs: name: failed-interface-test-diffs-${{ inputs.backend_name }} path: ${{ inputs.test_interface_directory }}/*/*.diff + - name: Run regression tests for library code with ${{ inputs.backend_name }} (binary restarts) + if: ${{ inputs.test_lib_directory }} + shell: bash + working-directory: ${{ inputs.test_lib_directory }} + env: + COLVARS_BINARY_RESTART: 1 + run: | + apptainer exec ${{github.workspace}}/devel-tools/${{ inputs.container_name }}.sif \ + ./run_tests.sh ${{github.workspace}}/${{ inputs.backend_name }}-source/${{ inputs.rpath_exe }} 0??_* diff --git a/gromacs/tests/library/run_tests.sh b/gromacs/tests/library/run_tests.sh index 103a09c8c..562273d7c 100755 --- a/gromacs/tests/library/run_tests.sh +++ b/gromacs/tests/library/run_tests.sh @@ -223,6 +223,12 @@ for dir in ${DIRLIST} ; do for f in AutoDiff/* do base=`basename $f` + + if [ "${base%.state.stripped}" != "${base}" ] && [ -n "${COLVARS_BINARY_RESTART}" ] ; then + # Do not try comparing binary state files, they will never match anyway + continue + fi + if [ ! -f $base ] ; then echo -e "\n*** File $(${TPUT_RED})$base$(${TPUT_CLEAR}) is missing. ***" SUCCESS=0 diff --git a/lammps/tests/library/run_tests.sh b/lammps/tests/library/run_tests.sh index 499b06b26..e972ce117 100755 --- a/lammps/tests/library/run_tests.sh +++ b/lammps/tests/library/run_tests.sh @@ -229,6 +229,10 @@ for dir in ${DIRLIST} ; do for f in AutoDiff/* do base=`basename $f` + if [ "${base%.state.stripped}" != "${base}" ] && [ -n "${COLVARS_BINARY_RESTART}" ] ; then + # Do not try comparing binary state files, they will never match anyway + continue + fi if [ "${base}" != "${base%.traj}" ] ; then # System force is now total force sed 's/fs_/ft_/g' < ${base} > ${TMPDIR}/${base} diff --git a/namd/tests/library/run_tests.sh b/namd/tests/library/run_tests.sh index 31a1e2c51..aa7fd7f33 100755 --- a/namd/tests/library/run_tests.sh +++ b/namd/tests/library/run_tests.sh @@ -161,6 +161,15 @@ for dir in ${DIRLIST} ; do script=`basename ${script}` basename=${script%.namd} + # If we are doing binary restarts, make an exception for tests that don't support it + if [ -n "${COLVARS_BINARY_RESTART}" ] ; then + if [ ${dir} == 004_10ala_moving_restart ] ; then + export COLVARS_BINARY_RESTART=0 + else + export COLVARS_BINARY_RESTART=1 + fi + fi + # Run the test (use a subshell to avoid cluttering stdout) # Use multiple threads to test SMP code (TODO: move SMP tests to interface?) NAMD_CUDASOA=$CUDASOA $BINARY +p ${NUM_THREADS} $script > ${basename}.out @@ -221,6 +230,10 @@ for dir in ${DIRLIST} ; do for f in AutoDiff/* do base=`basename $f` + if [ "${base%.state.stripped}" != "${base}" ] && [ -n "${COLVARS_BINARY_RESTART}" ] ; then + # Do not try comparing binary state files, they will never match anyway + continue + fi if [ ! -f $base ] ; then echo -e "\n*** File $(${TPUT_RED})$base$(${TPUT_CLEAR}) is missing. ***" SUCCESS=0 diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 4969de9da..8ffa10eaa 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -7,13 +7,14 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. -#include +#include +#include +#include #include +#include +#include #include -#include -#include #include -#include #include "colvarmodule.h" #include "colvarparse.h" @@ -123,7 +124,12 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) // set initial default values - binary_restart = true; + binary_restart = false; + if (getenv("COLVARS_BINARY_RESTART") != nullptr) { + if (atoi(getenv("COLVARS_BINARY_RESTART"))) { + binary_restart = true; + } + } // "it_restart" will be set by the input state file, if any; // "it" should be updated by the proxy @@ -1381,14 +1387,16 @@ int colvarmodule::setup_output() std::string(proxy->restart_output_prefix()+".colvars.state") : std::string(""); + std::string const state_file_format(binary_restart ? " (binary format)" : ""); + if (restart_out_name.size()) { - cvm::log("The restart output state file will be \""+ + cvm::log("The restart output state file" + state_file_format + " will be \""+ restart_out_name+"\".\n"); } output_prefix() = proxy->output_prefix(); if (output_prefix().size()) { - cvm::log("The final output state file will be \""+ + cvm::log("The final output state file" + state_file_format + " will be \""+ (output_prefix().size() ? std::string(output_prefix()+".colvars.state") : std::string("colvars.state"))+"\".\n"); From 6b2e8fe73b12e4af94ba1dac36c83577ca787912 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 1 Sep 2023 17:44:40 -0400 Subject: [PATCH 073/162] Fix forgotten renaming of functions --- lammps/src/COLVARS/colvarproxy_lammps.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lammps/src/COLVARS/colvarproxy_lammps.cpp b/lammps/src/COLVARS/colvarproxy_lammps.cpp index 95513547c..cce3a0889 100644 --- a/lammps/src/COLVARS/colvarproxy_lammps.cpp +++ b/lammps/src/COLVARS/colvarproxy_lammps.cpp @@ -209,7 +209,7 @@ double colvarproxy_lammps::compute() void colvarproxy_lammps::serialize_status(std::string &rst) { std::ostringstream os; - colvars->write_restart(os); + colvars->write_state(os); rst = os.str(); } From 7271c2e375cf63a314d7d5d324750cdfe04a4198 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 1 Sep 2023 19:25:05 -0400 Subject: [PATCH 074/162] Remove non-essential debug call to avoid segfault --- src/colvars_memstream.cpp | 3 --- src/colvars_memstream.h | 3 --- 2 files changed, 6 deletions(-) diff --git a/src/colvars_memstream.cpp b/src/colvars_memstream.cpp index ed5518d9a..2243dc96a 100644 --- a/src/colvars_memstream.cpp +++ b/src/colvars_memstream.cpp @@ -34,9 +34,6 @@ template <> void cvm::memory_stream::write_object(std::string const &t) { size_t const string_length = t.size(); size_t const new_data_size = sizeof(size_t) + sizeof(char) * string_length; - if (cvm::debug()) { - cvm::log("Writing object of type std::string, value = " + cvm::to_str(t)); - } if (expand_ouput_buffer(new_data_size)) { std::memcpy(output_location(), &string_length, sizeof(size_t)); incr_write_pos(sizeof(size_t)); diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index a856b5b12..9c2b30896 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -161,9 +161,6 @@ class cvm::memory_stream { template void cvm::memory_stream::write_object(T const &t) { - if (cvm::debug()) { - cvm::log("Writing object of type " + std::string(typeid(T).name()) + "\n"); - } static_assert(IS_TRIVIALLY_COPYABLE(T), "Cannot use write_object() on complex type"); size_t const new_data_size = sizeof(T); if (expand_ouput_buffer(new_data_size)) { From 0a139f5ebec4a89dcdf576cda2dfdfc47df3c425 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 8 Sep 2023 12:48:51 -0400 Subject: [PATCH 075/162] Embed unformatted state in LAMMPS restart file --- lammps/src/COLVARS/fix_colvars.cpp | 28 ++++++++++++++++++---------- src/colvarmodule.cpp | 18 ++++++++++++++++++ src/colvarmodule.h | 6 ++++++ 3 files changed, 42 insertions(+), 10 deletions(-) diff --git a/lammps/src/COLVARS/fix_colvars.cpp b/lammps/src/COLVARS/fix_colvars.cpp index bca3a37e1..246e905a5 100644 --- a/lammps/src/COLVARS/fix_colvars.cpp +++ b/lammps/src/COLVARS/fix_colvars.cpp @@ -45,9 +45,11 @@ #include #include -#include "colvarproxy_lammps.h" #include "colvarmodule.h" +#include "colvarproxy.h" +#include "colvarproxy_lammps.h" #include "colvarscript.h" +#include "colvars_memstream.h" /* struct for packed data communication of coordinates and forces. */ @@ -888,13 +890,17 @@ void FixColvars::end_of_step() void FixColvars::write_restart(FILE *fp) { if (me == 0) { - std::string rest_text; - proxy->serialize_status(rest_text); - // TODO call write_output_files() - const char *cvm_state = rest_text.c_str(); - int len = strlen(cvm_state) + 1; // need to include terminating null byte. - fwrite(&len,sizeof(int),1,fp); - fwrite(cvm_state,1,len,fp); + cvm::memory_stream ms; + if (proxy->colvars->write_state(ms)) { + int len_cv_state = ms.length(); + // Will write the buffer's length twice, so that the fix can read it later, too + int len = len_cv_state + sizeof(int); + fwrite(&len, sizeof(int), 1, fp); + fwrite(&len, sizeof(int), 1, fp); + fwrite(ms.output_buffer(), 1, len_cv_state, fp); + } else { + error->all(FLERR, "Failed to write Colvars state to binary file"); + } } } @@ -903,8 +909,10 @@ void FixColvars::write_restart(FILE *fp) void FixColvars::restart(char *buf) { if (me == 0) { - std::string rest_text(buf); - if (!proxy->deserialize_status(rest_text)) { + // Read the buffer's length, then load it into Colvars starting right past that location + int length = *(reinterpret_cast(buf)); + unsigned char *colvars_state_buffer = reinterpret_cast(buf + sizeof(int)); + if (proxy->colvars->set_input_state_buffer(length, colvars_state_buffer) != COLVARS_OK) { error->all(FLERR, "Failed to set the Colvars input state from string buffer"); } } diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 8ffa10eaa..55a7b3f16 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -1374,6 +1374,16 @@ int colvarmodule::setup_input() proxy->delete_input_stream("input state string"); } + if (input_state_buffer_.size() > 0) { + cvm::log(cvm::line_marker); + cvm::log("Loading state from unformatted memory.\n"); + cvm::memory_stream ms(input_state_buffer_.size(), input_state_buffer_.data()); + read_state(ms); + cvm::log(cvm::line_marker); + + input_state_buffer_.clear(); + } + return cvm::get_error(); } @@ -1523,6 +1533,14 @@ cvm::memory_stream &colvarmodule::read_state(cvm::memory_stream &is) } +int colvarmodule::set_input_state_buffer(size_t n, unsigned char *buf) +{ + input_state_buffer_.clear(); + std::copy(buf, buf + n, std::back_inserter(input_state_buffer_)); + return COLVARS_OK; +} + + std::istream & colvarmodule::read_objects_state(std::istream &is) { auto pos = is.tellg(); diff --git a/src/colvarmodule.h b/src/colvarmodule.h index 393718058..8f776e4b0 100644 --- a/src/colvarmodule.h +++ b/src/colvarmodule.h @@ -448,6 +448,9 @@ class colvarmodule { template IST & read_state_template_(IST &is); + /// Internal state buffer, to be read as an unformatted stream + std::vector input_state_buffer_; + public: /// Read all objects' state fron a formatted (text) stream @@ -456,6 +459,9 @@ class colvarmodule { /// Read all objects' state fron an unformatted (binary) stream memory_stream & read_state(memory_stream &is); + /// Set an internal state buffer, to be read later as an unformatted stream when ready + int set_input_state_buffer(size_t n, unsigned char *buf); + /// Read the states of individual objects; allows for changes std::istream & read_objects_state(std::istream &is); From e8a218091c95be141eee2bb190e3f8a35d2e0e4c Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 8 Sep 2023 12:34:11 -0400 Subject: [PATCH 076/162] Remove now unneeded LAMMPS proxy wrappers --- lammps/src/COLVARS/colvarproxy_lammps.cpp | 17 ----------------- lammps/src/COLVARS/colvarproxy_lammps.h | 6 ------ 2 files changed, 23 deletions(-) diff --git a/lammps/src/COLVARS/colvarproxy_lammps.cpp b/lammps/src/COLVARS/colvarproxy_lammps.cpp index cce3a0889..c2435cd2b 100644 --- a/lammps/src/COLVARS/colvarproxy_lammps.cpp +++ b/lammps/src/COLVARS/colvarproxy_lammps.cpp @@ -206,23 +206,6 @@ double colvarproxy_lammps::compute() return bias_energy; } -void colvarproxy_lammps::serialize_status(std::string &rst) -{ - std::ostringstream os; - colvars->write_state(os); - rst = os.str(); -} - -// set status from string -bool colvarproxy_lammps::deserialize_status(std::string &rst) -{ - if (! colvarproxy_io::input_stream_from_string("input state string", rst)) { - return false; - } else { - return true; - } -} - cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) diff --git a/lammps/src/COLVARS/colvarproxy_lammps.h b/lammps/src/COLVARS/colvarproxy_lammps.h index df624960a..d55a334a2 100644 --- a/lammps/src/COLVARS/colvarproxy_lammps.h +++ b/lammps/src/COLVARS/colvarproxy_lammps.h @@ -76,12 +76,6 @@ class colvarproxy_lammps : public colvarproxy { // perform colvars computation. returns biasing energy double compute(); - // dump status to string - void serialize_status(std::string &); - - // set status from string - bool deserialize_status(std::string &); - // Request to set the units used internally by Colvars int set_unit_system(std::string const &units_in, bool check_only = false) override; From f63ae0fe0e56a8f408363afb87a489381731b3e9 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 8 Sep 2023 20:25:14 -0400 Subject: [PATCH 077/162] Auto-detect unformatted vs. formatted input --- src/colvarmodule.cpp | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 55a7b3f16..7e3974bb9 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -1337,11 +1337,24 @@ int colvarmodule::setup_input() cvm::log(cvm::line_marker); - if (binary_restart) { - cvm::log("Loading state from binary file \""+restart_in_name+"\".\n"); - input_is->seekg(0, std::ios::end); - auto const file_size = input_is->tellg(); - input_is->seekg(0, std::ios::beg); + input_is->seekg(0, std::ios::end); + size_t const file_size = input_is->tellg(); + input_is->seekg(0, std::ios::beg); + + bool binary_state_file = false; + + uint32_t file_magic_number = 0; + if (file_size > sizeof(uint32_t)) { + if (input_is->read(reinterpret_cast(&file_magic_number), sizeof(uint32_t))) { + if (file_magic_number == colvars_magic_number) { + binary_state_file = true; + } + input_is->seekg(0, std::ios::beg); + } + } + + if (binary_state_file) { + cvm::log("Loading state from binary file \"" + restart_in_name + "\".\n"); // TODO integrate istream.read() into memory_stream to avoid copying auto *buf = new unsigned char[file_size]; if (input_is->read(reinterpret_cast(buf), file_size)) { From e61339733583e01de467b21ad1f7f06b015eda75 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 8 Sep 2023 20:25:40 -0400 Subject: [PATCH 078/162] Cosmetic changes --- src/colvarmodule.cpp | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 7e3974bb9..b6d7bccd9 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -1314,17 +1314,15 @@ int colvarmodule::reset() int colvarmodule::setup_input() { if (proxy->input_prefix().size()) { - // Read a state file - std::string restart_in_name(proxy->input_prefix()+ - std::string(".colvars.state")); - std::istream *input_is = &(proxy->input_stream(restart_in_name, - "restart file/channel", - false)); + + // Read state from a file + + std::string restart_in_name(proxy->input_prefix() + std::string(".colvars.state")); + std::istream *input_is = &(proxy->input_stream(restart_in_name, "restart file/channel", false)); if (!*input_is) { // Try without the suffix ".colvars.state" restart_in_name = proxy->input_prefix(); - input_is = &(proxy->input_stream(restart_in_name, - "restart file/channel")); + input_is = &(proxy->input_stream(restart_in_name, "restart file/channel")); if (!*input_is) { // Error message has already been printed, return now return COLVARS_FILE_ERROR; @@ -1361,14 +1359,15 @@ int colvarmodule::setup_input() cvm::memory_stream mem_is(file_size, buf); if (!read_state(mem_is)) { input_is->setstate(std::ios::failbit); - cvm::error("Error: cannot interpret contents of binary file \""+restart_in_name+"\".\n", + cvm::error("Error: cannot interpret contents of binary file \"" + restart_in_name + + "\".\n", COLVARS_INPUT_ERROR); } } else { cvm::error("Error: cannot read from binary file \"" + restart_in_name + "\".\n", COLVARS_INPUT_ERROR); } - delete [] buf; + delete[] buf; } else { cvm::log("Loading state from text file \"" + restart_in_name + "\".\n"); read_state(*input_is); @@ -1379,8 +1378,9 @@ int colvarmodule::setup_input() } if (proxy->input_stream_exists("input state string")) { + cvm::log(cvm::line_marker); - cvm::log("Loading state from string.\n"); + cvm::log("Loading state from formatted string.\n"); read_state(proxy->input_stream("input state string")); cvm::log(cvm::line_marker); From 5829dcb760e6a69d7254cec6b479d7df7fac1e81 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 8 Sep 2023 20:27:00 -0400 Subject: [PATCH 079/162] Add warning about mismatched binary state versions --- src/colvarmodule.cpp | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index b6d7bccd9..664e28293 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -1340,7 +1340,7 @@ int colvarmodule::setup_input() input_is->seekg(0, std::ios::beg); bool binary_state_file = false; - + uint32_t file_magic_number = 0; if (file_size > sizeof(uint32_t)) { if (input_is->read(reinterpret_cast(&file_magic_number), sizeof(uint32_t))) { @@ -1484,8 +1484,11 @@ template IST & colvarmodule::read_state_template_(IST &is) } if (restart_version() != version()) { - cvm::log("This state file was generated with version "+ - restart_version()+"\n"); + cvm::log("This state file was generated with version " + restart_version() + "\n"); + if (std::is_same::value) { + cvm::log("Warning: compatibility between differetn Colvars versions is not " + "guaranteed for unformatted (binary) state files.\n"); + } } if (restart_version_number() < 20160810) { From 767bff031f9a0c4c46a4278ea50c35f34dcc793c Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 8 Sep 2023 20:54:33 -0400 Subject: [PATCH 080/162] Ignore unformatted input state buffer (e.g. LAMMPS restart) if explicit input state is defined --- src/colvarmodule.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 664e28293..e6e7d3f20 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -1374,6 +1374,9 @@ int colvarmodule::setup_input() } cvm::log(cvm::line_marker); + // Now that the explicit input file was read, we shall ignore any unformatted buffer + input_state_buffer_.clear(); + proxy->delete_input_stream(restart_in_name); } From f4f7c88b05e80690c7921f061d3971c50c673c60 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 8 Sep 2023 21:06:20 -0400 Subject: [PATCH 081/162] Only write output state if the prefix is not null --- src/colvarmodule.cpp | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index e6e7d3f20..a5e082b85 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -807,7 +807,9 @@ int colvarmodule::calc() // Write restart file, if different from main output error_code |= write_restart_file(restart_out_name); } else { - error_code |= write_restart_file(output_prefix()+".colvars.state"); + if (output_prefix().size()) { + error_code |= write_restart_file(output_prefix()+".colvars.state"); + } } cvm::increase_depth(); From 1ff08639a93bf00f8df90fb34a10e51e56760e34 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 8 Sep 2023 21:36:14 -0400 Subject: [PATCH 082/162] Clarify that an empty output prefix is allowed in LAMMPS --- doc/colvars-refman-main.tex | 4 +++- lammps/doc/src/fix_colvars.rst | 7 ++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index 1c5285eb8..64d19a264 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -481,7 +481,9 @@ string}{% ``out''}{% If a value is provided, it is interpreted as the prefix to all output files that will be written by the Colvars module (see \ref{sec:colvars_output}). - A value must be defined and is set by default, even when Colvars embeds its state information in a LAMMPS restart files, to allow the output of other files (see \ref{sec:colvars_output}). + This includes output state files for checkpointing, as well as accumu;ated information such as PMFs or histograms and trajectories of the collective variables. + Because this information is often useful, a default value is set for this keyword when not provided. + However, supplying an empty string suppresses any file output from Colvars to file, except for data saved into the LAMMPS binary restart file. } \item % diff --git a/lammps/doc/src/fix_colvars.rst b/lammps/doc/src/fix_colvars.rst index 9ac9893c2..936fdaa83 100644 --- a/lammps/doc/src/fix_colvars.rst +++ b/lammps/doc/src/fix_colvars.rst @@ -85,9 +85,10 @@ selection keywords in the Colvars configuration file or files. There is no need to define multiple "fix colvars" instances and it is not allowed. -The "output" keyword allows to specify the prefix of output files -generated by Colvars, for example "*output*.colvars.traj" or -"output.pmf". +The "output" keyword allows to specify the prefix of output files generated +by Colvars, for example "*output*.colvars.traj" or "output.pmf". Supplying +an empty string suppresses any file output from Colvars to file, except for +data saved into the LAMMPS :doc:`binary restart ` files. The "input" keyword allows to specify an optional state file that contains the restart information needed to continue a previous simulation state. From c82fd2fd1794b8aad27b0f5b1bc0009cb4fe3dab Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 8 Sep 2023 22:09:03 -0400 Subject: [PATCH 083/162] Document binary vs. formatted state file format --- doc/colvars-refman-main.tex | 53 +++++++++++++++++++++++-------------- 1 file changed, 33 insertions(+), 20 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index 64d19a264..b77eea380 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -958,36 +958,49 @@ \cvsubsec{Input state file}{sec:colvars_input} -A \emph{state file} contains the information produced during a Colvars-based simulation besides atomic data, which is provided by \MDENGINE{}. - -Because many of the methods implemented in Colvars are history-dependent, this file is often needed to continue a long simulation over consecutive runs. -Such state file is written automatically at the end of any simulation with Colvars, and contains data accumulated during that simulation along with the step number at the end of it. -The step number read from the state file is then used to control such time-dependent biases: because of this essential role, the step number internal to Colvars may not always match the step number reported by the MD program that carried during the simulation (which may instead restart from zero each time). -\cvnamdonly{If a state file is not given, the NAMD command \texttt{firstTimestep} may be used to control the Colvars step number.} - -Depending on the configuration, a state file may need to be loaded issued at the beginning of a new simulation when time-dependent biasing methods are applied (moving restraints, metadynamics, ABF, ...). -\cvnamdonly{When the Colvars module is initialized in NAMD, the \texttt{colvarsInput} keyword can be used to give the name of the state file}. -\cvlammpsonly{When the Colvars fix is defined in LAMMPS, the keyword \texttt{input} can be used to load the state file, although it is typically easier to use the LAMMPS \texttt{read\_restart} to re-initialize Colvars together with other fixes.} -After initialization of the Colvars module, a state file may be loaded at any time \cvnamdonly{with the Tcl command \texttt{cv load}}% -\cvvmdonly{with the Tcl command \texttt{cv load}}% -\cvlammpsonly{with the \texttt{fix\_modify load } LAMMPS command}. - -It is possible to load a state file even if the configuration has changed: -for example, new variables may be defined or restraints be added in between consecutive runs. +Several of the sampling methods implemented in Colvars are time- or history-dependent, i.e.\ they work by accumulating data as a simulation progresses and use this data to change their biasing forces. When continuing a simulation over consecutive runs, a \emph{state file} needs to be loaded into Colvars. + +The Colvars state file may be in either one of two formats: +\begin{itemize} +\item Unformatted (binary) format, which is both space-efficient and quick to load/save, but requires that the same \MDENGINE{} build was used to save the file in the first place. Most importantly, no changes are allowed in the Colvars configuration between the original run. +\item Formatted (text) format, which takes more space and is slower to to load/save but is also portable across different platforms and even different engines (except for changes in physical units). Formatted state files are also the only format previously supported by Colvars version until late 2023. % TODO Add specific version? +\end{itemize} + +\cvsubsubsec{Contents of the state file.}{} +In either format, the state file contains accumulated data as well as the step number at the end of the run. +The step number read from a state file overrides any value that \MDENGINE{} provides, and will be incremented if the simulation proceeds. +This means that the step number used internally by Colvars may not always match the step number reported by \MDENGINE{}. +\cvnamdonly{This is particularly inmportant in NAMD, which represents step numbers as a 32-bit integers that overflows after $\sim$ 2 billion steps, effectively rendering neutralizing the usefulness of \texttt{firstTimeStep}.} + +% \cvgromacsonly{\cvsubsubsec{Restarting in GROMACS.}{} TODO } + +\cvlammpsonly{\cvsubsubsec{Restarting in LAMMPS.}{} +For continuing a Colvars-based simulation, the recommended method is using the standard LAMMPS \texttt{read\_restart} command, which effectively reads the Colvars state in unformatted (binary) format embedded in the LAMMPS restart file. Alternatively, restarting from a formatted Colvars-only state file is also possible by using the \texttt{input} keyword of the \texttt{fix colvars} command, which overrides the information read from the LAMMPS restart file. +Furthermore, a state file may also be loaded after initialization with the \texttt{fix\_modify load } LAMMPS command. +} + +\cvnamdonly{\cvsubsubsec{Restarting in NAMD.}{} +Before the Colvars module is initialized in NAMD, the \texttt{colvarsInput} keyword can be used to give the name of a state file. +After initialization of the Colvars module, a state file may be loaded at any time with the Tcl command \texttt{cv load}.} + +\cvsubsubsec{Restarting after a change in Colvars configuration.}{} +A unique advantage of the formatted Colvars state files is that they can be loaded even if the configuration has changed. +For example, new restraints may have been added or removed from the Colvars configuration between consecutive runs. For each newly defined variable or bias, no information will be read from the state file if this is unavailable: such new objects will remain uninitialized until the first compute step. Conversely, any information that the state file has about variables or biases that are no longer defined is silently ignored. -\emph{Because these checks are performed based on the names of variables and biases, it is the user's responsibility to ensure that these definitions are consistent between runs.} +\emph{Because these checks are performed based solely on the names of variables and biases, it is your responsibility to ensure that these names correspond to consistent definitions between runs.} \cvsubsec{Output files}{sec:colvars_output} -During a simulation with collective variables defined, the following three output files are written: +If the output prefix \outputName{} is defined, the following output files are written during a simulation run: \begin{itemize} -\item A \emph{state file}, named \outputName\texttt{.colvars.state}; this file is in ASCII (plain text) format\cvnamdonly{, regardless of the value of \texttt{binaryOutput} in the NAMD configuration}. This file is written at the end of the specified run\cvscriptonly{, but can also be written at any time with the command \texttt{cv save} (\ref{sec:cv_command_loadsave})}.\\ - \emph{This is the only Colvars output file needed to continue a simulation.} +\item A \emph{state file}, named \outputName\texttt{.colvars.state}, which is written at the end of the specified run\cvscriptonly{, and can also be written at any time with the scripting command \texttt{save} (\ref{sec:cv_command_loadsave})}. +This file is in plain text format by default\cvnamdonly{, regardless of the value of \texttt{binaryOutput} of the NAMD coordinate and velocity files}, or in binary format if the environment variable \texttt{COLVARS\_BINARY\_RESTART} is set to a non-zero integer. +\emph{The state is the only Colvars output file needed to continue a simulation.} \item If the parameter \refkey{colvarsRestartFrequency}{Colvars-global|colvarsRestartFrequency} is larger than zero, a \emph{restart file} is written every that many steps: this file is fully equivalent to the final state file. The name of this file is \restartName\texttt{.colvars.state}. From c15f5a6b367b14fe819e4122772e74c232fcd227 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sat, 9 Sep 2023 11:25:57 -0400 Subject: [PATCH 084/162] Remove last instance of #include in widely included header --- src/colvar_geometricpath.h | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/src/colvar_geometricpath.h b/src/colvar_geometricpath.h index ae28f6dda..51f97bb67 100644 --- a/src/colvar_geometricpath.h +++ b/src/colvar_geometricpath.h @@ -8,13 +8,13 @@ // Colvars repository at GitHub. -#include "colvarmodule.h" - -#include -#include #include +#include #include -#include +#include + +#include "colvarmodule.h" + namespace GeometricPathCV { @@ -172,10 +172,14 @@ void GeometricPathBase::determineClosestFr sign = -1; } if (cvm::fabs(static_cast(frame_index[0]) - static_cast(frame_index[1])) > 1) { - std::cout << "Warning: Geometrical pathCV relies on the assumption that the second closest frame is the neighbouring frame\n"; - std::cout << " Please check your configuration or increase restraint on z(σ)\n"; + std::string message( + "Warning: Geometrical pathCV relies on the assumption that the second closest frame is " + "the neighbouring frame\n" + " Please check your configuration or increase restraint on z(σ)\n"); for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) { - std::cout << "Frame index: " << frame_index[i_frame] << " ; optimal RMSD = " << frame_distances[frame_index[i_frame]] << "\n"; + message += "Frame index: " + cvm::to_str(frame_index[i_frame]) + + " ; optimal RMSD = " + cvm::to_str(frame_distances[frame_index[i_frame]]) + + "\n"; } } min_frame_index_1 = frame_index[0]; // s_m From 060e71d2cb38a3d90ae45140038e67ce22820f00 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sat, 9 Sep 2023 16:21:32 -0400 Subject: [PATCH 085/162] Move include to where it is required --- src/colvarmodule.h | 1 - src/colvartypes.h | 1 + 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/src/colvarmodule.h b/src/colvarmodule.h index 8f776e4b0..7cc479035 100644 --- a/src/colvarmodule.h +++ b/src/colvarmodule.h @@ -33,7 +33,6 @@ You can browse the class hierarchy or the list of source files. /// shared between all object instances) to be accessed from other /// objects. -#include #include #include #include diff --git a/src/colvartypes.h b/src/colvartypes.h index 765166fd7..455e628f1 100644 --- a/src/colvartypes.h +++ b/src/colvartypes.h @@ -10,6 +10,7 @@ #ifndef COLVARTYPES_H #define COLVARTYPES_H +#include // TODO specialize templates and replace this with iosfwd #include #ifdef COLVARS_LAMMPS From 8e83ba237d63bb15d8f2db7fd3ac60bd5013c4df Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sat, 9 Sep 2023 19:57:24 -0400 Subject: [PATCH 086/162] More consistent naming of stream I/O template functions --- src/colvarbias.cpp | 13 +++++++------ src/colvarbias.h | 4 ++-- src/colvarbias_abf.cpp | 12 ++++++------ src/colvarbias_abf.h | 4 ++-- src/colvargrid_def.h | 12 ++++++------ src/colvarvalue.cpp | 12 ++++++------ src/colvarvalue.h | 11 +++++++++-- 7 files changed, 38 insertions(+), 30 deletions(-) diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp index 451d82aac..169fc073b 100644 --- a/src/colvarbias.cpp +++ b/src/colvarbias.cpp @@ -540,7 +540,7 @@ void raise_error_rewind(IST &is, SPT start_pos, std::string const &bias_type, } -template IST & colvarbias::read_state_from_stream(IST &is) +template IST & colvarbias::read_state_template_(IST &is) { auto const start_pos = is.tellg(); @@ -603,13 +603,13 @@ template IST & colvarbias::read_state_from_stream(IST &is) std::istream &colvarbias::read_state(std::istream &is) { - return read_state_from_stream(is); + return read_state_template_(is); } cvm::memory_stream &colvarbias::read_state(cvm::memory_stream &is) { - return read_state_from_stream(is); + return read_state_template_(is); } @@ -699,7 +699,8 @@ cvm::memory_stream &colvarbias::write_state_data_key(cvm::memory_stream &os, std } -template IST &colvarbias::read_state_data_key_template(IST &is, std::string const &key) +template +IST &colvarbias::read_state_data_key_template_(IST &is, std::string const &key) { auto const start_pos = is.tellg(); std::string key_in; @@ -718,13 +719,13 @@ template IST &colvarbias::read_state_data_key_template(IST &is, s std::istream & colvarbias::read_state_data_key(std::istream &is, std::string const &key) { - return read_state_data_key_template(is, key); + return read_state_data_key_template_(is, key); } cvm::memory_stream & colvarbias::read_state_data_key(cvm::memory_stream &is, std::string const &key) { - return read_state_data_key_template(is, key); + return read_state_data_key_template_(is, key); } diff --git a/src/colvarbias.h b/src/colvarbias.h index 1217a2b2b..9a51f9d51 100644 --- a/src/colvarbias.h +++ b/src/colvarbias.h @@ -181,7 +181,7 @@ class colvarbias /// Read a keyword header for a data sequence from a stream /// \param[in,out] Input stream /// \param[in] Keyword labeling the header block; an error will be raised if not matching - template IST &read_state_data_key_template(IST &is, std::string const &key); + template IST &read_state_data_key_template_(IST &is, std::string const &key); public: @@ -198,7 +198,7 @@ class colvarbias private: /// Generic stream reading function (formatted and not) - template IST & read_state_from_stream(IST &is); + template IST & read_state_template_(IST &is); public: diff --git a/src/colvarbias_abf.cpp b/src/colvarbias_abf.cpp index d8927e29a..acca85efa 100644 --- a/src/colvarbias_abf.cpp +++ b/src/colvarbias_abf.cpp @@ -742,7 +742,7 @@ int colvarbias_abf::read_gradients_samples() } -template OST & colvarbias_abf::write_to_stream(OST &os) +template OST & colvarbias_abf::write_state_data_template_(OST &os) { auto flags = os.flags(); @@ -770,17 +770,17 @@ template OST & colvarbias_abf::write_to_stream(OST &os) std::ostream & colvarbias_abf::write_state_data(std::ostream& os) { - return write_to_stream(os); + return write_state_data_template_(os); } cvm::memory_stream & colvarbias_abf::write_state_data(cvm::memory_stream& os) { - return write_to_stream(os); + return write_state_data_template_(os); } -template IST &colvarbias_abf::read_from_stream(IST &is) +template IST &colvarbias_abf::read_state_data_template_(IST &is) { if ( input_prefix.size() > 0 ) { cvm::error("ERROR: cannot provide both inputPrefix and a colvars state file.\n", COLVARS_INPUT_ERROR); @@ -827,13 +827,13 @@ template IST &colvarbias_abf::read_from_stream(IST &is) std::istream & colvarbias_abf::read_state_data(std::istream& is) { - return read_from_stream(is); + return read_state_data_template_(is); } cvm::memory_stream & colvarbias_abf::read_state_data(cvm::memory_stream& is) { - return read_from_stream(is); + return read_state_data_template_(is); } diff --git a/src/colvarbias_abf.h b/src/colvarbias_abf.h index e9887562d..635e0fbfd 100644 --- a/src/colvarbias_abf.h +++ b/src/colvarbias_abf.h @@ -162,10 +162,10 @@ class colvarbias_abf : public colvarbias { private: /// Generic stream writing function (formatted and not) - template OST &write_to_stream(OST &os); + template OST &write_state_data_template_(OST &os); /// Generic stream readingx function (formatted and not) - template IST &read_from_stream(IST &is); + template IST &read_state_data_template_(IST &is); public: diff --git a/src/colvargrid_def.h b/src/colvargrid_def.h index c109ef1bf..92861f43b 100644 --- a/src/colvargrid_def.h +++ b/src/colvargrid_def.h @@ -22,7 +22,7 @@ #include "colvars_memstream.h" -template IST &read_restart_template(colvar_grid &g, IST &is) +template IST &read_restart_template_(colvar_grid &g, IST &is) { auto const start_pos = is.tellg(); std::string conf; @@ -43,13 +43,13 @@ template IST &read_restart_template(colvar_grid &g, IST template std::istream &colvar_grid::read_restart(std::istream &is) { - return read_restart_template(*this, is); + return read_restart_template_(*this, is); } template cvm::memory_stream &colvar_grid::read_restart(cvm::memory_stream &is) { - return read_restart_template(*this, is); + return read_restart_template_(*this, is); } @@ -69,7 +69,7 @@ template cvm::memory_stream &colvar_grid::write_restart(cvm::memory } -template IST &read_raw_template(colvar_grid &g, IST &is) +template IST &read_raw_template_(colvar_grid &g, IST &is) { auto const start_pos = is.tellg(); @@ -99,13 +99,13 @@ template IST &read_raw_template(colvar_grid &g, IST &is) template std::istream &colvar_grid::read_raw(std::istream &is) { - return read_raw_template(*this, is); + return read_raw_template_(*this, is); } template cvm::memory_stream &colvar_grid::read_raw(cvm::memory_stream &is) { - return read_raw_template(*this, is); + return read_raw_template_(*this, is); } diff --git a/src/colvarvalue.cpp b/src/colvarvalue.cpp index 8d0f63212..64436db98 100644 --- a/src/colvarvalue.cpp +++ b/src/colvarvalue.cpp @@ -723,7 +723,7 @@ int colvarvalue::from_simple_string(std::string const &s) } -template void colvarvalue::write_to_stream(OST &os) const +template void colvarvalue::write_to_stream_template_(OST &os) const { switch (type()) { case colvarvalue::type_scalar: @@ -751,14 +751,14 @@ template void colvarvalue::write_to_stream(OST &os) const std::ostream & operator << (std::ostream &os, colvarvalue const &x) { - x.write_to_stream(os); + x.write_to_stream_template_(os); return os; } cvm::memory_stream & operator << (cvm::memory_stream &os, colvarvalue const &x) { - x.write_to_stream(os); + x.write_to_stream_template_(os); return os; } @@ -773,7 +773,7 @@ std::ostream & operator << (std::ostream &os, std::vector const &v) } -template void colvarvalue::read_from_stream(IST &is) +template void colvarvalue::read_from_stream_template_(IST &is) { if (type() == colvarvalue::type_notset) { cvm::error("Trying to read from a stream a colvarvalue, " @@ -811,14 +811,14 @@ template void colvarvalue::read_from_stream(IST &is) std::istream & operator >> (std::istream &is, colvarvalue &x) { - x.read_from_stream(is); + x.read_from_stream_template_(is); return is; } cvm::memory_stream & operator >> (cvm::memory_stream &is, colvarvalue &x) { - x.read_from_stream(is); + x.read_from_stream_template_(is); return is; } diff --git a/src/colvarvalue.h b/src/colvarvalue.h index b2edaa5a5..5670906cd 100644 --- a/src/colvarvalue.h +++ b/src/colvarvalue.h @@ -298,9 +298,12 @@ class colvarvalue { /// Undefined operation void undef_op() const; +private: /// Generic stream writing function (formatted and not) - template void write_to_stream(OST &os) const; + template void write_to_stream_template_(OST &os) const; + +public: /// Formatted output operator friend std::ostream & operator << (std::ostream &os, colvarvalue const &x); @@ -308,8 +311,12 @@ class colvarvalue { /// Unformatted output operator friend cvm::memory_stream & operator << (cvm::memory_stream &os, colvarvalue const &x); +private: + /// Generic stream reading function (formatted and not) - template void read_from_stream(IST &is); + template void read_from_stream_template_(IST &is); + +public: /// Formatted input operator friend std::istream & operator >> (std::istream &is, colvarvalue &x); From 3c9076c7bfde7f9c22a8a0439af47761a118650a Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 15 Sep 2023 14:08:23 -0400 Subject: [PATCH 087/162] Silence redundant Clang analyzer warning --- src/colvarmodule.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index a5e082b85..c6fba2c46 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -125,8 +125,9 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) // set initial default values binary_restart = false; - if (getenv("COLVARS_BINARY_RESTART") != nullptr) { - if (atoi(getenv("COLVARS_BINARY_RESTART"))) { + char const *env_var = getenv("COLVARS_BINARY_RESTART"); + if (env_var) { + if (atoi(env_var ? env_var : "0")) { binary_restart = true; } } From 529d64a4788a529a0feda49144e1f7ec08f65bbb Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 15 Sep 2023 17:02:43 -0400 Subject: [PATCH 088/162] Support external output buffer in memory_stream --- src/colvars_memstream.cpp | 16 ++++++---------- src/colvars_memstream.h | 21 ++++++++++++++------- 2 files changed, 20 insertions(+), 17 deletions(-) diff --git a/src/colvars_memstream.cpp b/src/colvars_memstream.cpp index 2243dc96a..13cb8fb34 100644 --- a/src/colvars_memstream.cpp +++ b/src/colvars_memstream.cpp @@ -14,17 +14,13 @@ #include "colvars_memstream.h" -bool cvm::memory_stream::expand_ouput_buffer(size_t add_bytes) +bool cvm::memory_stream::expand_output_buffer(size_t add_bytes) { - if (external_output_buffer_) { - // Cannot resize an external buffer - setstate(std::ios::badbit); + auto &buffer = external_output_buffer_ ? *external_output_buffer_ : internal_buffer_; + if ((buffer.size() + add_bytes) <= max_length_) { + buffer.resize((buffer.size() + add_bytes)); } else { - if ((internal_buffer_.size() + add_bytes) <= max_length_) { - internal_buffer_.resize((internal_buffer_.size() + add_bytes)); - } else { - setstate(std::ios::badbit); - } + setstate(std::ios::badbit); } return bool(*this); } @@ -34,7 +30,7 @@ template <> void cvm::memory_stream::write_object(std::string const &t) { size_t const string_length = t.size(); size_t const new_data_size = sizeof(size_t) + sizeof(char) * string_length; - if (expand_ouput_buffer(new_data_size)) { + if (expand_output_buffer(new_data_size)) { std::memcpy(output_location(), &string_length, sizeof(size_t)); incr_write_pos(sizeof(size_t)); std::memcpy(output_location(), t.c_str(), t.size() * sizeof(char)); diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index 9c2b30896..374bc70eb 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -41,13 +41,19 @@ class cvm::memory_stream { { } + /// Set up a stream based on an external output buffer + memory_stream(std::vector &buf) : memory_stream() + { + external_output_buffer_ = &buf; + } + /// Length of the buffer inline size_t length() const { return data_length_; } /// Output buffer inline unsigned char *output_buffer() { - return (external_output_buffer_ ? external_output_buffer_ : internal_buffer_.data()); + return (external_output_buffer_ ? external_output_buffer_->data() : internal_buffer_.data()); } /// Next location to write to @@ -120,7 +126,7 @@ class cvm::memory_stream { protected: /// External output buffer - unsigned char *external_output_buffer_ = nullptr; + std::vector *external_output_buffer_ = nullptr; /// External input buffer unsigned char const *external_input_buffer_ = nullptr; @@ -138,7 +144,7 @@ class cvm::memory_stream { std::ios::iostate state_ = std::ios::goodbit; /// Add the requester number of bytes to the array capacity; return false if buffer is external - bool expand_ouput_buffer(size_t add_bytes); + bool expand_output_buffer(size_t add_bytes); /// Move the buffer position past the data just written inline void incr_write_pos(size_t c) { data_length_ += c; } @@ -155,15 +161,16 @@ class cvm::memory_stream { /// Move the buffer position past the data just read inline void incr_read_pos(size_t c) { read_pos_ += c; } - /// Check that the buffer contains enough bytes to read as the argument says, set error otherwise + /// Check that the buffer contains enough bytes to read as the argument says, set error + /// otherwise inline bool has_remaining(size_t c) { return c <= (data_length_ - read_pos_); } -}; + }; template void cvm::memory_stream::write_object(T const &t) { static_assert(IS_TRIVIALLY_COPYABLE(T), "Cannot use write_object() on complex type"); size_t const new_data_size = sizeof(T); - if (expand_ouput_buffer(new_data_size)) { + if (expand_output_buffer(new_data_size)) { std::memcpy(output_location(), &t, sizeof(T)); incr_write_pos(new_data_size); } @@ -180,7 +187,7 @@ template void cvm::memory_stream::write_vector(std::vector const static_assert(IS_TRIVIALLY_COPYABLE(T), "Cannot use write_vector() on complex type"); size_t const vector_length = t.size(); size_t const new_data_size = sizeof(size_t) + sizeof(T) * vector_length; - if (expand_ouput_buffer(new_data_size)) { + if (expand_output_buffer(new_data_size)) { std::memcpy(output_location(), &vector_length, sizeof(size_t)); incr_write_pos(sizeof(T)); std::memcpy(output_location(), t.data(), t.size() * sizeof(T)); From 195fdfa1299ba5919cface509c5986c4c0e382a2 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 15 Sep 2023 17:34:23 -0400 Subject: [PATCH 089/162] Silence compiler warning --- src/colvars_memstream.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h index 374bc70eb..0d80d2794 100644 --- a/src/colvars_memstream.h +++ b/src/colvars_memstream.h @@ -100,7 +100,7 @@ class cvm::memory_stream { // Compatibility with STL stream functions /// Report the current position in the buffer - inline size_t const tellg() const { return read_pos_; } + inline size_t tellg() const { return read_pos_; } /// Report the current position in the buffer inline memory_stream & seekg(size_t pos) { read_pos_ = pos; return *this; } From a34502d87924212c80ea3b5b35b728bcdf0d519c Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 15 Sep 2023 17:05:22 -0400 Subject: [PATCH 090/162] Add wrapper code to serialize/deserialize to std::vector --- src/colvarmodule.cpp | 17 +++++++++++++++++ src/colvarmodule.h | 6 ++++++ 2 files changed, 23 insertions(+) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index c6fba2c46..3b04867d5 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -1563,6 +1563,13 @@ int colvarmodule::set_input_state_buffer(size_t n, unsigned char *buf) } +int colvarmodule::set_input_state_buffer(std::vector &buf) +{ + input_state_buffer_ = std::move(buf); + return COLVARS_OK; +} + + std::istream & colvarmodule::read_objects_state(std::istream &is) { auto pos = is.tellg(); @@ -1829,6 +1836,16 @@ cvm::memory_stream &colvarmodule::write_state(cvm::memory_stream &os) } +int colvarmodule::write_state_buffer(std::vector &buffer) +{ + cvm::memory_stream os(buffer); + if (os << colvars_magic_number) { + write_state_template_(os); + } + return os ? COLVARS_OK : COLVARS_ERROR; +} + + std::ostream &colvarmodule::write_traj_label(std::ostream &os) { os.setf(std::ios::scientific, std::ios::floatfield); diff --git a/src/colvarmodule.h b/src/colvarmodule.h index 7cc479035..bc4855225 100644 --- a/src/colvarmodule.h +++ b/src/colvarmodule.h @@ -461,6 +461,9 @@ class colvarmodule { /// Set an internal state buffer, to be read later as an unformatted stream when ready int set_input_state_buffer(size_t n, unsigned char *buf); + /// Same as set_input_state_buffer() for C array, but uses std::move + int set_input_state_buffer(std::vector &buf); + /// Read the states of individual objects; allows for changes std::istream & read_objects_state(std::istream &is); @@ -481,6 +484,9 @@ class colvarmodule { /// Write the state of the module to an unformatted (binary) file memory_stream & write_state(memory_stream &os); + /// Write the state of the module to an array of bytes (wrapped as a memory_stream object) + int write_state_buffer(std::vector &buffer); + /// Strips .colvars.state from filename and checks that it is not empty static std::string state_file_prefix(char const *filename); From 53b7ee0357b10a5d6083162a675d626a37292fc1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Thu, 21 Sep 2023 14:40:26 +0200 Subject: [PATCH 091/162] Simplify test --- src/colvarmodule.cpp | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 3b04867d5..617a74a75 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -126,10 +126,8 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) binary_restart = false; char const *env_var = getenv("COLVARS_BINARY_RESTART"); - if (env_var) { - if (atoi(env_var ? env_var : "0")) { - binary_restart = true; - } + if (env_var && atoi(env_var)) { + binary_restart = true; } // "it_restart" will be set by the input state file, if any; From 799c34307bfbf6464295a44404a1788a941999e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Thu, 21 Sep 2023 15:55:43 +0200 Subject: [PATCH 092/162] Expand doc on binary restart in addition, a general round of spelling fixes --- doc/colvars-refman-main.tex | 51 +++++++++++++++++++------------------ 1 file changed, 26 insertions(+), 25 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index b77eea380..a6bdac5fe 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -171,7 +171,7 @@ Alternately, use the Automatic colvars features in the Actions tab. -Now, clicking ``Edit'' in the Dashboard window (or right-clikcing on a colvar in the list view), you can modify the collective variable to reflect interesting geometric properties of the system. +Now, clicking ``Edit'' in the Dashboard window (or right-clicking on a colvar in the list view), you can modify the collective variable to reflect interesting geometric properties of the system. The power of the collective variables approach lies in the variety of geometric functions (``components'') and their combinations. The editor window provides a number of helpers to make it easy and quick to define the most relevant variables. See section \ref{sec:dashboard_config_editor} for details. @@ -381,7 +381,7 @@ The ``internal units'' of the Colvars module are the units in which values are expected to be in the configuration file, and in which collective variable values, energies, etc. are expressed in the output and colvars trajectory files. Generally \textbf{the Colvars module uses internally the same units as its back-end MD engine, with the exception of VMD}, where different unit sets are supported to allow for easy setup, visualization and analysis of Colvars simulations performed with any simulation engine. -Note that \textbf{angles} are expressed in degrees, and derived quantites such as force constants are based on degrees as well. +Note that \textbf{angles} are expressed in degrees, and derived quantities such as force constants are based on degrees as well. Some colvar components have default values, expressed in \AA{}ngstr\"om in this documentation. They are converted to the current length unit as needed. Atomic coordinates read from \textbf{XYZ files} (and PDB files where applicable) are expected to be expressed in \AA{}ngstr\"om, no matter what unit system is in use by the back-end (\MDENGINE) or the Colvars Module. They are converted internally to the current length unit as needed. Note that force constants in \texttt{harmonic} and \texttt{harmonicWalls} biases (\ref{sec:colvarbias_harmonic}) are rescaled according to the \refkey{width}{colvar|width} parameter of colvars, so that they are formally in energy units, although if \refkey{width}{colvar|width} is given its default value of 1.0, force constants are effectively expressed in \energyunit/\textit{(colvar unit)}$^2$. @@ -481,7 +481,7 @@ string}{% ``out''}{% If a value is provided, it is interpreted as the prefix to all output files that will be written by the Colvars module (see \ref{sec:colvars_output}). - This includes output state files for checkpointing, as well as accumu;ated information such as PMFs or histograms and trajectories of the collective variables. + This includes output state files for checkpointing, as well as accumulated information such as PMFs or histograms and trajectories of the collective variables. Because this information is often useful, a default value is set for this keyword when not provided. However, supplying an empty string suppresses any file output from Colvars to file, except for data saved into the LAMMPS binary restart file. } @@ -524,11 +524,11 @@ Thermostating fix (optional)}{% string}{% NULL}{% - This keyword provides the \emph{ID} of an applicable thermostating fix command. This will be used to provide the Colvars module with the current thermostat target temperature when using a method that needs this information.} + This keyword provides the \emph{ID} of an applicable thermostatting fix command. This will be used to provide the Colvars module with the current thermostat target temperature when using a method that needs this information.} \end{itemize} -All of the above keywords except for the name of the configuration file may also be given (or overriden) using \texttt{fix\_modify}, as well as new Colvars configuration files (see \ref{sec:cv_scripting} for more details). +All of the above keywords except for the name of the configuration file may also be given (or overridden) using \texttt{fix\_modify}, as well as new Colvars configuration files (see \ref{sec:cv_scripting} for more details). } @@ -696,7 +696,7 @@ \end{mdexampleinput} The step number contained by the loaded file will be used internally by Colvars to control time-dependent biases, unless \texttt{firstTimestep} is issued, in which case that value will be used.} -\cvnamdonly{When the system's topology is changed during simulation via the \texttt{structure} command (e.g.{} in constant-pH simulations), it is generally best to reset and re-initalize the module from scratch before loading the corresponding snapshot: +\cvnamdonly{When the system's topology is changed during simulation via the \texttt{structure} command (e.g.{} in constant-pH simulations), it is generally best to reset and re-initialize the module from scratch before loading the corresponding snapshot: \begin{mdexampleinput} \-structure~newsystem.psf\\ \-reinitatoms~$<$snapshot$>$\\ @@ -811,7 +811,7 @@ \cvvmdonly{Note that in VMD, any forces applied via \texttt{addforce} do not have any effect on the movement of atoms: this feature is only available for compatibility.} For certain types of variable, the force applied directly on a colvar may be combined with those acting \emph{indirectly} on it via the interatomic force field, making up the \emph{total force}. -When the \refkey{outputTotalForce}{colvar|outputTotalForce} kewyord is enabled, or when a biasing method that makes explicit use of the total force is enabled, the total force may be obtained as: +When the \refkey{outputTotalForce}{colvar|outputTotalForce} keyword is enabled, or when a biasing method that makes explicit use of the total force is enabled, the total force may be obtained as: \cvscriptexampleinputcolvar{gettotalforce}{}{"xi"} \noindent{}Note that not all types of variable support total-force computation, and the value of the total force may not be available immediately within the same simulation step: see the documentation of \refkey{outputTotalForce}{colvar|outputTotalForce} for more details. @@ -962,8 +962,9 @@ The Colvars state file may be in either one of two formats: \begin{itemize} -\item Unformatted (binary) format, which is both space-efficient and quick to load/save, but requires that the same \MDENGINE{} build was used to save the file in the first place. Most importantly, no changes are allowed in the Colvars configuration between the original run. -\item Formatted (text) format, which takes more space and is slower to to load/save but is also portable across different platforms and even different engines (except for changes in physical units). Formatted state files are also the only format previously supported by Colvars version until late 2023. % TODO Add specific version? +\item Unformatted (binary) format, which is both space-efficient and quick to load/save, but requires that the same \MDENGINE{} build was used to save the file in the first place. Most importantly, no changes are allowed in the Colvars configuration between the original run. Binary state files are supported by Colvars versions starting late 2023. % TODO Add specific version? +Binary checkpointing is enabled by setting the environment variable COLVARS_BINARY_RESTART to 1. +\item Formatted (text) format, which takes more space and is slower to to load/save but is also portable across different platforms and even different engines (except for changes in physical units). \end{itemize} \cvsubsubsec{Contents of the state file.}{} @@ -1111,7 +1112,7 @@ \cvsubsubsec{Grid files: multicolumn text format}{sec:colvar_multicolumn_grid} -Many simulation methods and analysis tools write files that contain functions of the collective variables tabulated on a grid (e.g.{} potentials of mean force or multidimentional histograms) for the purpose of analyzing results. +Many simulation methods and analysis tools write files that contain functions of the collective variables tabulated on a grid (e.g.{} potentials of mean force or multidimensional histograms) for the purpose of analyzing results. Such files are produced by ABF (\ref{sec:colvarbias_abf}), metadynamics (\ref{sec:colvarbias_meta}), multidimensional histograms (\ref{sec:colvarbias_histogram}), as well as any restraint with optional thermodynamic integration support (\ref{sec:colvarbias_ti}). In some cases, these files may also be read as input of a new simulation. @@ -1143,7 +1144,7 @@ \item $\mathtt{periodic}(\xi_{i})$ is set to 1 if and only if $\xi_{i}$ is periodic and the grids' boundaries cover its period. \end{itemize} -How the grid's boundaries affect the sequence of points depends on how the contents of the file were computed. In many cases, such as histograms and PMFs computed by metadynamics (\ref{sec:colvarbias_ebmeta}), the values of $\xi_i$ in the first few columns correspond to the \emph{midpoints} of the corresponing bins, i.e.\ $\xi^{1}_{1} = \mathtt{min}(\xi_{i}) + \mathtt{width}(\xi_{i})/2$. +How the grid's boundaries affect the sequence of points depends on how the contents of the file were computed. In many cases, such as histograms and PMFs computed by metadynamics (\ref{sec:colvarbias_ebmeta}), the values of $\xi_i$ in the first few columns correspond to the \emph{midpoints} of the corresponding bins, i.e.\ $\xi^{1}_{1} = \mathtt{min}(\xi_{i}) + \mathtt{width}(\xi_{i})/2$. However, there is a slightly different format in PMF files computed by ABF (\ref{sec:colvarbias_abf}) or other biases that use thermodynamic integration (\ref{sec:colvarbias_ti}). In these cases, it is free-energy gradients that are accumulated on an \texttt{(npoints)}-long grid along each variable $\xi$: after these gradients are integrated, the resulting PMF is discretized on a slightly larger grid with \texttt{(npoints+1)} points along $\xi$ (unless the interval is periodic). Therefore, the grid's outer edges extend by $\mathtt{width}(\xi_{i})/2$ above and below the specified boundaries, so that for instance $\mathtt{min}(\xi_{i})$ in the header appears to be shifted back by $\mathtt{width}(\xi_{i})/2$ compared to what would be expected. \emph{Please keep this difference in mind when comparing PMFs computed by different methods.} @@ -1811,7 +1812,7 @@ \texttt{coordNum}}{% Pairlist control}{% decimal}{% - 0.0}{This controls the pairlist feature, dictating the minimum value for each summation element in Eq.~\ref{eq:cvc_coordNum} such that the pair that contributed the summation element is included in subsequent simulation timesteps until the next pairlist recalculation. For most applications, this value should be small (eg. 0.001) to avoid missing important contributions to the overall sum. Higher values will improve performance by reducing the number of pairs that contribute to the sum. Values above 1 will exclude all possible pair interactions. Similarly, values below 0 will never exclude a pair from consideration. To ensure continuous forces, Eq.~\ref{eq:cvc_coordNum} is further modified by subtracting the tolerance and then rescaling so that each pair covers the range $\left[0, 1\right]$. + 0.0}{This controls the pair list feature, dictating the minimum value for each summation element in Eq.~\ref{eq:cvc_coordNum} such that the pair that contributed the summation element is included in subsequent simulation timesteps until the next pai r list recalculation. For most applications, this value should be small (eg. 0.001) to avoid missing important contributions to the overall sum. Higher values will improve performance by reducing the number of pairs that contribute to the sum. Values above 1 will exclude all possible pair interactions. Similarly, values below 0 will never exclude a pair from consideration. To ensure continuous forces, Eq.~\ref{eq:cvc_coordNum} is further modified by subtracting the tolerance and then rescaling so that each pair covers the range $\left[0, 1\right]$. } \item % @@ -1821,7 +1822,7 @@ \texttt{coordNum}}{% Pairlist regeneration frequency}{% positive integer}{% - 100}{This controls the pairlist feature, dictating how many steps are taken between regenerating pairlists if the tolerance is greater than 0. + 100}{This controls the pairlist feature, dictating how many steps are taken between regenerating pair lists if the tolerance is greater than 0. } \end{cvcoptions} @@ -1831,7 +1832,7 @@ are less than the cutoff), or $N_{\mathtt{group1}}$ if \texttt{group2CenterOnly} is used. For performance reasons, at least one of \texttt{group1} and \texttt{group2} should be of limited size or \texttt{group2CenterOnly} should be used: the cost of the loop over all pairs grows as $N_{\mathtt{group1}} \times N_{\mathtt{group2}}$. -Setting $\mathtt{tolerance} > 0$ ameliorates this to some degree, although every pair is still checked to regenerate the pairlist. +Setting $\mathtt{tolerance} > 0$ ameliorates this to some degree, although every pair is still checked to regenerate the pair list. @@ -1890,7 +1891,7 @@ 3.3~\AA{}), \texttt{expNumer} (with a default value of 6) and \texttt{expDenom} (with a default value of 8). Unlike \texttt{coordNum}, it requires two atom numbers, \texttt{acceptor} and -\texttt{donor}, to be defined. It returns an adimensional number, +\texttt{donor}, to be defined. It returns a dimensionless number, with values between 0 (acceptor and donor far outside the cutoff distance) and 1 (acceptor and donor much closer than the cutoff). @@ -2302,7 +2303,7 @@ Altogether, these are sufficient to represent all three degrees of freedom of a full rotation. However, they also suffer from the potential ``gimbal lock'' problem, which emerges whenever $\theta \simeq \pm 90^\circ$, which includes also the case where the full rotation is small. Under such conditions, the angles $\phi$ and $\psi$ are both ill-defined and cannot be used as collective variables. -For these reasons, it is highly recommmended that Euler angles are used only in simulations where their range of applicability is \emph{known ahead of time}, and excludes configurations where $\theta \simeq \pm 90^\circ$ altogether. +For these reasons, it is highly recommended that Euler angles are used only in simulations where their range of applicability is \emph{known ahead of time}, and excludes configurations where $\theta \simeq \pm 90^\circ$ altogether. \cvsubsubsec{\texttt{orientation}: orientation from reference coordinates.}{sec:cvc_orientation} \labelkey{colvar|orientation} @@ -3222,7 +3223,7 @@ \texttt{aspathCV} and \texttt{azpathCV}}{% The file name of the path file.}{% UNIX filename}{% - Defines the nodes or images that constitutes the path in CV space. The CVs of an image are listed in a line of \texttt{pathFile} using space-seperated format. Lines from top to button in \texttt{pathFile} corresponds images from initial to last. + Defines the nodes or images that constitutes the path in CV space. The CVs of an image are listed in a line of \texttt{pathFile} using space-separated format. Lines from top to button in \texttt{pathFile} corresponds images from initial to last. } \end{cvcoptions} @@ -4119,7 +4120,7 @@ Histograms (\ref{sec:colvarbias_histogram}), ABF (\ref{sec:colvarbias_abf}) and metadynamics (\ref{sec:colvarbias_meta}) all use this number as the initial choice for the grid spacing along this variable. As a typical rule of thumb, \texttt{width} should be no larger than the standard deviation of the colvar in an unbiased simulation (to characterize a local free-energy minimum with at least two points). - Further, many restraints such as harmonic potentials (\ref{sec:colvarbias_harmonic}), harmonic walls (\ref{sec:colvarbias_harmonic_walls}) and linear restraints (\ref{sec:colvarbias_linear}) also use this parameter to define the \emph{expected fluctuations} of the colvar, alowing to express the force constant in terms of this unit. + Further, many restraints such as harmonic potentials (\ref{sec:colvarbias_harmonic}), harmonic walls (\ref{sec:colvarbias_harmonic_walls}) and linear restraints (\ref{sec:colvarbias_linear}) also use this parameter to define the \emph{expected fluctuations} of the colvar, allowing to express the force constant in terms of this unit. This is most useful with multi-dimensional restraints acting on variables that have very different units (for examples, working with \lengthunit{} and degrees $^\circ$ simultaneously): a single force constant can be used for all, which is converted to the respective unit of each variable when forces are applied (the are printed at initialization time. } @@ -5220,7 +5221,7 @@ free energy gradient at the current point $\bm{\xi}$ in the collective variable subspace, and $\alpha(N_\xi)$ is a scaling factor that is ramped from 0 to 1 as the local number of samples $N_\xi$ increases -to prevent nonequilibrium effects in the early phase of the simulation, +to prevent non-equilibrium effects in the early phase of the simulation, when the gradient estimate has a large variance. See the \texttt{fullSamples} parameter below for details. @@ -5229,7 +5230,7 @@ force introduced in the equations of motion guarantees that in the bin centered around $\bm{\xi}$, the forces acting along the selected collective variables average -to zero over time. Eventually, as the undelying free energy surface is canceled +to zero over time. Eventually, as the underlying free energy surface is canceled by the adaptive bias, evolution of the system along $\bm{\xi}$ is governed mainly by diffusion. Although this implementation of ABF can in principle be used in @@ -5297,7 +5298,7 @@ to application of the ABF} {positive integer} {200} - {To avoid nonequilibrium effects due to large fluctuations of the force exerted along the + {To avoid non-equilibrium effects due to large fluctuations of the force exerted along the colvars, it is recommended to apply a biasing force only after a the estimate has started converging. If \texttt{fullSamples} is non-zero, the applied biasing force is scaled by a factor $\alpha(N_\xi)$ between 0 and 1. @@ -5768,13 +5769,13 @@ V_{\mathrm{meta}}(\bm{\xi},t)dt} } \end{equation} -where $t_{e}$ is the time after which the bias potential grows (approximately) evenly during the simulation and $t_{tot}$ is the total simulation time. The free energy calculated according to eq.~\ref{eq:colvars_meta_fes_av} can thus be obtained averaging on time mutiple time-dependent free energy estimates, that can be printed out through the keyword \texttt{keepFreeEnergyFiles}. An alternative is to obtain the free energy profiles by summing the hills added during the simulation; the hills trajectory can be printed out by enabling the option \texttt{writeHillsTrajectory}. +where $t_{e}$ is the time after which the bias potential grows (approximately) evenly during the simulation and $t_{tot}$ is the total simulation time. The free energy calculated according to eq.~\ref{eq:colvars_meta_fes_av} can thus be obtained averaging on time multiple time-dependent free energy estimates, that can be printed out through the keyword \texttt{keepFreeEnergyFiles}. An alternative is to obtain the free energy profiles by summing the hills added during the simulation; the hills trajectory can be printed out by enabling the option \texttt{writeHillsTrajectory}. \cvsubsubsec{Treatment of the PMF boundaries}{sec:colvarbias_meta_boundaries} In typical scenarios the Gaussian hills of a metadynamics potential are interpolated and summed together onto a grid, which is much more efficient than computing each hill independently at every step (the keyword \refkey{useGrids}{metadynamics|useGrids} is \texttt{on} by default). -This numerical approximation typically yields neglibile errors in the resulting PMF \cite{Fiorin2013}. +This numerical approximation typically yields negligible errors in the resulting PMF \cite{Fiorin2013}. However, due to the finite thickness of the Gaussian function, the metadynamics potential would suddenly vanish each time a variable exceeds its grid boundaries. To avoid such discontinuity the Colvars metadynamics code will keep an explicit copy of each hill that straddles a grid's boundary, and will use it to compute metadynamics forces outside the grid. @@ -6120,7 +6121,7 @@ \\ \end{tabular} -\textbf{Tip:} Besides setting a meaninful value for \texttt{targetDistMinVal}, the exploration of unphysically low values of the target distribution (which would lead to very large hills and possibly numerical instabilities) can be also prevented by restricting sampling to a given interval, using e.g.{} \texttt{harmonicWalls} restraint (\ref{sec:colvarbias_harmonic_walls}). +\textbf{Tip:} Besides setting a meaningful value for \texttt{targetDistMinVal}, the exploration of unphysically low values of the target distribution (which would lead to very large hills and possibly numerical instabilities) can be also prevented by restricting sampling to a given interval, using e.g.{} \texttt{harmonicWalls} restraint (\ref{sec:colvarbias_harmonic_walls}). @@ -6387,7 +6388,7 @@ boolean}{% \texttt{off}}{% If this option is chosen and \texttt{colvarsTrajFrequency} is not zero, the positions of the restraint centers will be written to the trajectory file during the simulation. - This option allows to conveniently extract the PMF from the colvars trajectory files in a steered MD calculation. + This option allows to conveniently extract the PMF from the Colvars trajectory files in a steered MD calculation. } \end{itemize} From f96861e7b8c4a96132de3df3f83e012cda14cee6 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 25 Sep 2023 16:33:03 -0400 Subject: [PATCH 093/162] Further improve doc --- doc/colvars-refman-main.tex | 51 ++++++++++++++++++++++++++++--------- 1 file changed, 39 insertions(+), 12 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index a6bdac5fe..c3f59a2f4 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -958,13 +958,22 @@ \cvsubsec{Input state file}{sec:colvars_input} -Several of the sampling methods implemented in Colvars are time- or history-dependent, i.e.\ they work by accumulating data as a simulation progresses and use this data to change their biasing forces. When continuing a simulation over consecutive runs, a \emph{state file} needs to be loaded into Colvars. +Several of the sampling methods implemented in Colvars are time- or history-dependent, i.e.\ they work by accumulating data as a simulation progresses and use these data to determine their biasing forces. + +This requires that the Colvars information + +a standard method for checkpointing (currently, these are only GROMACS and LAMMPS) + +When continuing a simulation over consecutive runs, a \emph{state file} needs to be loaded into Colvars. The Colvars state file may be in either one of two formats: \begin{itemize} -\item Unformatted (binary) format, which is both space-efficient and quick to load/save, but requires that the same \MDENGINE{} build was used to save the file in the first place. Most importantly, no changes are allowed in the Colvars configuration between the original run. Binary state files are supported by Colvars versions starting late 2023. % TODO Add specific version? -Binary checkpointing is enabled by setting the environment variable COLVARS_BINARY_RESTART to 1. -\item Formatted (text) format, which takes more space and is slower to to load/save but is also portable across different platforms and even different engines (except for changes in physical units). +\item Unformatted, i.e.\ \emph{``binary''} format, which is both space-efficient and quick to load/save, but requires that the same \MDENGINE{} build was used to save the file in the first place, and the the Colvars configuration was the same. This format is supported by Colvars versions starting late 2023. % TODO Add specific version? +Binary checkpointing can b + +enabled by setting the environment variable ``COLVARS_BINARY_RESTART'' to 1. +\item Formatted, i.e.\ \emph{``text''} format, which takes more space and is slower to to load/save but is also portable across different platforms and even different simulation engines (save for changes in physical units). +This format is supported by all versions of Colvars. \end{itemize} \cvsubsubsec{Contents of the state file.}{} @@ -976,21 +985,39 @@ % \cvgromacsonly{\cvsubsubsec{Restarting in GROMACS.}{} TODO } \cvlammpsonly{\cvsubsubsec{Restarting in LAMMPS.}{} -For continuing a Colvars-based simulation, the recommended method is using the standard LAMMPS \texttt{read\_restart} command, which effectively reads the Colvars state in unformatted (binary) format embedded in the LAMMPS restart file. Alternatively, restarting from a formatted Colvars-only state file is also possible by using the \texttt{input} keyword of the \texttt{fix colvars} command, which overrides the information read from the LAMMPS restart file. -Furthermore, a state file may also be loaded after initialization with the \texttt{fix\_modify load } LAMMPS command. -} +For continuing a Colvars-based simulation, the recommended method is using the standard LAMMPS \texttt{read\_restart} command, which reads the Colvars state data from the LAMMPS restart file (in binary format). +\begin{mdexampleinput}{} +\-read\_restart~\emph{filename} +\end{mdexampleinput} +Alternatively, restarting from a Colvars-specific state file is also possible by providing the \texttt{input} keyword to the \texttt{fix colvars} command: +\begin{mdexampleinput}{} +\-fix~Colvars~all~colvars~\emph{configfile}~input~\emph{input\_prefix} +\end{mdexampleinput} +When the ``\texttt{input}'' keyword is used, the contents of the file \texttt{$<$\emph{input\_prefix}$>$.colvar.state} override the information read from the LAMMPS restart file. Finally, a state file may also be loaded after initialization through the ``\texttt{fix\_modify}'' command: +\begin{mdexampleinput}{% +}fix\_modify~Colvars~\texttt{input}~\emph{new\_input\_prefix} +\end{mdexampleinput} +} % end \cvlammpsonly + \cvnamdonly{\cvsubsubsec{Restarting in NAMD.}{} Before the Colvars module is initialized in NAMD, the \texttt{colvarsInput} keyword can be used to give the name of a state file. -After initialization of the Colvars module, a state file may be loaded at any time with the Tcl command \texttt{cv load}.} +After initialization of the Colvars module, a state file may be loaded at any time with the Tcl command \texttt{cv load}. +Both versions support loading Colvars state files in either format (binary or text). +} % end \cvnamdonly + \cvsubsubsec{Restarting after a change in Colvars configuration.}{} -A unique advantage of the formatted Colvars state files is that they can be loaded even if the configuration has changed. -For example, new restraints may have been added or removed from the Colvars configuration between consecutive runs. +It useful in some cases to modify the configuration of variables or biases between consecutive runs: a typical example would the addition or removal of a restraint in a simulation. +By restarting using formatted (i.e.\ text) Colvars state files, it is possible to read previous data while allowing for changes in configuration. For each newly defined variable or bias, no information will be read from the state file if this is unavailable: such new objects will remain uninitialized until the first compute step. Conversely, any information that the state file has about variables or biases that are no longer defined is silently ignored. \emph{Because these checks are performed based solely on the names of variables and biases, it is your responsibility to ensure that these names correspond to consistent definitions between runs.} +When restarting using unformatted (i.e.\ binary) state files, configuration changes are not allowed. The easiest solution would be to produce a formatted (i.e.\ text) state file specifically for that purpose. +\ifdefined\cvscriptapi{% +Alternatively, after restarting Colvars using a state file consistent with the previous configuration, the configuration may be changed using the scripting interface (see \ref{sec:cv_scripting}). +}\fi \cvsubsec{Output files}{sec:colvars_output} @@ -1000,8 +1027,8 @@ \begin{itemize} \item A \emph{state file}, named \outputName\texttt{.colvars.state}, which is written at the end of the specified run\cvscriptonly{, and can also be written at any time with the scripting command \texttt{save} (\ref{sec:cv_command_loadsave})}. -This file is in plain text format by default\cvnamdonly{, regardless of the value of \texttt{binaryOutput} of the NAMD coordinate and velocity files}, or in binary format if the environment variable \texttt{COLVARS\_BINARY\_RESTART} is set to a non-zero integer. -\emph{The state is the only Colvars output file needed to continue a simulation.} +This file is in plain text format by default\cvnamdonly{, regardless of the value of \texttt{binaryOutput} of the NAMD coordinate and velocity files}, or in unformatted (i.e.\ binary) format if the environment variable \texttt{COLVARS\_BINARY\_RESTART} is set to a non-zero integer. +The state file is used to continue a simulation, and is required to restart a simulation unless the engine supports embedding information into their checkpoint file (as GROMACS or LAMMPS currently do). \item If the parameter \refkey{colvarsRestartFrequency}{Colvars-global|colvarsRestartFrequency} is larger than zero, a \emph{restart file} is written every that many steps: this file is fully equivalent to the final state file. The name of this file is \restartName\texttt{.colvars.state}. From 12f73be2566e5116087b823e95ae4896246436f7 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 25 Sep 2023 18:18:21 -0400 Subject: [PATCH 094/162] Fix incomplete sections --- doc/colvars-refman-main.tex | 24 +++++++++--------------- 1 file changed, 9 insertions(+), 15 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index c3f59a2f4..50cdb9d83 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -958,29 +958,23 @@ \cvsubsec{Input state file}{sec:colvars_input} -Several of the sampling methods implemented in Colvars are time- or history-dependent, i.e.\ they work by accumulating data as a simulation progresses and use these data to determine their biasing forces. +Several of the sampling methods implemented in Colvars are time- or history-dependent, i.e.\ they work by accumulating data as a simulation progresses, and use these data to determine their biasing forces. If the simulation engine uses a checkpoint or restart file (as GROMACS and LAMMPS do), any data needed by Colvars are embedded inti that file. Otherwise, a dedicated \emph{state file} can be loaded into Colvars directly. -This requires that the Colvars information - -a standard method for checkpointing (currently, these are only GROMACS and LAMMPS) +When a dedicated Colvars state file is used, it may be in either one of two formats: +\begin{itemize} -When continuing a simulation over consecutive runs, a \emph{state file} needs to be loaded into Colvars. +\item Formatted, i.e.\ \emph{``text''} format, which takes more space and is slower to to load/save but is also portable across different platforms and even different simulation engines (save for changes in physical units). This format is used by default, unless explicitly requested otherwise. -The Colvars state file may be in either one of two formats: -\begin{itemize} -\item Unformatted, i.e.\ \emph{``binary''} format, which is both space-efficient and quick to load/save, but requires that the same \MDENGINE{} build was used to save the file in the first place, and the the Colvars configuration was the same. This format is supported by Colvars versions starting late 2023. % TODO Add specific version? -Binary checkpointing can b +\item Unformatted, i.e.\ \emph{``binary''} format, which is both space-efficient and quick to load/save, but requires that the same \MDENGINE{} build was used to write the file and that the Colvars configuration remains the same. This format is supported by Colvars versions starting 2023-09-25. +Colvars state files are written in binary format by setting the environment variable ``\texttt{COLVARS\_BINARY\_RESTART}'' to 1. -enabled by setting the environment variable ``COLVARS_BINARY_RESTART'' to 1. -\item Formatted, i.e.\ \emph{``text''} format, which takes more space and is slower to to load/save but is also portable across different platforms and even different simulation engines (save for changes in physical units). -This format is supported by all versions of Colvars. \end{itemize} \cvsubsubsec{Contents of the state file.}{} In either format, the state file contains accumulated data as well as the step number at the end of the run. The step number read from a state file overrides any value that \MDENGINE{} provides, and will be incremented if the simulation proceeds. This means that the step number used internally by Colvars may not always match the step number reported by \MDENGINE{}. -\cvnamdonly{This is particularly inmportant in NAMD, which represents step numbers as a 32-bit integers that overflows after $\sim$ 2 billion steps, effectively rendering neutralizing the usefulness of \texttt{firstTimeStep}.} +\cvnamdonly{This is particularly inmportant in NAMD, which represents step numbers as a 32-bit integers that overflows after $\sim$ 2 billion steps, effectively negating the usefulness of the \texttt{firstTimeStep} keyword. However, step numbers are implemented correctly in the Colvars state file.} % \cvgromacsonly{\cvsubsubsec{Restarting in GROMACS.}{} TODO } @@ -1014,7 +1008,7 @@ Conversely, any information that the state file has about variables or biases that are no longer defined is silently ignored. \emph{Because these checks are performed based solely on the names of variables and biases, it is your responsibility to ensure that these names correspond to consistent definitions between runs.} -When restarting using unformatted (i.e.\ binary) state files, configuration changes are not allowed. The easiest solution would be to produce a formatted (i.e.\ text) state file specifically for that purpose. +When restarting using binary state files, configuration changes are not allowed. The easiest solution would be to produce a text-format state file specifically for that purpose. \ifdefined\cvscriptapi{% Alternatively, after restarting Colvars using a state file consistent with the previous configuration, the configuration may be changed using the scripting interface (see \ref{sec:cv_scripting}). }\fi @@ -1027,7 +1021,7 @@ \begin{itemize} \item A \emph{state file}, named \outputName\texttt{.colvars.state}, which is written at the end of the specified run\cvscriptonly{, and can also be written at any time with the scripting command \texttt{save} (\ref{sec:cv_command_loadsave})}. -This file is in plain text format by default\cvnamdonly{, regardless of the value of \texttt{binaryOutput} of the NAMD coordinate and velocity files}, or in unformatted (i.e.\ binary) format if the environment variable \texttt{COLVARS\_BINARY\_RESTART} is set to a non-zero integer. +This file is in plain text format by default\cvnamdonly{, regardless of the value of \texttt{binaryOutput} of the NAMD coordinate and velocity files}, or in binary format if the environment variable \texttt{COLVARS\_BINARY\_RESTART} is set to a non-zero integer. The state file is used to continue a simulation, and is required to restart a simulation unless the engine supports embedding information into their checkpoint file (as GROMACS or LAMMPS currently do). \item If the parameter \refkey{colvarsRestartFrequency}{Colvars-global|colvarsRestartFrequency} is larger than zero, a \emph{restart file} is written every that many steps: this file is fully equivalent to the final state file. From 4d2751586908db57fcccf98c567e0b27ad8714fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Tue, 26 Sep 2023 00:24:56 +0200 Subject: [PATCH 095/162] Mini-edit in doc --- doc/colvars-refman-main.tex | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index 50cdb9d83..c0545db2d 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -1003,7 +1003,7 @@ \cvsubsubsec{Restarting after a change in Colvars configuration.}{} It useful in some cases to modify the configuration of variables or biases between consecutive runs: a typical example would the addition or removal of a restraint in a simulation. -By restarting using formatted (i.e.\ text) Colvars state files, it is possible to read previous data while allowing for changes in configuration. +By restarting using text-format Colvars state files, it is possible to read previous data while allowing for changes in configuration. For each newly defined variable or bias, no information will be read from the state file if this is unavailable: such new objects will remain uninitialized until the first compute step. Conversely, any information that the state file has about variables or biases that are no longer defined is silently ignored. \emph{Because these checks are performed based solely on the names of variables and biases, it is your responsibility to ensure that these names correspond to consistent definitions between runs.} From 571926fb34aadbfdc9398443614ff07be3e2f160 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sun, 24 Sep 2023 15:25:41 -0400 Subject: [PATCH 096/162] Get updated output/restart prefixes from NAMD --- namd/src/colvarproxy_namd.C | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C index d20bf19dd..08680c2be 100644 --- a/namd/src/colvarproxy_namd.C +++ b/namd/src/colvarproxy_namd.C @@ -72,7 +72,7 @@ colvarproxy_namd::colvarproxy_namd() // both fields are taken from data structures already available updated_masses_ = updated_charges_ = true; - // take the output prefixes from the namd input + // Take the output prefixes from the NAMD input colvarproxy_io::set_output_prefix(std::string(simparams->outputFilename)); colvarproxy_io::set_restart_output_prefix(std::string(simparams->restartFilename)); colvarproxy_io::set_default_restart_frequency(simparams->restartFrequency); @@ -323,6 +323,8 @@ void colvarproxy_namd::calculate() if (first_timestep) { + // First run after the proxy is constructed + colvarproxy_namd::setup(); colvars->update_engine_parameters(); colvars->setup_input(); @@ -331,17 +333,26 @@ void colvarproxy_namd::calculate() first_timestep = false; } else { + // Use the time step number inherited from GlobalMaster if ( step - previous_NAMD_step == 1 ) { colvars->it++; b_simulation_continuing = false; } else { + // Cases covered by this condition: // - run 0 // - beginning of a new run statement // The internal counter is not incremented, and the objects are made // aware of this via the following flag b_simulation_continuing = true; + + // Update NAMD output and restart prefixes + colvarproxy_io::set_output_prefix(std::string(simparams->outputFilename)); + colvarproxy_io::set_restart_output_prefix(std::string(simparams->restartFilename)); + colvarproxy_io::set_default_restart_frequency(simparams->restartFrequency); + colvars->setup_output(); + } } From e20f16ea2167cfab2be11eb8ca9528198c9d66b6 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sun, 24 Sep 2023 16:35:49 -0400 Subject: [PATCH 097/162] Update patch offsets --- namd/Makefile.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/namd/Makefile.patch b/namd/Makefile.patch index 5e812279c..a1349b313 100644 --- a/namd/Makefile.patch +++ b/namd/Makefile.patch @@ -1,8 +1,8 @@ diff --git a/Makefile b/Makefile -index 57618904..b51789b3 100644 +index 1456d146..4bae1b7a 100644 --- a/Makefile +++ b/Makefile -@@ -406,13 +406,7 @@ SBLIB = \ +@@ -404,13 +404,7 @@ SBLIB = \ include colvars/src/Makefile.namd From 1bb9fbeb763c10f9ff1c55431625d8b17f6eceeb Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sun, 24 Sep 2023 16:39:00 -0400 Subject: [PATCH 098/162] Avoid writing output files if output prefix is empty --- src/colvarmodule.cpp | 30 +++++++++++++----------------- 1 file changed, 13 insertions(+), 17 deletions(-) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 617a74a75..5106b7aff 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -800,30 +800,26 @@ int colvarmodule::calc() // write restart files and similar data if (restart_out_freq && (cvm::step_relative() > 0) && - ((cvm::step_absolute() % restart_out_freq) == 0) ) { + ((cvm::step_absolute() % restart_out_freq) == 0)) { if (restart_out_name.size()) { // Write restart file, if different from main output error_code |= write_restart_file(restart_out_name); - } else { - if (output_prefix().size()) { - error_code |= write_restart_file(output_prefix()+".colvars.state"); - } + } else if (output_prefix().size()) { + error_code |= write_restart_file(output_prefix() + ".colvars.state"); } - cvm::increase_depth(); - for (std::vector::iterator cvi = colvars.begin(); - cvi != colvars.end(); - cvi++) { - // TODO remove this when corrFunc becomes a bias - error_code |= (*cvi)->write_output_files(); - } - for (std::vector::iterator bi = biases.begin(); - bi != biases.end(); - bi++) { - error_code |= (*bi)->write_state_to_replicas(); + if (output_prefix().size()) { + cvm::increase_depth(); + for (std::vector::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { + // TODO remove this when corrFunc becomes a bias + error_code |= (*cvi)->write_output_files(); + } + for (std::vector::iterator bi = biases.begin(); bi != biases.end(); bi++) { + error_code |= (*bi)->write_state_to_replicas(); + } + cvm::decrease_depth(); } - cvm::decrease_depth(); } // Write output files for biases, at the specified frequency for each From aad10c26ee94c1463a7ab0c5143224140d47d3ea Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sun, 24 Sep 2023 16:39:43 -0400 Subject: [PATCH 099/162] Allow quiet redefinition of the output prefix --- src/colvarmodule.cpp | 37 ++++++++++++++++--------------------- 1 file changed, 16 insertions(+), 21 deletions(-) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 5106b7aff..572d6f35e 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -1417,31 +1417,26 @@ int colvarmodule::setup_output() restart_out_name+"\".\n"); } - output_prefix() = proxy->output_prefix(); - if (output_prefix().size()) { - cvm::log("The final output state file" + state_file_format + " will be \""+ - (output_prefix().size() ? - std::string(output_prefix()+".colvars.state") : - std::string("colvars.state"))+"\".\n"); - // cvm::log (cvm::line_marker); - } + if (output_prefix() != proxy->output_prefix()) { + output_prefix() = proxy->output_prefix(); + if (output_prefix().size()) { + cvm::log("The final output state file will be \"" + + (output_prefix().size() ? std::string(output_prefix() + ".colvars.state") + : std::string("colvars.state")) + + "\".\n"); + } - cv_traj_name = - (output_prefix().size() ? - std::string(output_prefix()+".colvars.traj") : - std::string("")); + cv_traj_name = + (output_prefix().size() ? std::string(output_prefix() + ".colvars.traj") : std::string("")); - for (std::vector::iterator bi = biases.begin(); - bi != biases.end(); - bi++) { - error_code |= (*bi)->setup_output(); - } - - if (error_code != COLVARS_OK || cvm::get_error()) { - set_error_bits(COLVARS_FILE_ERROR); + for (std::vector::iterator bi = biases.begin(); + bi != biases.end(); + bi++) { + error_code |= (*bi)->setup_output(); + } } - return cvm::get_error(); + return error_code; } From b3d40e4280380e02ae2ed2eec3cf7855cd120a92 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sun, 24 Sep 2023 17:35:20 -0400 Subject: [PATCH 100/162] Close existing trajectory and let code know that a new one was opened --- src/colvarmodule.cpp | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 572d6f35e..5786d7603 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -1426,6 +1426,12 @@ int colvarmodule::setup_output() "\".\n"); } + if (proxy->output_stream_exists(cv_traj_name)) { + // Close old file + proxy->close_output_stream(cv_traj_name); + cv_traj_write_labels = true; + } + cv_traj_name = (output_prefix().size() ? std::string(output_prefix() + ".colvars.traj") : std::string("")); From 953f2308c1c6e4d8f30762656456c3ecbc326d3d Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Sun, 24 Sep 2023 17:35:01 -0400 Subject: [PATCH 101/162] Test redefinition of outputName in NAMD --- .../AutoDiff/test.Tcl.out | 108 +++++++++++ .../AutoDiff/test.alt.colvars.traj | 12 ++ .../AutoDiff/test.colvars.out | 171 ++++++++++++++++++ .../AutoDiff/test.colvars.state.stripped | 17 ++ .../AutoDiff/test.colvars.traj | 12 ++ .../008_change_outputName/namd-version.txt | 3 + .../interface/008_change_outputName/test.in | 30 +++ .../interface/008_change_outputName/test.namd | 22 +++ 8 files changed, 375 insertions(+) create mode 100644 namd/tests/interface/008_change_outputName/AutoDiff/test.Tcl.out create mode 100644 namd/tests/interface/008_change_outputName/AutoDiff/test.alt.colvars.traj create mode 100644 namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.out create mode 100644 namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.state.stripped create mode 100644 namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.traj create mode 100644 namd/tests/interface/008_change_outputName/namd-version.txt create mode 100644 namd/tests/interface/008_change_outputName/test.in create mode 100644 namd/tests/interface/008_change_outputName/test.namd diff --git a/namd/tests/interface/008_change_outputName/AutoDiff/test.Tcl.out b/namd/tests/interface/008_change_outputName/AutoDiff/test.Tcl.out new file mode 100644 index 000000000..b2de5837b --- /dev/null +++ b/namd/tests/interface/008_change_outputName/AutoDiff/test.Tcl.out @@ -0,0 +1,108 @@ +TCL: Running for 10 steps +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: Setting parameter outputName to test.alt +TCL: Running for 10 steps +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: NUM. ATOMS REQUESTED: 0 +TCL: NUM. ATOMS USED: 0 +TCL: NUM. ATOM GROUPS USED: 2 +TCL: TOTAL FORCE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } +TCL: TOTAL TORQUE: { 0.0000000000000000 0.0000000000000000 0.0000000000000000 } diff --git a/namd/tests/interface/008_change_outputName/AutoDiff/test.alt.colvars.traj b/namd/tests/interface/008_change_outputName/AutoDiff/test.alt.colvars.traj new file mode 100644 index 000000000..ec7c88344 --- /dev/null +++ b/namd/tests/interface/008_change_outputName/AutoDiff/test.alt.colvars.traj @@ -0,0 +1,12 @@ +# step one fa_one E_h + 10 3.21732987848069e+00 -1.24693195139228e-02 1.94354911425369e-02 + 11 3.21949341092696e+00 -1.24779736437079e-02 1.94624782816335e-02 + 12 3.22129300880163e+00 -1.24851720352065e-02 1.94849400935879e-02 + 13 3.22262098902515e+00 -1.24904839561006e-02 1.95015236822008e-02 + 14 3.22340199261010e+00 -1.24936079704404e-02 1.95112800148814e-02 + 15 3.22359705879087e+00 -1.24943882351635e-02 1.95137171713739e-02 + 16 3.22320445242483e+00 -1.24928178096993e-02 1.95088121032925e-02 + 17 3.22225759147620e+00 -1.24890303659048e-02 1.94969849350616e-02 + 18 3.22082078911784e+00 -1.24832831564714e-02 1.94790447955802e-02 + 19 3.21898355455808e+00 -1.24759342182323e-02 1.94561168272076e-02 + 20 3.21685399837991e+00 -1.24674159935196e-02 1.94295576944337e-02 diff --git a/namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.out b/namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.out new file mode 100644 index 000000000..cb131694e --- /dev/null +++ b/namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.out @@ -0,0 +1,171 @@ +colvars: ---------------------------------------------------------------------- +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. +colvars: This version was built with the C++11 standard or higher. +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "test.in": +colvars: # units = "" [default] +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) +colvars: # smp = on [default] +colvars: # colvarsTrajFrequency = 1 +colvars: # colvarsRestartFrequency = 10 +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "one" +colvars: Initializing a new "distance" component. +colvars: # name = "" [default] +colvars: # componentCoeff = 1 [default] +colvars: # componentExp = 1 [default] +colvars: # period = 0 [default] +colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] +colvars: # scalable = on [default] +colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group1" +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableFitGradients = on [default] +colvars: Enabling scalable calculation for group "group1". +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group2" +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableFitGradients = on [default] +colvars: Enabling scalable calculation for group "group2". +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] +colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] +colvars: # width = 0.5 +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0.5 [default] +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = off [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = on +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "harmonic" instance. +colvars: # name = "h" +colvars: # colvars = { one } +colvars: # stepZeroData = off [default] +colvars: # outputEnergy = on +colvars: # outputFreq = 10 [default] +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] +colvars: # centers = { 0.1 } +colvars: # targetCenters = { 0.1 } [default] +colvars: # outputCenters = off [default] +colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] +colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (0 atoms). +colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 0, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Updating NAMD interface: +colvars: updating atomic data (0 atoms). +colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 0, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Saving collective variables state to "test.colvars.state". +colvars: The final output state file will be "test.alt.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.alt.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.alt.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Saving collective variables state to "test.alt.colvars.state". diff --git a/namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.state.stripped b/namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.state.stripped new file mode 100644 index 000000000..63e4dfd0e --- /dev/null +++ b/namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.state.stripped @@ -0,0 +1,17 @@ +configuration { + step 10 + dt 1.000000e+00 +} + +colvar { + name one + x 3.21732987848069e+00 +} + +restraint { + configuration { + step 10 + name h + } +} + diff --git a/namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.traj b/namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.traj new file mode 100644 index 000000000..cb3f3f619 --- /dev/null +++ b/namd/tests/interface/008_change_outputName/AutoDiff/test.colvars.traj @@ -0,0 +1,12 @@ +# step one fa_one E_h + 0 3.20554673468334e+00 -1.24221869387334e-02 1.92888410426048e-02 + 1 3.20437138788663e+00 -1.24174855515465e-02 1.92742434278583e-02 + 2 3.20383990619321e+00 -1.24153596247728e-02 1.92676443265549e-02 + 3 3.20396636247149e+00 -1.24158654498859e-02 1.92692143587090e-02 + 4 3.20472667452156e+00 -1.24189066980862e-02 1.92786554469713e-02 + 5 3.20606076202988e+00 -1.24242430481195e-02 1.92952269148432e-02 + 6 3.20787658913670e+00 -1.24315063565468e-02 1.93177937866079e-02 + 7 3.21005554475098e+00 -1.24402221790039e-02 1.93448909828726e-02 + 8 3.21245889760366e+00 -1.24498355904146e-02 1.93748007785444e-02 + 9 3.21493536150581e+00 -1.24597414460232e-02 1.94056446127186e-02 + 10 3.21732987848069e+00 -1.24693195139228e-02 1.94354911425369e-02 diff --git a/namd/tests/interface/008_change_outputName/namd-version.txt b/namd/tests/interface/008_change_outputName/namd-version.txt new file mode 100644 index 000000000..e26da9c13 --- /dev/null +++ b/namd/tests/interface/008_change_outputName/namd-version.txt @@ -0,0 +1,3 @@ +Info: NAMD 2.15alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2023-09-21. +colvars: Using NAMD interface, version "2023-09-19". diff --git a/namd/tests/interface/008_change_outputName/test.in b/namd/tests/interface/008_change_outputName/test.in new file mode 100644 index 000000000..27fbcab06 --- /dev/null +++ b/namd/tests/interface/008_change_outputName/test.in @@ -0,0 +1,30 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + width 0.5 + + distance { + group1 { + indexGroup group1 + } + group2 { + indexGroup group2 + } + } +} + +harmonic { + name h + colvars one + centers 0.1 + forceConstant 0.001 + outputEnergy yes +# outputCenters yes +} diff --git a/namd/tests/interface/008_change_outputName/test.namd b/namd/tests/interface/008_change_outputName/test.namd new file mode 100644 index 000000000..8bb95fc6c --- /dev/null +++ b/namd/tests/interface/008_change_outputName/test.namd @@ -0,0 +1,22 @@ +# -*- tcl -*- + + +source ../Common/common.namd +source ../Common/measure_net_force_torque.tcl + +stepspercycle 5 + +colvars on +colvarsConfig test.in + +if { [file exists test.prerun.tcl] > 0 } { + source test.prerun.tcl +} + +run 10 + +outputName test.alt + +run 10 + +source ../Common/delete_tmp_files.tcl From 30fb3d5bcd69cf631eaeca65d47d3c6c5a2f0f8f Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 25 Sep 2023 20:50:09 -0400 Subject: [PATCH 102/162] Update version strings --- doc/cv_version.tex | 2 +- lammps/src/COLVARS/colvarproxy_lammps_version.h | 2 +- src/colvars_version.h | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/cv_version.tex b/doc/cv_version.tex index 654ab903f..761a18ca0 100644 --- a/doc/cv_version.tex +++ b/doc/cv_version.tex @@ -1 +1 @@ -\newcommand{\cvversion}{2023-09-21} +\newcommand{\cvversion}{2023-09-25} diff --git a/lammps/src/COLVARS/colvarproxy_lammps_version.h b/lammps/src/COLVARS/colvarproxy_lammps_version.h index cf70c1d84..4e7a57535 100644 --- a/lammps/src/COLVARS/colvarproxy_lammps_version.h +++ b/lammps/src/COLVARS/colvarproxy_lammps_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2023-09-19" +#define COLVARPROXY_VERSION "2023-09-25" #endif diff --git a/src/colvars_version.h b/src/colvars_version.h index b4b482933..77028e485 100644 --- a/src/colvars_version.h +++ b/src/colvars_version.h @@ -1,3 +1,3 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2023-09-21" +#define COLVARS_VERSION "2023-09-25" #endif From de0cbbc37e7ada069cfff56fb6f1578099b50349 Mon Sep 17 00:00:00 2001 From: Hubert Date: Thu, 14 Sep 2023 17:14:26 +0200 Subject: [PATCH 103/162] Support the colvars MdModule version for GROMACS --- gromacs/gromacs-mdmodules.patch | 183 ++++++++ .../applied_forces/colvars/CMakeLists.txt | 42 ++ .../colvars/colvarproxygromacs.cpp | 255 +++++++++++ .../colvars/colvarproxygromacs.h | 144 ++++++ .../colvars/colvarsMDModule.cpp | 275 ++++++++++++ .../applied_forces/colvars/colvarsMDModule.h | 70 +++ .../colvars/colvarsforceprovider.cpp | 423 ++++++++++++++++++ .../colvars/colvarsforceprovider.h | 205 +++++++++ .../applied_forces/colvars/colvarsoptions.cpp | 295 ++++++++++++ .../applied_forces/colvars/colvarsoptions.h | 183 ++++++++ .../colvars/colvarspreprocessor.cpp | 95 ++++ .../colvars/colvarspreprocessor.h | 95 ++++ .../colvars/colvarssimulationsparameters.cpp | 123 +++++ .../colvars/colvarssimulationsparameters.h | 135 ++++++ 14 files changed, 2523 insertions(+) create mode 100644 gromacs/gromacs-mdmodules.patch create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/CMakeLists.txt create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.h create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.cpp create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.h create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.h diff --git a/gromacs/gromacs-mdmodules.patch b/gromacs/gromacs-mdmodules.patch new file mode 100644 index 000000000..1a468952d --- /dev/null +++ b/gromacs/gromacs-mdmodules.patch @@ -0,0 +1,183 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 45ebd45340..db90705c29 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -586,6 +586,9 @@ include(gmxManageLmfit) + + include(gmxManageMuparser) + ++include(gmxManageColvars) ++include(gmxManageLepton) ++ + ################################################## + # Process SIMD instruction settings + ################################################## +diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt +index c8ec2dd0cc..9051910fe6 100644 +--- a/src/gromacs/CMakeLists.txt ++++ b/src/gromacs/CMakeLists.txt +@@ -143,6 +143,11 @@ if (WIN32) + endif() + list(APPEND libgromacs_object_library_dependencies thread_mpi) + ++gmx_manage_colvars() ++gmx_manage_lepton() ++list(APPEND libgromacs_object_library_dependencies colvars) ++list(APPEND libgromacs_object_library_dependencies lepton) ++ + # This code is here instead of utility/CMakeLists.txt, because CMake + # custom commands and source file properties can only be set in the directory + # that contains the target that uses them. +@@ -205,6 +210,8 @@ add_library(legacy_modules INTERFACE) + target_include_directories(legacy_modules INTERFACE $) + target_link_libraries(libgromacs PRIVATE $) + ++gmx_include_colvars_headers() ++ + # Add these contents first because linking their tests can take a lot + # of time, so we want lots of parallel work still available after + # linking starts. +diff --git a/src/gromacs/applied_forces/CMakeLists.txt b/src/gromacs/applied_forces/CMakeLists.txt +index 3c4987f892..53e6b91d70 100644 +--- a/src/gromacs/applied_forces/CMakeLists.txt ++++ b/src/gromacs/applied_forces/CMakeLists.txt +@@ -67,6 +67,7 @@ gmx_add_libgromacs_sources( + add_subdirectory(awh) + add_subdirectory(densityfitting) + add_subdirectory(qmmm) ++add_subdirectory(colvars) + + if (BUILD_TESTING) + add_subdirectory(tests) +diff --git a/src/gromacs/mdrun/mdmodules.cpp b/src/gromacs/mdrun/mdmodules.cpp +index 5399f06d02..cd0ab4d2d6 100644 +--- a/src/gromacs/mdrun/mdmodules.cpp ++++ b/src/gromacs/mdrun/mdmodules.cpp +@@ -40,6 +40,7 @@ + #include "gromacs/applied_forces/densityfitting/densityfitting.h" + #include "gromacs/applied_forces/electricfield.h" + #include "gromacs/applied_forces/qmmm/qmmm.h" ++#include "gromacs/applied_forces/colvars/colvarsMDModule.h" + #include "gromacs/imd/imd.h" + #include "gromacs/mdtypes/iforceprovider.h" + #include "gromacs/mdtypes/imdmodule.h" +@@ -67,7 +68,8 @@ public: + field_(createElectricFieldModule()), + imd_(createInteractiveMolecularDynamicsModule()), + qmmm_(QMMMModuleInfo::create()), +- swapCoordinates_(createSwapCoordinatesModule()) ++ swapCoordinates_(createSwapCoordinatesModule()), ++ colvars_(ColvarsModuleInfo::create()) + { + } + +@@ -78,6 +80,7 @@ public: + field_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); + densityFitting_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); + qmmm_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); ++ colvars_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); + // In future, other sections would also go here. + } + +@@ -106,6 +109,7 @@ public: + std::unique_ptr imd_; + std::unique_ptr qmmm_; + std::unique_ptr swapCoordinates_; ++ std::unique_ptr colvars_; + + /*! \brief List of registered MDModules + * +@@ -129,6 +133,7 @@ void MDModules::initMdpTransform(IKeyValueTreeTransformRules* rules) + impl_->field_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); + impl_->densityFitting_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); + impl_->qmmm_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); ++ impl_->colvars_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); + } + + void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder* builder) +@@ -136,6 +141,7 @@ void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder* builder) + impl_->field_->mdpOptionProvider()->buildMdpOutput(builder); + impl_->densityFitting_->mdpOptionProvider()->buildMdpOutput(builder); + impl_->qmmm_->mdpOptionProvider()->buildMdpOutput(builder); ++ impl_->colvars_->mdpOptionProvider()->buildMdpOutput(builder); + } + + void MDModules::assignOptionsToModules(const KeyValueTreeObject& params, IKeyValueTreeErrorHandler* errorHandler) +@@ -173,6 +179,7 @@ ForceProviders* MDModules::initForceProviders() + impl_->field_->initForceProviders(impl_->forceProviders_.get()); + impl_->densityFitting_->initForceProviders(impl_->forceProviders_.get()); + impl_->qmmm_->initForceProviders(impl_->forceProviders_.get()); ++ impl_->colvars_->initForceProviders(impl_->forceProviders_.get()); + for (auto&& module : impl_->modules_) + { + module->initForceProviders(impl_->forceProviders_.get()); +@@ -184,12 +191,14 @@ void MDModules::subscribeToPreProcessingNotifications() + { + impl_->densityFitting_->subscribeToPreProcessingNotifications(&impl_->notifiers_); + impl_->qmmm_->subscribeToPreProcessingNotifications(&impl_->notifiers_); ++ impl_->colvars_->subscribeToPreProcessingNotifications(&impl_->notifiers_); + } + + void MDModules::subscribeToSimulationSetupNotifications() + { + impl_->densityFitting_->subscribeToSimulationSetupNotifications(&impl_->notifiers_); + impl_->qmmm_->subscribeToSimulationSetupNotifications(&impl_->notifiers_); ++ impl_->colvars_->subscribeToSimulationSetupNotifications(&impl_->notifiers_); + } + + void MDModules::add(std::shared_ptr module) +diff --git a/src/gromacs/fileio/checkpoint.h b/src/gromacs/fileio/checkpoint.h +index fa886f6e47..762a9ad349 100644 +--- a/src/gromacs/fileio/checkpoint.h ++++ b/src/gromacs/fileio/checkpoint.h +@@ -99,6 +99,11 @@ extern template void readKvtCheckpointValue(compat::not_null value, + const std::string& name, + const std::string& identifier, + const KeyValueTreeObject& kvt); ++//! \copydoc readKvtCheckpointValue ++extern template void readKvtCheckpointValue(compat::not_null value, ++ const std::string& name, ++ const std::string& identifier, ++ const KeyValueTreeObject& kvt); + + /*! \brief Write to a key-value-tree used for checkpointing. + * +@@ -125,6 +130,11 @@ extern template void writeKvtCheckpointValue(const real& value, + const std::string& name, + const std::string& identifier, + KeyValueTreeObjectBuilder kvtBuilder); ++//! \copydoc writeKvtCheckpointValue ++extern template void writeKvtCheckpointValue(const std::string& value, ++ const std::string& name, ++ const std::string& identifier, ++ KeyValueTreeObjectBuilder kvtBuilder); + + /*! \libinternal + * \brief Provides the MDModules with the checkpointed data on the main rank. +diff --git a/src/gromacs/fileio/checkpoint.cpp b/src/gromacs/fileio/checkpoint.cpp +index b493a9a82f..25299addec 100644 +--- a/src/gromacs/fileio/checkpoint.cpp ++++ b/src/gromacs/fileio/checkpoint.cpp +@@ -119,7 +119,10 @@ template void readKvtCheckpointValue(compat::not_null value, + const std::string& name, + const std::string& identifier, + const KeyValueTreeObject& kvt); +- ++template void readKvtCheckpointValue(compat::not_null value, ++ const std::string& name, ++ const std::string& identifier, ++ const KeyValueTreeObject& kvt); + template + void writeKvtCheckpointValue(const ValueType& value, + const std::string& name, +@@ -137,7 +140,10 @@ template void writeKvtCheckpointValue(const real& value, + const std::string& name, + const std::string& identifier, + KeyValueTreeObjectBuilder kvtBuilder); +- ++template void writeKvtCheckpointValue(const std::string& value, ++ const std::string& name, ++ const std::string& identifier, ++ KeyValueTreeObjectBuilder kvtBuilder); + + } // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/CMakeLists.txt b/gromacs/gromacs-mdmodules/applied_forces/colvars/CMakeLists.txt new file mode 100644 index 000000000..3ec3bf57a --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/CMakeLists.txt @@ -0,0 +1,42 @@ +# +# This file is part of the GROMACS molecular simulation package. +# +# Copyright 2023- The GROMACS Authors +# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. +# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. +# +# GROMACS is free software; you can redistribute it and/or +# modify it under the terms of the GNU Lesser General Public License +# as published by the Free Software Foundation; either version 2.1 +# of the License, or (at your option) any later version. +# +# GROMACS is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with GROMACS; if not, see +# https://www.gnu.org/licenses, or write to the Free Software Foundation, +# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +# +# If you want to redistribute modifications to GROMACS, please +# consider that scientific software is very special. Version +# control is crucial - bugs must be traceable. We will be happy to +# consider code for inclusion in the official distribution, but +# derived work must not be called official GROMACS. Details are found +# in the README & COPYING files - if they are missing, get the +# official version at https://www.gromacs.org. +# +# To help us fund GROMACS development, we humbly ask that you cite +# the research papers on the package. Check out https://www.gromacs.org. + +gmx_add_libgromacs_sources( + colvarsMDModule.cpp + colvarsoptions.cpp + colvarspreprocessor.cpp + colvarssimulationsparameters.cpp + colvarsforceprovider.cpp + colvarproxygromacs.cpp + ) + diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp new file mode 100644 index 000000000..e6e3325ba --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp @@ -0,0 +1,255 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Implements the Colvars GROMACS proxy class + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ + +#include "colvarproxygromacs.h" + + +namespace gmx +{ + +ColvarProxyGromacs::ColvarProxyGromacs(const std::string& colvarsConfigString, + t_atoms atoms, + PbcType pbcType, + const MDLogger* logger, + bool doParsing, + const std::map& input_strings, + real ensTemp) : + gmx_atoms(atoms), pbcType_(pbcType), logger_(logger), doParsing_(doParsing) +{ + + //! From colvarproxy + + // Retrieve masses and charges from input file + updated_masses_ = updated_charges_ = true; + + // User-scripted forces are not available in GROMACS + have_scripts = false; + + angstrom_value_ = 0.1; + + // From Gnu units + // $ units -ts 'k' 'kJ/mol/K/avogadro' + // 0.0083144621 + boltzmann_ = 0.0083144621; + + // Get the thermostat temperature. + set_target_temperature(ensTemp); + + // GROMACS random number generation. + rng.seed(makeRandomSeed()); + + + // Read configuration file and set up the proxy during Pre processing + // and during simulation phase but only on the master node. + if (doParsing) + { + + // Retrieve input files stored as string in the KVT + // Add them to the map of colvars input data. + for (const auto& [input_name, content] : input_strings) + { + input_streams_[input_name] = new std::istringstream(content); + } + + colvars = new colvarmodule(this); + cvm::log(cvm::line_marker); + cvm::log("Start colvars Initialization."); + + + colvars->cite_feature("GROMACS engine"); + colvars->cite_feature("Colvars-GROMACS interface"); + + if (cvm::debug()) + { + cvm::log("Initializing the colvars proxy object.\n"); + } + + + add_config("config", colvarsConfigString); + + colvarproxy::parse_module_config(); + colvars->update_engine_parameters(); + colvars->setup_input(); + + + // Citation Reporter + cvm::log(std::string("\n") + colvars->feature_report(0) + std::string("\n")); + + // TODO: Retrieve step + // if (step != 0) { + // cvm::log("Initializing step number to "+cvm::to_str(step)+".\n"); + // } + + // colvars->it = colvars->it_restart = step; + colvars->it = 0; + } +} + + +cvm::real ColvarProxyGromacs::rand_gaussian() +{ + return normal_distribution(rng); +} + +void ColvarProxyGromacs::log(std::string const& message) +{ + if (logger_) + { + GMX_LOG(logger_->info).appendText(message); + } +} + +void ColvarProxyGromacs::error(std::string const& message) +{ + // In GROMACS, all errors are fatal. + fatal_error(message); +} + +void ColvarProxyGromacs::fatal_error(std::string const& message) +{ + log(message); + GMX_THROW(InternalError("Error in collective variables module.\n")); +} + + +int ColvarProxyGromacs::set_unit_system(std::string const& units_in, bool /*colvars_defined*/) +{ + if (units_in != "gromacs") + { + cvm::error( + "Specified unit system \"" + units_in + + "\" is unsupported in Gromacs. Supported units are \"gromacs\" (nm, kJ/mol).\n"); + return COLVARS_ERROR; + } + return COLVARS_OK; +} + + +// **************** ATOMS **************** + +int ColvarProxyGromacs::check_atom_id(int atom_number) +{ + // GROMACS uses zero-based arrays. + int const aid = (atom_number - 1); + + if (cvm::debug()) + { + log("Adding atom " + cvm::to_str(atom_number) + " for collective variables calculation.\n"); + } + if ((aid < 0) || (aid >= gmx_atoms.nr)) + { + cvm::error("Error: invalid atom number specified, " + cvm::to_str(atom_number) + "\n", + COLVARS_INPUT_ERROR); + return COLVARS_INPUT_ERROR; + } + + return aid; +} + + +int ColvarProxyGromacs::init_atom(int atom_number) +{ + // GROMACS uses zero-based arrays. + int aid = atom_number - 1; + + for (size_t i = 0; i < atoms_ids.size(); i++) + { + if (atoms_ids[i] == aid) + { + // this atom id was already recorded + atoms_refcount[i] += 1; + return i; + } + } + + aid = check_atom_id(atom_number); + + if (aid < 0) + { + return COLVARS_INPUT_ERROR; + } + + int const index = add_atom_slot(aid); + update_atom_properties(index); + return index; +} + +void ColvarProxyGromacs::update_atom_properties(int index) +{ + + // update mass + double const mass = gmx_atoms.atom[atoms_ids[index]].m; + if (mass <= 0.001) + { + this->log("Warning: near-zero mass for atom " + cvm::to_str(atoms_ids[index] + 1) + + "; expect unstable dynamics if you apply forces to it.\n"); + } + atoms_masses[index] = mass; + // update charge + atoms_charges[index] = gmx_atoms.atom[atoms_ids[index]].q; +} + +ColvarProxyGromacs::~ColvarProxyGromacs() +{ + if (colvars != nullptr) + { + delete colvars; + colvars = nullptr; + } +} + + +cvm::rvector ColvarProxyGromacs::position_distance(cvm::atom_pos const& pos1, cvm::atom_pos const& pos2) const +{ + rvec r1, r2, dr; + r1[0] = pos1.x; + r1[1] = pos1.y; + r1[2] = pos1.z; + r2[0] = pos2.x; + r2[1] = pos2.y; + r2[2] = pos2.z; + + pbc_dx(&gmx_pbc, r2, r1, dr); + return cvm::atom_pos(dr[0], dr[1], dr[2]); +} + + +} // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h new file mode 100644 index 000000000..c3ac6baf5 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h @@ -0,0 +1,144 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Declares the Colvars GROMACS proxy class + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ + +#ifndef GMX_APPLIED_FORCES_COLVARPROXYGROMACS_H +#define GMX_APPLIED_FORCES_COLVARPROXYGROMACS_H + +#include "external/colvars/colvaratoms.h" +#include "external/colvars/colvarproxy.h" + +#include "gromacs/pbcutil/pbc.h" +#include "gromacs/random/tabulatednormaldistribution.h" +#include "gromacs/random/threefry.h" +#include "gromacs/topology/atoms.h" +#include "gromacs/utility/logger.h" + + +namespace gmx +{ + + +/*! \internal \brief + * Implements a GROMACS version of colvarproxy. + * This class hold for the communication between colvars and GROMACS. + * 2 child class will inherit from this one: one during pre processing (ColvarsPreProcessor) + * and one during the simulation (ColvarsForceProvider). + * Most of the work needed for the communication will be implemented in this class. + */ +class ColvarProxyGromacs : public colvarproxy +{ + +protected: + //! Atoms topology + t_atoms gmx_atoms; + + //! Box infos + PbcType pbcType_; + t_pbc gmx_pbc; + + // GROMACS logger instance + const MDLogger* logger_ = nullptr; + + //! Activate or not the parsing of the Colvars config file + bool doParsing_; + + + // GROMACS random number generation. + DefaultRandomEngine rng; // gromacs random number generator + TabulatedNormalDistribution<> normal_distribution; + + +public: + friend class cvm::atom; + + /*! \brief Construct ColvarProxyGromacs from its parameters + * + * \param[in] colvarsConfigString Content of the colvars input file. + * \param[in] atoms Atoms topology + * \param[in] pbcType Periodic boundary conditions + * \param[in] logger GROMACS logger instance + * \param[in] doParsing Wether the input file should be parsed. + * \param[in] input_strings Input files stored as string in the KVT + * \param[in] ensTemp the constant ensemble temperature + */ + ColvarProxyGromacs(const std::string& colvarsConfigString, + t_atoms atoms, + PbcType pbcType, + const MDLogger* logger, + bool doParsing, + const std::map& input_strings, + real ensTemp); + ~ColvarProxyGromacs() override; + + /// Update colvars topology of one atom mass and charge from the GROMACS topology + void update_atom_properties(int index); + + //! From colvarproxy + + // **************** SYSTEM-WIDE PHYSICAL QUANTITIES **************** + cvm::real rand_gaussian() override; + + // **************** INPUT/OUTPUT **************** + /// Print a message to the main log + void log(std::string const& message) override; + /// Print a message to the main log and let the rest of the program handle the error + void error(std::string const& message) override; + /// Print a message to the main log and exit with error code + /// possible suppression + [[noreturn]] void fatal_error(std::string const& message); + /// Request to set the units used internally by Colvars + int set_unit_system(std::string const& units_in, bool colvars_defined) override; + + /// Initialize colvars atom from GROMACS topology + int init_atom(int atom_number) override; + + /*! \brief Check if atom belongs to the global index of atoms + * \param[in] atom_number Colvars index of the atom to check + */ + int check_atom_id(int atom_number) override; + + // **************** PERIODIC BOUNDARY CONDITIONS **************** + cvm::rvector position_distance(cvm::atom_pos const& pos1, cvm::atom_pos const& pos2) const override; +}; + +} // namespace gmx + +#endif // GMX_APPLIED_FORCES_COLVARPROXYGROMACS_H diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp new file mode 100644 index 000000000..03ea70c73 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp @@ -0,0 +1,275 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Implements Colvars MDModule class + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ +#include "gmxpre.h" + +#include "colvarsMDModule.h" + +#include +#include + +#include "gromacs/domdec/localatomsetmanager.h" +#include "gromacs/fileio/checkpoint.h" +#include "gromacs/mdtypes/commrec.h" +#include "gromacs/mdtypes/imdmodule.h" +#include "gromacs/utility/keyvaluetreebuilder.h" + +#include "colvarsforceprovider.h" +#include "colvarsoptions.h" +#include "colvarssimulationsparameters.h" + + +namespace gmx +{ + +namespace +{ + +/*! \internal + * \brief Colvars module + * + * Class that implements the colvars MDModule + */ +class ColvarsMDModule final : public IMDModule +{ +public: + //! \brief Construct the colvars module. + explicit ColvarsMDModule() = default; + + // Now callbacks for several kinds of MdModuleNotification are created + // and subscribed, and will be dispatched correctly at run time + // based on the type of the parameter required by the lambda. + + /*! \brief Requests to be notified during pre-processing. + * + * \param[in] notifier allows the module to subscribe to notifications from MdModules. + * + * The colvars code subscribes to these notifications: + * - storing its internal parameters in a tpr file by writing to a + * key-value-tree during pre-processing by a function taking a + * KeyValueTreeObjectBuilder as parameter + * - Acess topology using gmx_mtop_t notification + * - Access MDLogger for notifications output + * - Access warninp for for grompp warnings output + * - Coordinates, PBC and box for setting up the proxy + */ + void subscribeToPreProcessingNotifications(MDModulesNotifiers* notifier) override + { + + if (!colvarsOptions_.isActive()) + { + return; + } + + // Writing internal parameters during pre-processing + const auto writeInternalParametersFunction = [this](KeyValueTreeObjectBuilder treeBuilder) { + colvarsOptions_.writeInternalParametersToKvt(treeBuilder); + }; + notifier->preProcessingNotifier_.subscribe(writeInternalParametersFunction); + + // Access of the topology during pre-processing + const auto gettTopologyFunction = [this](gmx_mtop_t* mtop) { + colvarsOptions_.getTopology(mtop); + }; + notifier->preProcessingNotifier_.subscribe(gettTopologyFunction); + + // Set Logger during pre-processing + const auto setLoggerFunction = [this](const MDLogger& logger) { + colvarsOptions_.setLogger(logger); + }; + notifier->preProcessingNotifier_.subscribe(setLoggerFunction); + + // Notification of the Coordinates, box and pbc during pre-processing + const auto processCoordinatesFunction = [this](const CoordinatesAndBoxPreprocessed& coord) { + colvarsOptions_.processCoordinates(coord); + }; + notifier->preProcessingNotifier_.subscribe(processCoordinatesFunction); + + // Notification for the temperature + const auto getTemperatureFunction = [this](const EnsembleTemperature& temp) { + colvarsOptions_.getTemperature(temp); + }; + notifier->preProcessingNotifier_.subscribe(getTemperatureFunction); + } + + + /*! \brief Request to be notified. + * The colvars code subscribes to these notifications: + * - the LocalAtomSetManager sets in the simulation parameter setup + * by taking a LocalAtomSetManager * as parameter + * - the type of periodic boundary conditions that are used + * by taking a PeriodicBoundaryConditionType as parameter + * - the topology of the system + * by taking a gmx_mtop_t * as parameter + * - the communicator + * by taking a t_commrec as parameter + * - the simulation time step + * by taking a SimulationTimeStep as a parameter + * - Access MDLogger for notifications output + */ + void subscribeToSimulationSetupNotifications(MDModulesNotifiers* notifier) override + { + if (!colvarsOptions_.isActive()) + { + return; + } + + // Reading internal parameters during simulation setup + const auto readInternalParametersFunction = [this](const KeyValueTreeObject& tree) { + colvarsOptions_.readInternalParametersFromKvt(tree); + }; + notifier->simulationSetupNotifier_.subscribe(readInternalParametersFunction); + // Retrieve the LocalAtomSetManager during simulation setup + const auto setLocalAtomManagerFunction = [this](LocalAtomSetManager* localAtomSetManager) { + this->ColvarsSimulationsParameters_.setLocalAtomSetManager(localAtomSetManager); + }; + notifier->simulationSetupNotifier_.subscribe(setLocalAtomManagerFunction); + + // constructing PBC during simulation setup + const auto setPeriodicBoundaryContionsFunction = [this](const PbcType& pbc) { + this->ColvarsSimulationsParameters_.setPeriodicBoundaryConditionType(pbc); + }; + notifier->simulationSetupNotifier_.subscribe(setPeriodicBoundaryContionsFunction); + + // Retrieve the topology during simulation setup + const auto setTopologyFunction = [this](const gmx_mtop_t& mtop) { + this->ColvarsSimulationsParameters_.setTopology(mtop); + }; + notifier->simulationSetupNotifier_.subscribe(setTopologyFunction); + + // Retrieve the Communication Record during simulations setup + const auto setCommFunction = [this](const t_commrec& cr) { + this->ColvarsSimulationsParameters_.setComm(cr); + }; + notifier->simulationSetupNotifier_.subscribe(setCommFunction); + + // setting the simulation time step + const auto setSimulationTimeStepFunction = [this](const SimulationTimeStep& simulationTimeStep) { + this->ColvarsSimulationsParameters_.setSimulationTimeStep(simulationTimeStep.delta_t); + }; + notifier->simulationSetupNotifier_.subscribe(setSimulationTimeStepFunction); + // Saving MDLogger during simulation setup + const auto setLoggerFunction = [this](const MDLogger& logger) { + this->ColvarsSimulationsParameters_.setLogger(logger); + }; + notifier->simulationSetupNotifier_.subscribe(setLoggerFunction); + + // Process tpr filename + const auto setTprFileNameFunction = [this](const MdRunInputFilename& tprName) { + colvarsOptions_.processTprFilename(tprName); + }; + notifier->simulationSetupNotifier_.subscribe(setTprFileNameFunction); + + // writing checkpoint data + const auto checkpointDataWriting = [this](MDModulesWriteCheckpointData checkpointData) { + colvarsForceProvider_->writeCheckpointData(checkpointData, ColvarsModuleInfo::name_); + }; + notifier->checkpointingNotifier_.subscribe(checkpointDataWriting); + + // reading checkpoint data + const auto checkpointDataReading = [this](MDModulesCheckpointReadingDataOnMain checkpointData) { + colvarsState_.readState(checkpointData.checkpointedData_, ColvarsModuleInfo::name_); + }; + notifier->checkpointingNotifier_.subscribe(checkpointDataReading); + + // Handle the atoms redistributed signal + const auto handleAtomsRedistributedSignal = + [this](const MDModulesAtomsRedistributedSignal& atomsRedistributedSignal) { + colvarsForceProvider_->processAtomsRedistributedSignal(atomsRedistributedSignal); + }; + notifier->simulationSetupNotifier_.subscribe(handleAtomsRedistributedSignal); + } + + //! From IMDModule + IMdpOptionProvider* mdpOptionProvider() override { return &colvarsOptions_; } + //! From IMDModule + //! Colvars provide its own output + IMDOutputProvider* outputProvider() override { return nullptr; } + + //! From IMDModule + //! Add this module to the force providers if active + void initForceProviders(ForceProviders* forceProviders) override + { + if (colvarsOptions_.isActive()) + { + + colvarsForceProvider_ = std::make_unique( + colvarsOptions_.colvarsInputContent(), + ColvarsSimulationsParameters_.localAtomSetManager(), + ColvarsSimulationsParameters_.periodicBoundaryConditionType(), + ColvarsSimulationsParameters_.simulationTimeStep(), + ColvarsSimulationsParameters_.topology(), + ColvarsSimulationsParameters_.comm(), + ColvarsSimulationsParameters_.logger(), + colvarsOptions_.colvarsAtomCoords(), + colvarsOptions_.colvarsOutputPrefix(), + colvarsOptions_.colvarsInputFiles(), + colvarsState_, + colvarsOptions_.colvarsEnsTemp()); + forceProviders->addForceProvider(colvarsForceProvider_.get()); + } + } + + +private: + //! The options provided for colvars + ColvarsOptions colvarsOptions_; + + //! Parameters that become available at simulation setup time. + ColvarsSimulationsParameters ColvarsSimulationsParameters_; + + //! Object that evaluates the forces + std::unique_ptr colvarsForceProvider_; + + //! The state of colvars force provider to be written in the checkpoint + ColvarsForceProviderState colvarsState_; +}; + + +} // namespace + +std::unique_ptr ColvarsModuleInfo::create() +{ + return std::make_unique(); +} + +const std::string ColvarsModuleInfo::name_ = "colvars"; + +} // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.h new file mode 100644 index 000000000..67cd450f9 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.h @@ -0,0 +1,70 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Declares factory structure for Colvars MDModule class + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ +#ifndef COLVARS_MDMODULE_H +#define COLVARS_MDMODULE_H + +#include +#include + +namespace gmx +{ + +class IMDModule; + +/*! \internal + \brief Information about the colvars module. + * + * Provides name and method to create a colvars module. + */ +struct ColvarsModuleInfo +{ + /*! \brief + * Creates a module for applying forces according to a colvar bias. + */ + static std::unique_ptr create(); + //! The name of the module + static const std::string name_; +}; + + +} // namespace gmx + +#endif diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp new file mode 100644 index 000000000..98aaa2571 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp @@ -0,0 +1,423 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Implements the force provider for colvars + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ + +#include "colvarsforceprovider.h" + +#include + +#include "gromacs/domdec/localatomsetmanager.h" +#include "gromacs/fileio/checkpoint.h" +#include "gromacs/gmxlib/network.h" +#include "gromacs/mdlib/broadcaststructs.h" +#include "gromacs/mdlib/groupcoord.h" +#include "gromacs/mdtypes/commrec.h" +#include "gromacs/mdtypes/enerdata.h" +#include "gromacs/mdtypes/forceoutput.h" + + +namespace gmx +{ + +/******************************************************************** + * ColvarsForceProviderState + */ + +const std::string ColvarsForceProviderState::nColvarsAtomsName_ = "nColvarsAtoms"; + +const std::string ColvarsForceProviderState::xOldWholeName_ = "xOldWhole"; + +const std::string ColvarsForceProviderState::colvarStateFileName_ = "colvarStateFile"; + +void ColvarsForceProviderState::writeState(KeyValueTreeObjectBuilder kvtBuilder, + const std::string& identifier) const +{ + writeKvtCheckpointValue(nColvarsAtoms_, nColvarsAtomsName_, identifier, kvtBuilder); + + // Write colvars atoms coords + auto DoubleArrayAdder = kvtBuilder.addUniformArray(xOldWholeName_); + for (int i = 0; i < nColvarsAtoms_; i++) + { + for (int j = 0; j < DIM; j++) + { + DoubleArrayAdder.addValue(static_cast(xOldWhole_[i][j])); + } + } + + + writeKvtCheckpointValue(colvarStateFile_, colvarStateFileName_, identifier, kvtBuilder); +} + +void ColvarsForceProviderState::readState(const KeyValueTreeObject& kvtData, const std::string& identifier) +{ + + stateRead_ = true; + + readKvtCheckpointValue(compat::make_not_null(&nColvarsAtoms_), nColvarsAtomsName_, identifier, kvtData); + + + // Read colvars atoms coords + auto kvtDoubleArray = kvtData[xOldWholeName_].asArray().values(); + + + // Make sure the coordinates saved are consistent with the dimensions + if (kvtDoubleArray.size() % DIM != 0) + { + GMX_THROW(InconsistentInputError( + "Coordinates saved in the checkpoint file are in the wrong format.")); + } + + snew(xOldWhole_, nColvarsAtoms_); + for (size_t i = 0; i < kvtDoubleArray.size() / DIM; i++) + { + for (int j = 0; j < DIM; j++) + { + xOldWhole_[i][j] = static_cast(kvtDoubleArray[i * DIM + j].cast()); + } + } + + readKvtCheckpointValue( + compat::make_not_null(&colvarStateFile_), colvarStateFileName_, identifier, kvtData); +} + + +/******************************************************************** + * ColvarsForceProvider + */ + +ColvarsForceProvider::ColvarsForceProvider(const std::string& colvarsConfigString, + LocalAtomSetManager* localAtomSetManager, + PbcType pbcType, + double simulationTimeStep, + t_atoms atoms, + const t_commrec* cr, + const MDLogger* logger, + const std::vector& colvarsCoords, + const std::string& outputPrefix, + const std::map& KVTInputs, + const ColvarsForceProviderState& state, + real ensTemp) : + ColvarProxyGromacs(colvarsConfigString, atoms, pbcType, logger, MAIN(cr), KVTInputs, ensTemp), + stateToCheckpoint_(state) +{ + + + // Total forces on each atom is not available in GROMACS + total_force_requested = false; + + // Neighbor Search boolean activated during initialization + gmx_bNS = true; + + // Get GROMACS timestep (picosecond to femtosecond) + set_integration_timestep(simulationTimeStep * 1000.0); + + output_prefix_str = outputPrefix; + + + if (doParsing_) + { + colvars->setup_output(); + } + + + // MPI initialisation + + // Initialise attributs for the MPI communication + if (MAIN(cr)) + { + // Retrieve the number of colvar atoms + n_colvars_atoms = atoms_ids.size(); + } + + if (PAR(cr)) + { + // Let the other nodes know the number of colvar atoms and their ids to construct a gmx::LocalAtomSet + block_bc(cr->mpi_comm_mygroup, n_colvars_atoms); + atoms_ids.resize(n_colvars_atoms); + nblock_bc(cr->mpi_comm_mygroup, n_colvars_atoms, atoms_ids.data()); + + // Initialise atoms_new_colvar_forces on non-MAIN nodes + if (!MAIN(cr)) + { + atoms_new_colvar_forces.resize(n_colvars_atoms); + } + } + + // Cast int into Index of the indices for the localAtomSetManager->add() function + std::vector index_atoms(atoms_ids.begin(), atoms_ids.end()); + colvars_atoms = std::make_unique(localAtomSetManager->add(index_atoms)); + + + snew(x_colvars_unwrapped, n_colvars_atoms); + snew(xa_shifts, n_colvars_atoms); + snew(xa_eshifts, n_colvars_atoms); + snew(f_colvars, n_colvars_atoms); + snew(xa_old_whole, n_colvars_atoms); + + + // Check state status (did we read a cpt file?) + if (MAIN(cr)) + { + if (stateToCheckpoint_.stateRead_) + { + if (stateToCheckpoint_.nColvarsAtoms_ != n_colvars_atoms) + { + cvm::error( + "Number of colvars atoms in the .cpt file differs from the one in .tpr " + "file"); + } + + // Copy back the last whole positions from the .cpt file + for (int i = 0; i < n_colvars_atoms; i++) + { + copy_rvec(stateToCheckpoint_.xOldWhole_[i], xa_old_whole[i]); + } + + // Read input state file + input_buffer_ = stateToCheckpoint_.colvarStateFile_.c_str(); + colvars->setup_input(); + } + else + { + // Initialize state variables + stateToCheckpoint_.nColvarsAtoms_ = n_colvars_atoms; + snew(stateToCheckpoint_.xOldWhole_, n_colvars_atoms); + + // Use input coords for the last whole positions. + for (int i = 0; i < n_colvars_atoms; i++) + { + copy_rvec(colvarsCoords[i], xa_old_whole[i]); + } + } + } + + + // // Communicate initial coordinates to all processes + if (PAR(cr)) + { + nblock_bc(cr->mpi_comm_mygroup, n_colvars_atoms, xa_old_whole); + } + + + if (MAIN(cr) && cvm::debug()) + { + cvm::log("atoms_ids = " + cvm::to_str(atoms_ids) + "\n"); + cvm::log("atoms_refcount = " + cvm::to_str(atoms_refcount) + "\n"); + cvm::log("positions = " + cvm::to_str(atoms_positions) + "\n"); + cvm::log("total_forces = " + cvm::to_str(atoms_total_forces) + "\n"); + cvm::log("atoms_new_colvar_forces = " + cvm::to_str(atoms_new_colvar_forces) + "\n"); + cvm::log(cvm::line_marker); + log("done initializing the colvars proxy object.\n"); + } + + if (MAIN(cr)) + { + cvm::log(cvm::line_marker); + cvm::log("End colvars Initialization.\n\n"); + } +} + +ColvarsForceProvider::~ColvarsForceProvider() +{ + if (doParsing_) + { + post_run(); + sfree(stateToCheckpoint_.xOldWhole_); + } + sfree(x_colvars_unwrapped); + sfree(xa_shifts); + sfree(xa_eshifts); + sfree(f_colvars); + sfree(xa_old_whole); +} + +void ColvarsForceProvider::calculateForces(const ForceProviderInput& forceProviderInput, + ForceProviderOutput* forceProviderOutput) +{ + + // Construct t_pbc struct + set_pbc(&gmx_pbc, pbcType_, forceProviderInput.box_); + + const t_commrec* cr = &(forceProviderInput.cr_); + // Local atom coords + const gmx::ArrayRef x = forceProviderInput.x_; + // Local atom coords (coerced into into old gmx type) + const rvec* x_pointer = &(x.data()->as_vec()); + const auto& box = forceProviderInput.box_; + + colvars->it = forceProviderInput.step_; + + + // Eventually there needs to be an interface to update local data upon neighbor search + // We could check if by chance all atoms are in one node, and skip communication + communicate_group_positions(cr, + x_colvars_unwrapped, + xa_shifts, + xa_eshifts, + gmx_bNS, + x_pointer, + colvars_atoms->numAtomsGlobal(), + colvars_atoms->numAtomsLocal(), + colvars_atoms->localIndex().data(), + colvars_atoms->collectiveIndex().data(), + xa_old_whole, + box); + + + // Communicate_group_positions takes care of removing shifts (unwrapping) + // in single node jobs, communicate_group_positions() is efficient and adds no overhead + + if (MAIN(cr)) + { + // On non-MAIN nodes, jump directly to applying the forces + + // backup applied forces if necessary to calculate total forces (if available in future + // version of Gromacs) if (total_force_requested) + // previous_atoms_new_colvar_forces = atoms_new_colvar_forces; + + // Zero the forces on the atoms, so that they can be accumulated by the colvars. + for (size_t i = 0; i < atoms_new_colvar_forces.size(); i++) + { + atoms_new_colvar_forces[i].x = atoms_new_colvar_forces[i].y = + atoms_new_colvar_forces[i].z = 0.0; + } + + // Get the atom positions from the Gromacs array. + for (size_t i = 0; i < atoms_ids.size(); i++) + { + atoms_positions[i] = cvm::rvector( + x_colvars_unwrapped[i][0], x_colvars_unwrapped[i][1], x_colvars_unwrapped[i][2]); + } + + // // Get total forces if required (if available in future version of Gromacs) + // if (total_force_requested && cvm::step_relative() > 0) { + // for (size_t i = 0; i < atoms_ids.size(); i++) { + // size_t aid = atoms_ids[i]; + // atoms_total_forces[i] = cvm::rvector(f[aid][0], f[aid][1], f[aid][2]); + // } + // } + + bias_energy = 0.0; + // Call the collective variable module to fill atoms_new_colvar_forces + if (colvars->calc() != COLVARS_OK) + { + cvm::error("Error calling colvars->calc()\n"); + } + + // Copy the forces to C array for broadcasting + for (int i = 0; i < n_colvars_atoms; i++) + { + f_colvars[i][0] = atoms_new_colvar_forces[i].x; + f_colvars[i][1] = atoms_new_colvar_forces[i].y; + f_colvars[i][2] = atoms_new_colvar_forces[i].z; + } + + forceProviderOutput->enerd_.term[F_COM_PULL] += bias_energy; + + // Copy last whole positions into State struct. + for (int i = 0; i < n_colvars_atoms; i++) + { + copy_rvec(xa_old_whole[i], stateToCheckpoint_.xOldWhole_[i]); + } + } // MAIN node + + + // Broadcast the forces to all the nodes + if (PAR(cr)) + { + nblock_bc(cr->mpi_comm_mygroup, n_colvars_atoms, f_colvars); + } + + + const gmx::ArrayRef& f_out = forceProviderOutput->forceWithVirial_.force_; + matrix local_colvars_virial = { { 0 } }; + const auto& localcolvarsIndex = colvars_atoms->localIndex(); + const auto& collectivecolvarsIndex = colvars_atoms->collectiveIndex(); + // Loop through local atoms to aply the colvars forces + for (gmx::Index l = 0; l < localcolvarsIndex.ssize(); l++) + { + /* Get the right index of the local colvars atoms */ + int i_local = localcolvarsIndex[l]; + /* Index of this local atom in the collective colvars atom arrays */ + int i_colvars = collectivecolvarsIndex[l]; + /* Add */ + rvec_inc(f_out[i_local], f_colvars[i_colvars]); + add_virial_term(local_colvars_virial, f_colvars[i_colvars], x_colvars_unwrapped[i_colvars]); + } + + forceProviderOutput->forceWithVirial_.addVirialContribution(local_colvars_virial); + + // Re-set the flag for proper update + gmx_bNS = false; +} + +void ColvarsForceProvider::add_virial_term(matrix vir, const rvec& f, const gmx::RVec& x) +{ + for (int j = 0; j < DIM; j++) + { + for (int m = 0; m < DIM; m++) + { + vir[j][m] -= 0.5 * f[j] * x[m]; + } + } +} + +// Pass restraint energy value for current timestep to MD engine +void ColvarsForceProvider::add_energy(cvm::real energy) +{ + bias_energy += energy; +} + + +void ColvarsForceProvider::writeCheckpointData(MDModulesWriteCheckpointData checkpointWriting, + const std::string& moduleName) +{ + colvars->write_restart_string(stateToCheckpoint_.colvarStateFile_); + stateToCheckpoint_.writeState(checkpointWriting.builder_, moduleName); +} + +void ColvarsForceProvider::processAtomsRedistributedSignal(const MDModulesAtomsRedistributedSignal& /*signal*/) +{ + // So far, just update the Neighbor Search boolean for the communicate_group_positions() in calculateForces() + gmx_bNS = true; +} + + +} // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h new file mode 100644 index 000000000..51fa5221e --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h @@ -0,0 +1,205 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Declares the force provider for colvars + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ + +#ifndef GMX_APPLIED_FORCES_COLVARSFORCEPROVIDER_H +#define GMX_APPLIED_FORCES_COLVARSFORCEPROVIDER_H + + +#include "gromacs/domdec/localatomset.h" +#include "gromacs/mdrunutility/mdmodulesnotifiers.h" +#include "gromacs/mdtypes/iforceprovider.h" + +#include "colvarproxygromacs.h" + + +namespace gmx +{ + + +/*! \internal + * \brief Parameters defining the internal colvars force provider state. + */ +struct ColvarsForceProviderState +{ + + /*! \brief Indicate if a colvars state was read. + */ + bool stateRead_ = false; + + /*! \brief The number of colvars atoms. + */ + std::int64_t nColvarsAtoms_ = 0; + + /*! \brief String naming variable holding the number of colvars atoms. + * \note Changing this name will break backwards compability for checkpoint file writing. + */ + static const std::string nColvarsAtomsName_; + + //! Last known whole positions of the colvars atoms + //! \todo Change the type to a standard one to avoid memory leak. + rvec* xOldWhole_ = nullptr; + + /*! \brief String naming variable holding the last known whole positions of the colvars atoms + * \note Changing this name will break backwards compability for checkpoint file writing. + */ + static const std::string xOldWholeName_; + + /*! \brief Content of the colvars state file. + */ + std::string colvarStateFile_; + + /*! \brief String naming variable holding the content of the colvars state file. + * \note Changing this name will break backwards compability for checkpoint file writing. + */ + static const std::string colvarStateFileName_; + + /*! \brief Write internal colvars data into a key value tree. + * The entries to the kvt are identified with identifier, so that a variable + * is indentified with the key "identifier-variablename" + * + * \param[in] kvtBuilder enables writing to the Key-Value-Tree + * the state is written to + * + * \param[in] identifier denotes the module that is checkpointing the data + */ + void writeState(KeyValueTreeObjectBuilder kvtBuilder, const std::string& identifier) const; + + /*! \brief Read the internal parameters from the checkpoint file on master + * \param[in] kvtData holding the checkpoint information + * \param[in] identifier identifies the data in a key-value-tree + */ + void readState(const KeyValueTreeObject& kvtData, const std::string& identifier); +}; + + +/*! \internal \brief + * Implements IForceProvider for colvars. + * Override the ColvarProxyGromacs generic class for the communication. + */ +class ColvarsForceProvider final : public ColvarProxyGromacs, public IForceProvider +{ + +private: + //! The total bias energy on all colvars atoms. + double bias_energy; + + //! Is this a neighbor-search step? + bool gmx_bNS; + + + // Node-local bookkepping data + //! The colvars atom indices + std::unique_ptr colvars_atoms; + //! Total number of Colvars atoms + int n_colvars_atoms = 0; + //! Unwrapped positions for all Colvars atoms, communicated to all nodes. + rvec* x_colvars_unwrapped = nullptr; + //! Shifts for all Colvars atoms, to make molecule(s) whole. + ivec* xa_shifts = nullptr; + //! Extra shifts since last DD step. + ivec* xa_eshifts = nullptr; + //! Old positions for all Colvars atoms on master. + rvec* xa_old_whole = nullptr; + //! Position of each local atom in the collective array. + int* xa_ind = nullptr; + //! Bias forces on all Colvars atoms + rvec* f_colvars = nullptr; + + ColvarsForceProviderState stateToCheckpoint_; + + +public: + friend class cvm::atom; + //! Construct force provider for colvars from its parameters + ColvarsForceProvider(const std::string& colvarsConfigString, + LocalAtomSetManager* localAtomSetManager, + PbcType pbcType, + double simulationTimeStep, + t_atoms atoms, + const t_commrec* cr, + const MDLogger* logger, + const std::vector& colvarsCoords, + const std::string& outputPrefix, + const std::map& KVTInputs, + const ColvarsForceProviderState& state, + real ensTemp); + + ~ColvarsForceProvider() override; + + /*! \brief Calculate colvars forces + * \param[in] forceProviderInput input for force provider + * \param[out] forceProviderOutput output for force provider + */ + void calculateForces(const ForceProviderInput& forceProviderInput, + ForceProviderOutput* forceProviderOutput) override; + + // Compute virial tensor for position r and force f, and add to matrix vir + void add_virial_term(matrix vir, const rvec& f, const gmx::RVec& x); + + /*! \brief Write internal colvars data to checkpoint file. + * \param[in] checkpointWriting enables writing to the Key-Value-Tree + * that is used for storing the checkpoint + * information + * \param[in] moduleName names the module that is checkpointing this force-provider + * + * \note The provided state to checkpoint has to change if checkpointing + * is moved before the force provider call in the MD-loop. + */ + void writeCheckpointData(MDModulesWriteCheckpointData checkpointWriting, const std::string& moduleName); + + /*! \brief Process atomsRedistributedSignal notification during mdrun. + * \param[in] atomsRedistributedSignal signal recieved + */ + void processAtomsRedistributedSignal(const MDModulesAtomsRedistributedSignal& atomsRedistributedSignal); + + + //! From colvarproxy + + /*! \brief add energy to the total count of bias energy bias_energy + * \param[in] energy the value of energy to add + * + */ + void add_energy(cvm::real energy) override; +}; + +} // namespace gmx + +#endif // GMX_APPLIED_FORCES_COLVARSFORCEPROVIDER_H diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp new file mode 100644 index 000000000..664066c1d --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp @@ -0,0 +1,295 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Implements options for Colvars. + */ +#include "gmxpre.h" + +#include "colvarsoptions.h" + +#include + +#include "gromacs/math/vec.h" +#include "gromacs/options/basicoptions.h" +#include "gromacs/options/optionsection.h" +#include "gromacs/topology/mtop_util.h" +#include "gromacs/utility/arrayref.h" +#include "gromacs/utility/keyvaluetreebuilder.h" +#include "gromacs/utility/keyvaluetreetransform.h" +#include "gromacs/utility/path.h" +#include "gromacs/utility/strconvert.h" + +#include "colvarspreprocessor.h" + + +namespace gmx +{ + +namespace +{ + +/*! \brief Helper to declare mdp transform rules. + * + * Enforces uniform mdp options that are always prepended with the correct + * string for the densityfitting mdp options. + * + * \tparam ToType type to be transformed to + * \tparam TransformWithFunctionType type of transformation function to be used + * + * \param[in] rules KVT transformation rules + * \param[in] transformationFunction the function to transform the flat kvt tree + * \param[in] optionTag string tag that describes the mdp option, appended to the + * default string for the density guided simulation + */ +template +void colvarsMdpTransformFromString(IKeyValueTreeTransformRules* rules, + TransformWithFunctionType transformationFunction, + const std::string& optionTag) +{ + rules->addRule().from("/colvars-" + optionTag).to("/colvars/" + optionTag).transformWith(transformationFunction); +} + +} // namespace + + +void ColvarsOptions::initMdpTransform(IKeyValueTreeTransformRules* rules) +{ + const auto& stringIdentityTransform = [](std::string s) { return s; }; + colvarsMdpTransformFromString(rules, &fromStdString, c_activeTag_); + colvarsMdpTransformFromString(rules, stringIdentityTransform, colvarsFileNameTag_); +} + + +void ColvarsOptions::buildMdpOutput(KeyValueTreeObjectBuilder* builder) const +{ + builder->addValue("comment-colvars-module", "; Colvars bias"); + builder->addValue("colvars-" + c_activeTag_, active_); + builder->addValue("comment-colvars-" + colvarsFileNameTag_, "; colvars input file"); + builder->addValue("colvars-" + colvarsFileNameTag_, colvarsFileName_); +} + + +void ColvarsOptions::initMdpOptions(IOptionsContainerWithSections* options) +{ + auto section = options->addSection(OptionSection("colvars")); + section.addOption(BooleanOption(c_activeTag_.c_str()).store(&active_)); + section.addOption(StringOption(colvarsFileNameTag_.c_str()).store(&colvarsFileName_)); +} + + +void ColvarsOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder) +{ + + // Copy the content of the colvars input file into a string for latter save in KVT + std::ifstream f(colvarsFileName_); + colvarsConfigString = + std::string((std::istreambuf_iterator(f)), std::istreambuf_iterator()); + + // Write colvars input file as a string + treeBuilder.addValue("colvars-configString", colvarsConfigString); + + + ColvarsPreProcessor colvarsPreProcess( + colvarsConfigString, gmx_atoms, pbc, logger_, box, x, ensembleTemperature); + //! Vector with colvars atoms coordinates + colvarsAtomCoords_ = colvarsPreProcess.getColvarsCoords(); + + // Save other colvars input files into the KVT + if (!colvarsPreProcess.inputStreamsToKVT(treeBuilder, "colvars-inputStreams")) + { + GMX_THROW(InternalError("Cannot save colvars input files into the tpr")); + } + + // Write colvars atoms coords + auto DoubleArrayAdder = treeBuilder.addUniformArray("colvars-startingCoords"); + for (const auto& indexValue : colvarsAtomCoords_) + { + for (int j = 0; j < DIM; j++) + { + DoubleArrayAdder.addValue(static_cast(indexValue[j])); + } + } + + // Write ensemble temperature + treeBuilder.addValue("colvars-ensTemp", ensembleTemperature); +} + + +void ColvarsOptions::readInternalParametersFromKvt(const KeyValueTreeObject& tree) +{ + + if (!active_) + { + return; + } + + + // Retrieve the content of all inputfiles listed in the KVT as "colvars-inputStreams-filename" + for (const auto& a : tree.properties()) + { + std::size_t pos = a.key().find("colvars-inputStreams"); + if (pos != std::string::npos) + { + std::string filename = a.key().substr(pos + std::string("colvars-inputStreams").size() + 1); + + inputFiles[filename] = tree[a.key()].cast(); + } + } + + if (!tree.keyExists("colvars-configString")) + { + GMX_THROW(InconsistentInputError( + "Cannot find colvars-configString required for colvars simulation.")); + } + colvarsConfigString = tree["colvars-configString"].cast(); + + + if (!tree.keyExists("colvars-startingCoords")) + { + GMX_THROW(InconsistentInputError( + "Cannot find colvars-startingCoords required for colvars simulation.")); + } + + auto kvtDoubleArray = tree["colvars-startingCoords"].asArray().values(); + + + // Make sure the coordinates saved are consistent with the dimensions + if (kvtDoubleArray.size() % DIM != 0) + { + GMX_THROW(InconsistentInputError( + "Coordinates saved in colvars-startingCoords are in the wrong format.")); + } + + for (size_t i = 0; i < kvtDoubleArray.size() / DIM; i++) + { + RVec x; + for (int j = 0; j < DIM; j++) + { + x[j] = static_cast(kvtDoubleArray[i * DIM + j].cast()); + } + colvarsAtomCoords_.push_back(x); + } + + ensembleTemperature = tree["colvars-ensTemp"].cast(); +} + +bool ColvarsOptions::isActive() const +{ + return active_; +} + +const std::string& ColvarsOptions::colvarsFileName() const +{ + return colvarsFileName_; +} + + +void ColvarsOptions::getTopology(gmx_mtop_t* mtop) +{ + gmx_atoms = gmx_mtop_global_atoms(*mtop); +} + + +const std::string& ColvarsOptions::colvarsInputContent() const +{ + return colvarsConfigString; +} + +const std::vector& ColvarsOptions::colvarsAtomCoords() const +{ + return colvarsAtomCoords_; +} + +const std::string& ColvarsOptions::colvarsOutputPrefix() const +{ + return output_prefix_; +} + +const std::map& ColvarsOptions::colvarsInputFiles() const +{ + return inputFiles; +} + +const real& ColvarsOptions::colvarsEnsTemp() const +{ + return ensembleTemperature; +} + +void ColvarsOptions::processCoordinates(const CoordinatesAndBoxPreprocessed& coord) +{ + + x = coord.coordinates_.unpaddedConstArrayRef(); + pbc = coord.pbc_; + copy_mat(coord.box_, box); +} + +void ColvarsOptions::setLogger(const MDLogger& logger) +{ + logger_ = &logger; +} + +void ColvarsOptions::processTprFilename(const MdRunInputFilename& tprFilename) +{ + // Exit if colvars module is not active + if (!active_) + { + return; + } + + // Provided name should not be empty + GMX_RELEASE_ASSERT(!tprFilename.mdRunFilename_.empty(), + "Filename of the *.tpr simulation file is empty"); + + if (!output_prefix_.empty()) + { + return; + } + + output_prefix_ = stripExtension(std::filesystem::path(tprFilename.mdRunFilename_).filename()); +} + +void ColvarsOptions::getTemperature(const EnsembleTemperature& temp) +{ + if (temp.constantEnsembleTemperature_) + { + ensembleTemperature = temp.constantEnsembleTemperature_.value(); + } + else + { + ensembleTemperature = -1; + } +} + +} // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h new file mode 100644 index 000000000..4e262de56 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h @@ -0,0 +1,183 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Declares options for Colvars. This class handles parameters set during + * pre-processing time. + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ +#ifndef GMX_APPLIED_FORCES_COLVARSOPTIONS_H +#define GMX_APPLIED_FORCES_COLVARSOPTIONS_H + +#include +#include +#include + +#include "gromacs/math/vectypes.h" +#include "gromacs/mdrunutility/mdmodulesnotifiers.h" +#include "gromacs/mdtypes/imdpoptionprovider.h" +#include "gromacs/topology/atoms.h" +#include "gromacs/utility/logger.h" +#include "gromacs/utility/real.h" + + +namespace gmx +{ + +class KeyValueTreeObject; +class KeyValueTreeBuilder; +struct CoordinatesAndBoxPreprocessed; +struct MdRunInputFilename; + + +/*! \internal + * \brief Input data storage for colvars + */ +class ColvarsOptions final : public IMdpOptionProvider +{ +public: + //! From IMdpOptionProvider + void initMdpTransform(IKeyValueTreeTransformRules* rules) override; + + /*! \brief + * Build mdp parameters for colvars to be output after pre-processing. + * \param[in, out] builder the builder for the mdp options output KV-tree. + */ + void buildMdpOutput(KeyValueTreeObjectBuilder* builder) const override; + + /*! \brief + * Connect option name and data. + */ + void initMdpOptions(IOptionsContainerWithSections* options) override; + + //! Store the paramers that are not mdp options in the tpr file + void writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder); + + //! Set the internal parameters that are stored in the tpr file + void readInternalParametersFromKvt(const KeyValueTreeObject& tree); + + /*! \brief Store the topology of the system. + * \param[in,out] mtop topology object + */ + void getTopology(gmx_mtop_t* mtop); + + /*! \brief Process coordinates, PbcType and Box in order to validate the colvars input. + * \param[in] coord structure with coordinates and box dimensions + */ + void processCoordinates(const CoordinatesAndBoxPreprocessed& coord); + + //! Set the MDLogger instance + void setLogger(const MDLogger& logger); + + /*! \brief Process MdRunInputFilename notification during mdrun. + * In case output_prefix is empty sets it to tpr name + * \param[in] tprFilename name of the *.tpr file that mdrun simulates + */ + void processTprFilename(const MdRunInputFilename& tprFilename); + + /*! \brief Store the ensemble temperature of the system if available. + * \param[in] temp temperature object + */ + void getTemperature(const EnsembleTemperature& temp); + + //! Report if this colvars module is active + bool isActive() const; + + //! Return the file name of the colvars input + const std::string& colvarsFileName() const; + + //! Return the content of the colvars input file + const std::string& colvarsInputContent() const; + + //! Return the colvars atoms coordinates + const std::vector& colvarsAtomCoords() const; + + //! Return the prefix for output colvars files + const std::string& colvarsOutputPrefix() const; + + //! Return the ensemble temperature + const real& colvarsEnsTemp() const; + + + const std::map& colvarsInputFiles() const; + + +private: + //! Indicate if colvars module is active + bool active_ = false; + + /*! \brief Following Tags denotes names of parameters from .mdp file + * \note Changing this strings will break .tpr backwards compability + */ + //! \{ + const std::string c_activeTag_ = "active"; + const std::string colvarsFileNameTag_ = "filename"; + //! \} + + //! Colvars input filename, default colvars.dat + std::string colvarsFileName_ = "colvars.dat"; + + + //! Content of the colvars input file + std::string colvarsConfigString; + //! Topology of the system + t_atoms gmx_atoms; + //! Coordinates + ArrayRef x; + //! PBC Type + PbcType pbc; + //! Box + matrix box; + //! Vector with colvars atoms coordinates + std::vector colvarsAtomCoords_; + //! Inputs files saved as strings inside KVT + std::map inputFiles; + + real ensembleTemperature; + + + //! Logger instance + const MDLogger* logger_ = nullptr; + + /*! \brief String containing the prefix for output colvars files + * default value empty, means will be deduced from *.tpr name during mdrun + */ + std::string output_prefix_; +}; + +} // namespace gmx + +#endif diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.cpp new file mode 100644 index 000000000..23414eba0 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.cpp @@ -0,0 +1,95 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Implements the Colvars GROMACS proxy class during pre-processing. + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ +#include "gmxpre.h" + +#include "colvarspreprocessor.h" + +#include + +namespace gmx +{ + +ColvarsPreProcessor::ColvarsPreProcessor(const std::string& colvarsConfigString, + t_atoms atoms, + PbcType pbcType, + const MDLogger* logger, + const matrix box, + ArrayRef x, + real ensTemp) : + ColvarProxyGromacs(colvarsConfigString, atoms, pbcType, logger, true, std::map(), ensTemp), + x_(x) +{ + + // Initialize t_pbc struct + set_pbc(&gmx_pbc, pbcType, box); + + cvm::log(cvm::line_marker); + cvm::log("End colvars Initialization.\n\n"); +} + +std::vector ColvarsPreProcessor::getColvarsCoords() +{ + + std::vector colvarsCoords; + + for (const auto& atom_id : atoms_ids) + { + colvarsCoords.push_back(x_[atom_id]); + } + return colvarsCoords; +} + +bool ColvarsPreProcessor::inputStreamsToKVT(KeyValueTreeObjectBuilder treeBuilder, const std::string& tag) +{ + + // Save full copy of the content of the input streams (aka input files) into the KVT. + for (const auto& input_name : list_input_stream_names()) + { + std::istream& stream = input_stream(input_name); + std::ostringstream os; + os << stream.rdbuf(); + treeBuilder.addValue(tag + "-" + input_name, os.str()); + } + return true; +} + + +} // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.h new file mode 100644 index 000000000..3f568fab0 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.h @@ -0,0 +1,95 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Declares the Colvars GROMACS proxy class during pre-processing. + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ +#ifndef GMX_APPLIED_FORCES_COLVARSPREPROCESSOR_H +#define GMX_APPLIED_FORCES_COLVARSPREPROCESSOR_H + + +#include "gromacs/utility/arrayref.h" +#include "gromacs/utility/keyvaluetreebuilder.h" + +#include "colvarproxygromacs.h" + + +namespace gmx +{ + +/*! \internal \brief + * Class that read a colvars configuration file during pre-processing and + * retrieve the colvars atoms coordinates to be stored in tpr KVT. + */ +class ColvarsPreProcessor : public ColvarProxyGromacs +{ +public: + /*! \brief Construct ColvarsPreProcessor from its parameters + * + + * \param[in] colvarsConfigString Content of the colvars input file. + * \param[in] atoms Atoms topology + * \param[in] pbcType Periodic boundary conditions + * \param[in] logger GROMACS logger instance + * \param[in] box Matrix with full box of the system + * \param[in] x Coordinates of each atom in the system + * \param[in] ensTemp the constant ensemble temperature + */ + ColvarsPreProcessor(const std::string& colvarsConfigString, + t_atoms atoms, + PbcType pbcType, + const MDLogger* logger, + const matrix box, + ArrayRef x, + real ensTemp); + + + //! Return a vector of the colvars atoms coordinates + std::vector getColvarsCoords(); + + //! Save all input files of colvars into the KVT + bool inputStreamsToKVT(KeyValueTreeObjectBuilder treeBuilder, const std::string& tag); + +private: + //! Atoms coordinates of the whole system + ArrayRef x_; +}; + + +} // namespace gmx + +#endif // GMX_APPLIED_FORCES_COLVARSPREPROCESSOR_H diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp new file mode 100644 index 000000000..9667f56d8 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp @@ -0,0 +1,123 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Implements the class holding parameters needed during simulation time + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ +#include "colvarssimulationsparameters.h" + +#include "gromacs/topology/mtop_util.h" +#include "gromacs/utility/exceptions.h" + +namespace gmx +{ + +void ColvarsSimulationsParameters::setLocalAtomSetManager(LocalAtomSetManager* localAtomSetManager) +{ + localAtomSetManager_ = localAtomSetManager; +} + +LocalAtomSetManager* ColvarsSimulationsParameters::localAtomSetManager() const +{ + return localAtomSetManager_; +} + +void ColvarsSimulationsParameters::setTopology(const gmx_mtop_t& mtop) +{ + gmx_atoms = gmx_mtop_global_atoms(mtop); +} + +t_atoms ColvarsSimulationsParameters::topology() const +{ + return gmx_atoms; +} + + +void ColvarsSimulationsParameters::setPeriodicBoundaryConditionType(const PbcType& pbcType) +{ + pbcType_ = std::make_unique(pbcType); +} + +PbcType ColvarsSimulationsParameters::periodicBoundaryConditionType() +{ + if (pbcType_ == nullptr) + { + GMX_THROW( + InternalError("Periodic boundary condition enum not set for colvars simulation.")); + } + return *pbcType_; +} + + +void ColvarsSimulationsParameters::setSimulationTimeStep(double timeStep) +{ + simulationTimeStep_ = timeStep; +} + +double ColvarsSimulationsParameters::simulationTimeStep() const +{ + return simulationTimeStep_; +} + + +void ColvarsSimulationsParameters::setComm(const t_commrec& cr) +{ + cr_ = &cr; +} + +const t_commrec* ColvarsSimulationsParameters::comm() const +{ + return cr_; +} + + +void ColvarsSimulationsParameters::setLogger(const MDLogger& logger) +{ + logger_ = &logger; +} + + +const MDLogger* ColvarsSimulationsParameters::logger() const +{ + if (logger_ == nullptr) + { + GMX_THROW(InternalError("Logger not set for Colvars simulation.")); + } + return logger_; +} + +} // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.h new file mode 100644 index 000000000..2f22631ad --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.h @@ -0,0 +1,135 @@ + +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Declares parameters needed during simulation time + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ +#ifndef GMX_APPLIED_FORCES_COLVARSIMULATIONSPARAMETERS_H +#define GMX_APPLIED_FORCES_COLVARSIMULATIONSPARAMETERS_H + +#include "gromacs/domdec/localatomsetmanager.h" +#include "gromacs/mdtypes/commrec.h" +#include "gromacs/pbcutil/pbc.h" +#include "gromacs/topology/atoms.h" +#include "gromacs/utility/logger.h" + +namespace gmx +{ + +/*! \internal + * \brief Collect colvars parameters only available during simulation setup. + * + * To build the colvars force provider during simulation setup, + * one needs access to parameters that become available only during simulation setup. + * + * This class collects these parameters via MdModuleNotifications in the + * simulation setup phase and provides a check if all necessary parameters have + * been provided. + */ +class ColvarsSimulationsParameters +{ +public: + ColvarsSimulationsParameters() = default; + + //! Set the local atom set Manager for colvars. + void setLocalAtomSetManager(LocalAtomSetManager* localAtomSetManager); + //! Get the local atom set Manager for colvars. + LocalAtomSetManager* localAtomSetManager() const; + + + /*! \brief Construct the topology of the system. + * + * \param[in] mtop is the pointer to the global topology struct + */ + void setTopology(const gmx_mtop_t& mtop); + + //! Get the topology + t_atoms topology() const; + + /*! \brief Set the periodic boundary condition via MdModuleNotifier. + * + * The pbc type is wrapped in PeriodicBoundaryConditionType to + * allow the MdModuleNotifier to statically distinguish the callback + * function type from other 'int' function callbacks. + * + * \param[in] pbcType enumerates the periodic boundary condition. + */ + void setPeriodicBoundaryConditionType(const PbcType& pbcType); + + //! Get the periodic boundary conditions + PbcType periodicBoundaryConditionType(); + + //! Set the simulation time step + void setSimulationTimeStep(double timeStep); + //! Return the simulation time step + double simulationTimeStep() const; + + //! Set the communicator + void setComm(const t_commrec& cr); + //! Return the communicator + const t_commrec* comm() const; + + /*! \brief Set the logger for QMMM during mdrun + * \param[in] logger Logger instance to be used for output + */ + void setLogger(const MDLogger& logger); + + //! Get the logger instance + const MDLogger* logger() const; + +private: + //! The LocalAtomSetManager + LocalAtomSetManager* localAtomSetManager_; + //! The type of periodic boundary conditions in the simulation + std::unique_ptr pbcType_; + //! The simulation time step + double simulationTimeStep_ = 1; + //! The topology + t_atoms gmx_atoms; + //! The communicator + const t_commrec* cr_; + //! MDLogger for notifications during mdrun + const MDLogger* logger_ = nullptr; + + + // GMX_DISALLOW_COPY_AND_ASSIGN(ColvarsSimulationsParameters); +}; + +} // namespace gmx + +#endif From 408f60ffe095dac914dbccdff1168a070ace7620 Mon Sep 17 00:00:00 2001 From: Hubert Date: Thu, 14 Sep 2023 17:14:26 +0200 Subject: [PATCH 104/162] Support GROMACS development branch in update script --- update-colvars-code.sh | 72 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) diff --git a/update-colvars-code.sh b/update-colvars-code.sh index d4b2edb96..c04a090e1 100755 --- a/update-colvars-code.sh +++ b/update-colvars-code.sh @@ -84,6 +84,10 @@ then elif [ -f "${target}/include/molfile_plugin.h" ] then code="VMD-PLUGINS" +elif [ -f "${target}/INSTALL-dev" ] +then + code="GROMACS-DEV" + echo "You are about to patch GROMACS developpement version with the alpha version of Colvars-MDModules." elif [ -f "${target}/src/gromacs/commandline/cmdlineinit.h" ] then code="GROMACS" @@ -603,3 +607,71 @@ then exit 0 fi + +if [ ${code} = "GROMACS-DEV" ] +then + + copy_lepton ${target}/src/external/ || exit 1 + + target_folder=${target}/src/external/colvars + patch_opts="-p1 --forward -s" + + echo "" + if [ -d ${target_folder} ] + then + echo "Your ${target} source tree seems to have already been patched." + echo "Update with the last Colvars source." + else + mkdir ${target_folder} + fi + + # Copy library files and proxy files to the "src/external/colvars" folder + for src in ${source}/src/*.h ${source}/src/*.cpp + do \ + tgt=$(basename ${src}) + condcopy "${src}" "${target_folder}/${tgt}" + done + echo "" + + # Copy CMake files + for src in ${source}/gromacs/cmake/gmxManage{Colvars,Lepton}.cmake + do \ + tgt=$(basename ${src}) + condcopy "${src}" "${target}/cmake/${tgt}" + done + echo "" + + # Copy MDModules files to the "src/gromacs/applied_forces/colvars" folder + target_folder=${target}/src/gromacs/applied_forces/colvars + if [ -d ${target_folder} ] + then + echo "Your ${target} source tree seems to have already been patched." + echo "Update with the last Colvars source." + else + mkdir ${target_folder} + fi + for src in ${source}/gromacs/gromacs-mdmodules/applied_forces/colvars/* + do \ + tgt=$(basename ${src}) + condcopy "${src}" "${target_folder}/${tgt}" + done + echo "" + + # Apply patch for Gromacs files + patch ${patch_opts} -d ${target} < ${source}/gromacs/gromacs-mdmodules.patch + ret_val=$? + if [ $ret_val -ne 0 ] + then + echo " ************************************************************************************************ " + echo " Patch fails. Your GROMACS developement tree may be different of one used for creating the patch. " + echo " ************************************************************************************************ " + else + echo ' done.' + echo "" + echo " *******************************************" + echo " Please create your build with cmake now." + echo " *******************************************" + fi + + exit 0 +fi From e1e69b34569700411070d742d0d28bb89b1974e9 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 14 Sep 2023 19:51:38 -0400 Subject: [PATCH 105/162] Update GROMACS script runner to handle MDModules interface --- gromacs/tests/library/Common/test.mdp | 4 +++ gromacs/tests/library/run_tests.sh | 41 +++++++++------------------ 2 files changed, 17 insertions(+), 28 deletions(-) diff --git a/gromacs/tests/library/Common/test.mdp b/gromacs/tests/library/Common/test.mdp index 63e8b6849..99b6001f5 100644 --- a/gromacs/tests/library/Common/test.mdp +++ b/gromacs/tests/library/Common/test.mdp @@ -51,3 +51,7 @@ pbc = xyz tcoupl = no ;Velocity generation gen_vel = no + +; Colvars configuration +colvars-active = Yes +colvars-filename = test.in diff --git a/gromacs/tests/library/run_tests.sh b/gromacs/tests/library/run_tests.sh index 562273d7c..03deb8fda 100755 --- a/gromacs/tests/library/run_tests.sh +++ b/gromacs/tests/library/run_tests.sh @@ -131,28 +131,14 @@ for dir in ${DIRLIST} ; do fi fi - SCRIPTS="../Common/test.tpr ../Common/test.restart.tpr" - restart=false - cleanup_files + # Run simulation(s) + for basename in test test.restart ; do - - # run simulation(s) - for script in ${SCRIPTS} ; do - - basename=`basename ${script}` - basename=${basename%.tpr} - - #prefix of the Gromacs generated files + # Prefix of the Gromacs generated files output="" - #Different command line if it's a restart (checkpoint needed) - if echo "${basename}" |grep -q "restart" - then - restart=true - fi - # Input files # Symbolink link to the colvars input file, index file, and xyz file ln -sf test.in test.dat @@ -169,26 +155,25 @@ for dir in ${DIRLIST} ; do fi # Try running the test - if [ "$restart" = "false" ] - then - $BINARY mdrun -s ${script} -deffnm ${basename} -colvars test.dat &> ${basename}.out + + if [ "${basename}" == "test" ] ; then + ${BINARY} grompp -f ../Common/test.mdp -c ../Common/da.pdb -p ../Common/da.top -t ../Common/da.trr -o ${basename}.tpr >& ${basename}.grompp.out + ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} >& ${basename}.out RETVAL=$? output=${basename} - else - if [ -f test.restart.in ] ; then - ln -fs test.restart.in test.dat - fi - $BINARY mdrun -s ${script} -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt -colvars test.dat -colvars_restart test.colvars.state.dat &> ${basename}.out - RETVAL=$? - output="${basename}.part0002" fi + if [ "${basename}" == "test.restart" ] ; then + ${BINARY} convert-tpr -s ${basename%.restart}.tpr -nsteps 40 -o ${basename}.tpr >& ${basename}.grompp.out + ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt >& ${basename}.out + RETVAL=$? + output=${basename} + fi # Output of Colvars module, minus the version numbers grep "^colvars:" ${basename}.out | grep -v 'Initializing the collective variables module' \ | grep -v 'Using GROMACS interface, version' > ${basename}.colvars.out - if [ -f ${output}.colvars.state ] ; then # Filter out the version number from the state files to allow comparisons grep -sv 'version' ${output}.colvars.state > ${TMPDIR}/${output}.colvars.state.stripped From a80682568d45b1435030882672bd8693151ff0c2 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 14 Sep 2023 19:47:55 -0400 Subject: [PATCH 106/162] Strip part number from output file names --- ...colvars.state.stripped => test.restart.colvars.state.stripped} | 0 ...st.restart.part0002.colvars.traj => test.restart.colvars.traj} | 0 ...colvars.state.stripped => test.restart.colvars.state.stripped} | 0 ...st.restart.part0002.colvars.traj => test.restart.colvars.traj} | 0 ...colvars.state.stripped => 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test.restart.colvars.traj} | 0 117 files changed, 0 insertions(+), 0 deletions(-) rename gromacs/tests/library/000_angle_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_angle_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_coordnum_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_coordnum_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_customfunction_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_customfunction_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_dihedral_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_dihedral_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_dihedralwalls/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_dihedralwalls/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/{test.restart.part0002.histogram1.dat => test.restart.histogram1.dat} (100%) rename gromacs/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance-dihedral_histogram2d-periodic/AutoDiff/{test.restart.part0002.histogram1.dat => test.restart.histogram1.dat} (100%) rename gromacs/tests/library/000_distance-extended/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance-extended/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance-grid-expand_metadynamics/AutoDiff/{test.restart.part0002.pmf => test.restart.pmf} (100%) rename gromacs/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance-grid_harmonic-centers-moving/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance-grid_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance-grid_harmonic-k-moving/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance-grid_histogram/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance-grid_histogram/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance-grid_histogram/AutoDiff/{test.restart.part0002.histogram1.dat => test.restart.histogram1.dat} (100%) rename gromacs/tests/library/000_distance-grid_metadynamics/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance-grid_metadynamics/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance-grid_metadynamics/AutoDiff/{test.restart.part0002.pmf => test.restart.pmf} (100%) rename gromacs/tests/library/000_distance/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_harmonic-centers-moving-full/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_harmonic-centers-moving-stages/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_harmonic-centers-moving/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_harmonic-centers-moving/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_harmonic-k-moving/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_harmonic-k-moving/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_harmonicwalls-both-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_harmonicwalls-both-k-moving/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_harmonicwalls-k-moving/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_harmonicwalls-upper-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_harmonicwalls-upper-k-moving/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_linear-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_linear-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distance_linear-k-moving/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distance_linear-k-moving/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distanceinv_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distancevec_harmonic-dvec-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distancewalls-compatible/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distancewalls-compatible/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distancewalls/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distancewalls/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distancexy-axis_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distancez-axis-fitgroup_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distancez-axis_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distancez-fitgroup_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_distancez_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_distancez_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_eigenvector-difference_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_eigenvector-normalized_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_eigenvector_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_gyration_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_gyration_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_inertia_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_inertia_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_inertiaz_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_orientation-fitgroup_harmonic-ori-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_orientation-fitgroup_harmonic-ori-moving/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_orientation_harmonic-ori-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_orientation_harmonic-ori-moving/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_rmsd-fitgroup_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_rmsd_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_rmsd_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_selfcoordnum-pairlist_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_spinangle_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_spinangle_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) rename gromacs/tests/library/000_tilt_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.state.stripped => test.restart.colvars.state.stripped} (100%) rename gromacs/tests/library/000_tilt_harmonic-fixed/AutoDiff/{test.restart.part0002.colvars.traj => test.restart.colvars.traj} (100%) diff --git a/gromacs/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped b/gromacs/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped similarity index 100% rename from gromacs/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped rename to gromacs/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped diff --git a/gromacs/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj b/gromacs/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj similarity index 100% rename from gromacs/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj rename to gromacs/tests/library/000_angle_harmonic-fixed/AutoDiff/test.restart.colvars.traj diff --git a/gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped b/gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped similarity index 100% rename from gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped rename to gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped diff --git a/gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj b/gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj similarity index 100% rename from gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj rename to gromacs/tests/library/000_coordnum-pairlist_harmonic-fixed/AutoDiff/test.restart.colvars.traj diff --git a/gromacs/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped b/gromacs/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped similarity index 100% rename from gromacs/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped rename to gromacs/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped diff --git a/gromacs/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj b/gromacs/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj similarity index 100% rename from gromacs/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj rename to gromacs/tests/library/000_coordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj diff --git a/gromacs/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped b/gromacs/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped similarity index 100% rename from gromacs/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped rename to gromacs/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped diff --git a/gromacs/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj b/gromacs/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj similarity index 100% rename from gromacs/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj rename to gromacs/tests/library/000_customfunction_harmonic-fixed/AutoDiff/test.restart.colvars.traj diff --git a/gromacs/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped b/gromacs/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped similarity index 100% rename from gromacs/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped rename to gromacs/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped diff --git a/gromacs/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj b/gromacs/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj similarity index 100% rename from gromacs/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj rename to gromacs/tests/library/000_dihedral_harmonic-fixed/AutoDiff/test.restart.colvars.traj diff --git a/gromacs/tests/library/000_dihedralwalls/AutoDiff/test.restart.part0002.colvars.state.stripped b/gromacs/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped similarity index 100% rename from gromacs/tests/library/000_dihedralwalls/AutoDiff/test.restart.part0002.colvars.state.stripped rename to gromacs/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.state.stripped diff --git a/gromacs/tests/library/000_dihedralwalls/AutoDiff/test.restart.part0002.colvars.traj b/gromacs/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj similarity index 100% rename from gromacs/tests/library/000_dihedralwalls/AutoDiff/test.restart.part0002.colvars.traj rename to gromacs/tests/library/000_dihedralwalls/AutoDiff/test.restart.colvars.traj diff --git a/gromacs/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped b/gromacs/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped similarity index 100% rename from gromacs/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped rename to gromacs/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped diff --git a/gromacs/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj b/gromacs/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj similarity index 100% rename from gromacs/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj rename to gromacs/tests/library/000_distance-coeffs_harmonic-fixed/AutoDiff/test.restart.colvars.traj diff --git a/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.part0002.colvars.state.stripped b/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped similarity index 100% rename from gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.part0002.colvars.state.stripped rename to gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped diff --git a/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.part0002.colvars.traj b/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj similarity index 100% rename from gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.part0002.colvars.traj rename to gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj diff --git a/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.part0002.histogram1.dat b/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat similarity index 100% rename from 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gromacs/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped diff --git a/gromacs/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj b/gromacs/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj similarity index 100% rename from gromacs/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj rename to gromacs/tests/library/000_selfcoordnum_harmonic-fixed/AutoDiff/test.restart.colvars.traj diff --git a/gromacs/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped b/gromacs/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped similarity index 100% rename from gromacs/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped rename to gromacs/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped diff --git a/gromacs/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj b/gromacs/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj similarity index 100% rename from gromacs/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj rename to gromacs/tests/library/000_spinangle_harmonic-fixed/AutoDiff/test.restart.colvars.traj diff --git a/gromacs/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped b/gromacs/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped similarity index 100% rename from gromacs/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.state.stripped rename to gromacs/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.state.stripped diff --git a/gromacs/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj b/gromacs/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj similarity index 100% rename from gromacs/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.part0002.colvars.traj rename to gromacs/tests/library/000_tilt_harmonic-fixed/AutoDiff/test.restart.colvars.traj From a2ad15df3890900d2da2d2034cae541bb7484c13 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 14 Sep 2023 19:55:03 -0400 Subject: [PATCH 107/162] Add backend CI runner for GROMACS main branch Also drop (temporarily) pre-MDModules GROMACS versions --- .github/workflows/test-backends.yml | 36 ++++------------------------- 1 file changed, 5 insertions(+), 31 deletions(-) diff --git a/.github/workflows/test-backends.yml b/.github/workflows/test-backends.yml index e9116e35d..dc21f9e97 100644 --- a/.github/workflows/test-backends.yml +++ b/.github/workflows/test-backends.yml @@ -99,40 +99,14 @@ jobs: private_key: ${{ secrets.PULL_VMD_KEY }} private_key_vmd_plugins: ${{ secrets.PULL_VMD_PLUGINS_KEY }} - gromacs-2021: - name: GROMACS 2021 - if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-2021') + gromacs-devel: + name: GROMACS (MDModules) + if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-devel') uses: ./.github/workflows/backend-template.yml with: - backend_name: GROMACS-2021 + backend_name: GROMACS-devel backend_repo: gromacs/gromacs - backend_repo_ref: release-2021 - container_name: CentOS9-devel - path_compile_script: devel-tools/compile-gromacs.sh - test_lib_directory: gromacs/tests/library - rpath_exe: install/bin/gmx_d - - gromacs-2022: - name: GROMACS 2022 - if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-2022') - uses: ./.github/workflows/backend-template.yml - with: - backend_name: GROMACS-2022 - backend_repo: gromacs/gromacs - backend_repo_ref: release-2022 - container_name: CentOS9-devel - path_compile_script: devel-tools/compile-gromacs.sh - test_lib_directory: gromacs/tests/library - rpath_exe: install/bin/gmx_d - - gromacs-2023: - name: GROMACS 2023 - if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-2023') - uses: ./.github/workflows/backend-template.yml - with: - backend_name: GROMACS-2023 - backend_repo: gromacs/gromacs - backend_repo_ref: release-2023 + backend_repo_ref: main container_name: CentOS9-devel path_compile_script: devel-tools/compile-gromacs.sh test_lib_directory: gromacs/tests/library From 357f4f1acf3c7e80b72078fac98003533b4fce41 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 14 Sep 2023 21:08:51 -0400 Subject: [PATCH 108/162] Use accessor to set initial step from MD engine --- .../applied_forces/colvars/colvarproxygromacs.cpp | 3 +-- lammps/src/COLVARS/colvarproxy_lammps.cpp | 13 +------------ namd/src/colvarproxy_namd.C | 4 +--- src/colvarmodule.cpp | 7 +++++++ src/colvarmodule.h | 3 +++ 5 files changed, 13 insertions(+), 17 deletions(-) diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp index e6e3325ba..aed0a674d 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp @@ -118,8 +118,7 @@ ColvarProxyGromacs::ColvarProxyGromacs(const std::string& colvarsConfigString, // cvm::log("Initializing step number to "+cvm::to_str(step)+".\n"); // } - // colvars->it = colvars->it_restart = step; - colvars->it = 0; + colvars->set_initial_step(static_cast(0L)); } } diff --git a/lammps/src/COLVARS/colvarproxy_lammps.cpp b/lammps/src/COLVARS/colvarproxy_lammps.cpp index c2435cd2b..bb1b2e8f0 100644 --- a/lammps/src/COLVARS/colvarproxy_lammps.cpp +++ b/lammps/src/COLVARS/colvarproxy_lammps.cpp @@ -67,18 +67,7 @@ void colvarproxy_lammps::init() set_integration_timestep(_lmp->update->dt * _lmp->force->femtosecond); if (_lmp->update->ntimestep != 0) { - cvm::log("Setting initial step number from LAMMPS: "+ - cvm::to_str(_lmp->update->ntimestep)+"\n"); - colvarmodule::it = colvarmodule::it_restart = - static_cast(_lmp->update->ntimestep); - } - - if (cvm::debug()) { - cvm::log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n"); - cvm::log("atoms_refcount = "+cvm::to_str(atoms_refcount)+"\n"); - cvm::log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n"); - cvm::log(cvm::line_marker); - cvm::log("Info: done initializing the colvars proxy object.\n"); + colvars->set_initial_step(static_cast(_lmp->update->ntimestep)); } } diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C index 08680c2be..32075eec4 100644 --- a/namd/src/colvarproxy_namd.C +++ b/namd/src/colvarproxy_namd.C @@ -122,9 +122,7 @@ colvarproxy_namd::colvarproxy_namd() #endif if (simparams->firstTimestep != 0) { - cvm::log("Initializing step number as firstTimestep.\n"); - colvars->it = colvars->it_restart = - static_cast(simparams->firstTimestep); + colvars->set_initial_step(static_cast(simparams->firstTimestep)); } reduction = ReductionMgr::Object()->willSubmit(REDUCTIONS_BASIC); diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp index 5786d7603..0d80edf38 100644 --- a/src/colvarmodule.cpp +++ b/src/colvarmodule.cpp @@ -194,6 +194,13 @@ size_t colvarmodule::size() const } +void colvarmodule::set_initial_step(step_number it_in) +{ + cvm::log("Setting initial step number from MD engine: " + cvm::to_str(it_in) + "\n"); + it = it_restart = it_in; +} + + int colvarmodule::read_config_file(char const *config_filename) { cvm::log(cvm::line_marker); diff --git a/src/colvarmodule.h b/src/colvarmodule.h index bc4855225..a602843b2 100644 --- a/src/colvarmodule.h +++ b/src/colvarmodule.h @@ -339,6 +339,9 @@ class colvarmodule { /// Destructor ~colvarmodule(); + /// Set the initial step number (it is 0 otherwise); may be overridden when reading a state + void set_initial_step(step_number it); + /// Actual function called by the destructor int reset(); From 2692302da02ac76c0d7d04826e339d5a53559e74 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 14 Sep 2023 21:38:37 -0400 Subject: [PATCH 109/162] Fix: Set input state string from GROMACS-MDModules interface --- .../applied_forces/colvars/colvarsforceprovider.cpp | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp index 98aaa2571..a9ac3f01b 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp @@ -211,7 +211,9 @@ ColvarsForceProvider::ColvarsForceProvider(const std::string& colvarsConfi } // Read input state file - input_buffer_ = stateToCheckpoint_.colvarStateFile_.c_str(); + input_stream_from_string("input state string", stateToCheckpoint_.colvarStateFile_); + // Clear input now that we have copied it + stateToCheckpoint_.colvarStateFile_.clear(); colvars->setup_input(); } else From b323e1efbc792a60a7e198690e130d4a3f3e7077 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 14 Sep 2023 21:38:59 -0400 Subject: [PATCH 110/162] Remove now unused colvarproxy member --- src/colvarproxy_io.cpp | 1 - src/colvarproxy_io.h | 3 --- 2 files changed, 4 deletions(-) diff --git a/src/colvarproxy_io.cpp b/src/colvarproxy_io.cpp index e3039afb8..df424c95e 100644 --- a/src/colvarproxy_io.cpp +++ b/src/colvarproxy_io.cpp @@ -29,7 +29,6 @@ colvarproxy_io::colvarproxy_io() { - input_buffer_ = NULL; restart_frequency_engine = 0; input_stream_error_ = new std::istringstream(); input_stream_error_->setstate(std::ios::badbit); diff --git a/src/colvarproxy_io.h b/src/colvarproxy_io.h index 1af3090ac..80f9f30d9 100644 --- a/src/colvarproxy_io.h +++ b/src/colvarproxy_io.h @@ -181,9 +181,6 @@ class colvarproxy_io { /// Object whose reference is returned when write errors occur std::ostream *output_stream_error_; - - /// Buffer from which the input state information may be read - char const *input_buffer_; }; From f78b9fe8ecb4951e3e5cdd4b8b9c705ca31adc09 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 14 Sep 2023 22:03:27 -0400 Subject: [PATCH 111/162] Add missing colvars: prefix from GROMACS log messages --- .../applied_forces/colvars/colvarproxygromacs.cpp | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp index aed0a674d..2ff2f34e5 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp @@ -41,6 +41,7 @@ #include "colvarproxygromacs.h" +#include namespace gmx { @@ -130,9 +131,12 @@ cvm::real ColvarProxyGromacs::rand_gaussian() void ColvarProxyGromacs::log(std::string const& message) { - if (logger_) - { - GMX_LOG(logger_->info).appendText(message); + if (logger_) { + std::istringstream is(message); + std::string line; + while (std::getline(is, line)) { + GMX_LOG(logger_->info).appendText("colvars: " + line + "\n"); + } } } From 53fcb467cd4e171cec75c1bb0515f0e8cff1df28 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 14 Sep 2023 22:04:32 -0400 Subject: [PATCH 112/162] Fix extraction of Colvars log messages in GROMACS test runner --- gromacs/tests/library/run_tests.sh | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gromacs/tests/library/run_tests.sh b/gromacs/tests/library/run_tests.sh index 03deb8fda..df2ebaebf 100755 --- a/gromacs/tests/library/run_tests.sh +++ b/gromacs/tests/library/run_tests.sh @@ -161,6 +161,8 @@ for dir in ${DIRLIST} ; do ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} >& ${basename}.out RETVAL=$? output=${basename} + grep "^colvars:" ${basename}.log | grep -v 'Initializing the collective variables module' \ + | grep -v 'Using GROMACS interface, version' > ${basename}.colvars.out fi if [ "${basename}" == "test.restart" ] ; then @@ -168,12 +170,10 @@ for dir in ${DIRLIST} ; do ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt >& ${basename}.out RETVAL=$? output=${basename} + grep "^colvars:" ${basename}.part0002.log | grep -v 'Initializing the collective variables module' \ + | grep -v 'Using GROMACS interface, version' > ${basename}.colvars.out fi - # Output of Colvars module, minus the version numbers - grep "^colvars:" ${basename}.out | grep -v 'Initializing the collective variables module' \ - | grep -v 'Using GROMACS interface, version' > ${basename}.colvars.out - if [ -f ${output}.colvars.state ] ; then # Filter out the version number from the state files to allow comparisons grep -sv 'version' ${output}.colvars.state > ${TMPDIR}/${output}.colvars.state.stripped From 060aac73d13f3f492022300b2097a3a63e9e4348 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 15 Sep 2023 12:06:07 -0400 Subject: [PATCH 113/162] Update gromacs-mdmodules.patch to add new serializable: types char and UChar --- gromacs/gromacs-mdmodules.patch | 193 ++++++++++++++++++++------------ 1 file changed, 119 insertions(+), 74 deletions(-) diff --git a/gromacs/gromacs-mdmodules.patch b/gromacs/gromacs-mdmodules.patch index 1a468952d..ba2039cf0 100644 --- a/gromacs/gromacs-mdmodules.patch +++ b/gromacs/gromacs-mdmodules.patch @@ -1,11 +1,11 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -index 45ebd45340..db90705c29 100644 +index 31e2bbbec5..bceb9ff32b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -586,6 +586,9 @@ include(gmxManageLmfit) - +@@ -646,6 +646,9 @@ include(gmxManageLmfit) + include(gmxManageMuparser) - + +include(gmxManageColvars) +include(gmxManageLepton) + @@ -13,13 +13,13 @@ index 45ebd45340..db90705c29 100644 # Process SIMD instruction settings ################################################## diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt -index c8ec2dd0cc..9051910fe6 100644 +index 96107341de..4628c15976 100644 --- a/src/gromacs/CMakeLists.txt +++ b/src/gromacs/CMakeLists.txt -@@ -143,6 +143,11 @@ if (WIN32) +@@ -146,6 +146,11 @@ if (WIN32) endif() list(APPEND libgromacs_object_library_dependencies thread_mpi) - + +gmx_manage_colvars() +gmx_manage_lepton() +list(APPEND libgromacs_object_library_dependencies colvars) @@ -28,10 +28,10 @@ index c8ec2dd0cc..9051910fe6 100644 # This code is here instead of utility/CMakeLists.txt, because CMake # custom commands and source file properties can only be set in the directory # that contains the target that uses them. -@@ -205,6 +210,8 @@ add_library(legacy_modules INTERFACE) +@@ -218,6 +223,8 @@ add_library(legacy_modules INTERFACE) target_include_directories(legacy_modules INTERFACE $) target_link_libraries(libgromacs PRIVATE $) - + +gmx_include_colvars_headers() + # Add these contents first because linking their tests can take a lot @@ -46,11 +46,67 @@ index 3c4987f892..53e6b91d70 100644 add_subdirectory(densityfitting) add_subdirectory(qmmm) +add_subdirectory(colvars) - + if (BUILD_TESTING) add_subdirectory(tests) +diff --git a/src/gromacs/fileio/checkpoint.cpp b/src/gromacs/fileio/checkpoint.cpp +index b493a9a82f..25299addec 100644 +--- a/src/gromacs/fileio/checkpoint.cpp ++++ b/src/gromacs/fileio/checkpoint.cpp +@@ -119,7 +119,10 @@ template void readKvtCheckpointValue(compat::not_null value, + const std::string& name, + const std::string& identifier, + const KeyValueTreeObject& kvt); +- ++template void readKvtCheckpointValue(compat::not_null value, ++ const std::string& name, ++ const std::string& identifier, ++ const KeyValueTreeObject& kvt); + template + void writeKvtCheckpointValue(const ValueType& value, + const std::string& name, +@@ -137,7 +140,10 @@ template void writeKvtCheckpointValue(const real& value, + const std::string& name, + const std::string& identifier, + KeyValueTreeObjectBuilder kvtBuilder); +- ++template void writeKvtCheckpointValue(const std::string& value, ++ const std::string& name, ++ const std::string& identifier, ++ KeyValueTreeObjectBuilder kvtBuilder); + + } // namespace gmx + +diff --git a/src/gromacs/fileio/checkpoint.h b/src/gromacs/fileio/checkpoint.h +index fa886f6e47..762a9ad349 100644 +--- a/src/gromacs/fileio/checkpoint.h ++++ b/src/gromacs/fileio/checkpoint.h +@@ -99,6 +99,11 @@ extern template void readKvtCheckpointValue(compat::not_null value, + const std::string& name, + const std::string& identifier, + const KeyValueTreeObject& kvt); ++//! \copydoc readKvtCheckpointValue ++extern template void readKvtCheckpointValue(compat::not_null value, ++ const std::string& name, ++ const std::string& identifier, ++ const KeyValueTreeObject& kvt); + + /*! \brief Write to a key-value-tree used for checkpointing. + * +@@ -125,6 +130,11 @@ extern template void writeKvtCheckpointValue(const real& value, + const std::string& name, + const std::string& identifier, + KeyValueTreeObjectBuilder kvtBuilder); ++//! \copydoc writeKvtCheckpointValue ++extern template void writeKvtCheckpointValue(const std::string& value, ++ const std::string& name, ++ const std::string& identifier, ++ KeyValueTreeObjectBuilder kvtBuilder); + + /*! \libinternal + * \brief Provides the MDModules with the checkpointed data on the main rank. diff --git a/src/gromacs/mdrun/mdmodules.cpp b/src/gromacs/mdrun/mdmodules.cpp -index 5399f06d02..cd0ab4d2d6 100644 +index 5221ff025c..715dafc20b 100644 --- a/src/gromacs/mdrun/mdmodules.cpp +++ b/src/gromacs/mdrun/mdmodules.cpp @@ -40,6 +40,7 @@ @@ -59,8 +115,8 @@ index 5399f06d02..cd0ab4d2d6 100644 #include "gromacs/applied_forces/qmmm/qmmm.h" +#include "gromacs/applied_forces/colvars/colvarsMDModule.h" #include "gromacs/imd/imd.h" + #include "gromacs/mdrunutility/mdmodulesnotifiers.h" #include "gromacs/mdtypes/iforceprovider.h" - #include "gromacs/mdtypes/imdmodule.h" @@ -67,7 +68,8 @@ public: field_(createElectricFieldModule()), imd_(createInteractiveMolecularDynamicsModule()), @@ -70,7 +126,7 @@ index 5399f06d02..cd0ab4d2d6 100644 + colvars_(ColvarsModuleInfo::create()) { } - + @@ -78,6 +80,7 @@ public: field_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); densityFitting_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); @@ -78,13 +134,13 @@ index 5399f06d02..cd0ab4d2d6 100644 + colvars_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); // In future, other sections would also go here. } - + @@ -106,6 +109,7 @@ public: std::unique_ptr imd_; std::unique_ptr qmmm_; std::unique_ptr swapCoordinates_; + std::unique_ptr colvars_; - + /*! \brief List of registered MDModules * @@ -129,6 +133,7 @@ void MDModules::initMdpTransform(IKeyValueTreeTransformRules* rules) @@ -93,7 +149,7 @@ index 5399f06d02..cd0ab4d2d6 100644 impl_->qmmm_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); + impl_->colvars_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); } - + void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder* builder) @@ -136,6 +141,7 @@ void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder* builder) impl_->field_->mdpOptionProvider()->buildMdpOutput(builder); @@ -101,7 +157,7 @@ index 5399f06d02..cd0ab4d2d6 100644 impl_->qmmm_->mdpOptionProvider()->buildMdpOutput(builder); + impl_->colvars_->mdpOptionProvider()->buildMdpOutput(builder); } - + void MDModules::assignOptionsToModules(const KeyValueTreeObject& params, IKeyValueTreeErrorHandler* errorHandler) @@ -173,6 +179,7 @@ ForceProviders* MDModules::initForceProviders() impl_->field_->initForceProviders(impl_->forceProviders_.get()); @@ -117,67 +173,56 @@ index 5399f06d02..cd0ab4d2d6 100644 impl_->qmmm_->subscribeToPreProcessingNotifications(&impl_->notifiers_); + impl_->colvars_->subscribeToPreProcessingNotifications(&impl_->notifiers_); } - + void MDModules::subscribeToSimulationSetupNotifications() { impl_->densityFitting_->subscribeToSimulationSetupNotifications(&impl_->notifiers_); impl_->qmmm_->subscribeToSimulationSetupNotifications(&impl_->notifiers_); + impl_->colvars_->subscribeToSimulationSetupNotifications(&impl_->notifiers_); } - + void MDModules::add(std::shared_ptr module) -diff --git a/src/gromacs/fileio/checkpoint.h b/src/gromacs/fileio/checkpoint.h -index fa886f6e47..762a9ad349 100644 ---- a/src/gromacs/fileio/checkpoint.h -+++ b/src/gromacs/fileio/checkpoint.h -@@ -99,6 +99,11 @@ extern template void readKvtCheckpointValue(compat::not_null value, - const std::string& name, - const std::string& identifier, - const KeyValueTreeObject& kvt); -+//! \copydoc readKvtCheckpointValue -+extern template void readKvtCheckpointValue(compat::not_null value, -+ const std::string& name, -+ const std::string& identifier, -+ const KeyValueTreeObject& kvt); - - /*! \brief Write to a key-value-tree used for checkpointing. - * -@@ -125,6 +130,11 @@ extern template void writeKvtCheckpointValue(const real& value, - const std::string& name, - const std::string& identifier, - KeyValueTreeObjectBuilder kvtBuilder); -+//! \copydoc writeKvtCheckpointValue -+extern template void writeKvtCheckpointValue(const std::string& value, -+ const std::string& name, -+ const std::string& identifier, -+ KeyValueTreeObjectBuilder kvtBuilder); - - /*! \libinternal - * \brief Provides the MDModules with the checkpointed data on the main rank. -diff --git a/src/gromacs/fileio/checkpoint.cpp b/src/gromacs/fileio/checkpoint.cpp -index b493a9a82f..25299addec 100644 ---- a/src/gromacs/fileio/checkpoint.cpp -+++ b/src/gromacs/fileio/checkpoint.cpp -@@ -119,7 +119,10 @@ template void readKvtCheckpointValue(compat::not_null value, - const std::string& name, - const std::string& identifier, - const KeyValueTreeObject& kvt); -- -+template void readKvtCheckpointValue(compat::not_null value, -+ const std::string& name, -+ const std::string& identifier, -+ const KeyValueTreeObject& kvt); - template - void writeKvtCheckpointValue(const ValueType& value, - const std::string& name, -@@ -137,7 +140,10 @@ template void writeKvtCheckpointValue(const real& value, - const std::string& name, - const std::string& identifier, - KeyValueTreeObjectBuilder kvtBuilder); -- -+template void writeKvtCheckpointValue(const std::string& value, -+ const std::string& name, -+ const std::string& identifier, -+ KeyValueTreeObjectBuilder kvtBuilder); - - } // namespace gmx +diff --git a/src/gromacs/utility/keyvaluetreeserializer.cpp b/src/gromacs/utility/keyvaluetreeserializer.cpp +index 964f60e130..81581fdf7f 100644 +--- a/src/gromacs/utility/keyvaluetreeserializer.cpp ++++ b/src/gromacs/utility/keyvaluetreeserializer.cpp +@@ -169,6 +169,30 @@ struct SerializationTraits + } + }; + ++template<> ++struct SerializationTraits ++{ ++ static void serialize(char value, ISerializer* serializer) { serializer->doChar(&value); } ++ static void deserialize(KeyValueTreeValueBuilder* builder, ISerializer* serializer) ++ { ++ char value = ' '; ++ serializer->doChar(&value); ++ builder->setValue(value); ++ } ++}; ++ ++template<> ++struct SerializationTraits ++{ ++ static void serialize(unsigned char value, ISerializer* serializer) { serializer->doUChar(&value); } ++ static void deserialize(KeyValueTreeValueBuilder* builder, ISerializer* serializer) ++ { ++ unsigned char value = '\0'; ++ serializer->doUChar(&value); ++ builder->setValue(value); ++ } ++}; ++ + template<> + struct SerializationTraits + { +@@ -245,6 +269,8 @@ void ValueSerializer::initSerializers() + SERIALIZER('A', KeyValueTreeArray), + SERIALIZER('s', std::string), + SERIALIZER('b', bool), ++ SERIALIZER('c', char), ++ SERIALIZER('u', unsigned char), + SERIALIZER('i', int), + SERIALIZER('l', int64_t), + SERIALIZER('f', float), From 45ff643ceffe5467c5a83ac3846e45da71ef48a4 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 15 Sep 2023 12:06:44 -0400 Subject: [PATCH 114/162] Serialize and deserialize formatted Colvars state file as an array of char --- .../colvars/colvarsforceprovider.cpp | 20 +++++++++++++++++-- .../colvars/colvarsforceprovider.h | 7 ++++++- 2 files changed, 24 insertions(+), 3 deletions(-) diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp index a9ac3f01b..16e5b14be 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp @@ -66,6 +66,8 @@ const std::string ColvarsForceProviderState::xOldWholeName_ = "xOldWhole"; const std::string ColvarsForceProviderState::colvarStateFileName_ = "colvarStateFile"; +const std::string ColvarsForceProviderState::colvarStateFileSizeName_ = "colvarStateFileSize"; + void ColvarsForceProviderState::writeState(KeyValueTreeObjectBuilder kvtBuilder, const std::string& identifier) const { @@ -81,8 +83,14 @@ void ColvarsForceProviderState::writeState(KeyValueTreeObjectBuilder kvtBuilder, } } + writeKvtCheckpointValue( + static_cast(colvarStateFile_.size()), colvarStateFileSizeName_, identifier, kvtBuilder); - writeKvtCheckpointValue(colvarStateFile_, colvarStateFileName_, identifier, kvtBuilder); + // Write formatted Colvars state file, one character at a time + auto charArrayAdder = kvtBuilder.addUniformArray(colvarStateFileName_); + for (const char &c : colvarStateFile_) { + charArrayAdder.addValue(c); + } } void ColvarsForceProviderState::readState(const KeyValueTreeObject& kvtData, const std::string& identifier) @@ -113,8 +121,16 @@ void ColvarsForceProviderState::readState(const KeyValueTreeObject& kvtData, con } } + int64_t colvarStateFileSize_ = 0L; readKvtCheckpointValue( - compat::make_not_null(&colvarStateFile_), colvarStateFileName_, identifier, kvtData); + compat::make_not_null(&colvarStateFileSize_), colvarStateFileSizeName_, identifier, kvtData); + + // Read Colvars state file + colvarStateFile_.reserve(colvarStateFileSize_); + auto charArray = kvtData[colvarStateFileName_].asArray().values(); + for (const auto &c: charArray) { + colvarStateFile_.append(1, c.cast()); + } } diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h index 51fa5221e..f9a035e77 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h @@ -86,11 +86,16 @@ struct ColvarsForceProviderState */ std::string colvarStateFile_; - /*! \brief String naming variable holding the content of the colvars state file. + /*! \brief String naming variable holding the content of the formatted Colvars state file. * \note Changing this name will break backwards compability for checkpoint file writing. */ static const std::string colvarStateFileName_; + /*! \brief String naming variable holding the size of the formatted Colvars state file. + * \note Changing this name will break backwards compability for checkpoint file writing. + */ + static const std::string colvarStateFileSizeName_; + /*! \brief Write internal colvars data into a key value tree. * The entries to the kvt are identified with identifier, so that a variable * is indentified with the key "identifier-variablename" From bdc2c157fac17988d1d7f454ad8ddef370b51918 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 15 Sep 2023 12:07:21 -0400 Subject: [PATCH 115/162] Add copy of GROMACS .clang-format to allow formatting code in Colvars worktree --- gromacs/gromacs-mdmodules/.clang-format | 131 ++++++++++++++++++++++++ 1 file changed, 131 insertions(+) create mode 100644 gromacs/gromacs-mdmodules/.clang-format diff --git a/gromacs/gromacs-mdmodules/.clang-format b/gromacs/gromacs-mdmodules/.clang-format new file mode 100644 index 000000000..258e4e29d --- /dev/null +++ b/gromacs/gromacs-mdmodules/.clang-format @@ -0,0 +1,131 @@ +--- +Language: Cpp +AccessModifierOffset: -4 +AlignAfterOpenBracket: Align +AlignConsecutiveAssignments: true +AlignConsecutiveDeclarations: true +AlignEscapedNewlinesLeft: true +AlignOperands: true +AlignTrailingComments: true +AllowAllParametersOfDeclarationOnNextLine: false +AllowShortBlocksOnASingleLine: true +AllowShortCaseLabelsOnASingleLine: true +AllowShortFunctionsOnASingleLine: Inline +AllowShortIfStatementsOnASingleLine: false +AllowShortLoopsOnASingleLine: false +AlwaysBreakAfterDefinitionReturnType: None +AlwaysBreakAfterReturnType: None +AlwaysBreakBeforeMultilineStrings: true +AlwaysBreakTemplateDeclarations: true +BinPackArguments: false +BinPackParameters: false +BraceWrapping: + AfterClass: true + AfterControlStatement: true + AfterEnum: true + AfterFunction: true + AfterNamespace: true + AfterObjCDeclaration: true + AfterStruct: true + AfterUnion: true + BeforeCatch: true + BeforeElse: true + IndentBraces: false +BreakBeforeBinaryOperators: NonAssignment +BreakBeforeBraces: Allman +BreakBeforeTernaryOperators: true +BreakConstructorInitializers: AfterColon +BreakAfterJavaFieldAnnotations: false +BreakInheritanceList: AfterColon +BreakStringLiterals: true +ColumnLimit: 100 +CommentPragmas: '^ IWYU pragma:|NOLINT' +ConstructorInitializerAllOnOneLineOrOnePerLine: true +ConstructorInitializerIndentWidth: 4 +ContinuationIndentWidth: 8 +Cpp11BracedListStyle: false +DerivePointerAlignment: false +DisableFormat: false +ExperimentalAutoDetectBinPacking: false +FixNamespaceComments: true +ForEachMacros: [ foreach, Q_FOREACH, BOOST_FOREACH ] +IncludeBlocks: Regroup +IncludeCategories: + # Make sure gmxpre.h goes first. + - Regex: 'gmxpre.h' + Priority: -1 + # config.h goes immediately after the main header. + - Regex: 'config.h' + Priority: 1 + # Group deprecated C compatibility headers. + - Regex: '^<[^/]*\.h>' + Priority: 2 + # Group C compatibility headers. + - Regex: '^' + Priority: 3 + # Get remaining C++ headers, as best we can tell. + - Regex: '^<[^/]*>' + Priority: 4 + # Get any other headers included from the system. + - Regex: '^<.*>' + Priority: 5 + # Group headers by API level. + # Non-private gromacs headers. + - Regex: 'gromacs/.*' + Priority: 20 + - Regex: 'testutils/.*' + Priority: 30 + - Regex: 'programs/.*' + Priority: 40 + - Regex: 'gmxapi/.*' + Priority: 50 + - Regex: 'nblib/.*' + Priority: 60 + # Try to match external headers by looking for paths not yet matched, + # but insert before recognized paths. + - Regex: '.*/.*' + Priority: 10 + # Private headers. Unfortunately, also matches headers without subdirectories or angle-brackets. + - Regex: '.*' + Priority: 100 +IncludeIsMainRegex: '(([-_](test|tests|unittest))?([-_][0-9]+)*)$' +IncludeIsMainSourceRegex: '(\.cu)$' +IndentPPDirectives: AfterHash +IndentCaseLabels: true +IndentWidth: 4 +IndentWrappedFunctionNames: false +JavaScriptQuotes: Leave +JavaScriptWrapImports: true +KeepEmptyLinesAtTheStartOfBlocks: true +MacroBlockBegin: '' +MacroBlockEnd: '' +MaxEmptyLinesToKeep: 2 +NamespaceIndentation: None +ObjCBlockIndentWidth: 2 +ObjCSpaceAfterProperty: false +ObjCSpaceBeforeProtocolList: false +PenaltyBreakBeforeFirstCallParameter: 1 +PenaltyBreakComment: 300 +PenaltyBreakFirstLessLess: 120 +PenaltyBreakString: 1000 +PenaltyExcessCharacter: 2 +PenaltyReturnTypeOnItsOwnLine: 100 +PointerAlignment: Left +ReflowComments: true +SortIncludes: true +SortUsingDeclarations: true +SpaceAfterCStyleCast: false +SpaceBeforeAssignmentOperators: true +SpaceBeforeParens: ControlStatements +SpaceInEmptyParentheses: false +SpacesBeforeTrailingComments: 1 +SpacesInAngles: false +SpaceAfterTemplateKeyword: false +SpacesInContainerLiterals: false +SpacesInCStyleCastParentheses: false +SpacesInParentheses: false +SpacesInSquareBrackets: false +Standard: Cpp11 +TabWidth: 8 +UseTab: Never +... From bd0a564c57654f855f58acb1f021ae50e489dd92 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 15 Sep 2023 12:26:56 -0400 Subject: [PATCH 116/162] Remove now unneeded changes to src/gromacs/fileio --- gromacs/gromacs-mdmodules.patch | 56 --------------------------------- 1 file changed, 56 deletions(-) diff --git a/gromacs/gromacs-mdmodules.patch b/gromacs/gromacs-mdmodules.patch index ba2039cf0..057092cfa 100644 --- a/gromacs/gromacs-mdmodules.patch +++ b/gromacs/gromacs-mdmodules.patch @@ -49,62 +49,6 @@ index 3c4987f892..53e6b91d70 100644 if (BUILD_TESTING) add_subdirectory(tests) -diff --git a/src/gromacs/fileio/checkpoint.cpp b/src/gromacs/fileio/checkpoint.cpp -index b493a9a82f..25299addec 100644 ---- a/src/gromacs/fileio/checkpoint.cpp -+++ b/src/gromacs/fileio/checkpoint.cpp -@@ -119,7 +119,10 @@ template void readKvtCheckpointValue(compat::not_null value, - const std::string& name, - const std::string& identifier, - const KeyValueTreeObject& kvt); -- -+template void readKvtCheckpointValue(compat::not_null value, -+ const std::string& name, -+ const std::string& identifier, -+ const KeyValueTreeObject& kvt); - template - void writeKvtCheckpointValue(const ValueType& value, - const std::string& name, -@@ -137,7 +140,10 @@ template void writeKvtCheckpointValue(const real& value, - const std::string& name, - const std::string& identifier, - KeyValueTreeObjectBuilder kvtBuilder); -- -+template void writeKvtCheckpointValue(const std::string& value, -+ const std::string& name, -+ const std::string& identifier, -+ KeyValueTreeObjectBuilder kvtBuilder); - - } // namespace gmx - -diff --git a/src/gromacs/fileio/checkpoint.h b/src/gromacs/fileio/checkpoint.h -index fa886f6e47..762a9ad349 100644 ---- a/src/gromacs/fileio/checkpoint.h -+++ b/src/gromacs/fileio/checkpoint.h -@@ -99,6 +99,11 @@ extern template void readKvtCheckpointValue(compat::not_null value, - const std::string& name, - const std::string& identifier, - const KeyValueTreeObject& kvt); -+//! \copydoc readKvtCheckpointValue -+extern template void readKvtCheckpointValue(compat::not_null value, -+ const std::string& name, -+ const std::string& identifier, -+ const KeyValueTreeObject& kvt); - - /*! \brief Write to a key-value-tree used for checkpointing. - * -@@ -125,6 +130,11 @@ extern template void writeKvtCheckpointValue(const real& value, - const std::string& name, - const std::string& identifier, - KeyValueTreeObjectBuilder kvtBuilder); -+//! \copydoc writeKvtCheckpointValue -+extern template void writeKvtCheckpointValue(const std::string& value, -+ const std::string& name, -+ const std::string& identifier, -+ KeyValueTreeObjectBuilder kvtBuilder); - - /*! \libinternal - * \brief Provides the MDModules with the checkpointed data on the main rank. diff --git a/src/gromacs/mdrun/mdmodules.cpp b/src/gromacs/mdrun/mdmodules.cpp index 5221ff025c..715dafc20b 100644 --- a/src/gromacs/mdrun/mdmodules.cpp From c60b231b58eb30db359008f9e2ed8136bb1bf657 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 15 Sep 2023 17:15:54 -0400 Subject: [PATCH 117/162] Use unformatted Colvars state --- .../colvars/colvarsforceprovider.cpp | 19 ++++++++++--------- .../colvars/colvarsforceprovider.h | 4 ++-- 2 files changed, 12 insertions(+), 11 deletions(-) diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp index 16e5b14be..e0aa6842b 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp @@ -40,6 +40,7 @@ */ #include "colvarsforceprovider.h" +#include "external/colvars/colvars_memstream.h" #include @@ -87,8 +88,8 @@ void ColvarsForceProviderState::writeState(KeyValueTreeObjectBuilder kvtBuilder, static_cast(colvarStateFile_.size()), colvarStateFileSizeName_, identifier, kvtBuilder); // Write formatted Colvars state file, one character at a time - auto charArrayAdder = kvtBuilder.addUniformArray(colvarStateFileName_); - for (const char &c : colvarStateFile_) { + auto charArrayAdder = kvtBuilder.addUniformArray(colvarStateFileName_); + for (const unsigned char &c : colvarStateFile_) { charArrayAdder.addValue(c); } } @@ -125,11 +126,13 @@ void ColvarsForceProviderState::readState(const KeyValueTreeObject& kvtData, con readKvtCheckpointValue( compat::make_not_null(&colvarStateFileSize_), colvarStateFileSizeName_, identifier, kvtData); - // Read Colvars state file - colvarStateFile_.reserve(colvarStateFileSize_); + // Read Colvars state file; use explicit loop because kvt types don't support std::copy auto charArray = kvtData[colvarStateFileName_].asArray().values(); + colvarStateFile_.resize(colvarStateFileSize_); + auto it = colvarStateFile_.begin(); for (const auto &c: charArray) { - colvarStateFile_.append(1, c.cast()); + *it = c.cast(); + it++; } } @@ -227,9 +230,7 @@ ColvarsForceProvider::ColvarsForceProvider(const std::string& colvarsConfi } // Read input state file - input_stream_from_string("input state string", stateToCheckpoint_.colvarStateFile_); - // Clear input now that we have copied it - stateToCheckpoint_.colvarStateFile_.clear(); + colvars->set_input_state_buffer(stateToCheckpoint_.colvarStateFile_); colvars->setup_input(); } else @@ -427,7 +428,7 @@ void ColvarsForceProvider::add_energy(cvm::real energy) void ColvarsForceProvider::writeCheckpointData(MDModulesWriteCheckpointData checkpointWriting, const std::string& moduleName) { - colvars->write_restart_string(stateToCheckpoint_.colvarStateFile_); + colvars->write_state_buffer(stateToCheckpoint_.colvarStateFile_); stateToCheckpoint_.writeState(checkpointWriting.builder_, moduleName); } diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h index f9a035e77..33aa6880a 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h @@ -82,9 +82,9 @@ struct ColvarsForceProviderState */ static const std::string xOldWholeName_; - /*! \brief Content of the colvars state file. + /*! \brief Content of the unformatted Colvars state file. */ - std::string colvarStateFile_; + std::vector colvarStateFile_; /*! \brief String naming variable holding the content of the formatted Colvars state file. * \note Changing this name will break backwards compability for checkpoint file writing. From 7967ca525d22f2a52ad9444e75c152ef9418d449 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 21 Sep 2023 16:05:31 -0400 Subject: [PATCH 118/162] Remove obsolete GROMACS patch section Contents were merged upstream: https://gitlab.com/gromacs/gromacs/-/merge_requests/3816 --- gromacs/gromacs-mdmodules.patch | 44 --------------------------------- 1 file changed, 44 deletions(-) diff --git a/gromacs/gromacs-mdmodules.patch b/gromacs/gromacs-mdmodules.patch index 057092cfa..4a7a5eb24 100644 --- a/gromacs/gromacs-mdmodules.patch +++ b/gromacs/gromacs-mdmodules.patch @@ -126,47 +126,3 @@ index 5221ff025c..715dafc20b 100644 } void MDModules::add(std::shared_ptr module) -diff --git a/src/gromacs/utility/keyvaluetreeserializer.cpp b/src/gromacs/utility/keyvaluetreeserializer.cpp -index 964f60e130..81581fdf7f 100644 ---- a/src/gromacs/utility/keyvaluetreeserializer.cpp -+++ b/src/gromacs/utility/keyvaluetreeserializer.cpp -@@ -169,6 +169,30 @@ struct SerializationTraits - } - }; - -+template<> -+struct SerializationTraits -+{ -+ static void serialize(char value, ISerializer* serializer) { serializer->doChar(&value); } -+ static void deserialize(KeyValueTreeValueBuilder* builder, ISerializer* serializer) -+ { -+ char value = ' '; -+ serializer->doChar(&value); -+ builder->setValue(value); -+ } -+}; -+ -+template<> -+struct SerializationTraits -+{ -+ static void serialize(unsigned char value, ISerializer* serializer) { serializer->doUChar(&value); } -+ static void deserialize(KeyValueTreeValueBuilder* builder, ISerializer* serializer) -+ { -+ unsigned char value = '\0'; -+ serializer->doUChar(&value); -+ builder->setValue(value); -+ } -+}; -+ - template<> - struct SerializationTraits - { -@@ -245,6 +269,8 @@ void ValueSerializer::initSerializers() - SERIALIZER('A', KeyValueTreeArray), - SERIALIZER('s', std::string), - SERIALIZER('b', bool), -+ SERIALIZER('c', char), -+ SERIALIZER('u', unsigned char), - SERIALIZER('i', int), - SERIALIZER('l', int64_t), - SERIALIZER('f', float), From 4b88bd378530867e830890d46fe1b01a5c739549 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 21 Sep 2023 16:51:20 -0400 Subject: [PATCH 119/162] clang-format --- .../applied_forces/colvars/colvarproxygromacs.cpp | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp index 2ff2f34e5..7bb3a52f6 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp @@ -131,10 +131,12 @@ cvm::real ColvarProxyGromacs::rand_gaussian() void ColvarProxyGromacs::log(std::string const& message) { - if (logger_) { + if (logger_) + { std::istringstream is(message); - std::string line; - while (std::getline(is, line)) { + std::string line; + while (std::getline(is, line)) + { GMX_LOG(logger_->info).appendText("colvars: " + line + "\n"); } } From 1ebd474572c4af4ea69ef6a793b3a34822613656 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 21 Sep 2023 16:51:10 -0400 Subject: [PATCH 120/162] Remove function that is no longer provided by colvarproxy base class --- .../applied_forces/colvars/colvarproxygromacs.cpp | 6 ------ .../applied_forces/colvars/colvarproxygromacs.h | 4 +--- 2 files changed, 1 insertion(+), 9 deletions(-) diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp index 7bb3a52f6..21e6b5291 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp @@ -143,12 +143,6 @@ void ColvarProxyGromacs::log(std::string const& message) } void ColvarProxyGromacs::error(std::string const& message) -{ - // In GROMACS, all errors are fatal. - fatal_error(message); -} - -void ColvarProxyGromacs::fatal_error(std::string const& message) { log(message); GMX_THROW(InternalError("Error in collective variables module.\n")); diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h index c3ac6baf5..3e2d76724 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h @@ -121,9 +121,7 @@ class ColvarProxyGromacs : public colvarproxy void log(std::string const& message) override; /// Print a message to the main log and let the rest of the program handle the error void error(std::string const& message) override; - /// Print a message to the main log and exit with error code - /// possible suppression - [[noreturn]] void fatal_error(std::string const& message); + /// Request to set the units used internally by Colvars int set_unit_system(std::string const& units_in, bool colvars_defined) override; From 112f672f72412e33c66d3b1579219a5406090c25 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 22 Sep 2023 11:11:29 -0400 Subject: [PATCH 121/162] Track GROMACS EDR filename to set Colvars output prefix --- gromacs/gromacs-mdmodules.patch | 55 +++++++++++++++++++ .../colvars/colvarsMDModule.cpp | 16 +++--- .../applied_forces/colvars/colvarsoptions.cpp | 14 ++--- .../applied_forces/colvars/colvarsoptions.h | 8 +-- 4 files changed, 72 insertions(+), 21 deletions(-) diff --git a/gromacs/gromacs-mdmodules.patch b/gromacs/gromacs-mdmodules.patch index 4a7a5eb24..fadc11dbc 100644 --- a/gromacs/gromacs-mdmodules.patch +++ b/gromacs/gromacs-mdmodules.patch @@ -126,3 +126,58 @@ index 5221ff025c..715dafc20b 100644 } void MDModules::add(std::shared_ptr module) +diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp +index bacb6321e9..68cbdc02c4 100644 +--- a/src/gromacs/mdrun/runner.cpp ++++ b/src/gromacs/mdrun/runner.cpp +@@ -1135,10 +1135,12 @@ int Mdrunner::mdrunner() + setupNotifier.notify(*inputrec->internalParameters); + } + +- // Let MdModules know the .tpr filename ++ // Let MdModules know the .tpr input and .edr output filenames + { + gmx::MdRunInputFilename mdRunInputFilename = { ftp2fn(efTPR, filenames.size(), filenames.data()) }; + setupNotifier.notify(mdRunInputFilename); ++ gmx::EdrOutputFilename edrOutputFilename = { ftp2fn(efEDR, filenames.size(), filenames.data()) }; ++ setupNotifier.notify(edrOutputFilename); + } + + if (fplog != nullptr) +diff --git a/src/gromacs/mdrunutility/mdmodulesnotifiers.h b/src/gromacs/mdrunutility/mdmodulesnotifiers.h +index 69872b3535..7d1520fc26 100644 +--- a/src/gromacs/mdrunutility/mdmodulesnotifiers.h ++++ b/src/gromacs/mdrunutility/mdmodulesnotifiers.h +@@ -167,6 +167,14 @@ struct MdRunInputFilename + std::string mdRunFilename_; + }; + ++/*! \libinternal \brief Energy trajectory output filename from Mdrun. ++ */ ++struct EdrOutputFilename ++{ ++ //! The name of energy output file ++ std::string edrOutputFilename_; ++}; ++ + /*! \libinternal \brief Notification for QM program input filename + * provided by user as command-line argument for grompp + */ +@@ -354,6 +362,7 @@ struct MDModulesNotifiers + * \tparam t_commrec& Provides a communicator to the modules during simulation + * setup + * \tparam MdRunInputFilename& Allows modules to know .tpr filename during mdrun ++ * \tparam EdrOutputFilename& Allows modules to know .edr filename during mdrun + */ + BuildMDModulesNotifier::type simulationSetupNotifier_; ++ const MdRunInputFilename&, ++ const EdrOutputFilename&>::type simulationSetupNotifier_; + }; + + } // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp index 03ea70c73..ddc51bb58 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp @@ -81,7 +81,7 @@ class ColvarsMDModule final : public IMDModule * * \param[in] notifier allows the module to subscribe to notifications from MdModules. * - * The colvars code subscribes to these notifications: + * The Colvars mdmodule code subscribes to these notifications: * - storing its internal parameters in a tpr file by writing to a * key-value-tree during pre-processing by a function taking a * KeyValueTreeObjectBuilder as parameter @@ -131,7 +131,7 @@ class ColvarsMDModule final : public IMDModule /*! \brief Request to be notified. - * The colvars code subscribes to these notifications: + * The Colvars mdmodule code subscribes to these notifications: * - the LocalAtomSetManager sets in the simulation parameter setup * by taking a LocalAtomSetManager * as parameter * - the type of periodic boundary conditions that are used @@ -142,7 +142,9 @@ class ColvarsMDModule final : public IMDModule * by taking a t_commrec as parameter * - the simulation time step * by taking a SimulationTimeStep as a parameter - * - Access MDLogger for notifications output + * - MDLogger for notifications output + * - the .edr filename + * to provide a user-defined output prefix for Colvars output files */ void subscribeToSimulationSetupNotifications(MDModulesNotifiers* notifier) override { @@ -191,11 +193,11 @@ class ColvarsMDModule final : public IMDModule }; notifier->simulationSetupNotifier_.subscribe(setLoggerFunction); - // Process tpr filename - const auto setTprFileNameFunction = [this](const MdRunInputFilename& tprName) { - colvarsOptions_.processTprFilename(tprName); + // Get edr filename + const auto setEdrFileNameFunction = [this](const EdrOutputFilename& filename) { + colvarsOptions_.processEdrFilename(filename); }; - notifier->simulationSetupNotifier_.subscribe(setTprFileNameFunction); + notifier->simulationSetupNotifier_.subscribe(setEdrFileNameFunction); // writing checkpoint data const auto checkpointDataWriting = [this](MDModulesWriteCheckpointData checkpointData) { diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp index 664066c1d..0b8463250 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp @@ -260,24 +260,18 @@ void ColvarsOptions::setLogger(const MDLogger& logger) logger_ = &logger; } -void ColvarsOptions::processTprFilename(const MdRunInputFilename& tprFilename) +void ColvarsOptions::processEdrFilename(const EdrOutputFilename& filename) { - // Exit if colvars module is not active + // Do nothing if Colvars is not active if (!active_) { return; } // Provided name should not be empty - GMX_RELEASE_ASSERT(!tprFilename.mdRunFilename_.empty(), - "Filename of the *.tpr simulation file is empty"); + GMX_RELEASE_ASSERT(!filename.edrOutputFilename_.empty(), "Empty name for the *.edr output file"); - if (!output_prefix_.empty()) - { - return; - } - - output_prefix_ = stripExtension(std::filesystem::path(tprFilename.mdRunFilename_).filename()); + output_prefix_ = stripExtension(std::filesystem::path(filename.edrOutputFilename_).filename()); } void ColvarsOptions::getTemperature(const EnsembleTemperature& temp) diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h index 4e262de56..f51e24f55 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h @@ -102,11 +102,11 @@ class ColvarsOptions final : public IMdpOptionProvider //! Set the MDLogger instance void setLogger(const MDLogger& logger); - /*! \brief Process MdRunInputFilename notification during mdrun. - * In case output_prefix is empty sets it to tpr name - * \param[in] tprFilename name of the *.tpr file that mdrun simulates + /*! \brief Process EdrOutputFilename notification during mdrun. + * Used to set the prefix of Colvars output files based on the .edr filename + * \param[in] filename name of the *.edr file that mdrun will produce */ - void processTprFilename(const MdRunInputFilename& tprFilename); + void processEdrFilename(const EdrOutputFilename& filename); /*! \brief Store the ensemble temperature of the system if available. * \param[in] temp temperature object From fb028ca47c66f1899836267b3f81ed8563ac5ed9 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 22 Sep 2023 12:06:36 -0400 Subject: [PATCH 122/162] Strip .partXXXX suffix when comparing GROMACS output files to reference --- gromacs/tests/library/run_tests.sh | 30 +++++++++++++----------------- 1 file changed, 13 insertions(+), 17 deletions(-) diff --git a/gromacs/tests/library/run_tests.sh b/gromacs/tests/library/run_tests.sh index df2ebaebf..b90bc5059 100755 --- a/gromacs/tests/library/run_tests.sh +++ b/gromacs/tests/library/run_tests.sh @@ -136,9 +136,6 @@ for dir in ${DIRLIST} ; do # Run simulation(s) for basename in test test.restart ; do - # Prefix of the Gromacs generated files - output="" - # Input files # Symbolink link to the colvars input file, index file, and xyz file ln -sf test.in test.dat @@ -160,30 +157,29 @@ for dir in ${DIRLIST} ; do ${BINARY} grompp -f ../Common/test.mdp -c ../Common/da.pdb -p ../Common/da.top -t ../Common/da.trr -o ${basename}.tpr >& ${basename}.grompp.out ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} >& ${basename}.out RETVAL=$? - output=${basename} - grep "^colvars:" ${basename}.log | grep -v 'Initializing the collective variables module' \ - | grep -v 'Using GROMACS interface, version' > ${basename}.colvars.out fi if [ "${basename}" == "test.restart" ] ; then ${BINARY} convert-tpr -s ${basename%.restart}.tpr -nsteps 40 -o ${basename}.tpr >& ${basename}.grompp.out ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt >& ${basename}.out RETVAL=$? - output=${basename} - grep "^colvars:" ${basename}.part0002.log | grep -v 'Initializing the collective variables module' \ - | grep -v 'Using GROMACS interface, version' > ${basename}.colvars.out + output=${basename}.part0002 + for file in ${output}.* ; do + # Remove the part number, our filenames are unique anyway + mv -f ${file} ${file/.part0002/} + done fi - if [ -f ${output}.colvars.state ] ; then - # Filter out the version number from the state files to allow comparisons - grep -sv 'version' ${output}.colvars.state > ${TMPDIR}/${output}.colvars.state.stripped - mv -f ${TMPDIR}/${output}.colvars.state.stripped ${output}.colvars.state.stripped - #Create symlink for restart input - ln -sf ${output}.colvars.state{,.dat} + # Filter out the version numbers to allow comparisons + grep "^colvars:" ${basename}.log \ + | grep -v 'Initializing the collective variables module' \ + | grep -v 'Using GROMACS interface, version' > ${basename}.colvars.out + if [ -f ${basename}.colvars.state ] ; then + grep -sv 'version' ${basename}.colvars.state \ + > ${TMPDIR}/${basename}.colvars.state.stripped && \ + mv -f ${TMPDIR}/${basename}.colvars.state.stripped ${basename}.colvars.state.stripped fi - #Convert the output of the traj files - # If this test is used to generate the reference output files, copy them if [ "x${gen_ref_output}" = 'xyes' ]; then grep ':-) GROMACS -' ${basename}.out | head -n 1 > gromacs-version.txt From a0c0af232a06cb60576d03697124da996935e9f7 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 22 Sep 2023 14:03:06 -0400 Subject: [PATCH 123/162] Add clarifying comment about why we need to fix MSVC's intentionally broken settings --- gromacs/cmake/gmxManageColvars.cmake | 1 + 1 file changed, 1 insertion(+) diff --git a/gromacs/cmake/gmxManageColvars.cmake b/gromacs/cmake/gmxManageColvars.cmake index 65dfd65aa..275d5bf72 100644 --- a/gromacs/cmake/gmxManageColvars.cmake +++ b/gromacs/cmake/gmxManageColvars.cmake @@ -9,6 +9,7 @@ function(gmx_manage_colvars) file(GLOB COLVARS_SOURCES ${PROJECT_SOURCE_DIR}/src/external/colvars/*.cpp) add_library(colvars OBJECT ${COLVARS_SOURCES}) # Colvars requires a correct definition of __cplusplus, which MSVC doesn't give by default + # See: https://learn.microsoft.com/en-us/cpp/build/reference/zc-cplusplus target_compile_options(colvars PRIVATE $<$:/Zc:__cplusplus>) endfunction() From a926e7755678d1e65538738fcda7d753f28f7b62 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 25 Sep 2023 07:43:07 -0400 Subject: [PATCH 124/162] Allow GROMACS test runner to handle different versions of Colvars interface --- gromacs/tests/library/run_tests.sh | 57 ++++++++++++++++++++++-------- 1 file changed, 43 insertions(+), 14 deletions(-) diff --git a/gromacs/tests/library/run_tests.sh b/gromacs/tests/library/run_tests.sh index b90bc5059..f26f61a0e 100755 --- a/gromacs/tests/library/run_tests.sh +++ b/gromacs/tests/library/run_tests.sh @@ -93,6 +93,12 @@ cleanup_files() { } +if ${BINARY} mdrun -colvars 2>&1 | grep -q 'Unknown command-line option -colvars' ; then + MDMODULES_INTERFACE=yes +else + MDMODULES_INTERFACE=no +fi + for dir in ${DIRLIST} ; do if [ -f ${dir}/disabled ] ; then @@ -153,21 +159,44 @@ for dir in ${DIRLIST} ; do # Try running the test - if [ "${basename}" == "test" ] ; then - ${BINARY} grompp -f ../Common/test.mdp -c ../Common/da.pdb -p ../Common/da.top -t ../Common/da.trr -o ${basename}.tpr >& ${basename}.grompp.out - ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} >& ${basename}.out - RETVAL=$? - fi + if [ "x${MDMODULES_INTERFACE}" == "xyes" ] ; then + + if [ "${basename}" == "test" ] ; then + ${BINARY} grompp -f ../Common/test.mdp -c ../Common/da.pdb -p ../Common/da.top -t ../Common/da.trr -o ${basename}.tpr >& ${basename}.grompp.out + ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} >& ${basename}.out + RETVAL=$? + fi + + if [ "${basename}" == "test.restart" ] ; then + ${BINARY} convert-tpr -s ${basename%.restart}.tpr -nsteps 40 -o ${basename}.tpr >& ${basename}.grompp.out + ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt >& ${basename}.out + RETVAL=$? + output=${basename}.part0002 + for file in ${output}.* ; do + # Remove the part number + mv -f ${file} ${file/.part0002/} + done + fi + + else + + if [ "${basename}" == "test" ] ; then + ln -fs ${basename}.in ${basename}.dat + ${BINARY} mdrun -s ../Common/${basename} -deffnm ${basename} -colvars test.dat &> ${basename}.out + RETVAL=$? + ln -fs ${basename}.colvars.state{,.dat} + fi + + if [ "${basename}" == "test.restart" ] ; then + ${BINARY} mdrun -s ../Common/${basename} -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt -colvars ${basename%.restart}.dat -colvars_restart ${basename%.restart}.colvars.state.dat &> ${basename}.out + RETVAL=$? + output="${basename}.part0002" + for file in ${output}.* ; do + # Remove the part number + mv -f ${file} ${file/.part0002/} + done + fi - if [ "${basename}" == "test.restart" ] ; then - ${BINARY} convert-tpr -s ${basename%.restart}.tpr -nsteps 40 -o ${basename}.tpr >& ${basename}.grompp.out - ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt >& ${basename}.out - RETVAL=$? - output=${basename}.part0002 - for file in ${output}.* ; do - # Remove the part number, our filenames are unique anyway - mv -f ${file} ${file/.part0002/} - done fi # Filter out the version numbers to allow comparisons From 15b49f66e8f80dbf43f4a51fae99718d8a07b250 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 25 Sep 2023 07:44:46 -0400 Subject: [PATCH 125/162] Restore CI jobs for patched GROMACS releases --- .github/workflows/test-backends.yml | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/.github/workflows/test-backends.yml b/.github/workflows/test-backends.yml index dc21f9e97..79233b8b3 100644 --- a/.github/workflows/test-backends.yml +++ b/.github/workflows/test-backends.yml @@ -99,6 +99,32 @@ jobs: private_key: ${{ secrets.PULL_VMD_KEY }} private_key_vmd_plugins: ${{ secrets.PULL_VMD_PLUGINS_KEY }} + gromacs-2022: + name: GROMACS 2022 + if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-2022') + uses: ./.github/workflows/backend-template.yml + with: + backend_name: GROMACS-2022 + backend_repo: gromacs/gromacs + backend_repo_ref: release-2022 + container_name: CentOS9-devel + path_compile_script: devel-tools/compile-gromacs.sh + test_lib_directory: gromacs/tests/library + rpath_exe: install/bin/gmx_d + + gromacs-2023: + name: GROMACS 2023 + if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-2023') + uses: ./.github/workflows/backend-template.yml + with: + backend_name: GROMACS-2023 + backend_repo: gromacs/gromacs + backend_repo_ref: release-2023 + container_name: CentOS9-devel + path_compile_script: devel-tools/compile-gromacs.sh + test_lib_directory: gromacs/tests/library + rpath_exe: install/bin/gmx_d + gromacs-devel: name: GROMACS (MDModules) if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-devel') From a08213e1664314e596b6f47d2dcb3257675ef3e3 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 25 Sep 2023 08:07:31 -0400 Subject: [PATCH 126/162] More robust GROMACS version detection in updater script --- update-colvars-code.sh | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/update-colvars-code.sh b/update-colvars-code.sh index c04a090e1..575cae2c5 100755 --- a/update-colvars-code.sh +++ b/update-colvars-code.sh @@ -84,11 +84,7 @@ then elif [ -f "${target}/include/molfile_plugin.h" ] then code="VMD-PLUGINS" -elif [ -f "${target}/INSTALL-dev" ] -then - code="GROMACS-DEV" - echo "You are about to patch GROMACS developpement version with the alpha version of Colvars-MDModules." -elif [ -f "${target}/src/gromacs/commandline/cmdlineinit.h" ] +elif [ -f "${target}/src/gromacs/version.h.cmakein" ] then code="GROMACS" else @@ -103,7 +99,7 @@ else elif [ -f "${target}/src/VMDApp.h" ] then code="VMD" - elif [ -f "${target}/src/gromacs/commandline/cmdlineinit.h" ] + elif [ -f "${target}/src/gromacs/version.h.cmakein" ] then code="GROMACS" else @@ -112,6 +108,12 @@ else fi fi +if [ ${code} == "GROMACS" ] ; then + if [ -f ${target}/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp ] ; then + # Code after https://gitlab.com/gromacs/gromacs/-/merge_requests/3566 + code=GROMACS-DEV + fi +fi COLVARS_VERSION=$(grep define $(dirname $0)/src/colvars_version.h | cut -d' ' -f 3 | tr -d '"') if [ -z "${COLVARS_VERSION}" ] ; then @@ -513,7 +515,7 @@ then echo ' done.' fi -# Update GROMACS tree +# Update GROMACS tree (legacy versions) if [ ${code} = "GROMACS" ] then @@ -608,6 +610,7 @@ then exit 0 fi +# Update GROMACS tree (MDModules interface-ready version) if [ ${code} = "GROMACS-DEV" ] then From 68a27d4f52fad0b7f1b64e1ef12ace0be50410a8 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 25 Sep 2023 08:34:12 -0400 Subject: [PATCH 127/162] Fix reference output regeneration commands --- gromacs/tests/library/run_tests.sh | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gromacs/tests/library/run_tests.sh b/gromacs/tests/library/run_tests.sh index f26f61a0e..7e30acbc5 100755 --- a/gromacs/tests/library/run_tests.sh +++ b/gromacs/tests/library/run_tests.sh @@ -214,14 +214,14 @@ for dir in ${DIRLIST} ; do grep ':-) GROMACS -' ${basename}.out | head -n 1 > gromacs-version.txt grep 'Initializing the collective variables module, version' ${basename}.out | head -n 1 >> gromacs-version.txt grep 'Using GROMACS interface, version' ${basename}.out | head -n 1 >> gromacs-version.txt - cp ${output}.colvars.state.stripped AutoDiff/ - cp ${output}.colvars.traj AutoDiff/ + cp ${basename}.colvars.state.stripped AutoDiff/ + cp ${basename}.colvars.traj AutoDiff/ cp ${basename}.colvars.out AutoDiff/ - if [ -f ${output}.histogram1.dat ] ; then - cp -f ${output}.histogram1.dat AutoDiff/ + if [ -f ${basename}.histogram1.dat ] ; then + cp -f ${basename}.histogram1.dat AutoDiff/ fi - if [ -f ${output}.pmf ] ; then - cp -f ${output}.pmf AutoDiff/ + if [ -f ${basename}.pmf ] ; then + cp -f ${basename}.pmf AutoDiff/ fi fi From be1b7a061188068588e06d5622de8d40f94a0024 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 25 Sep 2023 08:35:10 -0400 Subject: [PATCH 128/162] Regenerate missing reference data using old code version --- .../AutoDiff/test.colvars.out | 109 ------------------ .../AutoDiff/test.colvars.state.stripped | 20 ++++ .../AutoDiff/test.colvars.traj | 22 ++++ .../AutoDiff/test.restart.colvars.out | 0 .../test.restart.colvars.state.stripped | 20 ++++ .../AutoDiff/test.restart.colvars.traj | 22 ++++ .../gromacs-version.txt | 4 +- .../test.in | 3 +- 8 files changed, 88 insertions(+), 112 deletions(-) create mode 100644 gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped create mode 100644 gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj create mode 100644 gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out create mode 100644 gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped create mode 100644 gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out index 43cfc3327..e69de29bb 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out @@ -1,109 +0,0 @@ -colvars: ---------------------------------------------------------------------- -colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. -colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "test.dat": -colvars: # units = "" [default] -colvars: # indexFile = "index.ndx" -colvars: The following index groups are currently defined: -colvars: Protein (104 atoms) -colvars: Protein_noH (51 atoms) -colvars: Protein_Backbone (40 atoms) -colvars: Protein_C-alpha (10 atoms) -colvars: RMSD_atoms (10 atoms) -colvars: Protein_C-alpha_1_2 (2 atoms) -colvars: Protein_C-alpha_9_10 (2 atoms) -colvars: Protein_C-alpha_1 (1 atoms) -colvars: group1 (4 atoms) -colvars: Protein_C-alpha_2 (1 atoms) -colvars: group2 (4 atoms) -colvars: Protein_C-alpha_3 (1 atoms) -colvars: group3 (4 atoms) -colvars: Protein_C-alpha_4 (1 atoms) -colvars: group4 (4 atoms) -colvars: Protein_C-alpha_5 (1 atoms) -colvars: group5 (4 atoms) -colvars: Protein_C-alpha_6 (1 atoms) -colvars: group6 (4 atoms) -colvars: Protein_C-alpha_7 (1 atoms) -colvars: group7 (4 atoms) -colvars: Protein_C-alpha_8 (1 atoms) -colvars: group8 (4 atoms) -colvars: Protein_C-alpha_9 (1 atoms) -colvars: group9 (4 atoms) -colvars: Protein_C-alpha_10 (1 atoms) -colvars: group10 (4 atoms) -colvars: heavy_atoms (51 atoms) -colvars: # smp = on [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 10 -colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = "one" -colvars: Initializing a new "distanceDir" component. -colvars: # name = "" [default] -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # scalable = on [default] -colvars: Initializing atom group "group1". -colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] -colvars: # atomsOfGroup = "" [default] -colvars: # indexGroup = "group1" -colvars: # psfSegID = [default] -colvars: # atomsFile = "" [default] -colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. -colvars: Initializing atom group "group2". -colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] -colvars: # atomsOfGroup = "" [default] -colvars: # indexGroup = "group2" -colvars: # psfSegID = [default] -colvars: # atomsFile = "" [default] -colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] -colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] -colvars: # width = 0.05 -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputTotalForce = off [default] -colvars: # outputAppliedForce = on -colvars: # subtractAppliedForce = off [default] -colvars: # runAve = off [default] -colvars: # corrFunc = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = "harmonic1" [default] -colvars: # colvars = { one } -colvars: # outputEnergy = on -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] -colvars: # centers = { ( 1 , 0 , 0 ) } -colvars: # targetCenters = { ( -1 , 0 , 0 ) } -colvars: # targetNumSteps = 10 -colvars: # targetNumStages = 0 [default] -colvars: # outputAccumulatedWork = on -colvars: Error: interpolation between ( 1 , 0 , 0 ) and ( -1 , 0 , 0 ) with lambda = 0.5 is undefined: result = ( 0 , 0 , 0 ) -colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG. diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped new file mode 100644 index 000000000..668eb79a8 --- /dev/null +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped @@ -0,0 +1,20 @@ +configuration { + step 20 + dt 1.000000e+00 +} + +colvar { + name one + x ( -3.10885706960921e-01 , 2.11412551292752e-01 , 9.26636288067383e-01 ) +} + +restraint { + configuration { + step 20 + name harmonic1 + firstStep 0 + centers ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) + accumulatedWork -5.55059495927072e-01 + } +} + diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj new file mode 100644 index 000000000..a0e19b09e --- /dev/null +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj @@ -0,0 +1,22 @@ +# step one fa_one E_harmonic1 x0_one W_harmonic1 + 0 ( -3.30999991751309e-01 , 2.15045331613065e-01 , 9.18800582722965e-01 ) ( 1.11378079309750e+00 , -1.79949933493813e-01 , -7.68852327622577e-01 ) 2.22756158619499e+00 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 + 1 ( -3.30676782623035e-01 , 2.14698535143340e-01 , 9.18998043763632e-01 ) ( 1.11048488664575e+00 , -1.08566615530599e-01 , -7.69017563021407e-01 ) 2.19449259764792e+00 ( 9.96384506389575e-01 , 8.49583158190100e-02 , 0.00000000000000e+00 ) -1.72056748042513e-02 + 2 ( -3.30191402709992e-01 , 2.14462744628538e-01 , 9.19227593549499e-01 ) ( 1.09445346557288e+00 , -3.77530718922370e-03 , -7.69209650282220e-01 ) 2.13853504700783e+00 ( 9.77711878328341e-01 , 2.09951144259006e-01 , 0.00000000000000e+00 ) -4.66529868068846e-02 + 3 ( -3.29533211475485e-01 , 2.14332374411399e-01 , 9.19494152136829e-01 ) ( 1.04314868322252e+00 , 1.54321220161941e-01 , -7.69432706508098e-01 ) 2.03632995237275e+00 ( 9.17059383197694e-01 , 3.98750658543737e-01 , 0.00000000000000e+00 ) -1.00805936302149e-01 + 4 ( -3.28699069057470e-01 , 2.14296787722334e-01 , 9.19800961497998e-01 ) ( 8.99582104322054e-01 , 3.77633009931505e-01 , -7.69689444581524e-01 ) 1.84545470089225e+00 ( 7.46327346241351e-01 , 6.65579065365146e-01 , 0.00000000000000e+00 ) -1.99926587941052e-01 + 5 ( -3.27691834282163e-01 , 2.14340399151662e-01 , 9.20150126357812e-01 ) ( 5.94442023130421e-01 , 5.93742346795334e-01 , -7.69981625736217e-01 ) 1.55205903108605e+00 ( 3.82683432365090e-01 , 9.23879532511287e-01 , 0.00000000000000e+00 ) -3.39925761052374e-01 + 6 ( -3.26525219575073e-01 , 2.14443853732057e-01 , 9.20540664271815e-01 ) ( 2.25456984382301e-01 , 6.55988226043346e-01 , -7.70308427862655e-01 ) 1.28408996002688e+00 ( -5.70976569767208e-02 , 9.98368598047719e-01 , 0.00000000000000e+00 ) -4.54082888609383e-01 + 7 ( -3.25217810308112e-01 , 2.14583532852425e-01 , 9.20970837370527e-01 ) ( -3.45446132883389e-02 , 5.99010452204356e-01 , -7.70668396711657e-01 ) 1.13998163222684e+00 ( -3.66499613950964e-01 , 9.30418203268721e-01 , 0.00000000000000e+00 ) -5.12696099304228e-01 + 8 ( -3.23796753972870e-01 , 2.14734087750040e-01 , 9.21436342714346e-01 ) ( -1.83336242013975e-01 , 5.23058985434512e-01 , -7.71057931583365e-01 ) 1.07759705274523e+00 ( -5.42888821389189e-01 , 8.39804577036026e-01 , 0.00000000000000e+00 ) -5.38347687996117e-01 + 9 ( -3.22294835838418e-01 , 2.14869803103587e-01 , 9.21931128938661e-01 ) ( -2.69600896841635e-01 , 4.60035016859046e-01 , -7.71471968695871e-01 ) 1.05101082552318e+00 ( -6.44475639903469e-01 , 7.64624842371090e-01 , 0.00000000000000e+00 ) -5.49741754293482e-01 + 10 ( -3.20749363670832e-01 , 2.14966659531062e-01 , 9.22447386572705e-01 ) ( -3.23303886977151e-01 , 4.11822853801310e-01 , -7.71903973084039e-01 ) 1.03962620687203e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 11 ( -3.19200405834927e-01 , 2.15004012199105e-01 , 9.22975826147741e-01 ) ( -3.24600054894236e-01 , 4.11791597088692e-01 , -7.72346171320430e-01 ) 1.04141506145259e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 12 ( -3.17690153264675e-01 , 2.14966086384984e-01 , 9.23505575631783e-01 ) ( -3.25863834245023e-01 , 4.11823333409948e-01 , -7.72789465688676e-01 ) 1.04324719728625e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 13 ( -3.16259183478589e-01 , 2.14842289084984e-01 , 9.24025389091761e-01 ) ( -3.27061269762020e-01 , 4.11926926990588e-01 , -7.73224445591986e-01 ) 1.04508713028118e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 14 ( -3.14945243314928e-01 , 2.14626623157147e-01 , 9.24524151304584e-01 ) ( -3.28160774890971e-01 , 4.12107396239002e-01 , -7.73641809811676e-01 ) 1.04689728740514e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 15 ( -3.13782120484417e-01 , 2.14317396540321e-01 , 9.24991261798987e-01 ) ( -3.29134076075543e-01 , 4.12366157071962e-01 , -7.74032687873392e-01 ) 1.04863968622001e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 16 ( -3.12796860422836e-01 , 2.13914513281047e-01 , 9.25418124480686e-01 ) ( -3.29958541695074e-01 , 4.12703289783323e-01 , -7.74389886565438e-01 ) 1.05028243433359e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 17 ( -3.12009150054690e-01 , 2.13419871583257e-01 , 9.25798168444686e-01 ) ( -3.30617697731138e-01 , 4.13117205956034e-01 , -7.74707907354513e-01 ) 1.05179998760465e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 18 ( -3.11428813565447e-01 , 2.12836854235221e-01 , 9.26127727454735e-01 ) ( -3.31103323305337e-01 , 4.13605074872870e-01 , -7.74983682334123e-01 ) 1.05317671671676e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 19 ( -3.11057435290019e-01 , 2.12166908276454e-01 , 9.26406214888051e-01 ) ( -3.31414092646215e-01 , 4.14165685651166e-01 , -7.75216720618321e-01 ) 1.05440903429928e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 20 ( -3.10885706960921e-01 , 2.11412551292752e-01 , 9.26636288067383e-01 ) ( -3.31557794912004e-01 , 4.14796931575128e-01 , -7.75409245854786e-01 ) 1.05550497653936e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out new file mode 100644 index 000000000..e69de29bb diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped new file mode 100644 index 000000000..bdc922a18 --- /dev/null +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped @@ -0,0 +1,20 @@ +configuration { + step 40 + dt 1.000000e+00 +} + +colvar { + name one + x ( -3.08639969524265e-01 , 1.95850147681302e-01 , 9.30797555253167e-01 ) +} + +restraint { + configuration { + step 40 + name harmonic1 + firstStep 0 + centers ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) + accumulatedWork -5.55059495927072e-01 + } +} + diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj new file mode 100644 index 000000000..fb24bade0 --- /dev/null +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj @@ -0,0 +1,22 @@ +# step one fa_one E_harmonic1 x0_one W_harmonic1 + 20 ( -3.10885706960921e-01 , 2.11412551292752e-01 , 9.26636288067383e-01 ) ( -3.31557794912004e-01 , 4.14796931575128e-01 , -7.75409245854786e-01 ) 1.05550497653936e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 21 ( -3.10897091374193e-01 , 2.10576898213230e-01 , 9.26822727663689e-01 ) ( -3.31548268434978e-01 , 4.15496206072072e-01 , -7.75565258508975e-01 ) 1.05648042754375e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 22 ( -3.11064705021948e-01 , 2.09664336230821e-01 , 9.26973362833311e-01 ) ( -3.31408009334537e-01 , 4.16259837938952e-01 , -7.75691310018915e-01 ) 1.05736200976446e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 23 ( -3.11357671914477e-01 , 2.08681834875126e-01 , 9.27096700421886e-01 ) ( -3.31162854638869e-01 , 4.17081995073397e-01 , -7.75794518913034e-01 ) 1.05817801443891e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 24 ( -3.11740853393812e-01 , 2.07639270301561e-01 , 9.27202013454421e-01 ) ( -3.30842208376961e-01 , 4.17954413108557e-01 , -7.75882644858660e-01 ) 1.05895833756397e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 25 ( -3.12177635464617e-01 , 2.06549698371545e-01 , 9.27298412604241e-01 ) ( -3.30476709140112e-01 , 4.18866166899594e-01 , -7.75963311667228e-01 ) 1.05973085816301e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 26 ( -3.12630971759631e-01 , 2.05428922422296e-01 , 9.27394648102437e-01 ) ( -3.30097357328444e-01 , 4.19804032213926e-01 , -7.76043841532119e-01 ) 1.06052071553325e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 27 ( -3.13066251934311e-01 , 2.04294843741088e-01 , 9.27498322758918e-01 ) ( -3.29733114878271e-01 , 4.20753029254360e-01 , -7.76130596484663e-01 ) 1.06134768340546e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 28 ( -3.13451817595270e-01 , 2.03166745880829e-01 , 9.27615885706156e-01 ) ( -3.29410473533181e-01 , 4.21697021543826e-01 , -7.76228973158911e-01 ) 1.06222640633799e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 29 ( -3.13760105408211e-01 , 2.02063706631599e-01 , 9.27752582705393e-01 ) ( -3.29152498291312e-01 , 4.22620044787581e-01 , -7.76343361207873e-01 ) 1.06316692624188e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 30 ( -3.13968838424589e-01 , 2.01004279720987e-01 , 9.27912090681096e-01 ) ( -3.28977830503207e-01 , 4.23506573226381e-01 , -7.76476837481941e-01 ) 1.06417364922862e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 31 ( -3.14060414173331e-01 , 2.00005821063283e-01 , 9.28096831041933e-01 ) ( -3.28901199916659e-01 , 4.24342083431148e-01 , -7.76631428215889e-01 ) 1.06524686707691e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 32 ( -3.14021712205281e-01 , 1.99084361748090e-01 , 9.28308020632710e-01 ) ( -3.28933585723524e-01 , 4.25113160586101e-01 , -7.76808151665451e-01 ) 1.06638313529438e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 33 ( -3.13844134973355e-01 , 1.98254442559562e-01 , 9.28545655823247e-01 ) ( -3.29082182351199e-01 , 4.25807636963061e-01 , -7.77007004792893e-01 ) 1.06757542057160e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 34 ( -3.13523097439585e-01 , 1.97529381671397e-01 , 9.28808597477653e-01 ) ( -3.29350826559459e-01 , 4.26414367914278e-01 , -7.77227034369300e-01 ) 1.06881338799430e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 35 ( -3.13056497779899e-01 , 1.96920823570625e-01 , 9.29095161133697e-01 ) ( -3.29741277154683e-01 , 4.26923609333004e-01 , -7.77466830836678e-01 ) 1.07008574464239e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 36 ( -3.12445608882840e-01 , 1.96438331222221e-01 , 9.29402885468116e-01 ) ( -3.30252468983742e-01 , 4.27327358930148e-01 , -7.77724334559719e-01 ) 1.07137966721610e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 37 ( -3.11693070648280e-01 , 1.96088634007210e-01 , 9.29729357029793e-01 ) ( -3.30882192978423e-01 , 4.27619985559669e-01 , -7.77997525962531e-01 ) 1.07268406797811e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 38 ( -3.10803479062424e-01 , 1.95875135976297e-01 , 9.30072109306026e-01 ) ( -3.31626603217466e-01 , 4.27798640711938e-01 , -7.78284341067283e-01 ) 1.07398947957346e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 39 ( -3.09783190290509e-01 , 1.95797219440961e-01 , 9.30428838693547e-01 ) ( -3.32480380861805e-01 , 4.27863841268707e-01 , -7.78582852218760e-01 ) 1.07528911100899e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 40 ( -3.08639969524265e-01 , 1.95850147681302e-01 , 9.30797555253167e-01 ) ( -3.33437027998998e-01 , 4.27819550917190e-01 , -7.78891394235850e-01 ) 1.07657937834902e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/gromacs-version.txt b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/gromacs-version.txt index 08734a593..1fcba9718 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/gromacs-version.txt +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/gromacs-version.txt @@ -1 +1,3 @@ - :-) GROMACS - gmx mdrun, 2020.3-MODIFIED (double precision) (-: + :-) GROMACS - gmx mdrun, 2020.7-Colvars-2023-01-31-dev-20230405-4336830f69-unknown (double precision) (-: +colvars: Initializing the collective variables module, version 2023-01-31. +colvars: Using GROMACS interface, version "2023-01-31". diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/test.in b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/test.in index 77d51bb9e..826133b94 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/test.in +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/test.in @@ -25,9 +25,8 @@ harmonic { centers (1.0, 0.0, 0.0) forceConstant 0.004184 - targetCenters (-1.0, 0.0, 0.0) + targetCenters (-0.707106781, 0.707106781, 0.0) targetNumSteps 10 - lambda = -0.5 outputEnergy yes outputCenters yes From 0bee6e5eaa3f47d90b6e1ba7a887be30c3f72cab Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 25 Sep 2023 09:32:35 -0400 Subject: [PATCH 129/162] Fix error in Doxygen comment --- .../applied_forces/colvars/colvarsforceprovider.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h index 33aa6880a..0647db0f7 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h @@ -86,12 +86,12 @@ struct ColvarsForceProviderState */ std::vector colvarStateFile_; - /*! \brief String naming variable holding the content of the formatted Colvars state file. + /*! \brief String naming variable holding the content of the unformatted Colvars state file. * \note Changing this name will break backwards compability for checkpoint file writing. */ static const std::string colvarStateFileName_; - /*! \brief String naming variable holding the size of the formatted Colvars state file. + /*! \brief String naming variable holding the size of the unformatted Colvars state file. * \note Changing this name will break backwards compability for checkpoint file writing. */ static const std::string colvarStateFileSizeName_; From f71b65f9fbb90e9b8ac3d8f148260600dcb4166a Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 26 Sep 2023 18:21:08 -0400 Subject: [PATCH 130/162] Update GROMACS patch from GROMACS MR #3671 --- gromacs/gromacs-mdmodules.patch | 85 ++++++++++++++++++++------------- 1 file changed, 51 insertions(+), 34 deletions(-) diff --git a/gromacs/gromacs-mdmodules.patch b/gromacs/gromacs-mdmodules.patch index fadc11dbc..b912f6e8e 100644 --- a/gromacs/gromacs-mdmodules.patch +++ b/gromacs/gromacs-mdmodules.patch @@ -1,85 +1,92 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -index 31e2bbbec5..bceb9ff32b 100644 +index 31e2bbbec5..5dc774e726 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -646,6 +646,9 @@ include(gmxManageLmfit) +@@ -646,6 +646,8 @@ include(gmxManageLmfit) include(gmxManageMuparser) +include(gmxManageColvars) -+include(gmxManageLepton) + ################################################## # Process SIMD instruction settings ################################################## diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt -index 96107341de..4628c15976 100644 +index 96107341de..a722ddd5da 100644 --- a/src/gromacs/CMakeLists.txt +++ b/src/gromacs/CMakeLists.txt -@@ -146,6 +146,11 @@ if (WIN32) +@@ -146,6 +146,14 @@ if (WIN32) endif() list(APPEND libgromacs_object_library_dependencies thread_mpi) ++ +gmx_manage_colvars() -+gmx_manage_lepton() -+list(APPEND libgromacs_object_library_dependencies colvars) -+list(APPEND libgromacs_object_library_dependencies lepton) ++if(NOT GMX_USE_COLVARS STREQUAL "NONE") ++ list(APPEND libgromacs_object_library_dependencies colvars) ++endif() ++ ++ + # This code is here instead of utility/CMakeLists.txt, because CMake # custom commands and source file properties can only be set in the directory # that contains the target that uses them. -@@ -218,6 +223,8 @@ add_library(legacy_modules INTERFACE) - target_include_directories(legacy_modules INTERFACE $) - target_link_libraries(libgromacs PRIVATE $) +@@ -210,6 +218,8 @@ if(GMX_GPU_FFT_ROCFFT) + target_link_libraries(libgromacs PRIVATE roc::rocfft) + endif() +gmx_include_colvars_headers() + - # Add these contents first because linking their tests can take a lot - # of time, so we want lots of parallel work still available after - # linking starts. + target_link_libraries(libgromacs PRIVATE $) + # As long as the libgromacs target has source files that reference headers from + # modules that don't provide CMake targets, libgromacs needs to use `src/` diff --git a/src/gromacs/applied_forces/CMakeLists.txt b/src/gromacs/applied_forces/CMakeLists.txt -index 3c4987f892..53e6b91d70 100644 +index 3c4987f892..cc5f50c7a6 100644 --- a/src/gromacs/applied_forces/CMakeLists.txt +++ b/src/gromacs/applied_forces/CMakeLists.txt -@@ -67,6 +67,7 @@ gmx_add_libgromacs_sources( +@@ -67,6 +67,10 @@ gmx_add_libgromacs_sources( add_subdirectory(awh) add_subdirectory(densityfitting) add_subdirectory(qmmm) -+add_subdirectory(colvars) ++if(NOT GMX_USE_COLVARS STREQUAL "NONE") ++ # Build Colvars interface files if the library is available (default) ++ add_subdirectory(colvars) ++endif() if (BUILD_TESTING) add_subdirectory(tests) diff --git a/src/gromacs/mdrun/mdmodules.cpp b/src/gromacs/mdrun/mdmodules.cpp -index 5221ff025c..715dafc20b 100644 +index 5221ff025c..5776736f7f 100644 --- a/src/gromacs/mdrun/mdmodules.cpp +++ b/src/gromacs/mdrun/mdmodules.cpp -@@ -40,6 +40,7 @@ +@@ -37,6 +37,7 @@ + + #include + ++#include "gromacs/applied_forces/colvars/colvarsMDModule.h" #include "gromacs/applied_forces/densityfitting/densityfitting.h" #include "gromacs/applied_forces/electricfield.h" #include "gromacs/applied_forces/qmmm/qmmm.h" -+#include "gromacs/applied_forces/colvars/colvarsMDModule.h" - #include "gromacs/imd/imd.h" - #include "gromacs/mdrunutility/mdmodulesnotifiers.h" - #include "gromacs/mdtypes/iforceprovider.h" -@@ -67,7 +68,8 @@ public: +@@ -67,6 +68,9 @@ public: field_(createElectricFieldModule()), imd_(createInteractiveMolecularDynamicsModule()), qmmm_(QMMMModuleInfo::create()), -- swapCoordinates_(createSwapCoordinatesModule()) -+ swapCoordinates_(createSwapCoordinatesModule()), -+ colvars_(ColvarsModuleInfo::create()) ++#ifdef HAVE_COLVARS ++ colvars_(ColvarsModuleInfo::create()), ++#endif + swapCoordinates_(createSwapCoordinatesModule()) { } - -@@ -78,6 +80,7 @@ public: +@@ -78,6 +82,9 @@ public: field_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); densityFitting_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); qmmm_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); ++#ifdef HAVE_COLVARS + colvars_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); ++#endif // In future, other sections would also go here. } -@@ -106,6 +109,7 @@ public: +@@ -106,6 +113,7 @@ public: std::unique_ptr imd_; std::unique_ptr qmmm_; std::unique_ptr swapCoordinates_; @@ -87,42 +94,52 @@ index 5221ff025c..715dafc20b 100644 /*! \brief List of registered MDModules * -@@ -129,6 +133,7 @@ void MDModules::initMdpTransform(IKeyValueTreeTransformRules* rules) +@@ -129,6 +137,9 @@ void MDModules::initMdpTransform(IKeyValueTreeTransformRules* rules) impl_->field_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); impl_->densityFitting_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); impl_->qmmm_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); ++#ifdef HAVE_COLVARS + impl_->colvars_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); ++#endif } void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder* builder) -@@ -136,6 +141,7 @@ void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder* builder) +@@ -136,6 +147,9 @@ void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder* builder) impl_->field_->mdpOptionProvider()->buildMdpOutput(builder); impl_->densityFitting_->mdpOptionProvider()->buildMdpOutput(builder); impl_->qmmm_->mdpOptionProvider()->buildMdpOutput(builder); ++#ifdef HAVE_COLVARS + impl_->colvars_->mdpOptionProvider()->buildMdpOutput(builder); ++#endif } void MDModules::assignOptionsToModules(const KeyValueTreeObject& params, IKeyValueTreeErrorHandler* errorHandler) -@@ -173,6 +179,7 @@ ForceProviders* MDModules::initForceProviders() +@@ -173,6 +187,9 @@ ForceProviders* MDModules::initForceProviders() impl_->field_->initForceProviders(impl_->forceProviders_.get()); impl_->densityFitting_->initForceProviders(impl_->forceProviders_.get()); impl_->qmmm_->initForceProviders(impl_->forceProviders_.get()); ++#ifdef HAVE_COLVARS + impl_->colvars_->initForceProviders(impl_->forceProviders_.get()); ++#endif for (auto&& module : impl_->modules_) { module->initForceProviders(impl_->forceProviders_.get()); -@@ -184,12 +191,14 @@ void MDModules::subscribeToPreProcessingNotifications() +@@ -184,12 +201,18 @@ void MDModules::subscribeToPreProcessingNotifications() { impl_->densityFitting_->subscribeToPreProcessingNotifications(&impl_->notifiers_); impl_->qmmm_->subscribeToPreProcessingNotifications(&impl_->notifiers_); ++#ifdef HAVE_COLVARS + impl_->colvars_->subscribeToPreProcessingNotifications(&impl_->notifiers_); ++#endif } void MDModules::subscribeToSimulationSetupNotifications() { impl_->densityFitting_->subscribeToSimulationSetupNotifications(&impl_->notifiers_); impl_->qmmm_->subscribeToSimulationSetupNotifications(&impl_->notifiers_); ++#ifdef HAVE_COLVARS + impl_->colvars_->subscribeToSimulationSetupNotifications(&impl_->notifiers_); ++#endif } void MDModules::add(std::shared_ptr module) From d39f0139a2a787bcc5254f68de40baa889200fa5 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 26 Sep 2023 18:27:32 -0400 Subject: [PATCH 131/162] Update GROMACS interface files from GROMACS MR #3671 --- gromacs/cmake/gmxManageColvars.cmake | 63 +++++-- .../applied_forces/colvars/CMakeLists.txt | 3 + .../colvars/colvarproxygromacs.cpp | 16 +- .../colvars/colvarproxygromacs.h | 1 - .../colvars/colvarsMDModule.cpp | 18 +- .../colvars/colvarsforceprovider.cpp | 22 ++- .../applied_forces/colvars/colvarsoptions.cpp | 155 +++++++++++------- .../applied_forces/colvars/colvarsoptions.h | 54 ++++-- .../colvars/colvarssimulationsparameters.cpp | 10 +- 9 files changed, 237 insertions(+), 105 deletions(-) diff --git a/gromacs/cmake/gmxManageColvars.cmake b/gromacs/cmake/gmxManageColvars.cmake index 275d5bf72..d548d60f2 100644 --- a/gromacs/cmake/gmxManageColvars.cmake +++ b/gromacs/cmake/gmxManageColvars.cmake @@ -1,18 +1,57 @@ -# This file is part of the Collective Variables module (Colvars). -# The original version of Colvars and its updates are located at: -# https://github.com/Colvars/colvars -# Please update all Colvars source files before making any changes. -# If you wish to distribute your changes, please submit them to the -# Colvars repository at GitHub. +# +# This file is part of the GROMACS molecular simulation package. +# +# Copyright 2023- The GROMACS Authors +# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. +# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. +# +# GROMACS is free software; you can redistribute it and/or +# modify it under the terms of the GNU Lesser General Public License +# as published by the Free Software Foundation; either version 2.1 +# of the License, or (at your option) any later version. +# +# GROMACS is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with GROMACS; if not, see +# https://www.gnu.org/licenses, or write to the Free Software Foundation, +# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +# +# If you want to redistribute modifications to GROMACS, please +# consider that scientific software is very special. Version +# control is crucial - bugs must be traceable. We will be happy to +# consider code for inclusion in the official distribution, but +# derived work must not be called official GROMACS. Details are found +# in the README & COPYING files - if they are missing, get the +# official version at https://www.gromacs.org. +# +# To help us fund GROMACS development, we humbly ask that you cite +# the research papers on the package. Check out https://www.gromacs.org. + +# Build Colvars library as bundled in a GROMACS worktree; not supporting external linkage yet +gmx_option_multichoice(GMX_USE_COLVARS + "Build the collective variables (Colvars) library interfaced with GROMACS" + INTERNAL + INTERNAL NONE) +mark_as_advanced(GMX_USE_COLVARS) function(gmx_manage_colvars) - file(GLOB COLVARS_SOURCES ${PROJECT_SOURCE_DIR}/src/external/colvars/*.cpp) - add_library(colvars OBJECT ${COLVARS_SOURCES}) - # Colvars requires a correct definition of __cplusplus, which MSVC doesn't give by default - # See: https://learn.microsoft.com/en-us/cpp/build/reference/zc-cplusplus - target_compile_options(colvars PRIVATE $<$:/Zc:__cplusplus>) + if(GMX_USE_COLVARS STREQUAL "INTERNAL") + file(GLOB COLVARS_SOURCES ${PROJECT_SOURCE_DIR}/src/external/colvars/*.cpp) + add_library(colvars OBJECT ${COLVARS_SOURCES}) + # Set correctly the value of __cplusplus, which MSVC doesn't do by default + target_compile_options(colvars PRIVATE $<$:/Zc:__cplusplus>) + set(HAVE_COLVARS 1 CACHE INTERNAL "Is Colvars available?") + else() + set(HAVE_COLVARS 0 CACHE INTERNAL "Is Colvars available?") + endif() endfunction() function(gmx_include_colvars_headers) - target_include_directories(libgromacs PRIVATE ${PROJECT_SOURCE_DIR}/src/external/colvars) + if(GMX_USE_COLVARS STREQUAL "INTERNAL") + target_include_directories(libgromacs PRIVATE ${PROJECT_SOURCE_DIR}/src/external/colvars) + endif() endfunction() diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/CMakeLists.txt b/gromacs/gromacs-mdmodules/applied_forces/colvars/CMakeLists.txt index 3ec3bf57a..caac6e083 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/CMakeLists.txt +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/CMakeLists.txt @@ -40,3 +40,6 @@ gmx_add_libgromacs_sources( colvarproxygromacs.cpp ) +if (BUILD_TESTING) + add_subdirectory(tests) +endif() diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp index 21e6b5291..934b19a36 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp @@ -43,6 +43,7 @@ #include + namespace gmx { @@ -103,13 +104,15 @@ ColvarProxyGromacs::ColvarProxyGromacs(const std::string& colvarsConfigString, cvm::log("Initializing the colvars proxy object.\n"); } + int error_code = colvarproxy::setup(); + error_code |= colvars->read_config_string(colvarsConfigString); + error_code |= colvars->update_engine_parameters(); + error_code |= colvars->setup_input(); - add_config("config", colvarsConfigString); - - colvarproxy::parse_module_config(); - colvars->update_engine_parameters(); - colvars->setup_input(); - + if (error_code != COLVARS_OK) + { + error("Error when initializing Colvars module."); + } // Citation Reporter cvm::log(std::string("\n") + colvars->feature_report(0) + std::string("\n")); @@ -119,6 +122,7 @@ ColvarProxyGromacs::ColvarProxyGromacs(const std::string& colvarsConfigString, // cvm::log("Initializing step number to "+cvm::to_str(step)+".\n"); // } + // colvars->it = colvars->it_restart = step; colvars->set_initial_step(static_cast(0L)); } } diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h index 3e2d76724..008a19410 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h @@ -121,7 +121,6 @@ class ColvarProxyGromacs : public colvarproxy void log(std::string const& message) override; /// Print a message to the main log and let the rest of the program handle the error void error(std::string const& message) override; - /// Request to set the units used internally by Colvars int set_unit_system(std::string const& units_in, bool colvars_defined) override; diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp index ddc51bb58..8130e1b52 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp @@ -81,7 +81,7 @@ class ColvarsMDModule final : public IMDModule * * \param[in] notifier allows the module to subscribe to notifications from MdModules. * - * The Colvars mdmodule code subscribes to these notifications: + * The Colvars MDModule subscribes to these notifications: * - storing its internal parameters in a tpr file by writing to a * key-value-tree during pre-processing by a function taking a * KeyValueTreeObjectBuilder as parameter @@ -105,10 +105,10 @@ class ColvarsMDModule final : public IMDModule notifier->preProcessingNotifier_.subscribe(writeInternalParametersFunction); // Access of the topology during pre-processing - const auto gettTopologyFunction = [this](gmx_mtop_t* mtop) { - colvarsOptions_.getTopology(mtop); + const auto processTopologyFunction = [this](gmx_mtop_t* mtop) { + colvarsOptions_.processTopology(mtop); }; - notifier->preProcessingNotifier_.subscribe(gettTopologyFunction); + notifier->preProcessingNotifier_.subscribe(processTopologyFunction); // Set Logger during pre-processing const auto setLoggerFunction = [this](const MDLogger& logger) { @@ -123,15 +123,15 @@ class ColvarsMDModule final : public IMDModule notifier->preProcessingNotifier_.subscribe(processCoordinatesFunction); // Notification for the temperature - const auto getTemperatureFunction = [this](const EnsembleTemperature& temp) { - colvarsOptions_.getTemperature(temp); + const auto processTemperatureFunction = [this](const EnsembleTemperature& temp) { + colvarsOptions_.processTemperature(temp); }; - notifier->preProcessingNotifier_.subscribe(getTemperatureFunction); + notifier->preProcessingNotifier_.subscribe(processTemperatureFunction); } /*! \brief Request to be notified. - * The Colvars mdmodule code subscribes to these notifications: + * The Colvars MDModule subscribes to these notifications: * - the LocalAtomSetManager sets in the simulation parameter setup * by taking a LocalAtomSetManager * as parameter * - the type of periodic boundary conditions that are used @@ -233,7 +233,7 @@ class ColvarsMDModule final : public IMDModule { colvarsForceProvider_ = std::make_unique( - colvarsOptions_.colvarsInputContent(), + colvarsOptions_.colvarsConfigContent(), ColvarsSimulationsParameters_.localAtomSetManager(), ColvarsSimulationsParameters_.periodicBoundaryConditionType(), ColvarsSimulationsParameters_.simulationTimeStep(), diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp index e0aa6842b..19031dc00 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp @@ -40,10 +40,11 @@ */ #include "colvarsforceprovider.h" -#include "external/colvars/colvars_memstream.h" #include +#include "external/colvars/colvars_memstream.h" + #include "gromacs/domdec/localatomsetmanager.h" #include "gromacs/fileio/checkpoint.h" #include "gromacs/gmxlib/network.h" @@ -84,12 +85,14 @@ void ColvarsForceProviderState::writeState(KeyValueTreeObjectBuilder kvtBuilder, } } + writeKvtCheckpointValue( static_cast(colvarStateFile_.size()), colvarStateFileSizeName_, identifier, kvtBuilder); - // Write formatted Colvars state file, one character at a time + // Write unformatted Colvars state file, one character at a time auto charArrayAdder = kvtBuilder.addUniformArray(colvarStateFileName_); - for (const unsigned char &c : colvarStateFile_) { + for (const unsigned char& c : colvarStateFile_) + { charArrayAdder.addValue(c); } } @@ -130,7 +133,8 @@ void ColvarsForceProviderState::readState(const KeyValueTreeObject& kvtData, con auto charArray = kvtData[colvarStateFileName_].asArray().values(); colvarStateFile_.resize(colvarStateFileSize_); auto it = colvarStateFile_.begin(); - for (const auto &c: charArray) { + for (const auto& c : charArray) + { *it = c.cast(); it++; } @@ -229,9 +233,15 @@ ColvarsForceProvider::ColvarsForceProvider(const std::string& colvarsConfi copy_rvec(stateToCheckpoint_.xOldWhole_[i], xa_old_whole[i]); } + int error_code = colvarproxy::setup(); // Read input state file - colvars->set_input_state_buffer(stateToCheckpoint_.colvarStateFile_); - colvars->setup_input(); + error_code |= colvars->set_input_state_buffer(stateToCheckpoint_.colvarStateFile_); + error_code |= colvars->setup_input(); + + if (error_code != COLVARS_OK) + { + error("Error when initializing Colvars module."); + } } else { diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp index 0b8463250..47a8e3fad 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp @@ -50,6 +50,7 @@ #include "gromacs/utility/keyvaluetreetransform.h" #include "gromacs/utility/path.h" #include "gromacs/utility/strconvert.h" +#include "gromacs/utility/textreader.h" #include "colvarspreprocessor.h" @@ -78,7 +79,10 @@ void colvarsMdpTransformFromString(IKeyValueTreeTransformRules* rules, TransformWithFunctionType transformationFunction, const std::string& optionTag) { - rules->addRule().from("/colvars-" + optionTag).to("/colvars/" + optionTag).transformWith(transformationFunction); + rules->addRule() + .from("/" + c_colvarsModuleName + "-" + optionTag) + .to("/" + c_colvarsModuleName + "/" + optionTag) + .transformWith(transformationFunction); } } // namespace @@ -88,24 +92,32 @@ void ColvarsOptions::initMdpTransform(IKeyValueTreeTransformRules* rules) { const auto& stringIdentityTransform = [](std::string s) { return s; }; colvarsMdpTransformFromString(rules, &fromStdString, c_activeTag_); - colvarsMdpTransformFromString(rules, stringIdentityTransform, colvarsFileNameTag_); + colvarsMdpTransformFromString(rules, stringIdentityTransform, c_colvarsFileNameTag_); } void ColvarsOptions::buildMdpOutput(KeyValueTreeObjectBuilder* builder) const { - builder->addValue("comment-colvars-module", "; Colvars bias"); - builder->addValue("colvars-" + c_activeTag_, active_); - builder->addValue("comment-colvars-" + colvarsFileNameTag_, "; colvars input file"); - builder->addValue("colvars-" + colvarsFileNameTag_, colvarsFileName_); + // new empty line before writing colvars mdp values + builder->addValue("comment-" + c_colvarsModuleName + "empty-line", ""); + + builder->addValue("comment-" + c_colvarsModuleName + "-module", "; Colvars bias"); + builder->addValue(c_colvarsModuleName + "-" + c_activeTag_, active_); + + if (active_) + { + builder->addValue("comment-" + c_colvarsModuleName + "-" + c_colvarsFileNameTag_, + "; colvars config file"); + builder->addValue(c_colvarsModuleName + "-" + c_colvarsFileNameTag_, colvarsFileName_); + } } void ColvarsOptions::initMdpOptions(IOptionsContainerWithSections* options) { - auto section = options->addSection(OptionSection("colvars")); + auto section = options->addSection(OptionSection(c_colvarsModuleName.c_str())); section.addOption(BooleanOption(c_activeTag_.c_str()).store(&active_)); - section.addOption(StringOption(colvarsFileNameTag_.c_str()).store(&colvarsFileName_)); + section.addOption(StringOption(c_colvarsFileNameTag_.c_str()).store(&colvarsFileName_)); } @@ -113,12 +125,10 @@ void ColvarsOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder tree { // Copy the content of the colvars input file into a string for latter save in KVT - std::ifstream f(colvarsFileName_); - colvarsConfigString = - std::string((std::istreambuf_iterator(f)), std::istreambuf_iterator()); + colvarsConfigString = TextReader::readFileToString(colvarsFileName_); // Write colvars input file as a string - treeBuilder.addValue("colvars-configString", colvarsConfigString); + treeBuilder.addValue(c_colvarsModuleName + "-" + c_configStringTag_, colvarsConfigString); ColvarsPreProcessor colvarsPreProcess( @@ -127,13 +137,14 @@ void ColvarsOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder tree colvarsAtomCoords_ = colvarsPreProcess.getColvarsCoords(); // Save other colvars input files into the KVT - if (!colvarsPreProcess.inputStreamsToKVT(treeBuilder, "colvars-inputStreams")) + if (!colvarsPreProcess.inputStreamsToKVT(treeBuilder, c_colvarsModuleName + "-" + c_inputStreamsTag_)) { - GMX_THROW(InternalError("Cannot save colvars input files into the tpr")); + GMX_THROW(InternalError("Cannot save colvars input files into the tpr.")); } // Write colvars atoms coords - auto DoubleArrayAdder = treeBuilder.addUniformArray("colvars-startingCoords"); + auto DoubleArrayAdder = + treeBuilder.addUniformArray(c_colvarsModuleName + "-" + c_startingCoordsTag_); for (const auto& indexValue : colvarsAtomCoords_) { for (int j = 0; j < DIM; j++) @@ -143,7 +154,7 @@ void ColvarsOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder tree } // Write ensemble temperature - treeBuilder.addValue("colvars-ensTemp", ensembleTemperature); + treeBuilder.addValue(c_colvarsModuleName + "-" + c_ensTempTag_, ensembleTemperature); } @@ -159,30 +170,31 @@ void ColvarsOptions::readInternalParametersFromKvt(const KeyValueTreeObject& tre // Retrieve the content of all inputfiles listed in the KVT as "colvars-inputStreams-filename" for (const auto& a : tree.properties()) { - std::size_t pos = a.key().find("colvars-inputStreams"); + std::size_t pos = a.key().find(c_colvarsModuleName + "-" + c_inputStreamsTag_); if (pos != std::string::npos) { - std::string filename = a.key().substr(pos + std::string("colvars-inputStreams").size() + 1); + std::string filename = a.key().substr( + pos + std::string(c_colvarsModuleName + "-" + c_inputStreamsTag_).size() + 1); inputFiles[filename] = tree[a.key()].cast(); } } - if (!tree.keyExists("colvars-configString")) + if (!tree.keyExists(c_colvarsModuleName + "-" + c_configStringTag_)) { GMX_THROW(InconsistentInputError( "Cannot find colvars-configString required for colvars simulation.")); } - colvarsConfigString = tree["colvars-configString"].cast(); + colvarsConfigString = tree[c_colvarsModuleName + "-" + c_configStringTag_].cast(); - if (!tree.keyExists("colvars-startingCoords")) + if (!tree.keyExists(c_colvarsModuleName + "-" + c_startingCoordsTag_)) { GMX_THROW(InconsistentInputError( "Cannot find colvars-startingCoords required for colvars simulation.")); } - auto kvtDoubleArray = tree["colvars-startingCoords"].asArray().values(); + auto kvtDoubleArray = tree[c_colvarsModuleName + "-" + c_startingCoordsTag_].asArray().values(); // Make sure the coordinates saved are consistent with the dimensions @@ -202,51 +214,21 @@ void ColvarsOptions::readInternalParametersFromKvt(const KeyValueTreeObject& tre colvarsAtomCoords_.push_back(x); } - ensembleTemperature = tree["colvars-ensTemp"].cast(); -} - -bool ColvarsOptions::isActive() const -{ - return active_; -} - -const std::string& ColvarsOptions::colvarsFileName() const -{ - return colvarsFileName_; + if (!tree.keyExists(c_colvarsModuleName + "-" + c_ensTempTag_)) + { + GMX_THROW(InconsistentInputError( + "Cannot find ensemble temperature required for colvars simulation.")); + } + ensembleTemperature = tree[c_colvarsModuleName + "-" + c_ensTempTag_].cast(); } -void ColvarsOptions::getTopology(gmx_mtop_t* mtop) +void ColvarsOptions::processTopology(gmx_mtop_t* mtop) { gmx_atoms = gmx_mtop_global_atoms(*mtop); } -const std::string& ColvarsOptions::colvarsInputContent() const -{ - return colvarsConfigString; -} - -const std::vector& ColvarsOptions::colvarsAtomCoords() const -{ - return colvarsAtomCoords_; -} - -const std::string& ColvarsOptions::colvarsOutputPrefix() const -{ - return output_prefix_; -} - -const std::map& ColvarsOptions::colvarsInputFiles() const -{ - return inputFiles; -} - -const real& ColvarsOptions::colvarsEnsTemp() const -{ - return ensembleTemperature; -} - void ColvarsOptions::processCoordinates(const CoordinatesAndBoxPreprocessed& coord) { @@ -274,7 +256,8 @@ void ColvarsOptions::processEdrFilename(const EdrOutputFilename& filename) output_prefix_ = stripExtension(std::filesystem::path(filename.edrOutputFilename_).filename()); } -void ColvarsOptions::getTemperature(const EnsembleTemperature& temp) + +void ColvarsOptions::processTemperature(const EnsembleTemperature& temp) { if (temp.constantEnsembleTemperature_) { @@ -286,4 +269,56 @@ void ColvarsOptions::getTemperature(const EnsembleTemperature& temp) } } +bool ColvarsOptions::isActive() const +{ + return active_; +} + +const std::string& ColvarsOptions::colvarsFileName() const +{ + return colvarsFileName_; +} + + +const std::string& ColvarsOptions::colvarsConfigContent() const +{ + return colvarsConfigString; +} + +const std::vector& ColvarsOptions::colvarsAtomCoords() const +{ + return colvarsAtomCoords_; +} + +const std::string& ColvarsOptions::colvarsOutputPrefix() const +{ + return output_prefix_; +} + +const real& ColvarsOptions::colvarsEnsTemp() const +{ + return ensembleTemperature; +} + +const std::map& ColvarsOptions::colvarsInputFiles() const +{ + return inputFiles; +} + +void ColvarsOptions::setParameters(const std::string& colvarsfile, + t_atoms topology, + ArrayRef coords, + PbcType pbcType, + const matrix boxValues, + real temperature) +{ + colvarsFileName_ = colvarsfile; + gmx_atoms = topology; + x = coords; + pbc = pbcType; + copy_mat(boxValues, box); + ensembleTemperature = temperature; +} + + } // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h index f51e24f55..208d7deb6 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h @@ -63,6 +63,10 @@ struct CoordinatesAndBoxPreprocessed; struct MdRunInputFilename; +//! Tag with name of the Colvars MDModule +static const std::string c_colvarsModuleName = "colvars"; + + /*! \internal * \brief Input data storage for colvars */ @@ -92,7 +96,7 @@ class ColvarsOptions final : public IMdpOptionProvider /*! \brief Store the topology of the system. * \param[in,out] mtop topology object */ - void getTopology(gmx_mtop_t* mtop); + void processTopology(gmx_mtop_t* mtop); /*! \brief Process coordinates, PbcType and Box in order to validate the colvars input. * \param[in] coord structure with coordinates and box dimensions @@ -111,16 +115,16 @@ class ColvarsOptions final : public IMdpOptionProvider /*! \brief Store the ensemble temperature of the system if available. * \param[in] temp temperature object */ - void getTemperature(const EnsembleTemperature& temp); + void processTemperature(const EnsembleTemperature& temp); //! Report if this colvars module is active bool isActive() const; - //! Return the file name of the colvars input + //! Return the file name of the colvars config const std::string& colvarsFileName() const; - //! Return the content of the colvars input file - const std::string& colvarsInputContent() const; + //! Return the content of the colvars config file + const std::string& colvarsConfigContent() const; //! Return the colvars atoms coordinates const std::vector& colvarsAtomCoords() const; @@ -131,9 +135,27 @@ class ColvarsOptions final : public IMdpOptionProvider //! Return the ensemble temperature const real& colvarsEnsTemp() const; - + //! Return the map of all others colvars input files const std::map& colvarsInputFiles() const; + /*! \brief Function to set internal paramaters outside the way done + * through the MDModule notifiers and callbacks. + * Use exclusively in the test framework. + * + * \param[in] colvarsfile Name of the colvars input file. + * \param[in] topology Atoms topology + * \param[in] coords Coordinates of each atom in the system + * \param[in] pbcType Periodic boundary conditions + * \param[in] boxValues Matrix with full box of the system + * \param[in] temperature the constant ensemble temperature + */ + void setParameters(const std::string& colvarsfile, + t_atoms topology, + ArrayRef coords, + PbcType pbcType, + const matrix boxValues, + real temperature); + private: //! Indicate if colvars module is active @@ -143,15 +165,27 @@ class ColvarsOptions final : public IMdpOptionProvider * \note Changing this strings will break .tpr backwards compability */ //! \{ - const std::string c_activeTag_ = "active"; - const std::string colvarsFileNameTag_ = "filename"; + const std::string c_activeTag_ = "active"; + const std::string c_colvarsFileNameTag_ = "configfile"; + //! \} + + + /*! \brief This tags for parameters which will be generated during grompp + * and stored into *.tpr file via KVT + */ + //! \{ + const std::string c_inputStreamsTag_ = "inputStreams"; + const std::string c_configStringTag_ = "configString"; + const std::string c_startingCoordsTag_ = "startingCoords"; + const std::string c_ensTempTag_ = "ensTemp"; + //! \} - //! Colvars input filename, default colvars.dat + //! Colvars config filename, default colvars.dat std::string colvarsFileName_ = "colvars.dat"; - //! Content of the colvars input file + //! Content of the colvars config file std::string colvarsConfigString; //! Topology of the system t_atoms gmx_atoms; diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp index 9667f56d8..238605028 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp @@ -53,6 +53,10 @@ void ColvarsSimulationsParameters::setLocalAtomSetManager(LocalAtomSetManager* l LocalAtomSetManager* ColvarsSimulationsParameters::localAtomSetManager() const { + if (localAtomSetManager_ == nullptr) + { + GMX_THROW(InternalError("Local atom manager not set for Colvars simulation.")); + } return localAtomSetManager_; } @@ -77,7 +81,7 @@ PbcType ColvarsSimulationsParameters::periodicBoundaryConditionType() if (pbcType_ == nullptr) { GMX_THROW( - InternalError("Periodic boundary condition enum not set for colvars simulation.")); + InternalError("Periodic boundary condition enum not set for Colvars simulation.")); } return *pbcType_; } @@ -101,6 +105,10 @@ void ColvarsSimulationsParameters::setComm(const t_commrec& cr) const t_commrec* ColvarsSimulationsParameters::comm() const { + if (cr_ == nullptr) + { + GMX_THROW(InternalError("Communication record not set for Colvars simulation.")); + } return cr_; } From c11635b5e5ba7e35d6d9219669f0da0f82d06d0d Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 26 Sep 2023 18:29:48 -0400 Subject: [PATCH 132/162] Add GROMACS test files from GROMACS MR #3671 --- .../applied_forces/colvars/tests/.clang-tidy | 9 + .../colvars/tests/CMakeLists.txt | 44 +++ .../applied_forces/colvars/tests/colvars.cpp | 126 +++++++ .../colvars/tests/colvars_sample.dat | 17 + .../colvars/tests/colvars_sample_alanine.dat | 26 ++ .../colvars/tests/colvarsforceprovider.cpp | 351 ++++++++++++++++++ .../colvars/tests/colvarsoptions.cpp | 282 ++++++++++++++ .../colvars/tests/colvarspreprocessor.cpp | 236 ++++++++++++ .../applied_forces/colvars/tests/index.ndx | 2 + ...orceProviderTest_CalculateForces4water.xml | 68 ++++ ...rceProviderTest_CalculateForcesAlanine.xml | 123 ++++++ ...ionsTest_OutputDefaultValuesWhenActive.xml | 10 + ...Test_OutputNoDefaultValuesWhenInactive.xml | 8 + ...varsOptionsTest_OutputValuesWhenActive.xml | 10 + ...PreProcessorTest_CheckValuesFourWaters.xml | 24 ++ update-colvars-code.sh | 13 +- 16 files changed, 1347 insertions(+), 2 deletions(-) create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/.clang-tidy create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/CMakeLists.txt create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars.cpp create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample.dat create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample_alanine.dat create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsforceprovider.cpp create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsoptions.cpp create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarspreprocessor.cpp create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/index.ndx create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForces4water.xml create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForcesAlanine.xml create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputDefaultValuesWhenActive.xml create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputNoDefaultValuesWhenInactive.xml create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputValuesWhenActive.xml create mode 100644 gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsPreProcessorTest_CheckValuesFourWaters.xml diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/.clang-tidy b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/.clang-tidy new file mode 100644 index 000000000..458c9c0ee --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/.clang-tidy @@ -0,0 +1,9 @@ +# List of rationales for check suppressions (where known). +# This have to precede the list because inline comments are not +# supported by clang-tidy. +# +# -cppcoreguidelines-avoid-non-const-global-variables +# There are quite a lot of static variables in the test code that +# can not be replaced. +Checks: -cppcoreguidelines-avoid-non-const-global-variables, +InheritParentConfig: true diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/CMakeLists.txt b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/CMakeLists.txt new file mode 100644 index 000000000..2e7eddcf4 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/CMakeLists.txt @@ -0,0 +1,44 @@ +# +# This file is part of the GROMACS molecular simulation package. +# +# Copyright 2021- The GROMACS Authors +# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. +# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. +# +# GROMACS is free software; you can redistribute it and/or +# modify it under the terms of the GNU Lesser General Public License +# as published by the Free Software Foundation; either version 2.1 +# of the License, or (at your option) any later version. +# +# GROMACS is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with GROMACS; if not, see +# https://www.gnu.org/licenses, or write to the Free Software Foundation, +# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +# +# If you want to redistribute modifications to GROMACS, please +# consider that scientific software is very special. Version +# control is crucial - bugs must be traceable. We will be happy to +# consider code for inclusion in the official distribution, but +# derived work must not be called official GROMACS. Details are found +# in the README & COPYING files - if they are missing, get the +# official version at https://www.gromacs.org. +# +# To help us fund GROMACS development, we humbly ask that you cite +# the research papers on the package. Check out https://www.gromacs.org. + +gmx_add_unit_test(ColvarsAppliedForcesUnitTest colvars_applied_forces-test + CPP_SOURCE_FILES + colvarspreprocessor.cpp + colvars.cpp + colvarsoptions.cpp + colvarsforceprovider.cpp + + ) +target_link_libraries(colvars_applied_forces-test PRIVATE applied_forces math topology mdlib + mdtypes) + diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars.cpp new file mode 100644 index 000000000..bc8a286f6 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars.cpp @@ -0,0 +1,126 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Tests for functionality of the Colvars module. + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ +#include "gmxpre.h" + +#include + +#include "gromacs/applied_forces/colvars/colvarsMDModule.h" +#include "gromacs/gmxlib/network.h" +#include "gromacs/math/paddedvector.h" +#include "gromacs/math/vec.h" +#include "gromacs/mdrunutility/mdmodulesnotifiers.h" +#include "gromacs/mdtypes/enerdata.h" +#include "gromacs/mdtypes/forceoutput.h" +#include "gromacs/mdtypes/iforceprovider.h" +#include "gromacs/mdtypes/imdmodule.h" +#include "gromacs/mdtypes/imdpoptionprovider.h" +#include "gromacs/mdtypes/mdatom.h" +#include "gromacs/options/options.h" +#include "gromacs/options/treesupport.h" +#include "gromacs/utility/keyvaluetreebuilder.h" +#include "gromacs/utility/keyvaluetreetransform.h" +#include "gromacs/utility/real.h" +#include "gromacs/utility/smalloc.h" +#include "gromacs/utility/stringcompare.h" + +#include "testutils/testasserts.h" +#include "testutils/testfilemanager.h" +#include "testutils/testmatchers.h" + +namespace gmx +{ + +namespace +{ + +class ColvarsTest : public ::testing::Test +{ +public: + void addMdpOptionColvarsActive() + { + mdpValueBuilder_.rootObject().addValue("colvars-active", std::string("yes")); + mdpValueBuilder_.rootObject().addValue("colvars-filename", std::string("colvars.dat")); + } + + //! build an mdp options tree that sets the options for the Colvars module + void makeColvarsModuleWithSetOptions() + { + KeyValueTreeObject mdpOptionsTree = mdpValueBuilder_.build(); + + ColvarsModule_ = ColvarsModuleInfo::create(); + + // set up options + Options ColvarsModuleOptions; + ColvarsModule_->mdpOptionProvider()->initMdpOptions(&ColvarsModuleOptions); + + // Add rules to transform mdp inputs to ColvarsModule data + KeyValueTreeTransformer transform; + transform.rules()->addRule().keyMatchType("/", StringCompareType::CaseAndDashInsensitive); + ColvarsModule_->mdpOptionProvider()->initMdpTransform(transform.rules()); + + // Execute the transform on the mdpValues + auto transformedMdpValues = transform.transform(mdpOptionsTree, nullptr); + assignOptionsFromKeyValueTree(&ColvarsModuleOptions, transformedMdpValues.object(), nullptr); + } + + void intializeForceProviders() { ColvarsModule_->initForceProviders(&ColvarsForces_); } + +protected: + KeyValueTreeBuilder mdpValueBuilder_; + ForceProviders ColvarsForces_; + std::unique_ptr ColvarsModule_; +}; + +TEST_F(ColvarsTest, ForceProviderLackingInputThrows) +{ + // Prepare MDP inputs + addMdpOptionColvarsActive(); + + // Initialize with default options + makeColvarsModuleWithSetOptions(); + + // Build the force provider with missing input data + EXPECT_ANY_THROW(intializeForceProviders()); +} + +} // namespace + +} // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample.dat b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample.dat new file mode 100644 index 000000000..818983e91 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample.dat @@ -0,0 +1,17 @@ +units gromacs +colvar { + name d_atoms + distance { + group1 { + atomNumbers 1 + } + group2 { + atomNumbers 5 + } + } +} +harmonic { + colvars d_atoms + forceConstant 2000 + centers 0.3 +} diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample_alanine.dat b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample_alanine.dat new file mode 100644 index 000000000..3cacd0d6c --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample_alanine.dat @@ -0,0 +1,26 @@ +units gromacs +colvar { + + name one + width 0.5 + dihedral { + group1 { + atomNumbers 1 + } + group2 { + atomNumbers 5 + } + group3 { + atomNumbers 11 + } + group4 { + atomNumbers 12 + } + } +} + +harmonic { + colvars one + centers 0.1 + forceConstant 0.01 +} diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsforceprovider.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsforceprovider.cpp new file mode 100644 index 000000000..34b655ac0 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsforceprovider.cpp @@ -0,0 +1,351 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Tests for ColvarsForceProvider class of Colvars MDModule. + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ +#include "gmxpre.h" + +#include "gromacs/applied_forces/colvars/colvarsforceprovider.h" + +#include + +#include + +#include "gromacs/applied_forces/colvars/colvarssimulationsparameters.h" +#include "gromacs/domdec/localatomsetmanager.h" +#include "gromacs/fileio/confio.h" +#include "gromacs/gmxpreprocess/grompp.h" +#include "gromacs/math/paddedvector.h" +#include "gromacs/math/vec.h" +#include "gromacs/mdlib/forcerec.h" +#include "gromacs/mdtypes/commrec.h" +#include "gromacs/mdtypes/enerdata.h" +#include "gromacs/mdtypes/forceoutput.h" +#include "gromacs/mdtypes/iforceprovider.h" +#include "gromacs/pbcutil/pbc.h" +#include "gromacs/topology/mtop_lookup.h" +#include "gromacs/topology/mtop_util.h" +#include "gromacs/topology/topology.h" +#include "gromacs/utility/arrayref.h" +#include "gromacs/utility/textreader.h" +#include "gromacs/utility/textwriter.h" + +#include "testutils/cmdlinetest.h" +#include "testutils/refdata.h" +#include "testutils/testasserts.h" +#include "testutils/testfilemanager.h" + +namespace gmx +{ + +class ColvarsForceProviderTest : public ::testing::Test +{ +public: + void PrepareInputForceProvider(const std::string& fileName) + { + + gmx::test::TestFileManager fileManager_; + const std::string simData = + gmx::test::TestFileManager::getTestSimulationDatabaseDirectory().u8string(); + + // Generate empty mdp file + const std::string mdpInputFileName = + fileManager_.getTemporaryFilePath(fileName + ".mdp").u8string(); + gmx::TextWriter::writeFileFromString(mdpInputFileName, ""); + + // Generate tpr file + const std::string tprName = fileManager_.getTemporaryFilePath(fileName + ".tpr").u8string(); + { + gmx::test::CommandLine caller; + caller.append("grompp"); + caller.addOption("-f", mdpInputFileName); + caller.addOption( + "-p", + std::filesystem::path(simData).append(fileName).replace_extension(".top").u8string()); + caller.addOption( + "-c", + std::filesystem::path(simData).append(fileName).replace_extension(".gro").u8string()); + caller.addOption("-o", tprName); + ASSERT_EQ(0, gmx_grompp(caller.argc(), caller.argv())); + } + + + bool fullTopology; + gmx_mtop_t mtop; + rvec* coords; + // Load topology + readConfAndTopology(tprName.c_str(), &fullTopology, &mtop, &pbcType_, &coords, nullptr, box_); + + x_ = gmx::constArrayRefFromArray(reinterpret_cast(coords), atoms_.nr); + atoms_ = gmx_mtop_global_atoms(mtop); + } + + void ColvarsConfigStringFromFile(const std::string& filename) + { + // Path to the sample colvars input file + std::string colvarsInputFile = gmx::test::TestFileManager::getInputFilePath(filename).u8string(); + + colvarsConfigString_ = TextReader::readFileToString(colvarsInputFile); + } + + void CorrectColvarsConfigString() + { + // atomNumbers start at 1 in colvars + colvarsConfigString_ = R"(units gromacs + colvar { + name d_atoms + distance { + group1 { + atomNumbers 1 + } + group2 { + atomNumbers 5 + } + } + } + harmonic { + colvars d_atoms + forceConstant 20000 + centers 0.3 + })"; + } + + void IncorrectColvarsConfigString() + { + // Path to the sample colvars input file + std::string colvarsInputFile = + gmx::test::TestFileManager::getInputFilePath("colvars_sample.dat").u8string(); + + colvarsConfigString_ = TextReader::readFileToString(colvarsInputFile); + } + +protected: + std::string colvarsConfigString_; + std::vector atomCoords_; + LocalAtomSetManager atomSetManager_; + PbcType pbcType_; + MDLogger logger_; + t_atoms atoms_; + t_commrec cr_; + std::map KVTInputs; + ColvarsForceProviderState colvarsState_; + + double simulationTimeStep_ = 0.002; + real temperature_ = 300; + std::string prefixOutput_; + + ArrayRef x_; + matrix box_; +}; + +TEST_F(ColvarsForceProviderTest, CanConstructOrNot) +{ + + EXPECT_NO_THROW(ColvarsForceProvider forceProvider(colvarsConfigString_, + &atomSetManager_, + pbcType_, + simulationTimeStep_, + atoms_, + &cr_, + &logger_, + atomCoords_, + prefixOutput_, + KVTInputs, + colvarsState_, + temperature_)); +} + +TEST_F(ColvarsForceProviderTest, SimpleInputs) +{ + PrepareInputForceProvider("4water"); + ColvarsConfigStringFromFile("colvars_sample.dat"); + + // Indexes taken from the Colvars Config file. + atomCoords_ = { RVec(x_[0]), RVec(x_[4]) }; + + + ColvarsForceProvider forceProvider(colvarsConfigString_, + &atomSetManager_, + pbcType_, + simulationTimeStep_, + atoms_, + &cr_, + &logger_, + atomCoords_, + prefixOutput_, + KVTInputs, + colvarsState_, + temperature_); + + + // Re-use the PreProcessorTest since the ForceProvider recalls colvars initilization and the input are identicals. + gmx::test::TestReferenceData data("ColvarsPreProcessorTest_CheckValuesFourWaters.xml"); + gmx::test::TestReferenceChecker checker(data.rootChecker()); + + // Check colvars & atoms values are correctly read + checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001)); + checker.checkVector(atomCoords_[1], "Coords Atom 4"); + + const auto* const atom_ids = forceProvider.get_atom_ids(); + checker.checkSequence(atom_ids->begin(), atom_ids->end(), "Index of colvars atoms"); + + const auto* const atom_masses = forceProvider.get_atom_masses(); + checker.checkSequence(atom_masses->begin(), atom_masses->end(), "Masses of colvars atoms"); + + const auto* const atom_charges = forceProvider.get_atom_charges(); + checker.checkSequence(atom_charges->begin(), atom_charges->end(), "Charges of colvars atoms"); +} + +TEST_F(ColvarsForceProviderTest, WrongColvarsInput) +{ + PrepareInputForceProvider("4water"); + + // atom 100 does not exist + colvarsConfigString_ = R"(units gromacs + colvar { + name d_atoms + distance { + group1 { + atomNumbers 100 + } + group2 { + atomNumbers 2 + } + } + } + harmonic { + colvars d_atoms + forceConstant 2000 + centers 0.6 + })"; + + EXPECT_ANY_THROW(ColvarsForceProvider forceProvider(colvarsConfigString_, + &atomSetManager_, + pbcType_, + simulationTimeStep_, + atoms_, + &cr_, + &logger_, + atomCoords_, + prefixOutput_, + KVTInputs, + colvarsState_, + temperature_)); +} + +TEST_F(ColvarsForceProviderTest, CalculateForces4water) +{ + gmx::test::TestReferenceData data; + gmx::test::TestReferenceChecker checker(data.rootChecker()); + + PrepareInputForceProvider("4water"); + ColvarsConfigStringFromFile("colvars_sample.dat"); + + // Indexes taken from the Colvars Config file. + atomCoords_ = { RVec(x_[0]), RVec(x_[4]) }; + + // Prepare a ForceProviderInput + ForceProviderInput forceProviderInput(x_, atoms_.nr, {}, {}, 0.0, 0, box_, cr_); + + // Prepare a ForceProviderOutput + std::vector forces(atoms_.nr, RVec{ 0, 0, 0 }); + ForceWithVirial forceWithVirial(forces, true); + gmx_enerdata_t enerdDummy(1, nullptr); + ForceProviderOutput forceProviderOutput(&forceWithVirial, &enerdDummy); + + ColvarsForceProvider forceProvider(colvarsConfigString_, + &atomSetManager_, + pbcType_, + simulationTimeStep_, + atoms_, + &cr_, + &logger_, + atomCoords_, + prefixOutput_, + KVTInputs, + colvarsState_, + temperature_); + + forceProvider.calculateForces(forceProviderInput, &forceProviderOutput); + + checker.setDefaultTolerance(gmx::test::defaultFloatTolerance()); + checker.checkDouble(enerdDummy.term[F_COM_PULL], "Bias Energy"); + checker.checkSequence(forces.begin(), forces.end(), "Forces"); +} + +TEST_F(ColvarsForceProviderTest, CalculateForcesAlanine) +{ + gmx::test::TestReferenceData data; + gmx::test::TestReferenceChecker checker(data.rootChecker()); + + PrepareInputForceProvider("ala"); + ColvarsConfigStringFromFile("colvars_sample_alanine.dat"); + + // Indexes taken from the Colvars Config file. + atomCoords_ = { RVec(x_[0]), RVec(x_[4]), RVec(x_[10]), RVec(x_[11]) }; + + // Prepare a ForceProviderInput + ForceProviderInput forceProviderInput(x_, atoms_.nr, {}, {}, 0.0, 0, box_, cr_); + + // Prepare a ForceProviderOutput + std::vector forces(atoms_.nr, RVec{ 0, 0, 0 }); + ForceWithVirial forceWithVirial(forces, true); + gmx_enerdata_t enerdDummy(1, nullptr); + ForceProviderOutput forceProviderOutput(&forceWithVirial, &enerdDummy); + + ColvarsForceProvider forceProvider(colvarsConfigString_, + &atomSetManager_, + pbcType_, + simulationTimeStep_, + atoms_, + &cr_, + &logger_, + atomCoords_, + prefixOutput_, + KVTInputs, + colvarsState_, + temperature_); + + forceProvider.calculateForces(forceProviderInput, &forceProviderOutput); + + checker.setDefaultTolerance(gmx::test::defaultFloatTolerance()); + checker.checkDouble(enerdDummy.term[F_COM_PULL], "Bias Energy"); + checker.checkSequence(forces.begin(), forces.end(), "Forces"); +} + +} // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsoptions.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsoptions.cpp new file mode 100644 index 000000000..2f966de02 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsoptions.cpp @@ -0,0 +1,282 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2023- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Tests for ColvarsOptions class of Colvars MDModule. + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ +#include "gmxpre.h" + +#include "gromacs/applied_forces/colvars/colvarsoptions.h" + +#include +#include + +#include + +#include "gromacs/fileio/confio.h" +#include "gromacs/gmxpreprocess/grompp.h" +#include "gromacs/math/paddedvector.h" +#include "gromacs/mdrunutility/mdmodulesnotifiers.h" +#include "gromacs/mdtypes/inputrec.h" +#include "gromacs/options/options.h" +#include "gromacs/options/treesupport.h" +#include "gromacs/selection/indexutil.h" +#include "gromacs/topology/index.h" +#include "gromacs/topology/mtop_util.h" +#include "gromacs/topology/topology.h" +#include "gromacs/utility/keyvaluetreebuilder.h" +#include "gromacs/utility/keyvaluetreemdpwriter.h" +#include "gromacs/utility/keyvaluetreetransform.h" +#include "gromacs/utility/smalloc.h" +#include "gromacs/utility/stringcompare.h" +#include "gromacs/utility/stringstream.h" +#include "gromacs/utility/textwriter.h" + +#include "testutils/cmdlinetest.h" +#include "testutils/refdata.h" +#include "testutils/testasserts.h" +#include "testutils/testfilemanager.h" +#include "testutils/testmatchers.h" + +namespace gmx +{ + +static const std::string colvarsConfig = "colvars_sample.dat"; + +class ColvarsOptionsTest : public ::testing::Test +{ +public: + void setFromMdpValues(const KeyValueTreeObject& ColvarsMdpValues) + { + // Setup options + Options colvarsModuleOptions; + colvarsOptions_.initMdpOptions(&colvarsModuleOptions); + + // Add rules to transform mdp inputs to densityFittingModule data + KeyValueTreeTransformer transform; + transform.rules()->addRule().keyMatchType("/", StringCompareType::CaseAndDashInsensitive); + + colvarsOptions_.initMdpTransform(transform.rules()); + + // Execute the transform on the mdpValues + auto transformedMdpValues = transform.transform(ColvarsMdpValues, nullptr); + assignOptionsFromKeyValueTree(&colvarsModuleOptions, transformedMdpValues.object(), nullptr); + } + + static KeyValueTreeObject ColvarsBuildDefaulMdpValues() + { + // Prepare MDP inputs + KeyValueTreeBuilder mdpValueBuilder; + mdpValueBuilder.rootObject().addValue(c_colvarsModuleName + "-active", std::string("true")); + return mdpValueBuilder.build(); + } + + static KeyValueTreeObject ColvarsBuildInputMdpValues() + { + // Prepare MDP inputs + KeyValueTreeBuilder mdpValueBuilder; + mdpValueBuilder.rootObject().addValue(c_colvarsModuleName + "-active", std::string("true")); + mdpValueBuilder.rootObject().addValue(c_colvarsModuleName + "-configfile", colvarsConfig); + return mdpValueBuilder.build(); + } + + void PrepareInputColvarsPreProcessor(const std::string& fileName) + { + + // Path to the sample colvars input file + std::string colvarsConfigFile = + gmx::test::TestFileManager::getInputFilePath("colvars_sample.dat").u8string(); + + gmx::test::TestFileManager fileManager_; + const std::string simData = + gmx::test::TestFileManager::getTestSimulationDatabaseDirectory().u8string(); + + // Generate empty mdp file + const std::string mdpInputFileName = + fileManager_.getTemporaryFilePath(fileName + ".mdp").u8string(); + gmx::TextWriter::writeFileFromString(mdpInputFileName, ""); + + // Generate tpr file + const std::string tprName = fileManager_.getTemporaryFilePath(fileName + ".tpr").u8string(); + { + gmx::test::CommandLine caller; + caller.append("grompp"); + caller.addOption("-f", mdpInputFileName); + caller.addOption( + "-p", + std::filesystem::path(simData).append(fileName).replace_extension(".top").u8string()); + caller.addOption( + "-c", + std::filesystem::path(simData).append(fileName).replace_extension(".gro").u8string()); + caller.addOption("-o", tprName); + ASSERT_EQ(0, gmx_grompp(caller.argc(), caller.argv())); + } + + + bool fullTopology; + PbcType pbcType; + matrix box; + gmx_mtop_t mtop; + rvec* coords; + // Load topology + readConfAndTopology(tprName.c_str(), &fullTopology, &mtop, &pbcType, &coords, nullptr, box); + + t_atoms atoms = gmx_mtop_global_atoms(mtop); + x = gmx::constArrayRefFromArray(reinterpret_cast(coords), atoms.nr); + + // Populate attributes outside the use of the defined callbacks. + colvarsOptions_.setParameters(colvarsConfigFile, atoms, x, pbcType, box, 300); + } + + +protected: + ColvarsOptions colvarsOptions_; + ArrayRef x; +}; + + +TEST_F(ColvarsOptionsTest, OptionSetsActive) +{ + EXPECT_FALSE(colvarsOptions_.isActive()); + setFromMdpValues(ColvarsBuildDefaulMdpValues()); + EXPECT_TRUE(colvarsOptions_.isActive()); +} + +TEST_F(ColvarsOptionsTest, OutputNoDefaultValuesWhenInactive) +{ + // Test buildMdpOutput() + StringOutputStream stream; + KeyValueTreeBuilder builder; + KeyValueTreeObjectBuilder builderObject = builder.rootObject(); + + colvarsOptions_.buildMdpOutput(&builderObject); + { + TextWriter writer(&stream); + writeKeyValueTreeAsMdp(&writer, builder.build()); + } + stream.close(); + + gmx::test::TestReferenceData data; + gmx::test::TestReferenceChecker checker(data.rootChecker()); + + checker.checkString(stream.toString(), "Mdp output"); +} + +TEST_F(ColvarsOptionsTest, OutputDefaultValuesWhenActive) +{ + + // Activate colvars + setFromMdpValues(ColvarsBuildDefaulMdpValues()); + + // Transform module data into a flat key-value tree for output. + StringOutputStream stream; + KeyValueTreeBuilder builder; + KeyValueTreeObjectBuilder builderObject = builder.rootObject(); + + colvarsOptions_.buildMdpOutput(&builderObject); + { + TextWriter writer(&stream); + writeKeyValueTreeAsMdp(&writer, builder.build()); + } + stream.close(); + + gmx::test::TestReferenceData data; + gmx::test::TestReferenceChecker checker(data.rootChecker()); + + checker.checkString(stream.toString(), "Mdp output"); +} + +TEST_F(ColvarsOptionsTest, OutputValuesWhenActive) +{ + + // Activate colvars + setFromMdpValues(ColvarsBuildInputMdpValues()); + + // Transform module data into a flat key-value tree for output. + StringOutputStream stream; + KeyValueTreeBuilder builder; + KeyValueTreeObjectBuilder builderObject = builder.rootObject(); + + colvarsOptions_.buildMdpOutput(&builderObject); + { + TextWriter writer(&stream); + writeKeyValueTreeAsMdp(&writer, builder.build()); + } + stream.close(); + + gmx::test::TestReferenceData data; + gmx::test::TestReferenceChecker checker(data.rootChecker()); + + checker.checkString(stream.toString(), "Mdp output"); +} + +TEST_F(ColvarsOptionsTest, InternalsToKvtAndBack) +{ + + // Activate colvars + setFromMdpValues(ColvarsBuildInputMdpValues()); + // Set up parameters with a test system + PrepareInputColvarsPreProcessor("4water"); + + // Write parameters to the KVT + KeyValueTreeBuilder builder; + colvarsOptions_.writeInternalParametersToKvt(builder.rootObject()); + const auto inputTree = builder.build(); + + // Copy internal parameters + auto refColvarsInputContent = colvarsOptions_.colvarsConfigContent(); + auto refColvarsCoordinates = colvarsOptions_.colvarsAtomCoords(); + auto refTemperature = colvarsOptions_.colvarsEnsTemp(); + + // Retrieve paramaters from the KVT + colvarsOptions_.readInternalParametersFromKvt(inputTree); + + // Check parameters taken back from KVT + EXPECT_EQ(refColvarsInputContent, colvarsOptions_.colvarsConfigContent()); + + auto actualColvarsCoordinates = colvarsOptions_.colvarsAtomCoords(); + EXPECT_REAL_EQ(refColvarsCoordinates[0][XX], actualColvarsCoordinates[0][XX]); + EXPECT_REAL_EQ(refColvarsCoordinates[0][YY], actualColvarsCoordinates[0][YY]); + EXPECT_REAL_EQ(refColvarsCoordinates[0][ZZ], actualColvarsCoordinates[0][ZZ]); + EXPECT_REAL_EQ(refColvarsCoordinates[1][XX], actualColvarsCoordinates[1][XX]); + EXPECT_REAL_EQ(refColvarsCoordinates[1][YY], actualColvarsCoordinates[1][YY]); + EXPECT_REAL_EQ(refColvarsCoordinates[1][ZZ], actualColvarsCoordinates[1][ZZ]); + + EXPECT_EQ(refTemperature, colvarsOptions_.colvarsEnsTemp()); +} + +} // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarspreprocessor.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarspreprocessor.cpp new file mode 100644 index 000000000..c360f4b92 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarspreprocessor.cpp @@ -0,0 +1,236 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright 2021- The GROMACS Authors + * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. + * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * https://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at https://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out https://www.gromacs.org. + */ +/*! \internal \file + * \brief + * Tests for ColvarsPreProcessor class for Colvars MDModule + * + * \author Hubert Santuz + * \ingroup module_applied_forces + */ +#include "gmxpre.h" + +#include "gromacs/applied_forces/colvars/colvarspreprocessor.h" + +#include +#include + +#include + +#include "gromacs/fileio/confio.h" +#include "gromacs/gmxpreprocess/grompp.h" +#include "gromacs/math/vec.h" +#include "gromacs/pbcutil/pbc.h" +#include "gromacs/topology/mtop_lookup.h" +#include "gromacs/topology/mtop_util.h" +#include "gromacs/topology/topology.h" +#include "gromacs/utility/arrayref.h" +#include "gromacs/utility/path.h" +#include "gromacs/utility/textwriter.h" + +#include "testutils/cmdlinetest.h" +#include "testutils/refdata.h" +#include "testutils/testasserts.h" +#include "testutils/testfilemanager.h" + +namespace gmx +{ + +class ColvarsPreProcessorTest : public ::testing::Test +{ +public: + /*! \brief Generates tpr file from *.top and *.gro existing in the simulation database directory + * and loads gmx_mtop_t from it + */ + void makeMtopFromFile(const std::string& fileName, const std::string& mdpContent) + { + const std::string simData = + gmx::test::TestFileManager::getTestSimulationDatabaseDirectory().u8string(); + + // Generate empty mdp file + const std::string mdpInputFileName = + fileManager_.getTemporaryFilePath(fileName + ".mdp").u8string(); + gmx::TextWriter::writeFileFromString(mdpInputFileName, mdpContent); + + // Generate tpr file + const std::string tprName = fileManager_.getTemporaryFilePath(fileName + ".tpr").u8string(); + { + gmx::test::CommandLine caller; + caller.append("grompp"); + caller.addOption("-f", mdpInputFileName); + caller.addOption( + "-p", + std::filesystem::path(simData).append(fileName).replace_extension(".top").u8string()); + caller.addOption( + "-c", + std::filesystem::path(simData).append(fileName).replace_extension(".gro").u8string()); + caller.addOption("-o", tprName); + ASSERT_EQ(0, gmx_grompp(caller.argc(), caller.argv())); + } + + // Load topology + bool fullTopology; + gmx_mtop_t mtop_; + rvec* coords; + readConfAndTopology(tprName.c_str(), &fullTopology, &mtop_, &pbcType_, &coords, nullptr, box_); + atoms_ = gmx_mtop_global_atoms(mtop_); + x_ = gmx::constArrayRefFromArray(reinterpret_cast(coords), atoms_.nr); + } + +protected: + gmx::test::TestFileManager fileManager_; + t_atoms atoms_; + PbcType pbcType_; + matrix box_; + ArrayRef x_; +}; + +TEST_F(ColvarsPreProcessorTest, CanConstructColvarsPreProcess) +{ + // Reference input 4x SPCE waters from database 4water.top + makeMtopFromFile("4water", ""); + + EXPECT_NO_THROW(ColvarsPreProcessor colvarsPreProcess("", atoms_, pbcType_, nullptr, box_, x_, 0)); +} + +TEST_F(ColvarsPreProcessorTest, CheckValuesFourWaters) +{ + // Reference input 4x SPCE waters from database 4water.top + makeMtopFromFile("4water", ""); + + // atomNumbers start at 1 in colvars + std::string colvarsInput = R"(units gromacs + colvar { + name d_atoms + distance { + group1 { + atomNumbers 1 + } + group2 { + atomNumbers 5 + } + } + } + harmonic { + colvars d_atoms + forceConstant 20000 + centers 0.3 + })"; + + ColvarsPreProcessor colvarsPreProcess(colvarsInput, atoms_, pbcType_, nullptr, box_, x_, 0); + + gmx::test::TestReferenceData data; + gmx::test::TestReferenceChecker checker(data.rootChecker()); + + // Check colvars & atoms values are correctly read + checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001)); + checker.checkVector(colvarsPreProcess.getColvarsCoords()[1], "Coords Atom 4"); + + const auto* const atom_ids = colvarsPreProcess.get_atom_ids(); + checker.checkSequence(atom_ids->begin(), atom_ids->end(), "Index of colvars atoms"); + + const auto* const atom_masses = colvarsPreProcess.get_atom_masses(); + checker.checkSequence(atom_masses->begin(), atom_masses->end(), "Masses of colvars atoms"); + + const auto* const atom_charges = colvarsPreProcess.get_atom_charges(); + checker.checkSequence(atom_charges->begin(), atom_charges->end(), "Charges of colvars atoms"); +} + + +TEST_F(ColvarsPreProcessorTest, CheckNestedInputFiles) +{ + // Reference input 4x SPCE waters from database 4water.top + makeMtopFromFile("4water", ""); + + // TODO: add ref xyz file + std::string colvarsInput = R"(units gromacs + indexFile + colvar { + name d_atoms + distance { + group1 { + atomNumbers 1 + } + group2 { + atomNumbers 5 + } + } + } + harmonic { + colvars d_atoms + forceConstant 20000 + centers 0.6 + })"; + + // Replace index.ndx by its absolute path so Colvars can parse it. + std::string pathIndex = gmx::test::TestFileManager::getInputFilePath("index.ndx").u8string(); + size_t index = colvarsInput.find(""); + colvarsInput.replace(index, std::string("").length(), pathIndex); + + ColvarsPreProcessor colvarsPreProcess(colvarsInput, atoms_, pbcType_, nullptr, box_, x_, 0); + + // Make sure the index file inside colvarsInput was correctly read + auto listInputStreams = colvarsPreProcess.list_input_stream_names(); + auto inputStreamIndex = listInputStreams.begin(); + EXPECT_EQ(pathIndex, *inputStreamIndex); +} + +TEST_F(ColvarsPreProcessorTest, WrongColvarsInput) +{ + // Reference input 4x SPCE waters from database 4water.top + makeMtopFromFile("4water", ""); + + // atom 100 does not exist + std::string colvarsInput = R"(units gromacs + colvar { + name d_atoms + distance { + group1 { + atomNumbers 100 + } + group2 { + atomNumbers 2 + } + } + } + harmonic { + colvars d_atoms + forceConstant 20000 + centers 0.6 + })"; + + EXPECT_ANY_THROW(ColvarsPreProcessor colvarsPreProcess( + colvarsInput, atoms_, pbcType_, nullptr, box_, x_, 0)); +} + +} // namespace gmx diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/index.ndx b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/index.ndx new file mode 100644 index 000000000..de5faf39d --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/index.ndx @@ -0,0 +1,2 @@ +[ Colvars ] +2 4 diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForces4water.xml b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForces4water.xml new file mode 100644 index 000000000..d452cb080 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForces4water.xml @@ -0,0 +1,68 @@ + + + + 49.728973388671875 + + 12 + + 48.608006 + 138.14906 + 421.2695 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + -48.608006 + -138.14906 + -421.2695 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForcesAlanine.xml b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForcesAlanine.xml new file mode 100644 index 000000000..6faa4aa7b --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForcesAlanine.xml @@ -0,0 +1,123 @@ + + + + 0.007179399486631155 + + 23 + + 2.6480298 + -0.60938436 + -9.4919109 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + -4.9235234 + 1.1406431 + 17.493099 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 5.8324962 + -1.3687972 + -20.363705 + + + -3.5570025 + 0.83753848 + 12.362517 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + 0 + 0 + 0 + + + diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputDefaultValuesWhenActive.xml b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputDefaultValuesWhenActive.xml new file mode 100644 index 000000000..ea71ed868 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputDefaultValuesWhenActive.xml @@ -0,0 +1,10 @@ + + + + +; Colvars bias +colvars-active = true +; colvars config file +colvars-configfile = colvars.dat + + diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputNoDefaultValuesWhenInactive.xml b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputNoDefaultValuesWhenInactive.xml new file mode 100644 index 000000000..e32ea031d --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputNoDefaultValuesWhenInactive.xml @@ -0,0 +1,8 @@ + + + + +; Colvars bias +colvars-active = false + + diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputValuesWhenActive.xml b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputValuesWhenActive.xml new file mode 100644 index 000000000..8bae24579 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputValuesWhenActive.xml @@ -0,0 +1,10 @@ + + + + +; Colvars bias +colvars-active = true +; colvars config file +colvars-configfile = colvars_sample.dat + + diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsPreProcessorTest_CheckValuesFourWaters.xml b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsPreProcessorTest_CheckValuesFourWaters.xml new file mode 100644 index 000000000..678fd5757 --- /dev/null +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsPreProcessorTest_CheckValuesFourWaters.xml @@ -0,0 +1,24 @@ + + + + + 0.82499999 + 1.306 + 1.517 + + + 2 + 0 + 4 + + + 2 + 15.99940013885498 + 1.0080000162124634 + + + 2 + -0.81999999284744263 + 0.40999999642372131 + + diff --git a/update-colvars-code.sh b/update-colvars-code.sh index 575cae2c5..3ddcb4880 100755 --- a/update-colvars-code.sh +++ b/update-colvars-code.sh @@ -652,12 +652,21 @@ then echo "Update with the last Colvars source." else mkdir ${target_folder} + mkdir -p ${target_folder}/tests/refdata fi - for src in ${source}/gromacs/gromacs-mdmodules/applied_forces/colvars/* - do \ + for src in ${source}/gromacs/gromacs-mdmodules/applied_forces/colvars/*.* ; do tgt=$(basename ${src}) condcopy "${src}" "${target_folder}/${tgt}" done + for src in ${source}/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/*.* ; do + tgt=$(basename ${src}) + condcopy "${src}" "${target_folder}/tests/${tgt}" + done + for src in ${source}/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/*.* ; do + tgt=$(basename ${src}) + condcopy "${src}" "${target_folder}/tests/refdata/${tgt}" + done + echo "" # Apply patch for Gromacs files From 7a9fb1bf169025a03a5885af91f6761b8e0b1b13 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 26 Sep 2023 18:38:51 -0400 Subject: [PATCH 133/162] Update testing input --- gromacs/tests/library/Common/test.mdp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gromacs/tests/library/Common/test.mdp b/gromacs/tests/library/Common/test.mdp index 99b6001f5..c3953c389 100644 --- a/gromacs/tests/library/Common/test.mdp +++ b/gromacs/tests/library/Common/test.mdp @@ -54,4 +54,4 @@ gen_vel = no ; Colvars configuration colvars-active = Yes -colvars-filename = test.in +colvars-configfile = test.in From 2888830ae79bc2c3aff7ee8c1e40421880682d24 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 26 Sep 2023 18:53:00 -0400 Subject: [PATCH 134/162] Fix preprocessor macro definition --- gromacs/gromacs-mdmodules.patch | 49 +++++++++++++++++++++++++-------- 1 file changed, 38 insertions(+), 11 deletions(-) diff --git a/gromacs/gromacs-mdmodules.patch b/gromacs/gromacs-mdmodules.patch index b912f6e8e..5220f5506 100644 --- a/gromacs/gromacs-mdmodules.patch +++ b/gromacs/gromacs-mdmodules.patch @@ -11,6 +11,20 @@ index 31e2bbbec5..5dc774e726 100644 ################################################## # Process SIMD instruction settings ################################################## +diff --git a/src/config.h.cmakein b/src/config.h.cmakein +index 470777bbff..5e3fac0c93 100644 +--- a/src/config.h.cmakein ++++ b/src/config.h.cmakein +@@ -457,6 +457,9 @@ + /* Define if we have muparser support */ + #cmakedefine01 HAVE_MUPARSER + ++/* Define if we are building with Colvars */ ++#cmakedefine01 HAVE_COLVARS ++ + /* Build using clang analyzer */ + #cmakedefine01 GMX_CLANG_ANALYZER + diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt index 96107341de..a722ddd5da 100644 --- a/src/gromacs/CMakeLists.txt @@ -55,28 +69,39 @@ index 3c4987f892..cc5f50c7a6 100644 if (BUILD_TESTING) add_subdirectory(tests) diff --git a/src/gromacs/mdrun/mdmodules.cpp b/src/gromacs/mdrun/mdmodules.cpp -index 5221ff025c..5776736f7f 100644 +index 5221ff025c..faa8ac0b9e 100644 --- a/src/gromacs/mdrun/mdmodules.cpp +++ b/src/gromacs/mdrun/mdmodules.cpp -@@ -37,6 +37,7 @@ +@@ -33,10 +33,15 @@ + */ + #include "gmxpre.h" + ++#include "config.h" // Allow conditional compilation of individual MDModules ++ + #include "mdmodules.h" #include ++#ifdef HAVE_COLVARS +#include "gromacs/applied_forces/colvars/colvarsMDModule.h" ++#endif #include "gromacs/applied_forces/densityfitting/densityfitting.h" #include "gromacs/applied_forces/electricfield.h" #include "gromacs/applied_forces/qmmm/qmmm.h" -@@ -67,6 +68,9 @@ public: +@@ -67,7 +72,12 @@ public: field_(createElectricFieldModule()), imd_(createInteractiveMolecularDynamicsModule()), qmmm_(QMMMModuleInfo::create()), +#ifdef HAVE_COLVARS -+ colvars_(ColvarsModuleInfo::create()), -+#endif ++ swapCoordinates_(createSwapCoordinatesModule()), ++ colvars_(ColvarsModuleInfo::create()) ++#else swapCoordinates_(createSwapCoordinatesModule()) ++#endif { } -@@ -78,6 +82,9 @@ public: + +@@ -78,6 +88,9 @@ public: field_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); densityFitting_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); qmmm_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions); @@ -86,15 +111,17 @@ index 5221ff025c..5776736f7f 100644 // In future, other sections would also go here. } -@@ -106,6 +113,7 @@ public: +@@ -106,6 +119,9 @@ public: std::unique_ptr imd_; std::unique_ptr qmmm_; std::unique_ptr swapCoordinates_; ++#ifdef HAVE_COLVARS + std::unique_ptr colvars_; ++#endif /*! \brief List of registered MDModules * -@@ -129,6 +137,9 @@ void MDModules::initMdpTransform(IKeyValueTreeTransformRules* rules) +@@ -129,6 +145,9 @@ void MDModules::initMdpTransform(IKeyValueTreeTransformRules* rules) impl_->field_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); impl_->densityFitting_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); impl_->qmmm_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules()); @@ -104,7 +131,7 @@ index 5221ff025c..5776736f7f 100644 } void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder* builder) -@@ -136,6 +147,9 @@ void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder* builder) +@@ -136,6 +155,9 @@ void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder* builder) impl_->field_->mdpOptionProvider()->buildMdpOutput(builder); impl_->densityFitting_->mdpOptionProvider()->buildMdpOutput(builder); impl_->qmmm_->mdpOptionProvider()->buildMdpOutput(builder); @@ -114,7 +141,7 @@ index 5221ff025c..5776736f7f 100644 } void MDModules::assignOptionsToModules(const KeyValueTreeObject& params, IKeyValueTreeErrorHandler* errorHandler) -@@ -173,6 +187,9 @@ ForceProviders* MDModules::initForceProviders() +@@ -173,6 +195,9 @@ ForceProviders* MDModules::initForceProviders() impl_->field_->initForceProviders(impl_->forceProviders_.get()); impl_->densityFitting_->initForceProviders(impl_->forceProviders_.get()); impl_->qmmm_->initForceProviders(impl_->forceProviders_.get()); @@ -124,7 +151,7 @@ index 5221ff025c..5776736f7f 100644 for (auto&& module : impl_->modules_) { module->initForceProviders(impl_->forceProviders_.get()); -@@ -184,12 +201,18 @@ void MDModules::subscribeToPreProcessingNotifications() +@@ -184,12 +209,18 @@ void MDModules::subscribeToPreProcessingNotifications() { impl_->densityFitting_->subscribeToPreProcessingNotifications(&impl_->notifiers_); impl_->qmmm_->subscribeToPreProcessingNotifications(&impl_->notifiers_); From cb7374abc89926e3ea2a0a7bb7d84cb3e7151e6c Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 26 Sep 2023 20:00:28 -0400 Subject: [PATCH 135/162] Temporarily disable GROMACS test that depends on Lepton --- gromacs/tests/library/000_customfunction_harmonic-fixed/disabled | 1 + 1 file changed, 1 insertion(+) create mode 100644 gromacs/tests/library/000_customfunction_harmonic-fixed/disabled diff --git a/gromacs/tests/library/000_customfunction_harmonic-fixed/disabled b/gromacs/tests/library/000_customfunction_harmonic-fixed/disabled new file mode 100644 index 000000000..9a3927eb6 --- /dev/null +++ b/gromacs/tests/library/000_customfunction_harmonic-fixed/disabled @@ -0,0 +1 @@ +Temporarily disabled to stay in sync with the GROMACS GitLab repository. From fecf569dd93baa2745e578db8fe7c70d3088ad1e Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 27 Sep 2023 09:10:05 -0400 Subject: [PATCH 136/162] Update version strings --- gromacs/src/colvarproxy_gromacs_version.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gromacs/src/colvarproxy_gromacs_version.h b/gromacs/src/colvarproxy_gromacs_version.h index cf70c1d84..fea42454b 100644 --- a/gromacs/src/colvarproxy_gromacs_version.h +++ b/gromacs/src/colvarproxy_gromacs_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2023-09-19" +#define COLVARPROXY_VERSION "2023-09-27" #endif From 6bd7dc6f604620271f1d3c147e098dda44f68be8 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 27 Sep 2023 17:01:28 -0400 Subject: [PATCH 137/162] Fix two typos detected by @zwpku --- doc/colvars-refman-main.tex | 2 +- namd/src/colvarproxy_namd.C | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index c0545db2d..2cf9970c4 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -6574,7 +6574,7 @@ V(\xi) = \left\{ \begin{array}{l l} \frac{1}{2} k \left(\frac{\xi - \xi_{\mathrm{upper}}}{w_{\xi}}\right)^2 & \mathrm{if }\ \xi > \xi_{\mathrm{upper}} \\ - 0 & \mathrm{if }\ \xi_{\mathrm{lower}} \leq \xi \geq \xi_{\mathrm{upper}} \\ + 0 & \mathrm{if }\ \xi_{\mathrm{lower}} \geq \xi \leq \xi_{\mathrm{upper}} \\ \frac{1}{2} k \left(\frac{\xi - \xi_{\mathrm{lower}}}{w_{\xi}}\right)^2 & \mathrm{if }\ \xi < \xi_{\mathrm{lower}} \end{array} \right. diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C index 32075eec4..1f6e00342 100644 --- a/namd/src/colvarproxy_namd.C +++ b/namd/src/colvarproxy_namd.C @@ -1148,7 +1148,7 @@ int colvarproxy_namd::backup_file(char const *filename) int colvarproxy_namd::init_atom_group(std::vector const &atoms_ids) { if (cvm::debug()) - cvm::log("Reguesting from NAMD a group of size "+cvm::to_str(atoms_ids.size())+ + cvm::log("Requesting from NAMD a group of size "+cvm::to_str(atoms_ids.size())+ " for collective variables calculation.\n"); colvars->cite_feature("Scalable center-of-mass computation (NAMD)"); From 718173862eb7e5cc55e71d70fb54c5c65ed403b9 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 29 Sep 2023 11:27:25 -0400 Subject: [PATCH 138/162] One more typo and fix a wrong correction --- doc/colvars-refman-main.tex | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index 2cf9970c4..e48361bb0 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -2349,7 +2349,7 @@ As for the component \texttt{rmsd}, the available options are \texttt{atoms}, \texttt{refPositionsFile}\cvnamebasedonly{, \texttt{refPositionsCol} and \texttt{refPositionsColValue}, } and \texttt{refPositions}. -\textbf{Note:} \texttt{refPositions}and \texttt{refPositionsFile} define the set of positions \emph{from which} the optimal rotation is calculated, but this rotation is not applied to the coordinates of the atoms involved: it is used instead to define the variable itself. +\textbf{Note:} \texttt{refPositions} and \texttt{refPositionsFile} define the set of positions \emph{from which} the optimal rotation is calculated, but this rotation is not applied to the coordinates of the atoms involved: it is used instead to define the variable itself. \begin{cvcoptions} \item % @@ -6574,7 +6574,7 @@ V(\xi) = \left\{ \begin{array}{l l} \frac{1}{2} k \left(\frac{\xi - \xi_{\mathrm{upper}}}{w_{\xi}}\right)^2 & \mathrm{if }\ \xi > \xi_{\mathrm{upper}} \\ - 0 & \mathrm{if }\ \xi_{\mathrm{lower}} \geq \xi \leq \xi_{\mathrm{upper}} \\ + 0 & \mathrm{if }\ \xi_{\mathrm{lower}} \leq \xi \leq \xi_{\mathrm{upper}} \\ \frac{1}{2} k \left(\frac{\xi - \xi_{\mathrm{lower}}}{w_{\xi}}\right)^2 & \mathrm{if }\ \xi < \xi_{\mathrm{lower}} \end{array} \right. From d495ea94cd4c69f470f74e83296c0f60c041e2bb Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 29 Sep 2023 12:40:53 -0400 Subject: [PATCH 139/162] Restore multi-threaded tests for NAMD --- namd/tests/library/run_tests.sh | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/namd/tests/library/run_tests.sh b/namd/tests/library/run_tests.sh index aa7fd7f33..efc896c29 100755 --- a/namd/tests/library/run_tests.sh +++ b/namd/tests/library/run_tests.sh @@ -59,11 +59,8 @@ if ! { echo ${DIRLIST} | grep -q 0 ; } then DIRLIST=`eval ls -d [0-9][0-9][0-9]_*` fi -NUM_THREADS=1 NUM_CPUS=$(nproc) -if [ ${NUM_THREADS} -gt ${NUM_CPUS} ] ; then - NUM_THREADS=${NUM_CPUS} -fi +NUM_THREADS=${NUM_THREADS:-${NUM_CPUS}} TPUT_RED='true' TPUT_GREEN='true' From 70acd3a532968384be0c6a0df06a7982983b0d18 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 2 Oct 2023 23:29:21 -0400 Subject: [PATCH 140/162] Use a single TPR file when testing the MDModule interface [test-gromacs-devel] --- gromacs/tests/library/run_tests.sh | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gromacs/tests/library/run_tests.sh b/gromacs/tests/library/run_tests.sh index 7e30acbc5..c04f204ae 100755 --- a/gromacs/tests/library/run_tests.sh +++ b/gromacs/tests/library/run_tests.sh @@ -163,13 +163,12 @@ for dir in ${DIRLIST} ; do if [ "${basename}" == "test" ] ; then ${BINARY} grompp -f ../Common/test.mdp -c ../Common/da.pdb -p ../Common/da.top -t ../Common/da.trr -o ${basename}.tpr >& ${basename}.grompp.out - ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} >& ${basename}.out + ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -nsteps 20 -deffnm ${basename} >& ${basename}.out RETVAL=$? fi if [ "${basename}" == "test.restart" ] ; then - ${BINARY} convert-tpr -s ${basename%.restart}.tpr -nsteps 40 -o ${basename}.tpr >& ${basename}.grompp.out - ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt >& ${basename}.out + ${BINARY} mdrun -s ${basename%.restart}.tpr -ntomp 1 -nsteps 20 -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt >& ${basename}.out RETVAL=$? output=${basename}.part0002 for file in ${output}.* ; do From ab60dcb6100aba15c79ab055ef47b1b5e296d075 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 3 Oct 2023 11:37:25 -0400 Subject: [PATCH 141/162] Revert "Use a single TPR file when testing the MDModule interface" I hadn't noticed earlier the deprecation warning about -nsteps. --- gromacs/tests/library/run_tests.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gromacs/tests/library/run_tests.sh b/gromacs/tests/library/run_tests.sh index c04f204ae..7e30acbc5 100755 --- a/gromacs/tests/library/run_tests.sh +++ b/gromacs/tests/library/run_tests.sh @@ -163,12 +163,13 @@ for dir in ${DIRLIST} ; do if [ "${basename}" == "test" ] ; then ${BINARY} grompp -f ../Common/test.mdp -c ../Common/da.pdb -p ../Common/da.top -t ../Common/da.trr -o ${basename}.tpr >& ${basename}.grompp.out - ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -nsteps 20 -deffnm ${basename} >& ${basename}.out + ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} >& ${basename}.out RETVAL=$? fi if [ "${basename}" == "test.restart" ] ; then - ${BINARY} mdrun -s ${basename%.restart}.tpr -ntomp 1 -nsteps 20 -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt >& ${basename}.out + ${BINARY} convert-tpr -s ${basename%.restart}.tpr -nsteps 40 -o ${basename}.tpr >& ${basename}.grompp.out + ${BINARY} mdrun -s ${basename}.tpr -ntomp 1 -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt >& ${basename}.out RETVAL=$? output=${basename}.part0002 for file in ${output}.* ; do From 08de9386b5abc7cad5382e86001ca3f17de65c73 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 27 Sep 2023 16:01:57 -0400 Subject: [PATCH 142/162] Silence warning about default parameters in virtual functions --- namd/src/colvarproxy_namd.h | 4 ++-- src/colvarproxy.h | 44 +++++++++++++++++-------------------- 2 files changed, 22 insertions(+), 26 deletions(-) diff --git a/namd/src/colvarproxy_namd.h b/namd/src/colvarproxy_namd.h index 4fea9a613..89ba25107 100644 --- a/namd/src/colvarproxy_namd.h +++ b/namd/src/colvarproxy_namd.h @@ -191,13 +191,13 @@ class colvarproxy_namd : public colvarproxy, public GlobalMaster { int load_atoms(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, - double const pdb_field_value = 0.0) override; + double const pdb_field_value) override; int load_coords(char const *filename, std::vector &pos, const std::vector &indices, std::string const &pdb_field, - double const pdb_field_value = 0.0) override; + double const pdb_field_value) override; int scalable_group_coms() override diff --git a/src/colvarproxy.h b/src/colvarproxy.h index f1bc947c0..4b49279fc 100644 --- a/src/colvarproxy.h +++ b/src/colvarproxy.h @@ -72,30 +72,26 @@ class colvarproxy_atoms { /// (costly) set the corresponding atoms_refcount to zero virtual void clear_atom(int index); - /// \brief Select atom IDs from a file (usually PDB) \param filename name of - /// the file \param atoms array to which atoms read from "filename" will be - /// appended \param pdb_field (optional) if the file is a PDB and this - /// string is non-empty, select atoms for which this field is non-zero - /// \param pdb_field_value (optional) if non-zero, select only atoms whose - /// pdb_field equals this - virtual int load_atoms(char const *filename, - cvm::atom_group &atoms, - std::string const &pdb_field, - double pdb_field_value = 0.0); - - /// \brief Load a set of coordinates from a file (usually PDB); if "pos" is - /// already allocated, the number of its elements must match the number of - /// entries in "filename" \param filename name of the file \param pos array - /// of coordinates \param sorted_ids array of sorted internal IDs, used to - /// loop through the file only once \param pdb_field (optional) if the file - /// is a PDB and this string is non-empty, select atoms for which this field - /// is non-zero \param pdb_field_value (optional) if non-zero, select only - /// atoms whose pdb_field equals this - virtual int load_coords(char const *filename, - std::vector &pos, - std::vector const &sorted_ids, - std::string const &pdb_field, - double pdb_field_value = 0.0); + /// \brief Read a selection of atom IDs from a coordinate file (only PDB is supported) + /// \param[in] filename name of the file + /// \param[in,out] atoms array into which atoms will be read from "filename" + /// \param[in] pdb_field if the file is a PDB and this string is non-empty, + /// select atoms for which this field is non-zero + /// \param[in] pdb_field_value if non-zero, select only atoms whose pdb_field equals this + virtual int load_atoms(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, + double pdb_field_value); + + /// \brief Load a set of coordinates from a file (PDB or XYZ) + /// \param[in] filename name of the file + /// \param[in,out] pos array of coordinates; if not empty, the number of its elements must match + /// the number of entries in "filename" + /// \param[in] sorted_ids array of sorted internal IDs, used to loop through the file only once + /// \param[in] pdb_field if the file is a PDB and this string is non-empty, only atoms for which + /// this field is non-zero will be processed + /// \param[in] pdb_field_value if non-zero, process only atoms whose pdb_field equals this + virtual int load_coords(char const *filename, std::vector &pos, + std::vector const &sorted_ids, std::string const &pdb_field, + double pdb_field_value); /// Clear atomic data int reset(); From 3a6554f674523981dce72ba6816f363f02e0e044 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 27 Sep 2023 16:26:44 -0400 Subject: [PATCH 143/162] Remove default/optional arguments in virtual functions --- namd/src/colvarproxy_namd.h | 2 +- src/colvar.cpp | 13 +++++-------- src/colvarbias_abf.cpp | 4 ++-- src/colvarbias_meta.cpp | 14 +++++++------- src/colvarproxy_io.h | 2 +- 5 files changed, 16 insertions(+), 19 deletions(-) diff --git a/namd/src/colvarproxy_namd.h b/namd/src/colvarproxy_namd.h index 89ba25107..8ada3d132 100644 --- a/namd/src/colvarproxy_namd.h +++ b/namd/src/colvarproxy_namd.h @@ -250,7 +250,7 @@ class colvarproxy_namd : public colvarproxy, public GlobalMaster { #endif std::ostream &output_stream(std::string const &output_name, - std::string const description = "file/channel") override; + std::string const description) override; int flush_output_stream(std::string const &output_name) override; diff --git a/src/colvar.cpp b/src/colvar.cpp index b90350737..610ff9c85 100644 --- a/src/colvar.cpp +++ b/src/colvar.cpp @@ -2974,14 +2974,11 @@ int colvar::calc_runave() runave_variance *= 1.0 / cvm::real(runave_length-1); if (runave_outfile.size() > 0) { - std::ostream &runave_os = proxy->output_stream(runave_outfile); - runave_os << std::setw(cvm::it_width) << cvm::step_relative() - << " " - << std::setprecision(cvm::cv_prec) - << std::setw(cvm::cv_width) - << runave << " " - << std::setprecision(cvm::cv_prec) - << std::setw(cvm::cv_width) + std::ostream &runave_os = + proxy->output_stream(runave_outfile, "running average output file"); + runave_os << std::setw(cvm::it_width) << cvm::step_relative() << " " + << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << runave << " " + << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << cvm::sqrt(runave_variance) << "\n"; } } diff --git a/src/colvarbias_abf.cpp b/src/colvarbias_abf.cpp index acca85efa..dcf58a319 100644 --- a/src/colvarbias_abf.cpp +++ b/src/colvarbias_abf.cpp @@ -602,7 +602,7 @@ int colvarbias_abf::replica_share() { template int colvarbias_abf::write_grid_to_file(T const *grid, std::string const &filename, bool close) { - std::ostream &os = cvm::proxy->output_stream(filename); + std::ostream &os = cvm::proxy->output_stream(filename, "multicolumn grid file"); if (!os) { return cvm::error("Error opening file " + filename + " for writing.\n", COLVARS_ERROR | COLVARS_FILE_ERROR); } @@ -620,7 +620,7 @@ template int colvarbias_abf::write_grid_to_file(T const *grid, // (could be implemented as multiple dx files) if (num_variables() > 2 && close) { std::string dx = filename + ".dx"; - std::ostream &dx_os = cvm::proxy->output_stream(dx); + std::ostream &dx_os = cvm::proxy->output_stream(dx, "OpenDX grid file"); if (!dx_os) { return cvm::error("Error opening file " + dx + " for writing.\n", COLVARS_ERROR | COLVARS_FILE_ERROR); } diff --git a/src/colvarbias_meta.cpp b/src/colvarbias_meta.cpp index b00b2482c..3a2bf6b59 100644 --- a/src/colvarbias_meta.cpp +++ b/src/colvarbias_meta.cpp @@ -624,7 +624,7 @@ int colvarbias_meta::update_bias() add_hill(hill(cvm::step_absolute(), hill_weight*hills_scale, colvar_values, colvar_sigmas, replica_id)); std::ostream &replica_hills_os = - cvm::proxy->output_stream(replica_hills_file); + cvm::proxy->output_stream(replica_hills_file, "replica hills file"); if (replica_hills_os) { write_hill(replica_hills_os, hills.back()); } else { @@ -1777,7 +1777,7 @@ int colvarbias_meta::setup_output() // if we're running without grids, use a growing list of "hills" files // otherwise, just one state file and one "hills" file as buffer - std::ostream &list_os = cvm::proxy->output_stream(replica_list_file); + std::ostream &list_os = cvm::proxy->output_stream(replica_list_file, "replica list file"); if (list_os) { list_os << "stateFile " << replica_state_file << "\n"; list_os << "hillsFile " << replica_hills_file << "\n"; @@ -1799,7 +1799,7 @@ int colvarbias_meta::setup_output() if (b_hills_traj) { std::ostream &hills_traj_os = - cvm::proxy->output_stream(hills_traj_file_name()); + cvm::proxy->output_stream(hills_traj_file_name(), "hills trajectory file"); if (!hills_traj_os) { error_code |= COLVARS_FILE_ERROR; } @@ -1902,7 +1902,7 @@ int colvarbias_meta::write_output_files() } if (b_hills_traj) { std::ostream &hills_traj_os = - cvm::proxy->output_stream(hills_traj_file_name()); + cvm::proxy->output_stream(hills_traj_file_name(), "hills trajectory file"); hills_traj_os << hills_traj_os_buf.str(); cvm::proxy->flush_output_stream(hills_traj_file_name()); // clear the buffer @@ -2008,7 +2008,7 @@ int colvarbias_meta::write_replica_state_file() // Write to temporary state file std::string const tmp_state_file(replica_state_file+".tmp"); error_code |= proxy->remove_file(tmp_state_file); - std::ostream &rep_state_os = cvm::proxy->output_stream(tmp_state_file); + std::ostream &rep_state_os = cvm::proxy->output_stream(tmp_state_file, "temporary state file"); if (rep_state_os) { if (!write_state(rep_state_os)) { error_code |= cvm::error("Error: in writing to temporary file \""+ @@ -2027,11 +2027,11 @@ int colvarbias_meta::reopen_replica_buffer_file() { int error_code = COLVARS_OK; colvarproxy *proxy = cvm::proxy; - if (proxy->output_stream(replica_hills_file)) { + if (proxy->output_stream(replica_hills_file, "replica hills file")) { error_code |= proxy->close_output_stream(replica_hills_file); } error_code |= proxy->remove_file(replica_hills_file); - std::ostream &replica_hills_os = proxy->output_stream(replica_hills_file); + std::ostream &replica_hills_os = proxy->output_stream(replica_hills_file, "replica hills file"); if (replica_hills_os) { replica_hills_os.setf(std::ios::scientific, std::ios::floatfield); } else { diff --git a/src/colvarproxy_io.h b/src/colvarproxy_io.h index 80f9f30d9..68f8482bc 100644 --- a/src/colvarproxy_io.h +++ b/src/colvarproxy_io.h @@ -139,7 +139,7 @@ class colvarproxy_io { /// \param output_name File name or identifier /// \param description Purpose of the file virtual std::ostream &output_stream(std::string const &output_name, - std::string const description = "file/channel"); + std::string const description); /// Check if the file/channel is open (without opening it if not) virtual bool output_stream_exists(std::string const &output_name); From 910d97d9436cbbd6e0150cac68c9fae70affd8a4 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 27 Sep 2023 16:43:41 -0400 Subject: [PATCH 144/162] Remove instances of redudant virtual + override declaration --- src/colvaratoms.h | 17 +++++++---------- src/colvarparse.h | 2 +- src/colvarproxy.h | 4 ++-- 3 files changed, 10 insertions(+), 13 deletions(-) diff --git a/src/colvaratoms.h b/src/colvaratoms.h index eaebcbd32..d16ca7bd5 100644 --- a/src/colvaratoms.h +++ b/src/colvaratoms.h @@ -183,7 +183,7 @@ class colvarmodule::atom_group int init(); /// \brief Initialize dependency tree - virtual int init_dependencies() override; + int init_dependencies() override; /// \brief Update data required to calculate cvc's int setup(); @@ -224,16 +224,13 @@ class colvarmodule::atom_group static std::vector ag_features; /// \brief Implementation of the feature list accessor for atom group - virtual const std::vector &features() const override - { - return ag_features; - } - virtual std::vector &modify_features() override + const std::vector &features() const override { return ag_features; } + + std::vector &modify_features() override { return ag_features; } + + static void delete_features() { - return ag_features; - } - static void delete_features() { - for (size_t i=0; i < ag_features.size(); i++) { + for (size_t i = 0; i < ag_features.size(); i++) { delete ag_features[i]; } ag_features.clear(); diff --git a/src/colvarparse.h b/src/colvarparse.h index 402997a31..0ac9c1117 100644 --- a/src/colvarparse.h +++ b/src/colvarparse.h @@ -40,7 +40,7 @@ class colvarparse : public colvarparams { void set_string(std::string const &conf); /// Default destructor - virtual ~colvarparse() override; + ~colvarparse() override; /// Get the configuration string (includes comments) inline std::string const & get_config() const diff --git a/src/colvarproxy.h b/src/colvarproxy.h index 4b49279fc..5011e3fa2 100644 --- a/src/colvarproxy.h +++ b/src/colvarproxy.h @@ -600,9 +600,9 @@ class colvarproxy colvarproxy(); /// Destructor - virtual ~colvarproxy() override; + ~colvarproxy() override; - virtual bool io_available() override; + bool io_available() override; /// Request deallocation of the module (currently only implemented by VMD) virtual int request_deletion(); From ed4c27e71601d2ade3fa085b37390e54f345d0e5 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 27 Sep 2023 16:44:29 -0400 Subject: [PATCH 145/162] Add a few more suggestions from clang-tidy --- src/colvarmodule.h | 2 +- src/colvarproxy.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/colvarmodule.h b/src/colvarmodule.h index a602843b2..32f8c6c7e 100644 --- a/src/colvarmodule.h +++ b/src/colvarmodule.h @@ -784,7 +784,7 @@ class colvarmodule { std::string restart_out_name; /// Pseudo-random number with Gaussian distribution - static real rand_gaussian(void); + static real rand_gaussian(); protected: diff --git a/src/colvarproxy.h b/src/colvarproxy.h index 5011e3fa2..b0bb33591 100644 --- a/src/colvarproxy.h +++ b/src/colvarproxy.h @@ -608,7 +608,7 @@ class colvarproxy virtual int request_deletion(); /// Whether deallocation was requested - inline bool delete_requested() + inline bool delete_requested() const { return b_delete_requested; } From ef715347805d2bc5ce2cd202ac6eb60bf3959a4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Tue, 3 Oct 2023 19:23:12 +0200 Subject: [PATCH 146/162] Revert #573 --- lammps/src/COLVARS/colvarproxy_lammps.h | 2 +- misc_interfaces/C_fortran/colvarproxy_C.h | 2 +- misc_interfaces/stubs/colvarproxy_stub.cpp | 2 +- misc_interfaces/stubs/colvarproxy_stub.h | 2 +- namd/src/colvarproxy_namd.h | 2 +- src/colvarproxy_system.h | 2 +- tests/functional/run_colvars_test.cpp | 2 +- tests/unittests/read_xyz_traj.cpp | 2 +- vmd/src/colvarproxy_vmd.h | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/lammps/src/COLVARS/colvarproxy_lammps.h b/lammps/src/COLVARS/colvarproxy_lammps.h index d55a334a2..5cad6a247 100644 --- a/lammps/src/COLVARS/colvarproxy_lammps.h +++ b/lammps/src/COLVARS/colvarproxy_lammps.h @@ -77,7 +77,7 @@ class colvarproxy_lammps : public colvarproxy { double compute(); // Request to set the units used internally by Colvars - int set_unit_system(std::string const &units_in, bool check_only = false) override; + int set_unit_system(std::string const &units_in, bool check_only) override; /// Convert a command-line argument to string char const *script_obj_to_str(unsigned char *obj); diff --git a/misc_interfaces/C_fortran/colvarproxy_C.h b/misc_interfaces/C_fortran/colvarproxy_C.h index b2e203cf9..8babb0c42 100644 --- a/misc_interfaces/C_fortran/colvarproxy_C.h +++ b/misc_interfaces/C_fortran/colvarproxy_C.h @@ -12,7 +12,7 @@ class colvarproxy_C : public colvarproxy { ~colvarproxy_C(); private: - int set_unit_system(std::string const &units, bool check_only = false) { return 0.; } + int set_unit_system(std::string const &units, bool check_only) { return 0.; } /// \brief Boltzmann constant cvm::real boltzmann() { return 0.; } diff --git a/misc_interfaces/stubs/colvarproxy_stub.cpp b/misc_interfaces/stubs/colvarproxy_stub.cpp index f94273557..bc656f728 100644 --- a/misc_interfaces/stubs/colvarproxy_stub.cpp +++ b/misc_interfaces/stubs/colvarproxy_stub.cpp @@ -78,7 +78,7 @@ int colvarproxy_stub::set_unit_system(std::string const &units_in, bool check_only) { // if check_only is specified, just test for compatibility - // cvolvarmodule does that if new units are requested while colvars are already defined + // colvarmodule sets this flag if new units are requested while colvars are already defined if (check_only) { if ((units != "" && units_in != units) || (units == "" && units_in != "real")) { cvm::error("Specified unit system \"" + units_in + "\" is incompatible with previous setting \"" diff --git a/misc_interfaces/stubs/colvarproxy_stub.h b/misc_interfaces/stubs/colvarproxy_stub.h index ca97d9d6e..ec2ffdd56 100644 --- a/misc_interfaces/stubs/colvarproxy_stub.h +++ b/misc_interfaces/stubs/colvarproxy_stub.h @@ -35,7 +35,7 @@ class colvarproxy_stub : public colvarproxy { void error(std::string const &message) override; - int set_unit_system(std::string const &units_in, bool check_only = false) override; + int set_unit_system(std::string const &units_in, bool check_only) override; int init_atom(int atom_number) override; diff --git a/namd/src/colvarproxy_namd.h b/namd/src/colvarproxy_namd.h index 8ada3d132..d2551c544 100644 --- a/namd/src/colvarproxy_namd.h +++ b/namd/src/colvarproxy_namd.h @@ -82,7 +82,7 @@ class colvarproxy_namd : public colvarproxy, public GlobalMaster { void log(std::string const &message) override; void error(std::string const &message) override; - int set_unit_system(std::string const &units_in, bool check_only = false) override; + int set_unit_system(std::string const &units_in, bool check_only) override; void add_energy(cvm::real energy) override; void request_total_force(bool yesno) override; diff --git a/src/colvarproxy_system.h b/src/colvarproxy_system.h index 6e117eccd..67d0938e5 100644 --- a/src/colvarproxy_system.h +++ b/src/colvarproxy_system.h @@ -32,7 +32,7 @@ class colvarproxy_system { std::string units; /// \brief Request to set the units used internally by Colvars - virtual int set_unit_system(std::string const &units, bool check_only = false); + virtual int set_unit_system(std::string const &units, bool check_only); /// \brief Convert a length from Angstrom to internal inline cvm::real angstrom_to_internal(cvm::real l) const diff --git a/tests/functional/run_colvars_test.cpp b/tests/functional/run_colvars_test.cpp index b10dd5ac5..5ddf4ebb2 100644 --- a/tests/functional/run_colvars_test.cpp +++ b/tests/functional/run_colvars_test.cpp @@ -18,7 +18,7 @@ extern "C" int main(int argc, char *argv[]) { colvarproxy_stub *proxy = new colvarproxy_stub(); // Initialize simple unit system to test file input - err |= proxy->set_unit_system("real"); + err |= proxy->set_unit_system("real", false); if (argc > 3) { err |= proxy->set_output_prefix(argv[3]); diff --git a/tests/unittests/read_xyz_traj.cpp b/tests/unittests/read_xyz_traj.cpp index 80b54cb3f..9a8751ad0 100644 --- a/tests/unittests/read_xyz_traj.cpp +++ b/tests/unittests/read_xyz_traj.cpp @@ -9,7 +9,7 @@ extern "C" int main(int argc, char *argv[]) { colvarproxy_stub *proxy = new colvarproxy_stub(); - proxy->set_unit_system("real"); + proxy->set_unit_system("real", false); proxy->set_output_prefix("test.out"); proxy->colvars->setup_input(); proxy->colvars->setup_output(); diff --git a/vmd/src/colvarproxy_vmd.h b/vmd/src/colvarproxy_vmd.h index fb08beb59..539bc31cb 100644 --- a/vmd/src/colvarproxy_vmd.h +++ b/vmd/src/colvarproxy_vmd.h @@ -68,7 +68,7 @@ class colvarproxy_vmd : public colvarproxy { virtual void error(std::string const &message); - virtual int set_unit_system(std::string const &units_in, bool check_only = false); + virtual int set_unit_system(std::string const &units_in, bool check_only); virtual int run_force_callback(); From 7318e2ceca6c08ad823f09829383ebfcb5be1e1f Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 3 Oct 2023 14:00:42 -0400 Subject: [PATCH 147/162] Update version strings --- doc/cv_version.tex | 2 +- gromacs/src/colvarproxy_gromacs_version.h | 2 +- lammps/src/COLVARS/colvarproxy_lammps_version.h | 2 +- namd/src/colvarproxy_namd_version.h | 2 +- src/colvars_version.h | 2 +- vmd/src/colvarproxy_vmd_version.h | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/cv_version.tex b/doc/cv_version.tex index 761a18ca0..1360e7493 100644 --- a/doc/cv_version.tex +++ b/doc/cv_version.tex @@ -1 +1 @@ -\newcommand{\cvversion}{2023-09-25} +\newcommand{\cvversion}{2023-10-03} diff --git a/gromacs/src/colvarproxy_gromacs_version.h b/gromacs/src/colvarproxy_gromacs_version.h index fea42454b..5f7e40b66 100644 --- a/gromacs/src/colvarproxy_gromacs_version.h +++ b/gromacs/src/colvarproxy_gromacs_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2023-09-27" +#define COLVARPROXY_VERSION "2023-10-03" #endif diff --git a/lammps/src/COLVARS/colvarproxy_lammps_version.h b/lammps/src/COLVARS/colvarproxy_lammps_version.h index 4e7a57535..5f7e40b66 100644 --- a/lammps/src/COLVARS/colvarproxy_lammps_version.h +++ b/lammps/src/COLVARS/colvarproxy_lammps_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2023-09-25" +#define COLVARPROXY_VERSION "2023-10-03" #endif diff --git a/namd/src/colvarproxy_namd_version.h b/namd/src/colvarproxy_namd_version.h index cf70c1d84..5f7e40b66 100644 --- a/namd/src/colvarproxy_namd_version.h +++ b/namd/src/colvarproxy_namd_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2023-09-19" +#define COLVARPROXY_VERSION "2023-10-03" #endif diff --git a/src/colvars_version.h b/src/colvars_version.h index 77028e485..7b21f44a7 100644 --- a/src/colvars_version.h +++ b/src/colvars_version.h @@ -1,3 +1,3 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2023-09-25" +#define COLVARS_VERSION "2023-10-03" #endif diff --git a/vmd/src/colvarproxy_vmd_version.h b/vmd/src/colvarproxy_vmd_version.h index cf70c1d84..5f7e40b66 100644 --- a/vmd/src/colvarproxy_vmd_version.h +++ b/vmd/src/colvarproxy_vmd_version.h @@ -1,3 +1,3 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2023-09-19" +#define COLVARPROXY_VERSION "2023-10-03" #endif From f9fe895a423c962fc161305843b449ee2128a1b8 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 10 Oct 2023 10:16:28 -0400 Subject: [PATCH 148/162] Use persistent GH cache key We can manually delete caches at https://github.com/Colvars/colvars/actions/caches to force updates --- .github/workflows/backend-template.yml | 2 +- .github/workflows/test-library.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/backend-template.yml b/.github/workflows/backend-template.yml index 2bb65b736..69831e80c 100644 --- a/.github/workflows/backend-template.yml +++ b/.github/workflows/backend-template.yml @@ -87,7 +87,7 @@ jobs: uses: actions/cache@v3 with: path: ~/.apptainer - key: Linux-x86_64-containers-build-2023-09-05 + key: Linux-x86_64-containers-build - name: Checkout OpenMM (for Lepton library) uses: actions/checkout@v3 diff --git a/.github/workflows/test-library.yml b/.github/workflows/test-library.yml index 5ac11ea42..232c7e94d 100644 --- a/.github/workflows/test-library.yml +++ b/.github/workflows/test-library.yml @@ -234,7 +234,7 @@ jobs: uses: actions/cache@v3 with: path: ~/.apptainer - key: Linux-x86_64-containers-build-2023-09-05 + key: Linux-x86_64-containers-build - name: Get small downloadable packages uses: actions/checkout@v3 @@ -388,7 +388,7 @@ jobs: uses: actions/cache@v3 with: path: ~/.apptainer - key: Linux-x86_64-containers-build-2023-09-05 + key: Linux-x86_64-containers-build - name: Checkout Sun compiler (Oracle Developer Studio) uses: actions/checkout@v3 From 51d30f57ec210a91f2d7d7feebde475c553695e4 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 10 Oct 2023 10:22:59 -0400 Subject: [PATCH 149/162] Add custom-built Tcl 8.6 to CentOS 7 container --- devel-tools/containers/CentOS7-devel.def | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/devel-tools/containers/CentOS7-devel.def b/devel-tools/containers/CentOS7-devel.def index 616659ec3..165d6dd08 100644 --- a/devel-tools/containers/CentOS7-devel.def +++ b/devel-tools/containers/CentOS7-devel.def @@ -10,8 +10,9 @@ From: centos:7 yum -y update yum -y install epel-release centos-release-scl yum -y install \ - redhat-lsb-core "@Development Tools" \ - ncurses which bc man-db vim emacs screen tmux \ + redhat-lsb-core \ + bc man-db vim emacs tcsh which bash-completion screen tmux \ + "@Development Tools" \ gcc gcc-c++ gcc-gfortran glibc-static libstdc++-static clang cppcheck \ autoconf automake cvs git git-cvs cvsps subversion mercurial \ rh-git227 devtoolset-{7..11} llvm-toolset-7 cmake3 ccache ninja-build \ @@ -55,3 +56,11 @@ EOF git clone https://github.com/jhenin/spiff /tmp/spiff && \ make -C /tmp/spiff && \ install /tmp/spiff/spiff /usr/local/bin/ + + # Build and install Tcl 8.6 to support newer NAMD versions + cd /tmp && \ + curl -O https://newcontinuum.dl.sourceforge.net/project/tcl/Tcl/8.6.13/tcl8.6.13-src.tar.gz && \ + tar xzf tcl8.6.13-src.tar.gz && \ + cd tcl8.6.13/unix && \ + ./configure --prefix=/usr/local && \ + make -j install From 5b39a5b31c6db5251fa9a0fa091c296e25e052a4 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 10 Oct 2023 10:23:22 -0400 Subject: [PATCH 150/162] Let NAMD use Tcl from /usr/local automatically if available --- devel-tools/compile-namd.sh | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/devel-tools/compile-namd.sh b/devel-tools/compile-namd.sh index 6f206b64a..ee4b946c0 100755 --- a/devel-tools/compile-namd.sh +++ b/devel-tools/compile-namd.sh @@ -64,13 +64,20 @@ EOF cmd+=(--charm-arch netlrts-linux-x86_64) fi - # Quick check for more recent Tcl using RH and Debian paths - if [ -f /usr/lib64/libtcl8.6.so ] || \ - [ -f /usr/lib/x86_64-linux-gnu/libtcl8.6.so ] ; then - sed -i 's/-ltcl8.5/-ltcl8.6/' arch/Linux-x86_64.tcl + if ! grep -q -- -ltcl8.6 arch/Linux-x86_64.tcl ; then + # Amend NAMD 2.x arch file for recent Tcl versions under RH and Debian paths + if [ -f /usr/lib64/libtcl8.6.so ] || \ + [ -f /usr/lib/x86_64-linux-gnu/libtcl8.6.so ] ; then + sed -i 's/-ltcl8.5/-ltcl8.6/' arch/Linux-x86_64.tcl + fi + fi + + if [ -f /usr/local/include/tcl.h ] ; then + cmd+=(--tcl-prefix /usr/local) + else + cmd+=(--tcl-prefix ${TCL_HOME:-/usr}) fi - cmd+=(--tcl-prefix ${TCL_HOME:-/usr}) cmd+=(--with-fftw3 --fftw-prefix ${FFTW_HOME:-/usr}) local python_version=$(python3 --version 2> /dev/null | cut -d' ' -f 2) @@ -83,10 +90,10 @@ EOF eval ${cmd[@]} - if pushd ${dirname} ; then + if pushd ${dirname} ; then make -j$(nproc --all) ret_code=$? - popd + popd else ret_code=1 fi From dc2a54e07741ffb09feeffc9e85161b7483b21ec Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 10 Oct 2023 12:01:33 -0400 Subject: [PATCH 151/162] Make cache key unique to not confuse actions cache --- .github/workflows/backend-template.yml | 2 +- .github/workflows/test-library.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/backend-template.yml b/.github/workflows/backend-template.yml index 69831e80c..d9c1f53b8 100644 --- a/.github/workflows/backend-template.yml +++ b/.github/workflows/backend-template.yml @@ -87,7 +87,7 @@ jobs: uses: actions/cache@v3 with: path: ~/.apptainer - key: Linux-x86_64-containers-build + key: Linux-x86_64-containers-build-code - name: Checkout OpenMM (for Lepton library) uses: actions/checkout@v3 diff --git a/.github/workflows/test-library.yml b/.github/workflows/test-library.yml index 232c7e94d..8faa870f3 100644 --- a/.github/workflows/test-library.yml +++ b/.github/workflows/test-library.yml @@ -234,7 +234,7 @@ jobs: uses: actions/cache@v3 with: path: ~/.apptainer - key: Linux-x86_64-containers-build + key: Linux-x86_64-containers-build-code - name: Get small downloadable packages uses: actions/checkout@v3 @@ -388,7 +388,7 @@ jobs: uses: actions/cache@v3 with: path: ~/.apptainer - key: Linux-x86_64-containers-build + key: Linux-x86_64-containers-build-code - name: Checkout Sun compiler (Oracle Developer Studio) uses: actions/checkout@v3 From 36e0d270240090bcba8e17437e12778687111a11 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 10 Oct 2023 14:42:45 -0400 Subject: [PATCH 152/162] Set TCL_HOME variable when building NAMD 3 --- .github/workflows/test-backends.yml | 2 ++ devel-tools/compile-namd.sh | 11 +++++++---- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/.github/workflows/test-backends.yml b/.github/workflows/test-backends.yml index 79233b8b3..a68b846e8 100644 --- a/.github/workflows/test-backends.yml +++ b/.github/workflows/test-backends.yml @@ -74,6 +74,8 @@ jobs: secrets: # Choice of license by UIUC prevents sharing the code, hence the secret private_key: ${{ secrets.PULL_NAMD_KEY }} + env: + TCL_HOME: /opt/tcl/8.6 vmd: name: VMD diff --git a/devel-tools/compile-namd.sh b/devel-tools/compile-namd.sh index ee4b946c0..18746b612 100755 --- a/devel-tools/compile-namd.sh +++ b/devel-tools/compile-namd.sh @@ -72,11 +72,14 @@ EOF fi fi - if [ -f /usr/local/include/tcl.h ] ; then - cmd+=(--tcl-prefix /usr/local) - else - cmd+=(--tcl-prefix ${TCL_HOME:-/usr}) + if [ -z "${TCL_HOME}" ] ; then + if [ -f /usr/local/include/tcl.h ] ; then + export TCL_HOME=/usr/local + else + export TCL_HOME=/usr + fi fi + cmd+=(--tcl-prefix ${TCL_HOME}) cmd+=(--with-fftw3 --fftw-prefix ${FFTW_HOME:-/usr}) From 0c2ef944a29a2eb79d2655c60383fd962d57fb94 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 10 Oct 2023 17:17:44 -0400 Subject: [PATCH 153/162] Only print warning once --- colvartools/plot_colvars_traj.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/colvartools/plot_colvars_traj.py b/colvartools/plot_colvars_traj.py index 00f3e42ab..981e0053f 100644 --- a/colvartools/plot_colvars_traj.py +++ b/colvartools/plot_colvars_traj.py @@ -26,6 +26,7 @@ def __init__(self, name): self._name = name self._step = np.zeros(shape=(0), dtype=np.int64) self._colvar = np.zeros(shape=(0), dtype=np.float64) + self._warned_dimensions = False def __len__(self): """Returns the length of the trajectory""" @@ -40,11 +41,12 @@ def __str__(self): def _set_num_dimensions(self, n_d): """Set the number of components of the collective variable""" - if (len(self) > 0): + if len(self) > 0 and not self._warned_dimensions: print("Warning: changing the number of dimensions " - "of collective variable \""+self._name+ + "of collective variable \""+self._name + "\" after it has already been read.") - if (n_d > 1): + self._warned_dimensions = True + if n_d > 1: self._colvar.resize((len(self), n_d)) else: self._colvar.resize((len(self))) From c29b614482bf8c559b67573bb6fa8ba9da17e504 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 10 Oct 2023 16:21:21 -0400 Subject: [PATCH 154/162] Remove illegal Actions syntax --- .github/workflows/test-backends.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/test-backends.yml b/.github/workflows/test-backends.yml index a68b846e8..79233b8b3 100644 --- a/.github/workflows/test-backends.yml +++ b/.github/workflows/test-backends.yml @@ -74,8 +74,6 @@ jobs: secrets: # Choice of license by UIUC prevents sharing the code, hence the secret private_key: ${{ secrets.PULL_NAMD_KEY }} - env: - TCL_HOME: /opt/tcl/8.6 vmd: name: VMD From e2c412046ebbc575eb32568225bc73deeb6c1f73 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 10 Oct 2023 14:42:45 -0400 Subject: [PATCH 155/162] Use pre-built Tcl 8.6 library from UIUC --- devel-tools/build_test_library.cmake | 4 ++-- devel-tools/compile-namd.sh | 7 ++++++- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/devel-tools/build_test_library.cmake b/devel-tools/build_test_library.cmake index 53fb22bd1..eb778c905 100644 --- a/devel-tools/build_test_library.cmake +++ b/devel-tools/build_test_library.cmake @@ -31,8 +31,8 @@ if(DEFINED CMAKE_SYSTEM_NAME AND COLVARS_TCL) if(EXISTS "${COLVARS_SOURCE_DIR}/devel-tools/packages") if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux") - set(TCL_DIR "${COLVARS_SOURCE_DIR}/devel-tools/packages/tcl8.5.9-linux-x86_64") - set(TCL_LIBRARY "libtcl8.5.a") + set(TCL_DIR "${COLVARS_SOURCE_DIR}/devel-tools/packages/tcl8.6.13-linux-x86_64-threaded") + set(TCL_LIBRARY "libtcl8.6.a") endif() if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") diff --git a/devel-tools/compile-namd.sh b/devel-tools/compile-namd.sh index 18746b612..949f2c77c 100755 --- a/devel-tools/compile-namd.sh +++ b/devel-tools/compile-namd.sh @@ -64,7 +64,11 @@ EOF cmd+=(--charm-arch netlrts-linux-x86_64) fi - if ! grep -q -- -ltcl8.6 arch/Linux-x86_64.tcl ; then + if grep -q -- -ltcl8.6 arch/Linux-x86_64.tcl ; then + if [ -d $(dirname $0)/packages/tcl8.6.13-linux-x86_64-threaded ] ; then + export TCL_HOME=$(dirname $0)/packages/tcl8.6.13-linux-x86_64-threaded + fi + else # Amend NAMD 2.x arch file for recent Tcl versions under RH and Debian paths if [ -f /usr/lib64/libtcl8.6.so ] || \ [ -f /usr/lib/x86_64-linux-gnu/libtcl8.6.so ] ; then @@ -79,6 +83,7 @@ EOF export TCL_HOME=/usr fi fi + cmd+=(--tcl-prefix ${TCL_HOME}) cmd+=(--with-fftw3 --fftw-prefix ${FFTW_HOME:-/usr}) From 6195ce15c0fa6393257fce6e6a4eb04bed5460cf Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 12 Oct 2023 13:34:48 -0400 Subject: [PATCH 156/162] Prepend directory to avoid error from action scanning root folder --- .github/workflows/backend-template.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/backend-template.yml b/.github/workflows/backend-template.yml index d9c1f53b8..6420e65f6 100644 --- a/.github/workflows/backend-template.yml +++ b/.github/workflows/backend-template.yml @@ -167,7 +167,7 @@ jobs: uses: actions/upload-artifact@v3 with: name: failed-library-test-diffs-${{ inputs.backend_name }} - path: ${{ inputs.test_lib_directory }}/*/*.diff + path: ${{ github.workspace }}/${{ inputs.test_lib_directory }}/*/*.diff - name: Run regression tests for ${{ inputs.backend_name }} interface code if: ${{ inputs.test_interface_directory }} @@ -182,7 +182,7 @@ jobs: uses: actions/upload-artifact@v3 with: name: failed-interface-test-diffs-${{ inputs.backend_name }} - path: ${{ inputs.test_interface_directory }}/*/*.diff + path: ${{ github.workspace }}/${{ inputs.test_interface_directory }}/*/*.diff - name: Run regression tests for library code with ${{ inputs.backend_name }} (binary restarts) if: ${{ inputs.test_lib_directory }} From b49199a02082589a37aad3a0fdf671983e14a698 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 12 Oct 2023 15:20:00 -0400 Subject: [PATCH 157/162] Fix install instructions for Tcl 8.6 in container --- devel-tools/containers/CentOS7-devel.def | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/devel-tools/containers/CentOS7-devel.def b/devel-tools/containers/CentOS7-devel.def index 165d6dd08..201b8f5c8 100644 --- a/devel-tools/containers/CentOS7-devel.def +++ b/devel-tools/containers/CentOS7-devel.def @@ -59,8 +59,9 @@ EOF # Build and install Tcl 8.6 to support newer NAMD versions cd /tmp && \ + rm -f tcl8.6.13-src.tar.gz && \ curl -O https://newcontinuum.dl.sourceforge.net/project/tcl/Tcl/8.6.13/tcl8.6.13-src.tar.gz && \ tar xzf tcl8.6.13-src.tar.gz && \ cd tcl8.6.13/unix && \ - ./configure --prefix=/usr/local && \ - make -j install + ./configure --prefix=/opt/tcl/8.6 && \ + make -j16 && make install From 3acfd2454791fe6d043eba8ec4b38da97519c28c Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 12 Oct 2023 15:20:13 -0400 Subject: [PATCH 158/162] Fix detection of pre-built Tcl --- devel-tools/compile-namd.sh | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/devel-tools/compile-namd.sh b/devel-tools/compile-namd.sh index 949f2c77c..ee772b32e 100755 --- a/devel-tools/compile-namd.sh +++ b/devel-tools/compile-namd.sh @@ -4,6 +4,9 @@ source $(dirname $0)/load-recent-git.sh source $(dirname $0)/set-ccache.sh +# Save path to be used later +devel_tools_folder=$(realpath $(dirname $0)) + compile_namd_target() { @@ -65,8 +68,8 @@ EOF fi if grep -q -- -ltcl8.6 arch/Linux-x86_64.tcl ; then - if [ -d $(dirname $0)/packages/tcl8.6.13-linux-x86_64-threaded ] ; then - export TCL_HOME=$(dirname $0)/packages/tcl8.6.13-linux-x86_64-threaded + if [ -d ${devel_tools_folder}/packages/tcl8.6.13-linux-x86_64-threaded ] ; then + export TCL_HOME=${devel_tools_folder}/packages/tcl8.6.13-linux-x86_64-threaded fi else # Amend NAMD 2.x arch file for recent Tcl versions under RH and Debian paths From 3616cbb4739b3ef21937a5a8dfa621366ff5ab9c Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 12 Oct 2023 15:56:59 -0400 Subject: [PATCH 159/162] Use pre-built Tcl in container as well --- devel-tools/containers/CentOS7-devel.def | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/devel-tools/containers/CentOS7-devel.def b/devel-tools/containers/CentOS7-devel.def index 201b8f5c8..7ea04a13b 100644 --- a/devel-tools/containers/CentOS7-devel.def +++ b/devel-tools/containers/CentOS7-devel.def @@ -57,11 +57,12 @@ EOF make -C /tmp/spiff && \ install /tmp/spiff/spiff /usr/local/bin/ - # Build and install Tcl 8.6 to support newer NAMD versions + # Install Tcl 8.6 to support newer NAMD versions cd /tmp && \ - rm -f tcl8.6.13-src.tar.gz && \ - curl -O https://newcontinuum.dl.sourceforge.net/project/tcl/Tcl/8.6.13/tcl8.6.13-src.tar.gz && \ - tar xzf tcl8.6.13-src.tar.gz && \ - cd tcl8.6.13/unix && \ - ./configure --prefix=/opt/tcl/8.6 && \ - make -j16 && make install + rm -f tcl8.6.13-linux-x86_64-threaded.tar.gz && \ + curl -O https://www.ks.uiuc.edu/Research/namd/libraries/tcl8.6.13-linux-x86_64-threaded.tar.gz && \ + tar xzf tcl8.6.13-linux-x86_64-threaded.tar.gz && \ + cd tcl8.6.13-linux-x86_64-threaded && \ + find . -type f -exec install -v -D "{}" "/opt/tcl/8.6/{}" \; && \ + cd && \ + rm -fr /tmp/tcl8.6.13-linux-x86_64-threaded /tmp/tcl8.6.13-linux-x86_64-threaded.tar.gz From 46f1d6d7bb154b7b307000356db00d51ed70b089 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Fri, 6 Oct 2023 18:32:20 +0200 Subject: [PATCH 160/162] Only compute virial if requested in GMX As done in other modules. Could improve performance in NVT simulations. --- gromacs/gromacs-2020.x/colvarproxy_gromacs.cpp | 13 ++++++++++--- gromacs/gromacs-2021.x/colvarproxy_gromacs.cpp | 13 ++++++++++--- gromacs/gromacs-2022.x/colvarproxy_gromacs.cpp | 13 ++++++++++--- gromacs/gromacs-2023.x/colvarproxy_gromacs.cpp | 13 ++++++++++--- .../applied_forces/colvars/colvarsforceprovider.cpp | 9 +++++++-- 5 files changed, 47 insertions(+), 14 deletions(-) diff --git a/gromacs/gromacs-2020.x/colvarproxy_gromacs.cpp b/gromacs/gromacs-2020.x/colvarproxy_gromacs.cpp index ab959e126..2db82a776 100644 --- a/gromacs/gromacs-2020.x/colvarproxy_gromacs.cpp +++ b/gromacs/gromacs-2020.x/colvarproxy_gromacs.cpp @@ -471,6 +471,7 @@ void colvarproxy_gromacs::calculateForces( const gmx::ArrayRef &f_out = forceProviderOutput->forceWithVirial_.force_; matrix local_colvars_virial = { { 0 } }; + const bool computeVirial = forceProviderOutput->forceWithVirial_.computeVirial_; // Pass the applied forces back to GROMACS for (int i = 0; i < n_colvars_atoms; i++) @@ -482,16 +483,22 @@ void colvarproxy_gromacs::calculateForces( const int *locndx = cr->dd->ga2la->findHome(i_global); if (locndx) { f_out[*locndx] += f_colvars[i]; - add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + if (computeVirial) { + add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + } } // Do nothing if atom is not local } else { // Non MPI-parallel f_out[i_global] += f_colvars[i]; - add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + if (computeVirial) { + add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + } } } - forceProviderOutput->forceWithVirial_.addVirialContribution(local_colvars_virial); + if (computeVirial) { + forceProviderOutput->forceWithVirial_.addVirialContribution(local_colvars_virial); + } return; } diff --git a/gromacs/gromacs-2021.x/colvarproxy_gromacs.cpp b/gromacs/gromacs-2021.x/colvarproxy_gromacs.cpp index 892637ea9..3ae4a69f2 100644 --- a/gromacs/gromacs-2021.x/colvarproxy_gromacs.cpp +++ b/gromacs/gromacs-2021.x/colvarproxy_gromacs.cpp @@ -473,6 +473,7 @@ void colvarproxy_gromacs::calculateForces( const gmx::ArrayRef &f_out = forceProviderOutput->forceWithVirial_.force_; matrix local_colvars_virial = { { 0 } }; + const bool computeVirial = forceProviderOutput->forceWithVirial_.computeVirial_; // Pass the applied forces back to GROMACS for (int i = 0; i < n_colvars_atoms; i++) @@ -484,16 +485,22 @@ void colvarproxy_gromacs::calculateForces( const int *locndx = cr->dd->ga2la->findHome(i_global); if (locndx) { f_out[*locndx] += f_colvars[i]; - add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + if (computeVirial) { + add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + } } // Do nothing if atom is not local } else { // Non MPI-parallel f_out[i_global] += f_colvars[i]; - add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + if (computeVirial) { + add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + } } } - forceProviderOutput->forceWithVirial_.addVirialContribution(local_colvars_virial); + if (computeVirial) { + forceProviderOutput->forceWithVirial_.addVirialContribution(local_colvars_virial); + } return; } diff --git a/gromacs/gromacs-2022.x/colvarproxy_gromacs.cpp b/gromacs/gromacs-2022.x/colvarproxy_gromacs.cpp index 59b8661f5..02b673f02 100644 --- a/gromacs/gromacs-2022.x/colvarproxy_gromacs.cpp +++ b/gromacs/gromacs-2022.x/colvarproxy_gromacs.cpp @@ -473,6 +473,7 @@ void colvarproxy_gromacs::calculateForces( const gmx::ArrayRef &f_out = forceProviderOutput->forceWithVirial_.force_; matrix local_colvars_virial = { { 0 } }; + const bool computeVirial = forceProviderOutput->forceWithVirial_.computeVirial_; // Pass the applied forces back to GROMACS for (int i = 0; i < n_colvars_atoms; i++) @@ -484,16 +485,22 @@ void colvarproxy_gromacs::calculateForces( const int *locndx = cr->dd->ga2la->findHome(i_global); if (locndx) { f_out[*locndx] += f_colvars[i]; - add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + if (computeVirial) { + add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + } } // Do nothing if atom is not local } else { // Non MPI-parallel f_out[i_global] += f_colvars[i]; - add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + if (computeVirial) { + add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + } } } - forceProviderOutput->forceWithVirial_.addVirialContribution(local_colvars_virial); + if (computeVirial) { + forceProviderOutput->forceWithVirial_.addVirialContribution(local_colvars_virial); + } return; } diff --git a/gromacs/gromacs-2023.x/colvarproxy_gromacs.cpp b/gromacs/gromacs-2023.x/colvarproxy_gromacs.cpp index 6b17cda5a..d9eba8713 100644 --- a/gromacs/gromacs-2023.x/colvarproxy_gromacs.cpp +++ b/gromacs/gromacs-2023.x/colvarproxy_gromacs.cpp @@ -473,6 +473,7 @@ void colvarproxy_gromacs::calculateForces( const gmx::ArrayRef &f_out = forceProviderOutput->forceWithVirial_.force_; matrix local_colvars_virial = { { 0 } }; + const bool computeVirial = forceProviderOutput->forceWithVirial_.computeVirial_; // Pass the applied forces back to GROMACS for (int i = 0; i < n_colvars_atoms; i++) @@ -484,16 +485,22 @@ void colvarproxy_gromacs::calculateForces( const int *locndx = cr->dd->ga2la->findHome(i_global); if (locndx) { f_out[*locndx] += f_colvars[i]; - add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + if (computeVirial) { + add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + } } // Do nothing if atom is not local } else { // Non MPI-parallel f_out[i_global] += f_colvars[i]; - add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + if (computeVirial) { + add_virial_term(local_colvars_virial, f_colvars[i], x_colvars_unwrapped[i]); + } } } - forceProviderOutput->forceWithVirial_.addVirialContribution(local_colvars_virial); + if (computeVirial) { + forceProviderOutput->forceWithVirial_.addVirialContribution(local_colvars_virial); + } return; } diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp index 19031dc00..bd414fda3 100644 --- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp +++ b/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp @@ -397,6 +397,7 @@ void ColvarsForceProvider::calculateForces(const ForceProviderInput& forceProvid const gmx::ArrayRef& f_out = forceProviderOutput->forceWithVirial_.force_; matrix local_colvars_virial = { { 0 } }; + const bool computeVirial = forceProviderOutput->forceWithVirial_.computeVirial_; const auto& localcolvarsIndex = colvars_atoms->localIndex(); const auto& collectivecolvarsIndex = colvars_atoms->collectiveIndex(); // Loop through local atoms to aply the colvars forces @@ -408,10 +409,14 @@ void ColvarsForceProvider::calculateForces(const ForceProviderInput& forceProvid int i_colvars = collectivecolvarsIndex[l]; /* Add */ rvec_inc(f_out[i_local], f_colvars[i_colvars]); - add_virial_term(local_colvars_virial, f_colvars[i_colvars], x_colvars_unwrapped[i_colvars]); + if (computeVirial) { + add_virial_term(local_colvars_virial, f_colvars[i_colvars], x_colvars_unwrapped[i_colvars]); + } } - forceProviderOutput->forceWithVirial_.addVirialContribution(local_colvars_virial); + if (computeVirial) { + forceProviderOutput->forceWithVirial_.addVirialContribution(local_colvars_virial); + } // Re-set the flag for proper update gmx_bNS = false; From ed44f84820c3f28bad87d9891f6ef0d3003fe378 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 13 Oct 2023 12:08:36 -0400 Subject: [PATCH 161/162] Use GitHub-hosted container images for CI workflows --- .github/workflows/backend-template.yml | 16 ++------------ .github/workflows/test-library.yml | 29 +++++--------------------- 2 files changed, 7 insertions(+), 38 deletions(-) diff --git a/.github/workflows/backend-template.yml b/.github/workflows/backend-template.yml index 6420e65f6..ed7c9f355 100644 --- a/.github/workflows/backend-template.yml +++ b/.github/workflows/backend-template.yml @@ -81,14 +81,6 @@ jobs: restore-keys: | ${{ runner.os }}-build-${{ inputs.backend_name }}- - # Using an exact key to forgo saving it in case of a match (tarring up - # is expensive); also including a date to allow a force-update. - - name: Load containers cache - uses: actions/cache@v3 - with: - path: ~/.apptainer - key: Linux-x86_64-containers-build-code - - name: Checkout OpenMM (for Lepton library) uses: actions/checkout@v3 with: @@ -132,12 +124,8 @@ jobs: shell: bash working-directory: devel-tools run: | - # Pull all containers used to build backends - # (contains build tools, OpenMPI, FFTW, Tcl/Tk and Charm++) - apptainer remote status SylabsCloud || apptainer remote add --no-login SylabsCloud cloud.sylabs.io - apptainer remote use SylabsCloud - apptainer pull CentOS7-devel.sif library://giacomofiorin/default/colvars_development:centos7 - apptainer pull CentOS9-devel.sif library://giacomofiorin/default/colvars_development:centos9 + apptainer pull CentOS7-devel.sif oras://ghcr.io/Colvars/devel-containers:CentOS7-devel + apptainer pull CentOS9-devel.sif oras://ghcr.io/Colvars/devel-containers:CentOS9-devel - name: Update and build ${{ inputs.backend_name }} shell: bash diff --git a/.github/workflows/test-library.yml b/.github/workflows/test-library.yml index 8faa870f3..875a16f13 100644 --- a/.github/workflows/test-library.yml +++ b/.github/workflows/test-library.yml @@ -228,14 +228,6 @@ jobs: key: ${{ runner.os }}-build-multiple-${{ github.sha }} restore-keys: ${{ runner.os }}-build-multiple- - # Using an exact key to forgo saving it in case of a match (tarring up - # is expensive); also including a date to allow a force-update. - - name: Load containers cache - uses: actions/cache@v3 - with: - path: ~/.apptainer - key: Linux-x86_64-containers-build-code - - name: Get small downloadable packages uses: actions/checkout@v3 with: @@ -250,14 +242,12 @@ jobs: sudo apt update sudo apt install -y apptainer-suid - - name: Get container image + - name: Get container images for build dependencies shell: bash working-directory: devel-tools run: | - apptainer remote status SylabsCloud || apptainer remote add --no-login SylabsCloud cloud.sylabs.io - apptainer remote use SylabsCloud - apptainer pull CentOS7-devel.sif library://giacomofiorin/default/colvars_development:centos7 - apptainer pull CentOS9-devel.sif library://giacomofiorin/default/colvars_development:centos9 + apptainer pull CentOS7-devel.sif oras://ghcr.io/Colvars/devel-containers:CentOS7-devel + apptainer pull CentOS9-devel.sif oras://ghcr.io/Colvars/devel-containers:CentOS9-devel - name: GCC 4.8, C++11 (CentOS 7) env: @@ -384,12 +374,6 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Load containers cache - uses: actions/cache@v3 - with: - path: ~/.apptainer - key: Linux-x86_64-containers-build-code - - name: Checkout Sun compiler (Oracle Developer Studio) uses: actions/checkout@v3 with: @@ -412,14 +396,11 @@ jobs: sudo apt update sudo apt install -y apptainer-suid - - name: Get container image + - name: Get container images for build dependencies shell: bash working-directory: devel-tools run: | - apptainer remote status SylabsCloud || apptainer remote add --no-login SylabsCloud cloud.sylabs.io - apptainer remote use SylabsCloud - apptainer pull CentOS7-devel.sif library://giacomofiorin/default/colvars_development:centos7 - apptainer pull CentOS9-devel.sif library://giacomofiorin/default/colvars_development:centos9 + apptainer pull CentOS7-devel.sif oras://ghcr.io/Colvars/devel-containers:CentOS7-devel - name: Build library with Sun compiler (Oracle Developer Studio) shell: bash From 7b12838a143171faea007d364cd01127c4650847 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 13 Oct 2023 12:34:31 -0400 Subject: [PATCH 162/162] Use GH-hosted image for TeXLive container as well --- .github/workflows/test-library.yml | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/.github/workflows/test-library.yml b/.github/workflows/test-library.yml index 875a16f13..3a3a9776e 100644 --- a/.github/workflows/test-library.yml +++ b/.github/workflows/test-library.yml @@ -93,12 +93,6 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Load containers cache - uses: actions/cache@v3 - with: - path: ~/.apptainer - key: Linux-x86_64-containers-build-doc-2023-07-19 - - name: Install Apptainer shell: bash run: | @@ -110,9 +104,7 @@ jobs: shell: bash working-directory: devel-tools run: | - apptainer remote status SylabsCloud || apptainer remote add --no-login SylabsCloud cloud.sylabs.io - apptainer remote use SylabsCloud - apptainer pull texlive.sif library://giacomofiorin/default/colvars_development:texlive + apptainer pull texlive.sif oras://ghcr.io/Colvars/devel-containers:texlive - name: Checkout website repository uses: actions/checkout@v3