def test_pcm_default_string():
"""
Make sure the default string is correctly formatted.
"""
pcm = PCMSettings(units="au", medium_Solvent="Water")
assert pcm.to_string() == '\n Units = au\n CODATA = 2010\n Medium {\n SolverType = IEFPCM\n Nonequilibrium = False\n Solvent = H2O\n MatrixSymm = True\n Correction = 0.0\n DiagonalScaling = 1.07\n ProbeRadius = 1.0}\n Cavity {\n Type = GePol\n Area = 0.3\n Scaling = True\n RadiiSet = Bondi\n MinRadius = 100\n Mode = Implicit}'
def test_pcm_solver(data):
"""
Make sure only IEFPCM and CPCM solvers are allowed.
"""
solver, error = data
if error is not None:
with pytest.raises(error):
_ = PCMSettings(units="au", medium_Solvent="water", medium_SolverType=solver)
else:
pcm = PCMSettings(units="au", medium_Solvent="water", medium_SolverType=solver)
assert pcm.medium_SolverType == solver
def test_pcm_cavity_mode():
"""
Make sure only the implicit mode is allowed for collection computing.
"""
# try and change to explicit
with pytest.raises(PCMSettingError):
_ = PCMSettings(units="au", medium_Solvent="water", cavity_Mode="Explicit")
# make sure the default is implicit
pcm = PCMSettings(units="au", medium_Solvent="water", cavity_Mode="implicit")
assert pcm.cavity_Mode == "Implicit"
def test_pcm_cavity():
"""
Make sure only the GePol cavity can be set.
"""
# try and change from GePol
with pytest.raises(PCMSettingError):
_ = PCMSettings(units="au", medium_Solvent="Water", cavity_Type="isosurface")
# make sure gepol is the default
pcm = PCMSettings(units="au", medium_Solvent="Water", cavity_Type="gepol")
assert pcm.cavity_Type == "GePol"
def test_pcm_codata(data):
"""
Make sure an accptable codata value is passed and an error is raised if not.
"""
codata, error = data
if error is not None:
with pytest.raises(error):
_ = PCMSettings(units="AU", medium_Solvent="water", codata=codata)
else:
pcm = PCMSettings(units="AU", medium_Solvent="water", codata=codata)
assert pcm.codata == codata
def test_pcm_units(data):
"""
Make sure proper units are validated.
"""
unit, error = data
if error is not None:
with pytest.raises(error):
_ = PCMSettings(units=unit, medium_Solvent="Water")
else:
pcm = PCMSettings(units=unit, medium_Solvent="Water")
assert pcm.medium_Solvent == "H2O"
def test_pcm_solvent(solvent_data):
"""
Make sure solvents can be accepted as either names or chemical formula but are always converted to formula.
"""
solvent, formula, error = solvent_data
if error is not None:
with pytest.raises(error):
_ = PCMSettings(units="au", medium_Solvent=solvent)
else:
pcm = PCMSettings(units="au", medium_Solvent=solvent)
assert pcm.medium_Solvent == formula
def test_pcm_radiisets(data):
"""
Make sure only valid radii are allowed
"""
radii, error = data
if error is not None:
with pytest.raises(error):
_ = PCMSettings(units="au", medium_Solvent="Water", cavity_RadiiSet=radii)
else:
pcm = PCMSettings(units="au", medium_Solvent="Water", cavity_RadiiSet=radii)
assert pcm.cavity_RadiiSet == radii
def test_pcm_unit_conversion_defaults():
"""
Make sure the the default settings are converted to the correct units.
"""
# make sure the au are kept as default
pcm = PCMSettings(units="au", medium_Solvent="water")
assert pcm.medium_ProbeRadius == 1.0
assert pcm.cavity_Area == 0.3
assert pcm.cavity_MinRadius == 100
pcm2 = PCMSettings(units="angstrom", medium_Solvent="water")
assert pcm2.medium_ProbeRadius == pcm.medium_ProbeRadius * constants.bohr2angstroms
assert pcm2.cavity_Area == pcm.cavity_Area * constants.bohr2angstroms**2
assert pcm2.cavity_MinRadius == pcm.cavity_MinRadius * constants.bohr2angstroms
def test_pcm_unit_conversion():
"""
Make sure only defaults are converted and given options are kept constant.
"""
# set the probe radius to 2 angstroms
pcm = PCMSettings(units="angstrom", medium_Solvent="water", medium_ProbeRadius=2)
assert pcm.medium_ProbeRadius == 2
# make sure this has been converted
assert pcm.cavity_Area != 0.3
def test_qcspec_with_solvent():
"""
Make sure we only allow PCM to be used with PSI4.
"""
# make sure an error is raised with any program that is not psi4
with pytest.raises(QCSpecificationError):
_ = QCSpec(method="ani2x",
basis=None,
program="torchani",
spec_name="ani2x",
spec_description="testing ani with solvent",
implicit_solvent=PCMSettings(units="au",
medium_Solvent="water"))
# now try with PSI4
qc_spec = QCSpec(
implicit_solvent=PCMSettings(units="au", medium_Solvent="water"))
assert qc_spec.implicit_solvent is not None
assert qc_spec.implicit_solvent.medium_Solvent == "H2O"
def test_optimization_submissions_with_pcm(fractal_compute_server):
"""Test submitting an Optimization dataset to a snowflake server with PCM."""
client = FractalClient(fractal_compute_server)
program = "psi4"
if not has_program(program):
pytest.skip(f"Program '{program}' not found.")
# use a single small molecule due to the extra time PCM takes
molecules = Molecule.from_smiles("C")
factory = OptimizationDatasetFactory(driver="gradient")
factory.add_qc_spec(method="hf",
basis="sto-3g",
program=program,
spec_name="default",
spec_description="test",
implicit_solvent=PCMSettings(units="au",
medium_Solvent="water"),
overwrite=True)
dataset = factory.create_dataset(
dataset_name="Test optimizations info with pcm water",
molecules=molecules,
description="Test optimization dataset",
tagline="Testing optimization datasets",
)
# force a metadata validation error
dataset.metadata.long_description = None
with pytest.raises(DatasetInputError):
dataset.submit(client=client)
# re-add the description so we can submit the data
dataset.metadata.long_description = "Test basics dataset"
# now submit again
dataset.submit(client=client)
fractal_compute_server.await_results()
# make sure of the results are complete
ds = client.get_collection("OptimizationDataset", dataset.dataset_name)
# check the metadata
meta = Metadata(**ds.data.metadata)
assert meta == dataset.metadata
# check the provenance
assert dataset.provenance == ds.data.provenance
# check the qc spec
for qc_spec in dataset.qc_specifications.values():
spec = ds.data.specs[qc_spec.spec_name]
assert spec.description == qc_spec.spec_description
assert spec.qc_spec.driver == dataset.driver
assert spec.qc_spec.method == qc_spec.method
assert spec.qc_spec.basis == qc_spec.basis
assert spec.qc_spec.program == qc_spec.program
# check the keywords
keywords = client.query_keywords(spec.qc_spec.keywords)[0]
assert keywords.values["maxiter"] == qc_spec.maxiter
assert keywords.values["scf_properties"] == qc_spec.scf_properties
# query the dataset
ds.query(qc_spec.spec_name)
for index in ds.df.index:
record = ds.df.loc[index].default
assert record.status.value == "COMPLETE"
assert record.error is None
assert len(record.trajectory) > 1
result = record.get_trajectory()[0]
assert "CURRENT DIPOLE X" in result.extras["qcvars"].keys()
assert "SCF QUADRUPOLE XX" in result.extras["qcvars"].keys()
# make sure the PCM result was captured
assert result.extras["qcvars"]["PCM POLARIZATION ENERGY"] < 0
def test_basic_submissions_single_pcm_spec(fractal_compute_server):
"""Test submitting a basic dataset to a snowflake server with pcm water in the specification."""
client = FractalClient(fractal_compute_server)
program = "psi4"
if not has_program(program):
pytest.skip(f"Program '{program}' not found.")
molecules = Molecule.from_file(get_data("butane_conformers.pdb"), "pdb")
factory = BasicDatasetFactory(driver="energy")
factory.add_qc_spec(method="hf",
basis="sto-3g",
program=program,
spec_name="default",
spec_description="testing the single points with pcm",
implicit_solvent=PCMSettings(units="au",
medium_Solvent="water"),
overwrite=True)
# only use one molecule due to the time it takes to run with pcm
dataset = factory.create_dataset(
dataset_name="Test single points with pcm water",
molecules=molecules[0],
description="Test basics dataset with pcm water",
tagline="Testing single point datasets with pcm water",
)
# force a metadata validation error
dataset.metadata.long_description = None
with pytest.raises(DatasetInputError):
dataset.submit(client=client)
# re-add the description so we can submit the data
dataset.metadata.long_description = "Test basics dataset"
# now submit again
dataset.submit(client=client)
fractal_compute_server.await_results()
# make sure of the results are complete
ds = client.get_collection("Dataset", dataset.dataset_name)
# check the metadata
meta = Metadata(**ds.data.metadata)
assert meta == dataset.metadata
assert ds.data.description == dataset.description
assert ds.data.tagline == dataset.dataset_tagline
assert ds.data.tags == dataset.dataset_tags
# check the provenance
assert dataset.provenance == ds.data.provenance
# check the qc spec
assert ds.data.default_driver == dataset.driver
# get the last ran spec
for specification in ds.data.history:
driver, program, method, basis, spec_name = specification
spec = dataset.qc_specifications[spec_name]
assert driver == dataset.driver
assert program == spec.program
assert method == spec.method
assert basis == spec.basis
break
else:
raise RuntimeError(
f"The requested compute was not found in the history {ds.data.history}"
)
for spec in dataset.qc_specifications.values():
query = ds.get_records(
method=spec.method,
basis=spec.basis,
program=spec.program,
)
for index in query.index:
result = query.loc[index].record
assert result.status.value.upper() == "COMPLETE"
assert result.error is None
assert result.return_result is not None
# make sure the PCM result was captured
assert result.extras["qcvars"]["PCM POLARIZATION ENERGY"] < 0