def get_version(self) -> str:
self.found(raise_error=True)
# Get the node configuration
config = get_config()
# Run NWChem
which_prog = which("nwchem")
if config.use_mpiexec:
command = create_mpi_invocation(which_prog, config)
else:
command = [which_prog]
command.append("v.nw")
if which_prog not in self.version_cache:
success, output = execute(command, {"v.nw": ""}, scratch_directory=config.scratch_directory)
if success:
for line in output["stdout"].splitlines():
if "nwchem branch" in line:
branch = line.strip().split()[-1]
if "nwchem revision" in line:
revision = line.strip().split()[-1]
self.version_cache[which_prog] = safe_version(branch + "+" + revision)
else:
raise UnknownError(output["stderr"])
return self.version_cache[which_prog]
def get_version(self) -> str:
self.found(raise_error=True)
# Get the node configuration
config = get_config()
# Run MADNESS
which_prog = which("moldft")
if config.use_mpiexec:
command = create_mpi_invocation(which_prog, config)
else:
command = [which_prog]
command.append("v.moldft")
if which_prog not in self.version_cache:
success, output = execute(
command,
{
"v.moldft":
"dft\nxc lda\nend\ngeometry\nBe 0.0 0.0 0.0\n\nend\n"
},
scratch_directory=config.scratch_directory,
)
if success:
for line in output["stdout"].splitlines():
if "multiresolution suite" in line:
version = line.strip().split()[1]
self.version_cache[which_prog] = safe_version(version)
else:
raise UnknownError(output["stderr"])
return self.version_cache[which_prog]
def test_gaussian_solvent_template(tmpdir, water):
"""
Make sure that the template rendered with solvent settings matches what we expect.
"""
with tmpdir.as_cwd():
# get the charge method and implicit solvent engine
charge_engine = DDECCharges()
solvent_settings = charge_engine._get_calculation_settings()
# now make an atomic input for the harness
task = AtomicInput(
molecule=water.to_qcschema(),
driver="energy",
model={
"method": "b3lyp-d3bj",
"basis": "6-311G"
},
keywords=solvent_settings,
)
# we need the harness as this will render the template
gaussian_harness = GaussianHarness()
config = get_config(task_config={"ncores": 1, "memory": 1})
job_inputs = gaussian_harness.build_input(task, config)
# make sure the job file matches or expected reference
with open(get_data("gaussian_solvent_example.com")) as g_out:
assert g_out.read() == job_inputs["infiles"]["gaussian.com"]
def get_version(self) -> str:
# excuse missing Q-Chem for QCEngineRecords tests
found = self.found()
if not found:
return safe_version("0.0.0")
self.found(raise_error=True)
# Get the node configuration
config = get_config()
which_prog = which("qchem")
if which_prog not in self.version_cache:
success, exc = execute(
[which_prog, "v.in"],
{"v.in": "$rem\n"},
scratch_directory=config.scratch_directory,
environment=self._get_qc_path(),
timeout=15,
)
mobj = re.search(r"Q-Chem\s+([\d.]+)\s+for", exc["stdout"])
if not mobj:
mobj = re.search(r"Q-Chem version:\s+([\d.]+)\s+",
exc["stdout"])
if mobj:
self.version_cache[which_prog] = safe_version(mobj.group(1))
# if "QC not defined" in exc["stdout"]:
else:
return safe_version("0.0.0")
return self.version_cache[which_prog]
def test_gaussian_no_solvent_template(tmpdir, water):
"""
Make sure that we can calculate the electron density with no implicit solvent.
"""
with tmpdir.as_cwd():
# get the charge method and implicit solvent engine
charge_engine = DDECCharges(solvent_settings=None)
settings = charge_engine._get_calculation_settings()
task = AtomicInput(
molecule=water.to_qcschema(),
driver="energy",
model={
"method": "b3lyp-d3bj",
"basis": "6-311G"
},
keywords=settings,
)
# we need the harness as this will render the template
gaussian_harness = GaussianHarness()
config = get_config(task_config={"ncores": 1, "memory": 1})
job_inputs = gaussian_harness.build_input(task, config)
with open(get_data("gaussian_gas_example.com")) as g_out:
assert g_out.read() == job_inputs["infiles"]["gaussian.com"]
def psi4(input_data):
"""
Runs Psi4 in API mode
"""
# Insert API path if needed
psiapi = config.get_config("psi_path")
if (psiapi is not None) and (psiapi not in sys.path):
sys.path.insert(1, psiapi)
try:
import psi4
except ImportError:
raise ImportError("Could not find Psi4 in the Python path.")
# Setup the job
input_data["nthreads"] = config.get_config("nthreads_per_job")
input_data["memory"] = int(
config.get_config("memory_per_job") * 1024 * 1024 * 1024 * 0.95)
input_data["success"] = False
scratch = config.get_config("scratch_directory")
if scratch is not None:
input_data["scratch_location"] = scratch
psi_version = _parse_psi_version(psi4.__version__)
if psi_version > parse_version("1.2rc2.dev500"):
# Handle slight RC2 weirdness
psi_12rc2_tweak = (psi_version == parse_version("1.2rc2"))
psi_12rc2_tweak &= psi4.metadata.version_formatter("") != '(inplace)'
if psi_12rc2_tweak:
input_data["schema_name"] = "QC_JSON"
input_data["schema_version"] = 0
psi4.set_num_threads(input_data["nthreads"], quiet=True)
mol = psi4.core.Molecule.from_schema(input_data)
if mol.multiplicity() != 1:
input_data["keywords"]["reference"] = "uks"
output_data = psi4.json_wrapper.run_json(input_data)
# Handle slight RC2 weirdness once more
if psi_12rc2_tweak:
output_data["schema_name"] = "qc_schema_output"
output_data["schema_version"] = 1
else:
raise TypeError("Psi4 version '{}' not understood".format(psi_version))
# Dispatch errors, PSIO Errors are not recoverable for future runs
if output_data["success"] is False:
if "PSIO Error" in output_data["error"]:
raise ValueError(output_data["error"])
# Move several pieces up a level
if output_data["success"]:
output_data["provenance"]["memory"] = round(
input_data["memory"] / (1024**3), 3)
output_data["provenance"]["nthreads"] = input_data["nthreads"]
del output_data["memory"], input_data["nthreads"]
return output_data
