Merge pull request #852 from openforcefield/openmm-ljpme

Better support LJPME in OpenMM export

devtools/conda-envs/beta_env.yaml

@@ -12,7 +12,7 @@ dependencies:
   - pydantic =1
   - openmm >=7.6
   # OpenFF stack
-  - openff-toolkit >=0.14.2
+  - openff-toolkit >=0.14.5
   - openff-models
   - openff-nagl
   - openff-nagl-models

devtools/conda-envs/dev_env.yaml

@@ -11,7 +11,7 @@ dependencies:
   - pydantic
   - openmm
   # OpenFF stack
-  - openff-toolkit ==0.14.3
+  - openff-toolkit ==0.14.5
   - openff-interchange-base
   - openff-models
   - smirnoff-plugins =2023

devtools/conda-envs/docs_env.yaml

@@ -10,7 +10,7 @@ dependencies:
   - pip
   - numpy >=1.21
   - pydantic =1
-  - openff-toolkit-base >=0.14.2
+  - openff-toolkit-base =0.14.5
   - openff-models
   - openmm >=7.6
   - mbuild

devtools/conda-envs/examples_env.yaml

@@ -10,7 +10,7 @@ dependencies:
   - pydantic =1
   - openmm >=7.6
   # OpenFF stack
-  - openff-toolkit >=0.14.2
+  - openff-toolkit >=0.14.5
   - openff-nagl ==0.3.1
   - openff-nagl-models ==0.1
   # Optional features

devtools/conda-envs/test_env.yaml

@@ -8,7 +8,7 @@ dependencies:
   - numpy
   - pydantic
   # OpenFF stack
-  - openff-toolkit-base >=0.14.3
+  - openff-toolkit-base >=0.14.5
   - openff-units
   - openff-models
   # Needs to be explicitly listed to not be dropped when AmberTools is removed

docs/releasehistory.md

@@ -16,6 +16,7 @@ Please note that all releases prior to a version 1.0.0 are considered pre-releas
 ### New Features
 
 * #848 Raises a more useful error when `Interchange.minimize` is called while positions are not present.
+* #852 Support LJPME in OpenMM export.
 
 ### Bugfixes
 

openff/interchange/_tests/energy_tests/components/tests_smirnoff.py → openff/interchange/_tests/energy_tests/components/test_smirnoff.py

@@ -2,25 +2,33 @@
 import pytest
 from openff.toolkit import ForceField, Molecule
 from openff.units import unit
-from openff.utilities import get_data_file_path, has_package
+from openff.utilities import get_data_file_path, has_package, skip_if_missing
 
 from openff.interchange import Interchange
 from openff.interchange._tests.unit_tests.smirnoff.test_valence import (
     TestBondOrderInterpolation,
 )
-from openff.interchange.drivers.openmm import _get_openmm_energies, get_openmm_energies
+from openff.interchange.drivers.openmm import (
+    _get_openmm_energies,
+    _process,
+    get_openmm_energies,
+)
 
 if has_package("openmm"):
     import openmm
     import openmm.app
     import openmm.unit
 
 
+@skip_if_missing("openmm")
 class TestBondOrderInterpolationEnergies(TestBondOrderInterpolation):
     @pytest.mark.slow()
     def test_basic_bond_order_interpolation_energies(self):
         forcefield = ForceField(
-            "test_forcefields/test_forcefield.offxml",
+            get_data_file_path(
+                "test_forcefields/test_forcefield.offxml",
+                "openff.toolkit",
+            ),
             self.xml_ff_bo_bonds,
         )
 
@@ -38,10 +46,19 @@ def test_basic_bond_order_interpolation_energies(self):
             out,
             combine_nonbonded_forces=True,
         ).energies["Bond"]
-        toolkit_bond_energy = _get_openmm_energies(
-            forcefield.create_openmm_system(top),
-            box_vectors=[[4, 0, 0], [0, 4, 0], [0, 0, 4]] * openmm.unit.nanometer,
-            positions=mol.conformers[0],
+
+        system = forcefield.create_openmm_system(top)
+        toolkit_bond_energy = _process(
+            _get_openmm_energies(
+                system=system,
+                box_vectors=[[4, 0, 0], [0, 4, 0], [0, 0, 4]] * openmm.unit.nanometer,
+                positions=mol.conformers[0].to_openmm(),
+                round_positions=None,
+                platform="Reference",
+            ),
+            system=system,
+            combine_nonbonded_forces=True,
+            detailed=False,
         ).energies["Bond"]
 
         assert abs(interchange_bond_energy - toolkit_bond_energy).m < 1e-2

openff/interchange/_tests/unit_tests/interop/openmm/test_nonbonded.py

@@ -39,14 +39,24 @@ def test_reaction_field(self, sage, periodic):
 
 @skip_if_missing("openmm")
 class TestEwaldSettings:
-    def test_set_ewald_tolerance(self, sage, basic_top):
+    @pytest.mark.parametrize("lj_method", ["cutoff", "pme"])
+    def test_set_ewald_tolerance(self, sage, basic_top, lj_method):
         import openmm
 
+        if lj_method == "pme":
+            sage["vdW"].periodic_method = "Ewald3D"
+
         system = sage.create_interchange(basic_top).to_openmm(ewald_tolerance=1.234e-5)
 
         for force in system.getForces():
             if isinstance(force, openmm.NonbondedForce):
+                if lj_method == "pme":
+                    assert force.getNonbondedMethod() == openmm.NonbondedForce.LJPME
+                elif lj_method == "cutoff":
+                    assert force.getNonbondedMethod() == openmm.NonbondedForce.PME
+
                 assert force.getEwaldErrorTolerance() == 1.234e-5
+
                 break
         else:
             pytest.fail("Found no `NonbondedForce`")

openff/interchange/smirnoff/_nonbonded.py

@@ -176,7 +176,10 @@ def store_potentials(self, parameter_handler: vdWHandler) -> None:
         Populate self.potentials with key-val pairs of [TopologyKey, PotentialKey].
 
         """
-        self.periodic_method = parameter_handler.periodic_method.lower()
+        self.periodic_method = parameter_handler.periodic_method.lower().replace(
+            "ewald3d",
+            "pme",
+        )
         self.nonperiodic_method = parameter_handler.nonperiodic_method.lower()
         self.cutoff = parameter_handler.cutoff
 
@@ -222,7 +225,10 @@ def create(
             scale_15=parameter_handler.scale15,
             cutoff=parameter_handler.cutoff,
             mixing_rule=parameter_handler.combining_rules.lower(),
-            periodic_method=parameter_handler.periodic_method.lower(),
+            periodic_method=parameter_handler.periodic_method.lower().replace(
+                "ewald3d",
+                "pme",
+            ),
             nonperiodic_method=parameter_handler.nonperiodic_method.lower(),
             switch_width=parameter_handler.switch_width,
         )