def test_phase_creation():
"""Phases are initialized correctly by Yank.create()."""
phase_name = 'my-solvent-phase'
toluene = testsystems.TolueneImplicit()
protocol = AbsoluteAlchemicalFactory.defaultSolventProtocolImplicit()
atom_indices = find_components(toluene.system, toluene.topology, 'resname TOL')
phase = AlchemicalPhase(phase_name, toluene.system, toluene.topology,
toluene.positions, atom_indices, protocol)
thermodynamic_state = ThermodynamicState(temperature=300.0*unit.kelvin)
# Create new simulation.
with enter_temp_directory():
output_dir = 'output'
utils.config_root_logger(verbose=False)
yank = Yank(store_directory=output_dir)
yank.create(thermodynamic_state, phase)
# Netcdf dataset has been created
nc_path = os.path.join(output_dir, phase_name + '.nc')
assert os.path.isfile(nc_path)
# Read data
try:
nc_file = netcdf.Dataset(nc_path, mode='r')
metadata_group = nc_file.groups['metadata']
serialized_topology = metadata_group.variables['topology'][0]
finally:
nc_file.close()
# Topology has been stored correctly
deserialized_topology = utils.deserialize_topology(serialized_topology)
assert deserialized_topology == mdtraj.Topology.from_openmm(toluene.topology)
def test_no_alchemical_atoms():
"""Test whether Yank raises exception when no alchemical atoms are specified."""
toluene = testsystems.TolueneImplicit()
# Create parameters. With the exception of atom_indices, all other
# parameters must be legal, we don't want to catch an exception
# different than the one we are testing.
phase = AlchemicalPhase(name='solvent-implicit', reference_system=toluene.system,
reference_topology=toluene.topology,
positions=toluene.positions, atom_indices={'ligand': []},
protocol=AbsoluteAlchemicalFactory.defaultSolventProtocolImplicit())
thermodynamic_state = ThermodynamicState(temperature=300.0*unit.kelvin)
# Create new simulation.
with enter_temp_directory():
yank = Yank(store_directory='output')
yank.create(thermodynamic_state, phase)
def test_resuming():
"""Test that sampling correctly resumes."""
# Prepare ModifiedHamiltonianExchange arguments
toluene_test = testsystems.TolueneImplicit()
ligand_atoms = range(15)
alchemical_factory = AbsoluteAlchemicalFactory(toluene_test.system,
ligand_atoms=ligand_atoms)
base_state = ThermodynamicState(temperature=300.0 * unit.kelvin)
base_state.system = alchemical_factory.alchemically_modified_system
alchemical_state1 = AlchemicalState(lambda_electrostatics=1.0,
lambda_sterics=1.0)
alchemical_state0 = AlchemicalState(lambda_electrostatics=0.0,
lambda_sterics=0.0)
alchemical_states = [alchemical_state1, alchemical_state0]
positions = toluene_test.positions
# We pass as fully_interacting_expanded_state and noninteracting_expanded_state the normal
# reference state as we just want to check that they are correctly
# set on resume
fully_interacting_expanded_state = ThermodynamicState(temperature=300.0 *
unit.kelvin)
fully_interacting_expanded_state.system = toluene_test.system
noninteracting_expanded_state = copy.deepcopy(base_state)
with enter_temp_directory():
store_file_name = 'simulation.nc'
simulation = ModifiedHamiltonianExchange(store_file_name)
simulation.create(
base_state,
alchemical_states,
positions,
mc_atoms=ligand_atoms,
fully_interacting_expanded_state=fully_interacting_expanded_state,
noninteracting_expanded_state=noninteracting_expanded_state)
# Clean up simulation and resume
del simulation
simulation = ModifiedHamiltonianExchange(store_file_name)
simulation.resume()
assert simulation.fully_interacting_expanded_state is not None
assert simulation.noninteracting_expanded_state is not None