def _setup_dummy_system(directory):
"""Generate a temporary parameterized system object."""
force_field_path = path.join(directory, "ff.json")
with open(force_field_path, "w") as file:
file.write(build_tip3p_smirnoff_force_field().json())
substance = Substance.from_components("O")
build_coordinates = BuildCoordinatesPackmol("build_coordinates")
build_coordinates.max_molecules = 10
build_coordinates.mass_density = 0.05 * unit.grams / unit.milliliters
build_coordinates.substance = substance
build_coordinates.execute(directory)
assign_parameters = BuildSmirnoffSystem("assign_parameters")
assign_parameters.force_field_path = force_field_path
assign_parameters.coordinate_file_path = build_coordinates.coordinate_file_path
assign_parameters.substance = substance
assign_parameters.execute(directory)
return (
build_coordinates.coordinate_file_path,
assign_parameters.parameterized_system,
)
def test_calculate_reduced_potential_openmm():
substance = Substance.from_components("O")
thermodynamic_state = ThermodynamicState(298 * unit.kelvin,
1.0 * unit.atmosphere)
with tempfile.TemporaryDirectory() as directory:
force_field_path = path.join(directory, "ff.json")
with open(force_field_path, "w") as file:
file.write(build_tip3p_smirnoff_force_field().json())
build_coordinates = BuildCoordinatesPackmol("build_coordinates")
build_coordinates.max_molecules = 10
build_coordinates.mass_density = 0.05 * unit.grams / unit.milliliters
build_coordinates.substance = substance
build_coordinates.execute(directory, None)
assign_parameters = BuildSmirnoffSystem("assign_parameters")
assign_parameters.force_field_path = force_field_path
assign_parameters.coordinate_file_path = build_coordinates.coordinate_file_path
assign_parameters.substance = substance
assign_parameters.execute(directory, None)
reduced_potentials = OpenMMReducedPotentials("reduced_potentials")
reduced_potentials.substance = substance
reduced_potentials.thermodynamic_state = thermodynamic_state
reduced_potentials.reference_force_field_paths = [force_field_path]
reduced_potentials.system_path = assign_parameters.system_path
reduced_potentials.trajectory_file_path = get_data_filename(
"test/trajectories/water.dcd")
reduced_potentials.coordinate_file_path = get_data_filename(
"test/trajectories/water.pdb")
reduced_potentials.kinetic_energies_path = get_data_filename(
"test/statistics/stats_pandas.csv")
reduced_potentials.high_precision = False
reduced_potentials.execute(directory, ComputeResources())
assert path.isfile(reduced_potentials.statistics_file_path)
final_array = StatisticsArray.from_pandas_csv(
reduced_potentials.statistics_file_path)
assert ObservableType.ReducedPotential in final_array