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___________________________________ TestSMIRNOFFTemplateGenerator.test_energies ___________________________________
self = <openmmforcefields.tests.test_template_generators.TestSMIRNOFFTemplateGenerator testMethod=test_energies>
def test_energies(self):
"""Test potential energies match between openff-toolkit and OpenMM ForceField"""
# Test all supported SMIRNOFF force fields
for small_molecule_forcefield in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS:
if "ff14sb" in small_molecule_forcefield:
continue
if "tip" in small_molecule_forcefield:
continue
if "opc" in small_molecule_forcefield:
continue
# We cannot test openff-2.0.0-rc.1 because it triggers an openmm.OpenMMException due to an equilibrium angle > \pi
# See https://github.com/openmm/openmm/issues/3185
if "openff-2.0.0-rc.1" not in small_molecule_forcefield:
continue
print(f'Testing energies for {small_molecule_forcefield}...')
# Create a generator that knows about a few molecules
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
generator = SMIRNOFFTemplateGenerator(molecules=self.molecules, forcefield=small_molecule_forcefield)
# Create a ForceField
openmm_forcefield = openmm.app.ForceField()
# Register the template generator
openmm_forcefield.registerTemplateGenerator(generator.generator)
# Parameterize some molecules
for molecule in self.molecules:
# Create OpenMM System using OpenMM app
openmm_system = openmm_forcefield.createSystem(molecule.to_topology().to_openmm(), removeCMMotion=False, nonbondedMethod=NoCutoff)
# Retrieve System generated by the SMIRNOFF typing engine
smirnoff_system = generator.get_openmm_system(molecule)
# Compare energies and forces
> self.compare_energies(molecule, openmm_system, smirnoff_system)
openmmforcefields/tests/test_template_generators.py:819:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
openmmforcefields/tests/test_template_generators.py:647: in compare_energies
reference_energy, reference_forces = cls.compute_energy(
openmmforcefields/tests/test_template_generators.py:612: in compute_energy
context = openmm.Context(system, integrator, platform)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <openmm.openmm.Context; >
args = (<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x170762b50> >, <openmm.openmm.VerletInteg...or *' at 0x170761560> >, <openmm.openmm.Platform; proxy of <Swig Object of type 'OpenMM::Platform *' at 0x170762d00> >)
def __init__(self, *args):
r"""
__init__(self, system, integrator) -> Context
__init__(self, system, integrator, platform) -> Context
__init__(self, system, integrator, platform, properties) -> Context
__init__(self, other) -> Context
Construct a new Context in which to run a simulation, explicitly specifying what Platform should be used to perform calculations and the values of platform-specific properties.
Parameters
----------
system : System
the System which will be simulated
integrator : Integrator
the Integrator which will be used to simulate the System
platform : Platform
the Platform to use for calculations
properties : map< std::string, std::string >
a set of values for platform-specific properties. Keys are the property names.
"""
> _openmm.Context_swiginit(self, _openmm.new_Context(*args))
E openmm.OpenMMException: HarmonicAngleForce: angle must be between 0 and pi
../../micromamba/envs/interchange-examples-env/lib/python3.11/site-packages/openmm/openmm.py:2471: OpenMMException
---------------------------------------------- Captured stdout call -----------------------------------------------
Testing energies for openff-2.0.0-rc.1...
================================================ warnings summary =================================================
openmmforcefields/tests/test_template_generators.py::TestGAFFTemplateGenerator::test_add_molecules
/Users/mattthompson/software/openmmforcefields/openmmforcefields/utils.py:36: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import resource_filename
openmmforcefields/tests/test_template_generators.py::TestGAFFTemplateGenerator::test_add_molecules
/Users/mattthompson/micromamba/envs/interchange-examples-env/lib/python3.11/site-packages/pkg_resources/__init__.py:2832: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
declare_namespace(pkg)
openmmforcefields/tests/test_template_generators.py::TestSMIRNOFFTemplateGenerator::test_14_scaling_from_offxml
/Users/mattthompson/micromamba/envs/interchange-examples-env/lib/python3.11/site-packages/lark/utils.py:163: DeprecationWarning: module 'sre_parse' is deprecated
import sre_parse
openmmforcefields/tests/test_template_generators.py::TestSMIRNOFFTemplateGenerator::test_14_scaling_from_offxml
/Users/mattthompson/micromamba/envs/interchange-examples-env/lib/python3.11/site-packages/lark/utils.py:164: DeprecationWarning: module 'sre_constants' is deprecated
import sre_constants
openmmforcefields/tests/test_template_generators.py::TestSMIRNOFFTemplateGenerator::test_14_scaling_from_offxml
/Users/mattthompson/micromamba/envs/interchange-examples-env/lib/python3.11/site-packages/mdtraj/formats/__init__.py:6: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13
from .xtc import XTCTrajectoryFile
openmmforcefields/tests/test_template_generators.py::TestSMIRNOFFTemplateGenerator::test_14_scaling_from_offxml
/Users/mattthompson/micromamba/envs/interchange-examples-env/lib/python3.11/site-packages/mbuild/recipes/__init__.py:13: DeprecationWarning: SelectableGroups dict interface is deprecated. Use select.
entry_points = metadata.entry_points()["mbuild.plugins"]
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================================= short test summary info =============================================
FAILED openmmforcefields/tests/test_template_generators.py::TestSMIRNOFFTemplateGenerator::test_energies - openmm.OpenMMException: HarmonicAngleForce: angle must be between 0 and pi
The text was updated successfully, but these errors were encountered:
While working on something else, haven't looked any deeper
The text was updated successfully, but these errors were encountered: