def test_thermoml_mole_constraints():
"""A collection of tests to ensure that the Mole fraction constraint is
implemented correctly alongside solvent constraints."""
# Mole fraction
data_set = ThermoMLDataSet.from_file(get_data_filename('test/properties/mole.xml'))
assert data_set is not None
assert len(data_set.properties) > 0
# Mole fraction + Solvent: Mass fraction
data_set = ThermoMLDataSet.from_file(get_data_filename('test/properties/mole_mass.xml'))
assert data_set is not None
assert len(data_set.properties) > 0
# Mole fraction + Solvent: Mole fraction
data_set = ThermoMLDataSet.from_file(get_data_filename('test/properties/mole_mole.xml'))
assert data_set is not None
assert len(data_set.properties) > 0
# Mole fraction + Solvent: Molality
data_set = ThermoMLDataSet.from_file(get_data_filename('test/properties/mole_molality.xml'))
assert data_set is not None
assert len(data_set.properties) > 0
def test_from_url():
data_set = ThermoMLDataSet.from_url('https://trc.nist.gov/journals/jct/2005v37/i04/j.jct.2004.09.022.xml')
assert data_set is not None
assert len(data_set.properties) > 0
data_set = ThermoMLDataSet.from_url('https://trc.nist.gov/journals/jct/2005v37/i04/j.jct.2004.09.022.xmld')
assert data_set is None
def test_thermoml_from_url():
"""A test to ensure that ThermoML archive files can be loaded from a url."""
data_set = ThermoMLDataSet.from_url('https://trc.nist.gov/journals/jct/2005v37/i04/j.jct.2004.09.022.xml')
assert data_set is not None
assert len(data_set.properties) > 0
data_set = ThermoMLDataSet.from_url('https://trc.nist.gov/journals/jct/2005v37/i04/j.jct.2004.09.022.xmld')
assert data_set is None
def test_from_files():
data_set = ThermoMLDataSet.from_file(get_data_filename('properties/j.jct.2004.09.014.xml'),
get_data_filename('properties/j.jct.2004.09.022.xml'),
get_data_filename('properties/j.jct.2007.09.004.xml'))
assert data_set is not None
assert len(data_set.properties) > 0
data_set = ThermoMLDataSet.from_file('properties/j.jct.2004.09.014.xmld')
assert data_set is None
def test_serialization():
"""A test to ensure that data sets are JSON serializable."""
data_set = ThermoMLDataSet.from_file(get_data_filename('properties/single_density.xml'))
data_set_json = data_set.json()
parsed_data_set = ThermoMLDataSet.parse_json(data_set_json)
assert data_set.number_of_properties == parsed_data_set.number_of_properties
parsed_data_set_json = parsed_data_set.json()
assert parsed_data_set_json == data_set_json
def test_thermoml_from_files():
"""A test to ensure that ThermoML archive files can be loaded from local sources."""
data_set = ThermoMLDataSet.from_file(get_data_filename('properties/single_density.xml'),
get_data_filename('properties/single_dielectric.xml'),
get_data_filename('properties/single_enthalpy_mixing.xml'))
assert data_set is not None
assert len(data_set.properties) == 3
data_set = ThermoMLDataSet.from_file('dummy_filename')
assert data_set is None
def test_from_doi():
data_set = ThermoMLDataSet.from_doi('10.1016/j.jct.2016.10.001')
assert data_set is not None
assert len(data_set.properties) > 0
for mixture_tag in data_set.properties:
for physical_property in data_set.properties[mixture_tag]:
physical_property_json = physical_property.json()
print(physical_property_json)
physical_property_recreated = PhysicalProperty.parse_json(physical_property_json)
print(physical_property_recreated)
data_set = ThermoMLDataSet.from_doi('10.1016/j.jct.2016.12.009')
assert data_set is None
data_set = ThermoMLDataSet.from_doi('10.1016/j.jct.2016.12.009x')
assert data_set is None
def test_thermoml_from_doi():
"""A test to ensure that ThermoML archive files can be loaded from a doi."""
data_set = ThermoMLDataSet.from_doi('10.1016/j.jct.2016.10.001')
assert data_set is not None
assert len(data_set.properties) > 0
for mixture_tag in data_set.properties:
for physical_property in data_set.properties[mixture_tag]:
physical_property_json = physical_property.json()
print(physical_property_json)
physical_property_recreated = PhysicalProperty.parse_json(physical_property_json)
print(physical_property_recreated)
data_set = ThermoMLDataSet.from_doi('10.1016/j.jct.2016.12.009')
assert data_set is None
data_set = ThermoMLDataSet.from_doi('10.1016/j.jct.2016.12.009x')
assert data_set is None
def compute_estimate_async():
"""Submit calculations to a running server instance"""
from openforcefield.typing.engines import smirnoff
setup_timestamp_logging()
# Load in the data set of interest.
data_set = ThermoMLDataSet.from_file(get_data_filename('properties/single_dielectric.xml'))
# Load in the force field to use.
force_field = smirnoff.ForceField(get_data_filename('forcefield/smirnoff99Frosst.offxml'))
# new_property_0 = copy.deepcopy(data_set.properties['COCCO{1.0}'][0])
# new_property_0.thermodynamic_state.temperature -= 2.0 * unit.kelvin
# new_property_0.id = str(uuid4())
#
# data_set.properties['COCCO{1.0}'].append(new_property_0)
#
# new_property_1 = copy.deepcopy(data_set.properties['COCCO{1.0}'][0])
# new_property_1.thermodynamic_state.temperature += 2.0 * unit.kelvin
# new_property_1.id = str(uuid4())
#
# data_set.properties['COCCO{1.0}'].append(new_property_1)
# Modify the submission options
submission_options = PropertyEstimatorOptions()
workflow_options = PropertyWorkflowOptions(PropertyWorkflowOptions.ConvergenceMode.RelativeUncertainty,
relative_uncertainty_fraction=100000)
submission_options.workflow_options = {
'Density': workflow_options,
'Dielectric': workflow_options,
'EnthalpyOfMixing': workflow_options
}
# submission_options.allowed_calculation_layers = ['SimulationLayer']
submission_options.allowed_calculation_layers = ['ReweightingLayer']
# Create the client object.
property_estimator = client.PropertyEstimatorClient()
# Submit the request to a running server.
request = property_estimator.request_estimate(data_set, force_field, submission_options)
logging.info('Request info: {}'.format(str(request)))
# Wait for the results.
result = request.results(synchronous=True)
logging.info('The server has returned a response: {}'.format(result.json()))
def compute_estimate_sync():
"""Submit calculations to a running server instance"""
from openforcefield.typing.engines import smirnoff
setup_timestamp_logging()
# Load in the data set of interest.
data_set = ThermoMLDataSet.from_file(get_data_filename('properties/single_density.xml'))
# Load in the force field to use.
force_field = smirnoff.ForceField(get_data_filename('forcefield/smirnoff99Frosst.offxml'))
# Create the client object.
property_estimator = client.PropertyEstimatorClient()
# Submit the request to a running server, and wait for the results.
result = property_estimator.request_estimate(data_set, force_field)
logging.info('The server has returned a response: {}'.format(result))
def parse_all_jct_files():
logging.basicConfig(filename='data_sets.log', filemode='w', level=logging.INFO)
data_path = get_data_filename('properties/JCT')
thermoml_files = []
for file_path in listdir(data_path):
full_path = join(data_path, file_path)
if not isfile(full_path):
continue
thermoml_files.append(full_path)
data_set = ThermoMLDataSet.from_file(*thermoml_files)
from propertyestimator.properties.density import Density
from propertyestimator.properties.dielectric import DielectricConstant
from propertyestimator.properties.enthalpy import EnthalpyOfMixing
properties_by_type = {Density.__name__: [], DielectricConstant.__name__: [],
EnthalpyOfMixing.__name__: []}
for substance_key in data_set.properties:
for data_property in data_set.properties[substance_key]:
if type(data_property).__name__ not in properties_by_type:
continue
properties_by_type[type(data_property).__name__].append(data_property.source.reference)
for type_key in properties_by_type:
with open('{}.dat'.format(type_key), 'w') as file:
for doi in properties_by_type[type_key]:
file.write('{}\n'.format(doi))