def test_density_dielectric_merging():
substance = Mixture()
substance.add_component('C', 1.0)
density = 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 = 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.get_default_workflow_schema(
'SimulationLayer', PropertyWorkflowOptions())
dielectric_schema = dielectric.get_default_workflow_schema(
'SimulationLayer', PropertyWorkflowOptions())
density_metadata = Workflow.generate_default_metadata(
density, get_data_filename('forcefield/smirnoff99Frosst.offxml'),
PropertyEstimatorOptions())
dielectric_metadata = Workflow.generate_default_metadata(
density, get_data_filename('forcefield/smirnoff99Frosst.offxml'),
PropertyEstimatorOptions())
density_workflow = Workflow(density, density_metadata)
density_workflow.schema = density_schema
dielectric_workflow = Workflow(dielectric, dielectric_metadata)
dielectric_workflow.schema = dielectric_schema
workflow_graph = WorkflowGraph('')
workflow_graph.add_workflow(density_workflow)
workflow_graph.add_workflow(dielectric_workflow)
merge_order_a = graph.topological_sort(density_workflow.dependants_graph)
merge_order_b = graph.topological_sort(
dielectric_workflow.dependants_graph)
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()
def test_group_replicators():
dummy_schema = WorkflowSchema()
replicator_id = 'replicator'
dummy_replicated_protocol = DummyInputOutputProtocol(f'dummy_$({replicator_id})')
dummy_replicated_protocol.input_value = ReplicatorValue(replicator_id)
dummy_group = ProtocolGroup('dummy_group')
dummy_group.add_protocols(dummy_replicated_protocol)
dummy_schema.protocols[dummy_group.id] = dummy_group.schema
dummy_protocol_single_value = DummyInputOutputProtocol(f'dummy_single_$({replicator_id})')
dummy_protocol_single_value.input_value = ProtocolPath('output_value', dummy_group.id,
dummy_replicated_protocol.id)
dummy_schema.protocols[dummy_protocol_single_value.id] = dummy_protocol_single_value.schema
dummy_protocol_list_value = AddValues(f'dummy_list')
dummy_protocol_list_value.values = ProtocolPath('output_value', dummy_group.id,
dummy_replicated_protocol.id)
dummy_schema.protocols[dummy_protocol_list_value.id] = dummy_protocol_list_value.schema
replicator = ProtocolReplicator(replicator_id)
replicator.template_values = [
EstimatedQuantity(1.0 * unit.kelvin, 1.0 * unit.kelvin, 'dummy_source'),
EstimatedQuantity(2.0 * unit.kelvin, 2.0 * unit.kelvin, 'dummy_source')
]
dummy_schema.replicators.append(replicator)
dummy_schema.validate_interfaces()
dummy_property = create_dummy_property(Density)
dummy_metadata = Workflow.generate_default_metadata(dummy_property,
'smirnoff99Frosst-1.1.0.offxml',
[])
dummy_workflow = Workflow(dummy_property, 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 == replicator.template_values[0]
assert dummy_workflow.protocols[dummy_group.id].protocols['dummy_1'].input_value == replicator.template_values[1]
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 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.protocols[dummy_protocol.id] = 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.replicators = [
replicator_a,
replicator_b
]
dummy_schema.validate_interfaces()
dummy_property = create_dummy_property(Density)
dummy_metadata = Workflow.generate_default_metadata(dummy_property,
'smirnoff99Frosst-1.1.0.offxml',
[])
dummy_workflow = Workflow(dummy_property, 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.protocols[dummy_protocol.id] = dummy_protocol.schema
dummy_schema.replicators = [replicator_a, replicator_b]
dummy_schema.validate_interfaces()
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_property, 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
print(dummy_workflow.schema)
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.protocols[dummy_protocol.id] = dummy_protocol.schema
dummy_schema.final_value_source = ProtocolPath('final_value',
dummy_protocol.id)
replicator_a = ProtocolReplicator(replicator_id='rep_a')
replicator_a.template_values = ['a', 'b']
replicator_a.protocols_to_replicate = [ProtocolPath('', dummy_protocol.id)]
replicator_b = ProtocolReplicator(replicator_id='rep_b')
replicator_b.template_values = [1, 2]
replicator_b.protocols_to_replicate = [ProtocolPath('', dummy_protocol.id)]
dummy_schema.replicators = [replicator_a, replicator_b]
dummy_schema.validate_interfaces()
dummy_property = create_dummy_property(Density)
dummy_metadata = Workflow.generate_default_metadata(
dummy_property,
get_data_filename('forcefield/smirnoff99Frosst.offxml'),
PropertyEstimatorOptions())
dummy_workflow = Workflow(dummy_property, dummy_metadata)
dummy_workflow.schema = dummy_schema
assert len(dummy_workflow.protocols) == 4
assert dummy_workflow.protocols[dummy_workflow.uuid +
'|dummy_0_0'].replicated_value_a == 'a'
assert dummy_workflow.protocols[dummy_workflow.uuid +
'|dummy_0_1'].replicated_value_a == 'a'
assert dummy_workflow.protocols[dummy_workflow.uuid +
'|dummy_1_0'].replicated_value_a == 'b'
assert dummy_workflow.protocols[dummy_workflow.uuid +
'|dummy_1_1'].replicated_value_a == 'b'
assert dummy_workflow.protocols[dummy_workflow.uuid +
'|dummy_0_0'].replicated_value_b == 1
assert dummy_workflow.protocols[dummy_workflow.uuid +
'|dummy_0_1'].replicated_value_b == 2
assert dummy_workflow.protocols[dummy_workflow.uuid +
'|dummy_1_0'].replicated_value_b == 1
assert dummy_workflow.protocols[dummy_workflow.uuid +
'|dummy_1_1'].replicated_value_b == 2
print(dummy_workflow.schema)