def default_simulation_schema(
absolute_tolerance=UNDEFINED, relative_tolerance=UNDEFINED, n_molecules=1000
):
"""Returns the default calculation schema to use when estimating
this class of property from direct simulations.
Parameters
----------
absolute_tolerance: openff.evaluator.unit.Quantity, optional
The absolute tolerance to estimate the property to within.
relative_tolerance: float
The tolerance (as a fraction of the properties reported
uncertainty) to estimate the property to within.
n_molecules: int
The number of molecules to use in the simulation.
Returns
-------
SimulationSchema
The schema to follow when estimating this property.
"""
assert absolute_tolerance == UNDEFINED or relative_tolerance == UNDEFINED
calculation_schema = SimulationSchema()
calculation_schema.absolute_tolerance = absolute_tolerance
calculation_schema.relative_tolerance = relative_tolerance
use_target_uncertainty = (
absolute_tolerance != UNDEFINED or relative_tolerance != UNDEFINED
)
# Define the protocols which will run the simulation itself.
protocols, value_source, output_to_store = generate_simulation_protocols(
AverageDielectricConstant("average_dielectric"),
use_target_uncertainty,
n_molecules=n_molecules,
)
# Add a protocol to compute the dipole moments and pass these to
# the analysis protocol.
compute_dipoles = ComputeDipoleMoments("compute_dipoles")
compute_dipoles.parameterized_system = ProtocolPath(
"parameterized_system", protocols.assign_parameters.id
)
compute_dipoles.trajectory_path = ProtocolPath(
"trajectory_file_path", protocols.production_simulation.id
)
compute_dipoles.gradient_parameters = ProtocolPath(
"parameter_gradient_keys", "global"
)
protocols.converge_uncertainty.add_protocols(compute_dipoles)
protocols.analysis_protocol.volumes = ProtocolPath(
f"observables[{ObservableType.Volume.value}]",
protocols.production_simulation.id,
)
protocols.analysis_protocol.dipole_moments = ProtocolPath(
"dipole_moments",
compute_dipoles.id,
)
# Build the workflow schema.
schema = WorkflowSchema()
schema.protocol_schemas = [
protocols.build_coordinates.schema,
protocols.assign_parameters.schema,
protocols.energy_minimisation.schema,
protocols.equilibration_simulation.schema,
protocols.converge_uncertainty.schema,
protocols.decorrelate_trajectory.schema,
protocols.decorrelate_observables.schema,
]
schema.outputs_to_store = {"full_system": output_to_store}
schema.final_value_source = value_source
calculation_schema.workflow_schema = schema
return calculation_schema
def default_simulation_schema(absolute_tolerance=UNDEFINED,
relative_tolerance=UNDEFINED,
n_molecules=1000):
"""Returns the default calculation schema to use when estimating
this class of property from direct simulations.
Parameters
----------
absolute_tolerance: pint.Quantity, optional
The absolute tolerance to estimate the property to within.
relative_tolerance: float
The tolerance (as a fraction of the properties reported
uncertainty) to estimate the property to within.
n_molecules: int
The number of molecules to use in the simulation.
Returns
-------
SimulationSchema
The schema to follow when estimating this property.
"""
assert absolute_tolerance == UNDEFINED or relative_tolerance == UNDEFINED
calculation_schema = SimulationSchema()
calculation_schema.absolute_tolerance = absolute_tolerance
calculation_schema.relative_tolerance = relative_tolerance
# Define the protocol which will extract the average dielectric constant
# from the results of a simulation.
extract_dielectric = ExtractAverageDielectric("extract_dielectric")
extract_dielectric.thermodynamic_state = ProtocolPath(
"thermodynamic_state", "global")
# Define the protocols which will run the simulation itself.
use_target_uncertainty = (absolute_tolerance != UNDEFINED
or relative_tolerance != UNDEFINED)
protocols, value_source, output_to_store = generate_base_simulation_protocols(
extract_dielectric,
use_target_uncertainty,
n_molecules=n_molecules,
)
# Make sure the input of the analysis protcol is properly hooked up.
extract_dielectric.system_path = ProtocolPath(
"system_path", protocols.assign_parameters.id)
# Dielectric constants typically take longer to converge, so we need to
# reflect this in the maximum number of convergence iterations.
protocols.converge_uncertainty.max_iterations = 400
# Set up the gradient calculations. For dielectric constants, we need to use
# a slightly specialised reweighting protocol which we set up here.
coordinate_source = ProtocolPath("output_coordinate_file",
protocols.equilibration_simulation.id)
trajectory_source = ProtocolPath(
"trajectory_file_path",
protocols.converge_uncertainty.id,
protocols.production_simulation.id,
)
statistics_source = ProtocolPath(
"statistics_file_path",
protocols.converge_uncertainty.id,
protocols.production_simulation.id,
)
gradient_mbar_protocol = ReweightDielectricConstant("gradient_mbar")
gradient_mbar_protocol.reference_dipole_moments = [
ProtocolPath(
"dipole_moments",
protocols.converge_uncertainty.id,
extract_dielectric.id,
)
]
gradient_mbar_protocol.reference_volumes = [
ProtocolPath("volumes", protocols.converge_uncertainty.id,
extract_dielectric.id)
]
gradient_mbar_protocol.thermodynamic_state = ProtocolPath(
"thermodynamic_state", "global")
gradient_mbar_protocol.reference_reduced_potentials = statistics_source
(
gradient_group,
gradient_replicator,
gradient_source,
) = generate_gradient_protocol_group(
gradient_mbar_protocol,
ProtocolPath("force_field_path", "global"),
coordinate_source,
trajectory_source,
statistics_source,
)
# Build the workflow schema.
schema = WorkflowSchema()
schema.protocol_schemas = [
protocols.build_coordinates.schema,
protocols.assign_parameters.schema,
protocols.energy_minimisation.schema,
protocols.equilibration_simulation.schema,
protocols.converge_uncertainty.schema,
protocols.extract_uncorrelated_trajectory.schema,
protocols.extract_uncorrelated_statistics.schema,
gradient_group.schema,
]
schema.protocol_replicators = [gradient_replicator]
schema.outputs_to_store = {"full_system": output_to_store}
schema.gradients_sources = [gradient_source]
schema.final_value_source = value_source
calculation_schema.workflow_schema = schema
return calculation_schema