def create_dummy_metadata(dummy_property, calculation_layer):
global_metadata = Workflow.generate_default_metadata(
dummy_property, "smirnoff99Frosst-1.1.0.offxml", [])
if calculation_layer == "ReweightingLayer":
schema = registered_calculation_schemas[calculation_layer][
dummy_property.__class__.__name__]
if callable(schema):
schema = schema()
for key, query in schema.storage_queries.items():
fake_data = [(f"data_path_{index}_{key}", f"ff_path_{index}_{key}")
for index in range(3)]
if (query.substance_query != UNDEFINED
and query.substance_query.components_only):
fake_data = []
for component_index in enumerate(
dummy_property.substance.components):
fake_data.append([(
f"data_path_{index}_{key}_{component_index}",
f"ff_path_{index}_{key}",
) for index in range(3)])
global_metadata[key] = fake_data
return global_metadata
def _get_workflow_metadata(
working_directory,
physical_property,
force_field_path,
parameter_gradient_keys,
storage_backend,
calculation_schema,
):
"""Returns the global metadata to pass to the workflow.
Parameters
----------
working_directory: str
The local directory in which to store all local,
temporary calculation data from this workflow.
physical_property : PhysicalProperty
The property that the workflow will estimate.
force_field_path : str
The path to the force field parameters to use in the workflow.
parameter_gradient_keys: list of ParameterGradientKey
A list of references to all of the parameters which all observables
should be differentiated with respect to.
storage_backend: StorageBackend
The backend used to store / retrieve data from previous calculations.
calculation_schema: WorkflowCalculationSchema
The schema containing all of this layers options.
Returns
-------
dict of str and Any, optional
The global metadata to make available to a workflow.
Returns `None` if the required metadata could not be
found / assembled.
"""
target_uncertainty = None
if calculation_schema.absolute_tolerance != UNDEFINED:
target_uncertainty = calculation_schema.absolute_tolerance
elif calculation_schema.relative_tolerance != UNDEFINED:
target_uncertainty = (physical_property.uncertainty *
calculation_schema.relative_tolerance)
global_metadata = Workflow.generate_default_metadata(
physical_property,
force_field_path,
parameter_gradient_keys,
target_uncertainty,
)
return global_metadata
def test_nested_replicators():
dummy_schema = WorkflowSchema()
dummy_protocol = DummyReplicableProtocol("dummy_$(rep_a)_$(rep_b)")
dummy_protocol.replicated_value_a = ReplicatorValue("rep_a")
dummy_protocol.replicated_value_b = ReplicatorValue("rep_b")
dummy_schema.protocol_schemas = [dummy_protocol.schema]
replicator_a = ProtocolReplicator(replicator_id="rep_a")
replicator_a.template_values = ["a", "b"]
replicator_b = ProtocolReplicator(replicator_id="rep_b")
replicator_b.template_values = [1, 2]
dummy_schema.protocol_replicators = [replicator_a, replicator_b]
dummy_schema.validate()
dummy_property = create_dummy_property(Density)
dummy_metadata = Workflow.generate_default_metadata(
dummy_property, "smirnoff99Frosst-1.1.0.offxml", [])
dummy_workflow = Workflow(dummy_metadata, "")
dummy_workflow.schema = dummy_schema
assert len(dummy_workflow.protocols) == 4
assert dummy_workflow.protocols["dummy_0_0"].replicated_value_a == "a"
assert dummy_workflow.protocols["dummy_0_1"].replicated_value_a == "a"
assert dummy_workflow.protocols["dummy_1_0"].replicated_value_a == "b"
assert dummy_workflow.protocols["dummy_1_1"].replicated_value_a == "b"
assert dummy_workflow.protocols["dummy_0_0"].replicated_value_b == 1
assert dummy_workflow.protocols["dummy_0_1"].replicated_value_b == 2
assert dummy_workflow.protocols["dummy_1_0"].replicated_value_b == 1
assert dummy_workflow.protocols["dummy_1_1"].replicated_value_b == 2
print(dummy_workflow.schema)
def test_advanced_nested_replicators():
dummy_schema = WorkflowSchema()
replicator_a = ProtocolReplicator(replicator_id="replicator_a")
replicator_a.template_values = ["a", "b"]
replicator_b = ProtocolReplicator(
replicator_id=f"replicator_b_{replicator_a.placeholder_id}")
replicator_b.template_values = ProtocolPath(
f"dummy_list[{replicator_a.placeholder_id}]", "global")
dummy_protocol = DummyReplicableProtocol(f"dummy_"
f"{replicator_a.placeholder_id}_"
f"{replicator_b.placeholder_id}")
dummy_protocol.replicated_value_a = ReplicatorValue(replicator_a.id)
dummy_protocol.replicated_value_b = ReplicatorValue(replicator_b.id)
dummy_schema.protocol_schemas = [dummy_protocol.schema]
dummy_schema.protocol_replicators = [replicator_a, replicator_b]
dummy_schema.validate()
dummy_property = create_dummy_property(Density)
dummy_metadata = Workflow.generate_default_metadata(
dummy_property, "smirnoff99Frosst-1.1.0.offxml", [])
dummy_metadata["dummy_list"] = [[1], [2]]
dummy_workflow = Workflow(dummy_metadata, "")
dummy_workflow.schema = dummy_schema
assert len(dummy_workflow.protocols) == 2
assert dummy_workflow.protocols["dummy_0_0"].replicated_value_a == "a"
assert dummy_workflow.protocols["dummy_0_0"].replicated_value_b == 1
assert dummy_workflow.protocols["dummy_1_0"].replicated_value_a == "b"
assert dummy_workflow.protocols["dummy_1_0"].replicated_value_b == 2
def test_group_replicators():
dummy_schema = WorkflowSchema()
replicator_id = "replicator"
dummy_replicated_protocol = DummyInputOutputProtocol(
f"dummy_$({replicator_id})")
dummy_replicated_protocol.input_value = ReplicatorValue(replicator_id)
dummy_group = ProtocolGroup("dummy_group")
dummy_group.add_protocols(dummy_replicated_protocol)
dummy_protocol_single_value = DummyInputOutputProtocol(
f"dummy_single_$({replicator_id})")
dummy_protocol_single_value.input_value = ProtocolPath(
"output_value", dummy_group.id, dummy_replicated_protocol.id)
dummy_protocol_list_value = AddValues("dummy_list")
dummy_protocol_list_value.values = ProtocolPath(
"output_value", dummy_group.id, dummy_replicated_protocol.id)
dummy_schema.protocol_schemas = [
dummy_group.schema,
dummy_protocol_single_value.schema,
dummy_protocol_list_value.schema,
]
replicator = ProtocolReplicator(replicator_id)
replicator.template_values = [
(1.0 * unit.kelvin).plus_minus(1.0 * unit.kelvin),
(2.0 * unit.kelvin).plus_minus(2.0 * unit.kelvin),
]
dummy_schema.protocol_replicators = [replicator]
dummy_schema.validate()
dummy_property = create_dummy_property(Density)
dummy_metadata = Workflow.generate_default_metadata(
dummy_property, "smirnoff99Frosst-1.1.0.offxml", [])
dummy_workflow = Workflow(dummy_metadata, "")
dummy_workflow.schema = dummy_schema
assert len(dummy_workflow.protocols) == 4
assert (dummy_workflow.protocols[dummy_group.id].protocols["dummy_0"].
input_value.value == replicator.template_values[0].value)
assert (dummy_workflow.protocols[dummy_group.id].protocols["dummy_1"].
input_value.value == replicator.template_values[1].value)
assert dummy_workflow.protocols[
"dummy_single_0"].input_value == ProtocolPath("output_value",
dummy_group.id,
"dummy_0")
assert dummy_workflow.protocols[
"dummy_single_1"].input_value == ProtocolPath("output_value",
dummy_group.id,
"dummy_1")
assert len(dummy_workflow.protocols["dummy_list"].values) == 2
assert dummy_workflow.protocols["dummy_list"].values[0] == ProtocolPath(
"output_value", dummy_group.id, "dummy_0")
assert dummy_workflow.protocols["dummy_list"].values[1] == ProtocolPath(
"output_value", dummy_group.id, "dummy_1")
def main():
setup_timestamp_logging()
# Retrieve the current version.
version = evaluator.__version__.replace(".", "-").replace("v", "")
if "+" in version:
version = "latest"
# Create a new directory to run the current versions results in.
os.makedirs(os.path.join(version, "results"))
with temporarily_change_directory(version):
# Load in the force field
force_field = ForceField(
"openff-1.2.0.offxml",
get_data_filename("forcefield/tip3p.offxml"),
)
force_field_source = SmirnoffForceFieldSource.from_object(force_field)
force_field_source.json("force-field.json")
# Load in the data set, retaining only a specific host / guest pair.
binding_affinity = TaproomDataSet(
host_codes=["acd"],
guest_codes=["bam"],
default_ionic_strength=150 * unit.millimolar,
).properties[0]
# Set up the calculation
schema = HostGuestBindingAffinity.default_paprika_schema(
n_solvent_molecules=2000).workflow_schema
schema.replace_protocol_types({
"BaseBuildSystem": ("BuildSmirnoffSystem" if isinstance(
force_field_source, SmirnoffForceFieldSource) else
"BuildTLeapSystem" if isinstance(
force_field_source, TLeapForceFieldSource)
else "BaseBuildSystem")
})
metadata = Workflow.generate_default_metadata(binding_affinity,
"force-field.json",
UNDEFINED)
workflow = Workflow.from_schema(schema, metadata, "acd_bam")
# Run the calculation
with DaskLSFBackend(
minimum_number_of_workers=1,
maximum_number_of_workers=50,
resources_per_worker=QueueWorkerResources(
number_of_gpus=1,
preferred_gpu_toolkit=QueueWorkerResources.GPUToolkit.CUDA,
per_thread_memory_limit=5 * unit.gigabyte,
wallclock_time_limit="05:59",
),
setup_script_commands=[
"conda activate openff-evaluator-paprika",
"module load cuda/10.0",
],
queue_name="gpuqueue",
) as calculation_backend:
results = workflow.execute(
root_directory="workflow",
calculation_backend=calculation_backend).result()
# Save the results
results.json("results.json", format=True)
def test_density_dielectric_merging(workflow_merge_function):
substance = Substance.from_components("C")
density = openff.evaluator.properties.Density(
thermodynamic_state=ThermodynamicState(
temperature=298 * unit.kelvin, pressure=1 * unit.atmosphere
),
phase=PropertyPhase.Liquid,
substance=substance,
value=10 * unit.gram / unit.mole,
uncertainty=1 * unit.gram / unit.mole,
)
dielectric = openff.evaluator.properties.DielectricConstant(
thermodynamic_state=ThermodynamicState(
temperature=298 * unit.kelvin, pressure=1 * unit.atmosphere
),
phase=PropertyPhase.Liquid,
substance=substance,
value=10 * unit.gram / unit.mole,
uncertainty=1 * unit.gram / unit.mole,
)
density_schema = density.default_simulation_schema().workflow_schema
dielectric_schema = dielectric.default_simulation_schema().workflow_schema
density_metadata = Workflow.generate_default_metadata(
density, "smirnoff99Frosst-1.1.0.offxml", []
)
dielectric_metadata = Workflow.generate_default_metadata(
density, "smirnoff99Frosst-1.1.0.offxml", []
)
density_workflow = Workflow(density_metadata)
density_workflow.schema = density_schema
dielectric_workflow = Workflow(dielectric_metadata)
dielectric_workflow.schema = dielectric_schema
workflow_merge_function(density_workflow, dielectric_workflow)
density_workflow_graph = density_workflow.to_graph()
dielectric_workflow_graph = dielectric_workflow.to_graph()
dependants_graph_a = density_workflow_graph._protocol_graph._build_dependants_graph(
density_workflow_graph.protocols, False, apply_reduction=True
)
dependants_graph_b = (
dielectric_workflow_graph._protocol_graph._build_dependants_graph(
dielectric_workflow_graph.protocols, False, apply_reduction=True
)
)
merge_order_a = graph.topological_sort(dependants_graph_a)
merge_order_b = graph.topological_sort(dependants_graph_b)
for protocol_id_A, protocol_id_B in zip(merge_order_a, merge_order_b):
if (
protocol_id_A.find("extract_traj") < 0
and protocol_id_A.find("extract_stats") < 0
):
assert (
density_workflow.protocols[protocol_id_A].schema.json()
== dielectric_workflow.protocols[protocol_id_B].schema.json()
)
else:
assert (
density_workflow.protocols[protocol_id_A].schema.json()
!= dielectric_workflow.protocols[protocol_id_B].schema.json()
)