def test_to_pandas():
"""A test to ensure that data sets are convertable to pandas objects."""
source = CalculationSource('Dummy', {})
pure_substance = Substance.from_components('C')
binary_substance = Substance.from_components('C', 'O')
data_set = PhysicalPropertyDataSet()
data_set.properties[pure_substance.identifier] = []
data_set.properties[binary_substance.identifier] = []
for temperature in [298 * unit.kelvin, 300 * unit.kelvin, 302 * unit.kelvin]:
thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=1.0 * unit.atmosphere)
density_property = Density(thermodynamic_state=thermodynamic_state,
phase=PropertyPhase.Liquid,
substance=pure_substance,
value=1 * unit.gram / unit.milliliter,
uncertainty=0.11 * unit.gram / unit.milliliter,
source=source)
dielectric_property = DielectricConstant(thermodynamic_state=thermodynamic_state,
phase=PropertyPhase.Liquid,
substance=pure_substance,
value=1 * unit.dimensionless,
uncertainty=0.11 * unit.dimensionless,
source=source)
data_set.properties[pure_substance.identifier].append(density_property)
data_set.properties[pure_substance.identifier].append(dielectric_property)
for temperature in [298 * unit.kelvin, 300 * unit.kelvin, 302 * unit.kelvin]:
thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=1.0 * unit.atmosphere)
enthalpy_property = EnthalpyOfMixing(thermodynamic_state=thermodynamic_state,
phase=PropertyPhase.Liquid,
substance=binary_substance,
value=1 * unit.kilojoules / unit.mole,
uncertainty=0.11 * unit.kilojoules / unit.mole,
source=source)
excess_property = ExcessMolarVolume(thermodynamic_state=thermodynamic_state,
phase=PropertyPhase.Liquid,
substance=binary_substance,
value=1 * unit.meter**3 / unit.mole,
uncertainty=0.11 * unit.meter**3 / unit.mole,
source=source)
data_set.properties[binary_substance.identifier].append(enthalpy_property)
data_set.properties[binary_substance.identifier].append(excess_property)
data_set_pandas = data_set.to_pandas()
assert data_set_pandas is not None
assert len(data_set_pandas) == 6
def save_results(force_field_key, results):
"""Saves the estimated results to disk.
Parameters
----------
force_field_key: str
The key of the force field which these results were
estimated for.
results: PropertyEstimatorResult
The results of an estimation request.
"""
with open(f'{force_field_key} results.json', 'w') as file:
json.dump(results,
file,
sort_keys=True,
indent=2,
separators=(',', ': '),
cls=TypedJSONEncoder)
# Save the estimated and unsuccessful properties in separate data sets.
estimated_data_set = PhysicalPropertyDataSet()
unsuccessful_data_set = PhysicalPropertyDataSet()
# Gather up the successfully estimated properties.
for substance_id in results.estimated_properties:
estimated_properties = results.estimated_properties[substance_id]
for estimated_property in estimated_properties:
if substance_id not in estimated_data_set.properties:
estimated_data_set.properties[substance_id] = []
estimated_property.source.provenance = {}
estimated_data_set.properties[substance_id].append(
estimated_property)
estimated_data_set.to_pandas().to_csv(f'{force_field_key}.csv')
with open(f'{force_field_key}.json', 'w') as file:
json.dump(estimated_data_set,
file,
sort_keys=True,
indent=2,
separators=(',', ': '),
cls=TypedJSONEncoder)
# Gather up the properties which could not be estimated.
for substance_id in results.unsuccessful_properties:
unsuccessful_properties = results.unsuccessful_properties[
substance_id][0]
for unsuccessful_property in unsuccessful_properties:
if substance_id not in unsuccessful_data_set.properties:
unsuccessful_data_set.properties[substance_id] = []
unsuccessful_property.source.provenance = None
unsuccessful_data_set.properties[substance_id].append(
unsuccessful_property)
with open(f'{force_field_key} unsuccessful.json', 'w') as file:
json.dump(unsuccessful_data_set,
file,
sort_keys=True,
indent=2,
separators=(',', ': '),
cls=TypedJSONEncoder)
# Save any exceptions that occured in a more human readable file.
with open(f'{force_field_key} exceptions.txt', 'w') as file:
for index, exception in enumerate(results.exceptions):
file.write(f'\n{exception.directory}\n')
file.write(exception.message.replace('\\n', '\n'))