def test_to_pandas():
"""A test to ensure that data sets are convertable to pandas objects."""
source = CalculationSource('Dummy', {})
pure_substance = Substance.from_components('C')
binary_substance = Substance.from_components('C', 'O')
data_set = PhysicalPropertyDataSet()
data_set.properties[pure_substance.identifier] = []
data_set.properties[binary_substance.identifier] = []
for temperature in [298 * unit.kelvin, 300 * unit.kelvin, 302 * unit.kelvin]:
thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=1.0 * unit.atmosphere)
density_property = Density(thermodynamic_state=thermodynamic_state,
phase=PropertyPhase.Liquid,
substance=pure_substance,
value=1 * unit.gram / unit.milliliter,
uncertainty=0.11 * unit.gram / unit.milliliter,
source=source)
dielectric_property = DielectricConstant(thermodynamic_state=thermodynamic_state,
phase=PropertyPhase.Liquid,
substance=pure_substance,
value=1 * unit.dimensionless,
uncertainty=0.11 * unit.dimensionless,
source=source)
data_set.properties[pure_substance.identifier].append(density_property)
data_set.properties[pure_substance.identifier].append(dielectric_property)
for temperature in [298 * unit.kelvin, 300 * unit.kelvin, 302 * unit.kelvin]:
thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=1.0 * unit.atmosphere)
enthalpy_property = EnthalpyOfMixing(thermodynamic_state=thermodynamic_state,
phase=PropertyPhase.Liquid,
substance=binary_substance,
value=1 * unit.kilojoules / unit.mole,
uncertainty=0.11 * unit.kilojoules / unit.mole,
source=source)
excess_property = ExcessMolarVolume(thermodynamic_state=thermodynamic_state,
phase=PropertyPhase.Liquid,
substance=binary_substance,
value=1 * unit.meter**3 / unit.mole,
uncertainty=0.11 * unit.meter**3 / unit.mole,
source=source)
data_set.properties[binary_substance.identifier].append(enthalpy_property)
data_set.properties[binary_substance.identifier].append(excess_property)
data_set_pandas = data_set.to_pandas()
assert data_set_pandas is not None
assert len(data_set_pandas) == 6
def test_weight_by_mole_fraction_protocol(component_smiles, value):
full_substance = Substance.from_components('C', 'CC', 'CCC')
component = Substance.from_components(component_smiles)
mole_fraction = next(iter(full_substance.get_amounts(component_smiles))).value
with tempfile.TemporaryDirectory() as temporary_directory:
weight_protocol = WeightByMoleFraction('weight')
weight_protocol.value = value
weight_protocol.full_substance = full_substance
weight_protocol.component = component
result = weight_protocol.execute(temporary_directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert weight_protocol.weighted_value == value * mole_fraction
def test_local_simulation_storage():
"""A simple test to that force fields can be stored and
retrieved using the local storage backend."""
substance = Substance.from_components(r'C', r'C/C=C/C=C/COC(=O)',
r'CCOC(=O)/C=C(/C)\O')
dummy_simulation_data = StoredSimulationData()
dummy_simulation_data.thermodynamic_state = ThermodynamicState(
298.0 * unit.kelvin, 1.0 * unit.atmosphere)
dummy_simulation_data.statistical_inefficiency = 1.0
dummy_simulation_data.force_field_id = 'tmp_ff_id'
dummy_simulation_data.substance = substance
with tempfile.TemporaryDirectory() as base_directory:
temporary_data_directory = os.path.join(base_directory, 'temp_data')
temporary_backend_directory = os.path.join(base_directory,
'storage_dir')
os.makedirs(temporary_data_directory)
os.makedirs(temporary_backend_directory)
local_storage = LocalFileStorage(temporary_backend_directory)
dummy_simulation_data.unique_id = local_storage.store_simulation_data(
dummy_simulation_data, temporary_data_directory)
retrieved_data_directories = local_storage.retrieve_simulation_data(
substance)
assert substance.identifier in retrieved_data_directories
assert len(retrieved_data_directories[substance.identifier]) == 1
retrieved_data, retrieved_data_directory = retrieved_data_directories[
substance.identifier][0]
assert dummy_simulation_data.thermodynamic_state == retrieved_data.thermodynamic_state
assert dummy_simulation_data.statistical_inefficiency == retrieved_data.statistical_inefficiency
assert dummy_simulation_data.force_field_id == retrieved_data.force_field_id
assert dummy_simulation_data.substance == retrieved_data.substance
local_storage_new = LocalFileStorage(temporary_backend_directory)
retrieved_data, retrieved_data_directory = local_storage_new.retrieve_simulation_data_by_id(
dummy_simulation_data.unique_id)
assert retrieved_data is not None
assert os.path.isdir(retrieved_data_directory)
def _build_input_output_substances():
"""Builds sets if input and expected substances for the
`test_build_coordinate_composition` test.
Returns
-------
list of tuple of Substance and Substance
A list of input and expected substances.
"""
# Start with some easy cases
substances = [
(Substance.from_components('O'), Substance.from_components('O')),
(Substance.from_components('O',
'C'), Substance.from_components('O', 'C')),
(Substance.from_components('O', 'C', 'CO'),
Substance.from_components('O', 'C', 'CO'))
]
# Handle some cases where rounding will need to occur.
input_substance = Substance()
input_substance.add_component(Substance.Component('O'),
Substance.MoleFraction(0.41))
input_substance.add_component(Substance.Component('C'),
Substance.MoleFraction(0.59))
expected_substance = Substance()
expected_substance.add_component(Substance.Component('O'),
Substance.MoleFraction(0.4))
expected_substance.add_component(Substance.Component('C'),
Substance.MoleFraction(0.6))
substances.append((input_substance, expected_substance))
input_substance = Substance()
input_substance.add_component(Substance.Component('O'),
Substance.MoleFraction(0.59))
input_substance.add_component(Substance.Component('C'),
Substance.MoleFraction(0.41))
expected_substance = Substance()
expected_substance.add_component(Substance.Component('O'),
Substance.MoleFraction(0.6))
expected_substance.add_component(Substance.Component('C'),
Substance.MoleFraction(0.4))
substances.append((input_substance, expected_substance))
return substances
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(f'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 = CalculateReducedPotentialOpenMM(f'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
result = reduced_potentials.execute(directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
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
def _setup_dummy_system(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())
substance = Substance.from_components('C')
build_coordinates = BuildCoordinatesPackmol('build_coordinates')
build_coordinates.max_molecules = 1
build_coordinates.mass_density = 0.001 * unit.grams / unit.milliliters
build_coordinates.substance = substance
build_coordinates.execute(directory, None)
assign_parameters = BuildSmirnoffSystem(f'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)
return build_coordinates.coordinate_file_path, assign_parameters.system_path
def test_gradient_reduced_potentials(use_subset):
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())
reduced_potentials = GradientReducedPotentials(f'reduced_potentials')
reduced_potentials.substance = substance
reduced_potentials.thermodynamic_state = thermodynamic_state
reduced_potentials.reference_force_field_paths = [force_field_path]
reduced_potentials.reference_statistics_path = get_data_filename(
'test/statistics/stats_pandas.csv')
reduced_potentials.force_field_path = force_field_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.use_subset_of_force_field = use_subset
reduced_potentials.enable_pbc = True
reduced_potentials.parameter_key = ParameterGradientKey(
'vdW', '[#1]-[#8X2H2+0:1]-[#1]', 'epsilon')
result = reduced_potentials.execute(directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert path.isfile(reduced_potentials.forward_potentials_path)
assert path.isfile(reduced_potentials.reverse_potentials_path)
for reference_path in reduced_potentials.reference_force_field_paths:
assert path.isfile(reference_path)
def generate_trajectories():
"""Generates trajectories to subsample.
"""
setup_timestamp_logging()
logger = logging.getLogger()
substance = Substance.from_components('C(C(C(C(C(F)(F)Br)(F)F)(F)F)(F)F)(C(C(C(F)(F)F)(F)F)(F)F)(F)F')
logger.info('Building system.')
build_system = BuildSmirnoffSystem('build_system')
build_system.coordinate_file_path = 'coords.pdb'
build_system.substance = substance
build_system.force_field_path = 'smirnoff99Frosst-1.1.0.offxml'
build_system.execute('', None)
logger.info('System built.')
production_simulation = RunOpenMMSimulation(f'production_simulation')
production_simulation.steps_per_iteration = 500
production_simulation.output_frequency = 1
production_simulation.timestep = 2.0 * unit.femtosecond
production_simulation.thermodynamic_state = ThermodynamicState(temperature=298.15*unit.kelvin,
pressure=1.0*unit.atmosphere)
production_simulation.input_coordinate_file = 'coords.pdb'
production_simulation.system_path = 'system.xml'
compute_resources = ComputeResources(number_of_threads=4)
logger.info(f'Simulation started.')
production_simulation_schema = production_simulation.schema
production_simulation.execute('', compute_resources)
production_simulation.schema = production_simulation_schema
logger.info(f'Simulation finished.')