def main():
setup_timestamp_logging()
# Load in the force field
force_field_path = "smirnoff99Frosst-1.1.0.offxml"
force_field_source = SmirnoffForceFieldSource.from_path(force_field_path)
# Load in the data set containing the pure and binary properties.
data_set = PhysicalPropertyDataSet.from_json("pure_data_set.json")
data_set.merge(PhysicalPropertyDataSet.from_json("binary_data_set.json"))
# Set up a server object to run the calculations using.
server = setup_server(backend_type=BackendType.LocalGPU,
max_number_of_workers=1,
port=8001)
with server:
# Request the estimates.
property_estimator = EvaluatorClient(
ConnectionOptions(server_port=8001))
for calculation_layer in ["SimulationLayer", "ReweightingLayer"]:
options = RequestOptions()
options.calculation_layers = [calculation_layer]
parameter_gradient_keys = [
ParameterGradientKey(tag="vdW",
smirks="[#6X4:1]",
attribute="epsilon"),
ParameterGradientKey(tag="vdW",
smirks="[#6X4:1]",
attribute="rmin_half"),
]
request, _ = property_estimator.request_estimate(
property_set=data_set,
force_field_source=force_field_source,
options=options,
parameter_gradient_keys=parameter_gradient_keys,
)
# Wait for the results.
results, _ = request.results(True, 5)
layer_name = re.sub(r"(?<!^)(?=[A-Z])", "_",
calculation_layer).lower()
results.json(f"pure_binary_{layer_name}.json", True)
def main():
setup_timestamp_logging()
# Load in the force field
force_field_path = "smirnoff99Frosst-1.1.0.offxml"
force_field_source = SmirnoffForceFieldSource.from_path(force_field_path)
# Create a data set containing three solvation free energies.
data_set = PhysicalPropertyDataSet.from_json("hydration_data_set.json")
data_set.json("hydration_data_set.json", format=True)
# Set up a server object to run the calculations using.
server = setup_server(backend_type=BackendType.LocalGPU,
max_number_of_workers=1,
port=8002)
with server:
# Request the estimates.
property_estimator = EvaluatorClient(
ConnectionOptions(server_port=8002))
options = RequestOptions()
options.calculation_layers = ["SimulationLayer"]
options.add_schema("SimulationLayer", "SolvationFreeEnergy",
_get_fixed_lambda_schema())
request, _ = property_estimator.request_estimate(
property_set=data_set,
force_field_source=force_field_source,
options=options,
)
# Wait for the results.
results, _ = request.results(True, 60)
# Save the result to file.
results.json(f"results.json", True)
def main():
setup_timestamp_logging()
# Load in the force field
force_field_path = 'smirnoff99Frosst-1.1.0.offxml'
force_field_source = SmirnoffForceFieldSource.from_path(force_field_path)
# Load in the data set containing a single dielectric
# property.
with open('pure_data_set.json') as file:
data_set = PhysicalPropertyDataSet.parse_json(file.read())
data_set.filter_by_property_types('DielectricConstant')
# Set up the server object which run the calculations.
setup_server(backend_type=BackendType.LocalGPU,
max_number_of_workers=1,
port=8001)
# Request the estimates.
property_estimator = client.PropertyEstimatorClient(
client.ConnectionOptions(server_port=8001))
options = PropertyEstimatorOptions()
options.allowed_calculation_layers = ['SimulationLayer']
options.workflow_options = {
'DielectricConstant': {
'SimulationLayer':
WorkflowOptions(WorkflowOptions.ConvergenceMode.NoChecks),
'ReweightingLayer':
WorkflowOptions(WorkflowOptions.ConvergenceMode.NoChecks)
}
}
parameter_gradient_keys = [
ParameterGradientKey(tag='vdW', smirks='[#6X4:1]',
attribute='epsilon'),
ParameterGradientKey(tag='vdW',
smirks='[#6X4:1]',
attribute='rmin_half')
]
request = property_estimator.request_estimate(
property_set=data_set,
force_field_source=force_field_source,
options=options,
parameter_gradient_keys=parameter_gradient_keys)
# Wait for the results.
results = request.results(True, 5)
# Save the result to file.
with open('dielectric_simulation.json', 'wb') as file:
json_results = json.dumps(results,
sort_keys=True,
indent=2,
separators=(',', ': '),
cls=TypedJSONEncoder)
file.write(json_results.encode('utf-8'))
# Attempt to reweight the cached data.
options.allowed_calculation_layers = ['ReweightingLayer']
request = property_estimator.request_estimate(
property_set=data_set,
force_field_source=force_field_source,
options=options,
parameter_gradient_keys=parameter_gradient_keys)
# Wait for the results.
results = request.results(True, 5)
# Save the result to file.
with open('dielectric_reweight.json', 'wb') as file:
json_results = json.dumps(results,
sort_keys=True,
indent=2,
separators=(',', ': '),
cls=TypedJSONEncoder)
file.write(json_results.encode('utf-8'))