merge torchann squash

doc/colvars-code-refs.bib

@@ -342,4 +342,5 @@ @article{White2014
 % coordNum pairlist
 % Custom functions (Lepton)
 % Scripted functions (Tcl)
+% torchANN colvar component 
 % --- END ---

gromacs/cmake/gmxManageColvars.cmake

@@ -55,3 +55,15 @@ function(gmx_include_colvars_headers)
         target_include_directories(libgromacs PRIVATE ${PROJECT_SOURCE_DIR}/src/external/colvars)
     endif()
 endfunction()
+
+function(gmx_set_colvars_torch)
+  find_package(Torch)
+  if (Torch_FOUND)
+    set_property(TARGET colvars PROPERTY CXX_STANDARD 17)
+    target_compile_definitions(colvars PRIVATE -DTORCH)
+    target_compile_options(colvars PRIVATE ${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS})
+    target_include_directories(colvars PRIVATE ${TORCH_INCLUDE_DIRS})
+    target_link_libraries(libgromacs PRIVATE "${TORCH_LIBRARIES}")
+  endif()
+endfunction()
+

gromacs/gromacs-2020.x.patch

@@ -3,23 +3,23 @@ index 0911eb2a45..5530c1576a 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
 @@ -200,6 +200,9 @@ option(GMX_USE_OPENCL "Enable OpenCL acceleration" OFF)
-
+ 
  option(GMX_INSTALL_LEGACY_API "Install legacy headers" OFF)
-
+ 
 +include(gmxManageColvars)
 +include(gmxManageLepton)
 +
  # The earliest version of the CUDA toolkit that supports c++14 is 9.0
  set(REQUIRED_CUDA_VERSION 9.0)
  set(REQUIRED_CUDA_COMPUTE_CAPABILITY 3.0)
 diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
-index 9249a7a08f..18b45ff01f 100644
+index 9249a7a08f..ab5a927fb7 100644
 --- a/src/gromacs/CMakeLists.txt
 +++ b/src/gromacs/CMakeLists.txt
 @@ -137,6 +137,12 @@ if (WIN32)
  endif()
  list(APPEND libgromacs_object_library_dependencies thread_mpi)
-
+ 
 +# Add Colvars and Lepton targets, embed their object code in libgromacs
 +gmx_manage_colvars()
 +gmx_manage_lepton()
@@ -29,11 +29,13 @@ index 9249a7a08f..18b45ff01f 100644
  configure_file(version.h.cmakein version.h)
  if(GMX_INSTALL_LEGACY_API)
    install(FILES
-@@ -195,6 +201,8 @@ else()
+@@ -195,6 +201,10 @@ else()
      add_library(libgromacs ${LIBGROMACS_SOURCES})
  endif()
-
+ 
 +gmx_include_colvars_headers()
++
++gmx_set_colvars_torch()
 +
  # Add these contents first because linking their tests can take a lot
  # of time, so we want lots of parallel work still available after
@@ -58,8 +60,8 @@ index 9c6cfe4213..ec2e64f61f 100644
 +/* COLVARS : add a value of 1000 for Colvars support and
 + * prevent regular GROMACS to read colvars .cpt files */
 +static const int cpt_version = cptv_Count - 1 + 1000;
-
-
+ 
+ 
  const char* est_names[estNR] = { "FE-lambda",
 @@ -1178,6 +1181,15 @@ static void do_cpt_header(XDR* xd, gmx_bool bRead, FILE* list, CheckpointHeaderC
      {
@@ -75,12 +77,12 @@ index 9c6cfe4213..ec2e64f61f 100644
 +    }
 +
  }
-
+ 
  static int do_cpt_footer(XDR* xd, int file_version)
 @@ -1909,6 +1921,35 @@ static int do_cpt_EDstate(XDR* xd, gmx_bool bRead, int nED, edsamhistory_t* EDst
      return 0;
  }
-
+ 
 +/* This function stores the last whole configuration of the colvars atoms in the .cpt file */
 +static int do_cpt_colvars(XDR* xd, gmx_bool bRead, int ecolvars, colvarshistory_t* colvarsstate, FILE* list)
 +{
@@ -116,7 +118,7 @@ index 9c6cfe4213..ec2e64f61f 100644
 @@ -2330,6 +2371,10 @@ void write_checkpoint(const char*                   fn,
      swaphistory_t* swaphist    = observablesHistory->swapHistory.get();
      int            eSwapCoords = (swaphist ? swaphist->eSwapCoords : eswapNO);
-
+ 
 +    /* COLVARS */
 +    colvarshistory_t* colvarshist = observablesHistory->colvarsHistory.get();
 +    int               ecolvars    = (colvarshist ? colvarshist->n_atoms : 0);
@@ -145,7 +147,7 @@ index 9c6cfe4213..ec2e64f61f 100644
 @@ -2802,6 +2849,17 @@ static void read_checkpoint(const char*                   fn,
          cp_error();
      }
-
+ 
 +    if (headerContents->ecolvars != 0 && observablesHistory->colvarsHistory == nullptr)
 +    {
 +        observablesHistory->colvarsHistory = std::make_unique<colvarshistory_t>(colvarshistory_t{});
@@ -163,7 +165,7 @@ index 9c6cfe4213..ec2e64f61f 100644
 @@ -2957,6 +3015,13 @@ static CheckpointHeaderContents read_checkpoint_data(t_fileio*
          cp_error();
      }
-
+ 
 +    colvarshistory_t colvarshist = {};
 +    ret = do_cpt_colvars(gmx_fio_getxdr(fp), TRUE, headerContents.ecolvars, &colvarshist, nullptr);
 +    if (ret)
@@ -172,12 +174,12 @@ index 9c6cfe4213..ec2e64f61f 100644
 +    }
 +
      ret = do_cpt_files(gmx_fio_getxdr(fp), TRUE, outputfiles, nullptr, headerContents.file_version);
-
+ 
      if (ret)
 @@ -3065,6 +3130,12 @@ void list_checkpoint(const char* fn, FILE* out)
          ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, headerContents.eSwapCoords, &swaphist, out);
      }
-
+ 
 +    if (ret == 0)
 +    {
 +        colvarshistory_t colvarshist = {};
@@ -198,7 +200,7 @@ index fb8f7268be..6feb181b30 100644
 +    //! Colvars
 +    int ecolvars;
  };
-
+ 
  /* Write a checkpoint to <fn>.cpt
 diff --git a/src/gromacs/mdlib/energyoutput.cpp b/src/gromacs/mdlib/energyoutput.cpp
 index f2532f3dfe..c761958854 100644
@@ -210,7 +212,7 @@ index f2532f3dfe..c761958854 100644
      bEner_[F_ORIRESDEV]  = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
 -    bEner_[F_COM_PULL]   = ((ir->bPull && pull_have_potential(pull_work)) || ir->bRot);
 +    bEner_[F_COM_PULL]   = ((ir->bPull && pull_have_potential(pull_work)) || ir->bRot || ir->bColvars);
-
+ 
      MdModulesEnergyOutputToDensityFittingRequestChecker mdModulesAddOutputToDensityFittingFieldRequest;
      mdModulesNotifier.notifier_.notify(&mdModulesAddOutputToDensityFittingFieldRequest);
 diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
@@ -220,7 +222,7 @@ index f2528d78b4..7f91cac83d 100644
 @@ -114,6 +114,8 @@
  #include "gromacs/utility/strconvert.h"
  #include "gromacs/utility/sysinfo.h"
-
+ 
 +#include "colvarproxy_gromacs.h"
 +
  using gmx::AtomLocality;
@@ -242,7 +244,7 @@ index f2528d78b4..7f91cac83d 100644
 +
          gmx::ForceProviderInput  forceProviderInput(x, *mdatoms, t, box, *cr);
          gmx::ForceProviderOutput forceProviderOutput(forceWithVirial, enerd);
-
+ 
 diff --git a/src/gromacs/mdrun/legacymdrunoptions.h b/src/gromacs/mdrun/legacymdrunoptions.h
 index 796e479490..8b20073b3b 100644
 --- a/src/gromacs/mdrun/legacymdrunoptions.h
@@ -255,7 +257,7 @@ index 796e479490..8b20073b3b 100644
 +                                          { efXVG, "-swap", "swapions", ffOPTWR },
 +                                          { efDAT, "-colvars",  "colvars",   ffOPTRDMULT },     /* COLVARS */
 +                                          { efDAT, "-colvars_restart", "colvars",  ffOPTRD },   /* COLVARS */}};
-
+ 
      //! Print a warning if any force is larger than this (in kJ/mol nm).
      real pforce = -1;
 diff --git a/src/gromacs/mdrun/replicaexchange.cpp b/src/gromacs/mdrun/replicaexchange.cpp
@@ -268,10 +270,10 @@ index 9ff4b3817d..eb31f1fa89 100644
      exchange_rvecs(ms, b, state->v.rvec_array(), state->natoms);
 +    exchange_rvecs(ms, b, state->xa_old_whole_colvars, state->n_colvars_atoms);
  }
-
+ 
  static void copy_state_serial(const t_state* src, t_state* dest)
 diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp
-index c2b3c088d7..bb38d44ab2 100644
+index c2b3c088d7..7a5f2b05a4 100644
 --- a/src/gromacs/mdrun/runner.cpp
 +++ b/src/gromacs/mdrun/runner.cpp
 @@ -115,6 +115,7 @@
@@ -285,7 +287,7 @@ index c2b3c088d7..bb38d44ab2 100644
 @@ -156,6 +157,8 @@
  #include "gromacs/utility/smalloc.h"
  #include "gromacs/utility/stringutil.h"
-
+ 
 +#include "colvarproxy_gromacs.h"
 +
  #include "isimulator.h"
@@ -294,7 +296,7 @@ index c2b3c088d7..bb38d44ab2 100644
 @@ -1536,6 +1539,51 @@ int Mdrunner::mdrunner()
                                 MASTER(cr) ? globalState->x.rvec_array() : nullptr, filenames.size(),
                                 filenames.data(), oenv, mdrunOptions.imdOptions, startingBehavior);
-
+ 
 +        /* COLVARS */
 +        if (opt2bSet("-colvars",filenames.size(), filenames.data()))
 +        {
@@ -346,7 +348,7 @@ index c2b3c088d7..bb38d44ab2 100644
 @@ -1654,6 +1702,16 @@ int Mdrunner::mdrunner()
          free_membed(membed);
      }
-
+ 
 +    /* COLVARS */
 +    if (inputrec->bColvars)
 +    {
@@ -387,28 +389,28 @@ index 0000000000..ea69e03419
 +
 +#endif
 diff --git a/src/gromacs/mdtypes/inputrec.h b/src/gromacs/mdtypes/inputrec.h
-index 266670f3ef..f1d287d35d 100644
+index 266670f3ef..86e4aa35d3 100644
 --- a/src/gromacs/mdtypes/inputrec.h
 +++ b/src/gromacs/mdtypes/inputrec.h
 @@ -53,6 +53,8 @@ struct gmx_enfrot;
  struct gmx_enfrotgrp;
  struct pull_params_t;
-
+ 
 +class colvarproxy_gromacs;
 +
  namespace gmx
  {
  class Awh;
 @@ -587,6 +589,10 @@ struct t_inputrec // NOLINT (clang-analyzer-optin.performance.Padding)
-
+ 
      //! KVT for storing simulation parameters that are not part of the mdp file.
      std::unique_ptr<gmx::KeyValueTreeObject> internalParameters;
 +
 +    /* COLVARS */
 +    gmx_bool                bColvars = false;       /* Do we do colvars calculations ? */
 +    colvarproxy_gromacs     *colvars_proxy = nullptr; /* The object for the colvars calculations */
  };
-
+ 
  int ir_optimal_nstcalcenergy(const t_inputrec* ir);
 diff --git a/src/gromacs/mdtypes/observableshistory.cpp b/src/gromacs/mdtypes/observableshistory.cpp
 index 0b5983a59c..57d851645a 100644
@@ -419,7 +421,7 @@ index 0b5983a59c..57d851645a 100644
  #include "gromacs/mdtypes/pullhistory.h"
  #include "gromacs/mdtypes/swaphistory.h"
 +#include "gromacs/mdtypes/colvarshistory.h"
-
+ 
  ObservablesHistory::ObservablesHistory()  = default;
  ObservablesHistory::~ObservablesHistory() = default;
 diff --git a/src/gromacs/mdtypes/observableshistory.h b/src/gromacs/mdtypes/observableshistory.h
@@ -431,18 +433,18 @@ index d2ba1d820f..a5747139d7 100644
  struct edsamhistory_t;
  struct swaphistory_t;
 +struct colvarshistory_t;
-
+ 
  /*! \libinternal \brief Observables history, for writing/reading to/from checkpoint file
   */
 @@ -76,6 +77,9 @@ struct ObservablesHistory
      //! Ion/water position swapping history
      std::unique_ptr<swaphistory_t> swapHistory;
-
+ 
 +    //! Colvars
 +    std::unique_ptr<colvarshistory_t> colvarsHistory;
 +
      ObservablesHistory();
-
+ 
      ~ObservablesHistory();
 diff --git a/src/gromacs/mdtypes/state.cpp b/src/gromacs/mdtypes/state.cpp
 index a949d589a3..957f7b7139 100644
@@ -456,7 +458,7 @@ index a949d589a3..957f7b7139 100644
 +    ddp_count_cg_gl(0),
 +    xa_old_whole_colvars(nullptr),
 +    n_colvars_atoms(0)
-
+ 
  {
      // It would be nicer to initialize these with {} or {{0}} in the
 diff --git a/src/gromacs/mdtypes/state.h b/src/gromacs/mdtypes/state.h
@@ -465,14 +467,14 @@ index a54bff29bb..8619c7935a 100644
 +++ b/src/gromacs/mdtypes/state.h
 @@ -257,6 +257,10 @@ public:
      std::vector<int> cg_gl;           //!< The global cg number of the local cgs
-
+ 
      std::vector<double> pull_com_prev_step; //!< The COM of the previous step of each pull group
 +
 +    int      n_colvars_atoms; //!< number of colvars atoms
 +    rvec*    xa_old_whole_colvars; //!< last whole positions of colvars atoms
 +
  };
-
+ 
  #ifndef DOXYGEN
 diff --git a/src/programs/mdrun/tests/refdata/MdrunTest_WritesHelp.xml b/src/programs/mdrun/tests/refdata/MdrunTest_WritesHelp.xml
 index c2973bb1af..cb4d1da254 100644
@@ -496,6 +498,6 @@ index c2973bb1af..cb4d1da254 100644
 +           Generic data file
 + -colvars_restart [&lt;.dat&gt;]  (colvars.dat)    (Opt.)
 +           Generic data file
-
+ 
  Options to specify output files:
-
+