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Fixed error in ANIPotential #141

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Merged
peastman merged 1 commit into from
Apr 28, 2026
+24 −12
Merged

Fixed error in ANIPotential #141

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2 changes: 1 addition & 1 deletion openmmml/models/anipotential.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ def _computeANI(state, model, species, pbc, indices):
_, energy = model((species, positions), cell=boxvectors, pbc=pbc)
energy *= torchani.units.hartree2kjoulemol(1)
energy.backward()
forces = (-positions.grad).detach().cpu().numpy()
forces = (-positions.grad[0]).detach().cpu().numpy()
if indices is not None:
f = np.zeros((numAtoms, 3), dtype=np.float32)
f[indices] = forces
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34 changes: 23 additions & 11 deletions test/TestANIPotential.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,34 +11,46 @@

torchani = pytest.importorskip("torchani", reason="torchani is not installed")

rtol = 1e-5
platform_ints = range(mm.Platform.getNumPlatforms())
# Get the path to the test data
test_data_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "data")


@pytest.mark.parametrize("implementation,platform_int", list(itertools.product(['nnpops', 'torchani'], list(platform_ints))))
@pytest.mark.parametrize("platform_int", list(platform_ints))
class TestANIPotential:
def testSimulate(self, platform_int):
pdb = app.PDBFile(os.path.join(test_data_dir, 'toluene', 'toluene.pdb'))
potential = MLPotential('ani2x')
system = potential.createSystem(pdb.topology)
platform = mm.Platform.getPlatform(platform_int)
integrator = mm.LangevinIntegrator(300.0, 1.0,0.001)
context = mm.Context(system, integrator, platform)
context.setPositions(pdb.positions)
integrator.step(10)
positions = context.getState(positions=True).getPositions(asNumpy=True).value_in_unit(unit.nanometer)
assert np.all(np.isfinite(positions))

def testCreateMixedSystem(self, implementation, platform_int):
def testCreateMixedSystem(self, platform_int):
pdb = app.PDBFile(os.path.join(test_data_dir, 'alanine-dipeptide', 'alanine-dipeptide-explicit.pdb'))
ff = app.ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
mmSystem = ff.createSystem(pdb.topology, nonbondedMethod=app.PME)
potential = MLPotential('ani2x')
mlAtoms = [a.index for a in next(pdb.topology.chains()).atoms()]
mixedSystem = potential.createMixedSystem(pdb.topology, mmSystem, mlAtoms, interpolate=False, implementation=implementation)
interpSystem = potential.createMixedSystem(pdb.topology, mmSystem, mlAtoms, interpolate=True, implementation=implementation)
mixedSystem = potential.createMixedSystem(pdb.topology, mmSystem, mlAtoms, interpolate=False)
interpSystem = potential.createMixedSystem(pdb.topology, mmSystem, mlAtoms, interpolate=True)
platform = mm.Platform.getPlatform(platform_int)
mmContext = mm.Context(mmSystem, mm.VerletIntegrator(0.001), platform)
mixedContext = mm.Context(mixedSystem, mm.VerletIntegrator(0.001), platform)
interpContext = mm.Context(interpSystem, mm.VerletIntegrator(0.001), platform)
mmContext.setPositions(pdb.positions)
mixedContext.setPositions(pdb.positions)
interpContext.setPositions(pdb.positions)
mmEnergy = mmContext.getState(getEnergy=True).getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole)
mixedEnergy = mixedContext.getState(getEnergy=True).getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole)
interpEnergy1 = interpContext.getState(getEnergy=True).getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole)
mmState = mmContext.getState(energy=True, forces=True)
mixedState = mixedContext.getState(energy=True, forces=True)
interpState1 = interpContext.getState(energy=True, forces=True)
interpContext.setParameter('lambda_interpolate', 0)
interpEnergy2 = interpContext.getState(getEnergy=True).getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole)
assert np.isclose(mixedEnergy, interpEnergy1, rtol=rtol)
assert np.isclose(mmEnergy, interpEnergy2, rtol=rtol)
interpState2 = interpContext.getState(energy=True, forces=True)
assert np.isclose(mixedState.getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole), interpState1.getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole), rtol=1e-5)
assert np.isclose(mmState.getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole), interpState2.getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole), rtol=1e-5)
assert np.allclose(mixedState.getForces().value_in_unit(unit.kilojoules_per_mole/unit.nanometer), interpState1.getForces().value_in_unit(unit.kilojoules_per_mole/unit.nanometer), rtol=1e-3)
assert np.allclose(mmState.getForces().value_in_unit(unit.kilojoules_per_mole/unit.nanometer), interpState2.getForces().value_in_unit(unit.kilojoules_per_mole/unit.nanometer), rtol=1e-3)
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