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