Merge pull request #11 from mattwthompson/energy-tests

Update energy tests

deforcefields/data/ethanol.sdf

@@ -0,0 +1,26 @@
+
+  -OEChem-02242314133D
+
+  9  8  0     0  0  0  0  0  0999 V2000
+    1.0616   -0.2681   -0.0006 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.9101    0.9126   -0.4220 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.5170    1.3236   -1.7228 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3393   -0.6108    1.0001 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0000   -0.0002   -0.0006 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.1801   -1.0990   -0.7040 H   0  0  0  0  0  0  0  0  0  0  0  0
+    2.9684    0.6361   -0.4446 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.7730    1.7499    0.2687 H   0  0  0  0  0  0  0  0  0  0  0  0
+    2.0787    2.0794   -1.9612 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  1  4  1  0  0  0  0
+  1  5  1  0  0  0  0
+  1  6  1  0  0  0  0
+  2  7  1  0  0  0  0
+  2  8  1  0  0  0  0
+  3  9  1  0  0  0  0
+M  END
+> <atom.dprop.PartialCharge>
+-0.097100 0.131430 -0.601340 0.044760 0.044760 0.044760 0.017320 0.017320 0.398090
+
+$$$$

deforcefields/data/water.sdf

@@ -0,0 +1,11 @@
+
+  -OEChem-02242314343D
+
+  3  2  0     0  0  0  0  0  0999 V2000
+    0.0611    0.3887    0.0589 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7238   -0.3116   -0.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7849   -0.0770   -0.0207 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+M  END
+$$$$

deforcefields/tests/conftest.py

@@ -0,0 +1,41 @@
+import os.path
+
+import pytest
+from openff.toolkit.topology import Molecule
+
+
+def get_data(relative_path: str) -> str:
+    """
+    Get the file path to some data in the package for testing.
+
+    Args:
+        relative_path: The relative path of the file to be loaded from deforcefields/data
+
+    Returns:
+        The absolute path to the requested file in deforcefields/data.
+    """
+    from pkg_resources import resource_filename
+
+    file_name = resource_filename("deforcefields", os.path.join("data", relative_path))
+    if not os.path.exists(file_name):
+        raise ValueError(
+            f"{relative_path} does not exist. If you have just added it, you'll have to re-install."
+        )
+    return file_name
+
+
+@pytest.fixture()
+def ethanol_with_charges() -> Molecule:
+    """
+    Return and OpenFF Molecule model of ethanol with `am1bccelf10` charges computed with openeye
+    """
+    ethanol = Molecule.from_file(get_data("ethanol.sdf"))
+    return ethanol
+
+
+@pytest.fixture()
+def water() -> Molecule:
+    """
+    Return an OpenFF Molecule model of water with no charges.
+    """
+    return Molecule.from_file(get_data("water.sdf"))

deforcefields/tests/test_deforcefields.py

@@ -2,10 +2,12 @@
 Test loading DE-Force fields via the plugin interface through the toolkit.
 """
 
+import numpy
 import openmm
 import pytest
+from openff.interchange.constants import kj_mol
 from openff.interchange.drivers.openmm import get_openmm_energies
-from openff.toolkit import ForceField, Molecule
+from openff.toolkit import ForceField, Molecule, Quantity, Topology
 from openmm import unit
 
 
@@ -16,17 +18,16 @@
         pytest.param("de-force_unconstrained-1.0.2.offxml", id="Constraints"),
     ],
 )
-def test_load_de_ff(forcefield):
+def test_load_de_ff(forcefield, ethanol_with_charges):
     """
     Load the DE FF and create an OpenMM system.
     """
 
     ff = ForceField(forcefield, load_plugins=True)
-    ethanol = Molecule.from_smiles("CCO")
 
-    system = ff.create_interchange(topology=ethanol.to_topology()).to_openmm(
-        combine_nonbonded_forces=False,
-    )
+    system = ff.create_interchange(
+        topology=ethanol_with_charges.to_topology(),
+    ).to_openmm(combine_nonbonded_forces=False)
 
     forces = {force.__class__.__name__: force for force in system.getForces()}
 
@@ -89,3 +90,88 @@ def test_fails_unsupported_chemistry():
         ).create_interchange(
             Molecule.from_mapped_smiles("[H:3][C:1]#[C:2][H:4]").to_topology()
         ).to_openmm(combine_nonbonded_forces=False)
+
+
+@pytest.mark.parametrize(
+    "forcefield, ref_energy",
+    [
+        pytest.param("de-force-1.0.2.offxml", 13.601144438830156, id="No constraints"),
+        pytest.param(
+            "de-force_unconstrained-1.0.2.offxml", 13.605201859835375, id="Constraints"
+        ),
+    ],
+)
+def test_energy_no_sites(forcefield, ref_energy, ethanol_with_charges):
+    """
+    Test calculating the single point energy of ethanol using constrained and unconstrained DE-FF with pre-computed
+    partial charges from openeye.
+    """
+
+    ff = ForceField(forcefield, load_plugins=True)
+
+    interchange = ff.create_interchange(
+        topology=ethanol_with_charges.to_topology(),
+        charge_from_molecules=[ethanol_with_charges],
+    )
+
+    found_energy = get_openmm_energies(
+        interchange,
+        combine_nonbonded_forces=False,
+    ).total_energy.m_as(kj_mol)
+
+    assert found_energy == pytest.approx(ref_energy)
+
+
+def evaluate_water_energy_at_distance(
+    force_field: ForceField,
+    distance: float,
+) -> list[Quantity]:
+    """
+    Evaluate a water dimer at specified distances (in Angstrom).
+
+    Taken from smirnoff_plugins.utilities.openmm, which collates virtual particles
+    between molecules. Interchange (with OpenMM) puts all virtual sites at the END
+    of the topology; mismatching these causes NaNs.
+    """
+
+    water = Molecule.from_smiles("O")
+    water.generate_conformers(n_conformers=1)
+    topology = Topology.from_molecules([water, water])
+    topology.box_vectors = unit.Quantity(numpy.eye(3) * 20, unit.nanometer)
+
+    topology.set_positions(
+        numpy.vstack(
+            [
+                water.conformers[0],
+                water.conformers[0]
+                + Quantity(
+                    numpy.array([distance, 0, 0]),
+                    "angstrom",
+                ),
+            ],
+        ),
+    )
+
+    return get_openmm_energies(
+        force_field.create_interchange(topology),
+        combine_nonbonded_forces=False,
+    ).total_energy
+
+
+@pytest.mark.parametrize(
+    ("distance", "ref_energy"),
+    [(2, 1005.0846252441406), (3, 44.696786403656006), (4, 10.453390896320343)],
+)
+def test_energy_sites(distance, ref_energy):
+    """
+    Test calculating the energy for a system with two waters with virtual sites at set distances.
+    """
+
+    ff = ForceField("de-force-1.0.2.offxml", load_plugins=True)
+
+    found_energy = evaluate_water_energy_at_distance(
+        force_field=ff,
+        distance=distance,
+    )
+
+    assert found_energy.m_as(kj_mol) == pytest.approx(ref_energy, abs=0.01)

devtools/conda-envs/test_env.yaml

@@ -11,8 +11,8 @@ dependencies:
   - pytest
 
     # Core-deps
-  - openff-toolkit >=0.14.3
-  - openff-interchange >=0.3.18
+  - openff-toolkit >=0.15
+  - openff-interchange >=0.3.23
   # the above two constraints are pulled in by smirnoff-plugins;
   # could just drop them, but maybe it's better to be explicit
-  - smirnoff-plugins >=2023.08.0
+  - smirnoff-plugins >=2024.01.0