Warn when switching function cannot be applied

.github/workflows/beta.yaml

@@ -22,6 +22,8 @@ jobs:
           - "3.9"
           - "3.10"
           - "3.11"
+        pydantic-version:
+          - "2"
         openeye:
           - true
           - false
@@ -37,9 +39,9 @@ jobs:
       uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: devtools/conda-envs/beta_env.yaml
-        channel-priority: "flexible"
         create-args: >-
           python=${{ matrix.python-version }}
+          pydantic=${{ matrix.pydantic-version }}
 
     - name: Install package
       run: |

devtools/conda-envs/beta_env.yaml

@@ -35,7 +35,7 @@ dependencies:
   - panedr
   # Examples
   - nglview
-  - pytest
+  - pytest =8.0
   - nbval
   # Typing
   - mypy

devtools/conda-envs/dev_env.yaml

@@ -24,7 +24,7 @@ dependencies:
   - mdtraj
   - intermol
   - openeye-toolkits >=2023.2
-  - pytest
+  - pytest =8.0
   - pytest-cov
   - pytest-xdist
   - pytest-randomly

devtools/conda-envs/examples_env.yaml

@@ -25,7 +25,7 @@ dependencies:
   - pdbfixer
   - nglview
   - openeye-toolkits >=2023.2
-  - pytest
+  - pytest =8.0
   - pytest-xdist
   - nbval
   - openmmforcefields >=0.11.2

devtools/conda-envs/test_env.yaml

@@ -21,7 +21,7 @@ dependencies:
   - mdtraj
   - intermol
   - jax
-  - pytest
+  - pytest =8.0
   - pytest-cov
   - pytest-xdist
   - pytest-randomly

docs/releasehistory.md

@@ -13,9 +13,11 @@ Please note that all releases prior to a version 1.0.0 are considered pre-releas
 
 ## Current development
 
+* #912 A warning is raised when writing an input/run file (not data file) to an engine that does not implement a switching function described by SMIRNOFF.
 * #916 Some internal code paths are re-organized, including removing the `openff.interchange.interop.internal` submodule.
 * #916 Improves speed of `Interchange.to_lammps`, particularly for larger systems.
 * #915 Deprecates `Interchange.__add__` in favor of `Interchange.combine`.
+* #897 Improves energy evaluation with LAMMPS when some bonds are constrained.
 
 ## 0.3.22 - 2023-02-27
 

docs/using/output.md

@@ -76,6 +76,8 @@ should be modified for the desired simulation:
 mdconfig.write_lammps_input(input_file="auto_generated.in")
 ```
 
+Note that LAMMPS does not seem to implement a switching function as [commonly used](https://openforcefield.github.io/standards/standards/smirnoff/#vdw) by SMIRNOFF force fields.
+
 ## OpenMM
 
 An [`Interchange`] object can be converted to an `openmm.System` object with
@@ -121,6 +123,8 @@ should be modified for the desired simulation:
 mdconfig.write_sander_input_file(input_file="auto_generated.in")
 ```
 
+Note that Amber does not implement a switching function as [commonly used](https://openforcefield.github.io/standards/standards/smirnoff/#vdw) by SMIRNOFF force fields.
+
 <!--
 ## CHARMM
 

docs/using/status.md

@@ -1,12 +1,12 @@
 # Capabilities
 
-| Engine | Known bugs | HMR | 4-site water models | 5-site water models | Virtual sites on ligands | Proteins | Nucleic acids | Lipids | Carbohydrates |
-|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|
-| All | | | | | | <td colspan=3>No supported SMIRNOFF force fields |
-| OpenMM | [Link](https://github.com/openforcefield/openff-interchange/issues?q=is%3Aissue+is%3Aopen+label%3Aopenmm+label%3Abug) | Mostly<sup>2</sup> supported | Supported | Supported | Supported | Supported |
-| GROMACS | [Link](https://github.com/openforcefield/openff-interchange/issues?q=is%3Aissue+is%3Aopen+label%3Agromacs+label%3Abug) | Mostly<sup>2</sup> supported | Partially supported | Supported | Partially supported | Supported |
-| Amber | [Link](https://github.com/openforcefield/openff-interchange/issues?q=is%3Aissue+is%3Aopen+label%3Aamber+label%3Abug) | Unsupported | Unsupported<sup>1</sup> | Unsupported<sup>1</sup> | Unsupported<sup>1</sup> | Supported |
-| LAMMPS | [Link](https://github.com/openforcefield/openff-interchange/issues?q=is%3Aissue+is%3Aopen+label%3Alammps+label%3Abug) | Unsupported | Not supported | Not supported | Not supported | Not tested |
+| Engine | Known bugs | HMR | Bond constraints | 4-site water models | 5-site water models | Virtual sites on ligands | Proteins | Nucleic acids | Lipids | Carbohydrates |
+|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|
+| OpenMM | [Link](https://github.com/openforcefield/openff-interchange/issues?q=is%3Aissue+is%3Aopen+label%3Aopenmm+label%3Abug) | Mostly<sup>2</sup> supported | Supported | Supported | Supported | Supported | Supported |
+| GROMACS | [Link](https://github.com/openforcefield/openff-interchange/issues?q=is%3Aissue+is%3Aopen+label%3Agromacs+label%3Abug) | Mostly<sup>2</sup> supported | Partially supported | Partially supported | Supported | Partially supported | Supported |
+| Amber | [Link](https://github.com/openforcefield/openff-interchange/issues?q=is%3Aissue+is%3Aopen+label%3Aamber+label%3Abug) | Unsupported | Partially supported | Unsupported<sup>1</sup> | Unsupported<sup>1</sup> | Unsupported<sup>1</sup> | Supported |
+| LAMMPS | [Link](https://github.com/openforcefield/openff-interchange/issues?q=is%3Aissue+is%3Aopen+label%3Alammps+label%3Abug) | Unsupported | Partially supported | Not supported | Not supported | Not supported | Not tested |
+| All | | | | | | | <td colspan=3>No available SMIRNOFF force fields |
 
 1. Unable to find upstream documentation
 2. See caveats in `Interchange.to_openmm` and `Interchange.to_gromacs` docstrings.

openff/interchange/_tests/conftest.py

@@ -24,6 +24,12 @@ def sage_unconstrained():
     return ForceField("openff_unconstrained-2.0.0.offxml")
 
 
+@pytest.fixture()
+def sage_no_switch(sage):
+    sage["vdW"].switch_width = Quantity(0.0, "angstrom")
+    return sage
+
+
 @pytest.fixture()
 def sage_with_bond_charge(sage):
     sage["Bonds"].add_parameter(

openff/interchange/_tests/data/ions.offxml

@@ -1,9 +1,13 @@
 <?xml version="1.0" encoding='ASCII'?>
 <SMIRNOFF version="0.3" aromaticity_model="OEAroModel_MDL">
-  <vdW version="0.3" potential="Lennard-Jones-12-6" combining_rules="Lorentz-Berthelot" scale12="0.0" scale13="0.0" scale14="0.5" scale15="1" switch_width="1.0 * angstroms" cutoff="9.0 * angstroms" method="cutoff">
-    <Atom smirks="[*:1]" id="n1" sigma="0.1 * nanometers" epsilon="0.0 * kilojoules_per_mole" />
+  <Bonds version="0.4" potential="harmonic" fractional_bondorder_method="AM1-Wiberg" fractional_bondorder_interpolation="linear">
+  </Bonds>
+  <Angles version="0.3" potential="harmonic">
+  </Angles>
+  <vdW version="0.4" potential="Lennard-Jones-12-6" combining_rules="Lorentz-Berthelot" scale12="0.0" scale13="0.0" scale14="0.5" scale15="1.0" cutoff="9.0 * angstrom ** 1" switch_width="1.0 * angstrom ** 1" periodic_method="cutoff" nonperiodic_method="no-cutoff">
+    <Atom smirks="[*:1]" epsilon="0.0868793154488 * mole ** -1 * kilocalorie ** 1" id="n14" rmin_half="1.953447017081 * angstrom ** 1"></Atom>
   </vdW>
-  <Electrostatics version="0.3" scale12="0.0" scale13="0.0" scale14="0.833333" scale15="1.0" cutoff="9.0 * angstrom" switch_width="0.0 * angstrom" method="PME"></Electrostatics>
+  <Electrostatics version="0.4" scale12="0.0" scale13="0.0" scale14="0.8333333333" scale15="1.0" cutoff="9.0 * angstrom ** 1" switch_width="0.0 * angstrom ** 1" periodic_potential="Ewald3D-ConductingBoundary" nonperiodic_potential="Coulomb" exception_potential="Coulomb"></Electrostatics>
   <LibraryCharges version="0.3">
     <LibraryCharge name="foobar" smirks="[#3:1]" charge1="1.0*elementary_charge"/>
     <LibraryCharge name="foobar" smirks="[#17:1]" charge1="-1.0*elementary_charge"/>

openff/interchange/_tests/energy_tests/interop/amber/__init__.py

@@ -0,0 +1 @@
+"""Energy tests specifically relevant to Amber behaviors."""

openff/interchange/_tests/energy_tests/interop/amber/test_energies.py

@@ -0,0 +1,33 @@
+import pytest
+from openff.toolkit import Quantity
+from openff.utilities import skip_if_missing
+
+from openff.interchange._tests import MoleculeWithConformer, requires_ambertools
+from openff.interchange.constants import kcal_mol
+from openff.interchange.drivers import get_amber_energies, get_openmm_energies
+
+
+@requires_ambertools
+@skip_if_missing("openmm")
+@pytest.mark.parametrize(
+    "smiles",
+    ["c1ccccc1", "C1#CC#CC#C1", "C1=CC=C2C(=C1)C=CC3=C2C=CC4=CC=CC=C43"],
+)
+def test_polycyclic_nonbonded(smiles, sage_no_switch):
+    molecule = MoleculeWithConformer.from_smiles(smiles)
+    topology = molecule.to_topology()
+    topology.box_vectors = Quantity([10, 10, 10], "nanometer")
+
+    interchange = sage_no_switch.create_interchange(topology)
+
+    openmm_vdw = get_openmm_energies(
+        interchange,
+        combine_nonbonded_forces=False,
+    ).energies["vdW"]
+
+    amber_vdw = get_amber_energies(interchange).energies["vdW"]
+
+    assert openmm_vdw.m == pytest.approx(
+        amber_vdw.m,
+        rel=1e-5,
+    ), f"{openmm_vdw.m_as(kcal_mol)=}, {amber_vdw.m_as(kcal_mol)=}"

openff/interchange/_tests/unit_tests/components/test_mdconfig.py

@@ -1,3 +1,4 @@
+import warnings
 from typing import Union
 
 import pytest
@@ -10,6 +11,7 @@
     get_smirnoff_defaults,
 )
 from openff.interchange.constants import _PME
+from openff.interchange.warnings import SwitchingFunctionNotImplementedWarning
 
 
 @pytest.fixture()
@@ -241,22 +243,80 @@ def test_unconstrained_ligand_rigid_water_box(
         assert options["cntrl"]["ntf"] == "2"
         assert options["cntrl"]["ntc"] == "1"
 
-    def test_fswitch_negative_when_no_switching_function(
+    def test_switching_function_warning(
         self,
-        unconstrained_ligand_rigid_water_box,
+        system_no_constraints,
     ):
         """Reproduce issue 745."""
-        MDConfig.from_interchange(
-            unconstrained_ligand_rigid_water_box,
-        ).write_sander_input_file("yes.in")
+        with pytest.warns(
+            SwitchingFunctionNotImplementedWarning,
+        ):
+            MDConfig.from_interchange(
+                system_no_constraints,
+            ).write_sander_input_file("yes.in")
 
-        # With OpenFF defaults, the switch starts at 8 A and the cutoff is at 9 A
-        assert parse_sander("yes.in")["cntrl"]["fswitch"] == "8.0"
+        # This should always be -1 (turned off) since Amber does not implement
+        # a switching function on the potential
+        assert parse_sander("yes.in")["cntrl"]["fswitch"] == "-1.0"
 
-        unconstrained_ligand_rigid_water_box["vdW"].switch_width = 0.0 * unit.nanometer
+        system_no_constraints["vdW"].switch_width = 0.0 * unit.nanometer
 
-        MDConfig.from_interchange(
-            unconstrained_ligand_rigid_water_box,
-        ).write_sander_input_file("no.in")
+        # this pattern forces warnings to become errors
+        with warnings.catch_warnings():
+            warnings.simplefilter("error")
+
+            MDConfig.from_interchange(
+                system_no_constraints,
+            ).write_sander_input_file("no.in")
 
         assert parse_sander("no.in")["cntrl"]["fswitch"] == "-1.0"
+
+
+class TestWriteLAMMPSInput:
+
+    def test_switching_function_warning(
+        self,
+        system_no_constraints,
+        tmp_path,
+    ):
+        with pytest.warns(
+            SwitchingFunctionNotImplementedWarning,
+        ):
+            MDConfig.from_interchange(
+                system_no_constraints,
+            ).write_lammps_input(
+                interchange=system_no_constraints,
+                input_file=tmp_path / "yes.in",
+            )
+
+    def test_no_error_if_no_constraints(
+        self,
+        system_no_constraints,
+        tmp_path,
+    ):
+        MDConfig.from_interchange(system_no_constraints).write_lammps_input(
+            interchange=system_no_constraints,
+            input_file=tmp_path / ".inp",
+        )
+
+    def test_error_if_unsupported_constrained(
+        self,
+        rigid_water_box,
+        constrained_ligand_rigid_water_box,
+        unconstrained_ligand_rigid_water_box,
+        tmp_path,
+    ):
+        for system in [
+            rigid_water_box,
+            constrained_ligand_rigid_water_box,
+            unconstrained_ligand_rigid_water_box,
+        ]:
+
+            with pytest.raises(
+                NotImplementedError,
+                match="unsupported constraints case",
+            ):
+                MDConfig.from_interchange(system).write_lammps_input(
+                    system,
+                    tmp_path / ".inp",
+                )

openff/interchange/_tests/unit_tests/drivers/test_all.py

@@ -6,14 +6,14 @@
 
 import pandas
 import pytest
-from openff.toolkit.topology import Molecule
+from openff.toolkit import Quantity
 from openff.utilities.testing import skip_if_missing
 
-from openff.interchange import Interchange
 from openff.interchange._tests import (
     HAS_GROMACS,
     HAS_LAMMPS,
     HAS_SANDER,
+    MoleculeWithConformer,
     needs_gmx,
     needs_lmp,
     needs_not_gmx,
@@ -29,16 +29,12 @@
 class TestDriversAll:
     @pytest.fixture()
     def basic_interchange(self, sage_unconstrained):
-        molecule = Molecule.from_smiles("CCO")
-        molecule.generate_conformers(n_conformers=1)
+        molecule = MoleculeWithConformer.from_smiles("CCO")
         molecule.name = "MOL"
         topology = molecule.to_topology()
+        topology.box_vectors = Quantity([4, 4, 4], "nanometer")
 
-        out = Interchange.from_smirnoff(sage_unconstrained, topology)
-        out.positions = molecule.conformers[0]
-        out.box = [4, 4, 4]
-
-        return out
+        return sage_unconstrained.create_interchange(topology)
 
     @needs_gmx
     @needs_lmp

openff/interchange/_tests/unit_tests/drivers/test_lammps.py

@@ -1,8 +1,9 @@
 import pytest
-from openff.units import unit
+from openff.toolkit import Quantity, unit
 
+from openff.interchange._tests import MoleculeWithConformer, needs_lmp
 from openff.interchange.constants import kj_mol
-from openff.interchange.drivers.lammps import _process
+from openff.interchange.drivers.lammps import _process, get_lammps_energies
 
 
 class TestProcess:
@@ -46,3 +47,12 @@ def test_detailed(self, dummy_energies):
             dummy_energies,
             detailed=True,
         )
+
+
+class TestLAMMPSDriver:
+    @needs_lmp
+    def test_can_write_without_torsions(self, sage):
+        topology = MoleculeWithConformer.from_smiles("N").to_topology()
+        topology.box_vectors = Quantity([4, 4, 4], unit.nanometer)
+
+        assert get_lammps_energies(sage.create_interchange(topology))["Bond"].m == 0.0

openff/interchange/_tests/unit_tests/interop/lammps/__init__.py

@@ -0,0 +1 @@
+"""Tests with LAMMPS."""

openff/interchange/_tests/unit_tests/interop/lammps/export/__init__.py

@@ -0,0 +1 @@
+"""Tests with LAMMPS exports."""

openff/interchange/components/interchange.py

@@ -500,7 +500,7 @@ def to_gro(self, file_path: Union[Path, str], decimal: int = 3):
     def to_lammps(self, file_path: Union[Path, str], writer="internal"):
         """Export this Interchange to a LAMMPS data file."""
         if writer == "internal":
-            from openff.interchange.interop.lammps.export import to_lammps
+            from openff.interchange.interop.lammps import to_lammps
 
             to_lammps(self, file_path)
         else: