def test_RunCritic2(self):
os.chdir(
os.path.join(
module_dir,
"..",
"..",
"test_files",
"critic_test_files",
"small_critic_example",
))
firetask = RunCritic2(molecule=self.mol, cube_file="dens.0.cube.gz")
firetask.run_task(fw_spec={})
with open("cpreport_correct.json") as f:
cpreport_reference = json.load(f)
with open("yt_correct.json") as f:
yt_reference = json.load(f)
with open("cpreport.json") as f:
cpreport = json.load(f)
with open("yt.json") as f:
yt = json.load(f)
# Context for below - reference files were built before units were added
# to Critic2, and we avoid testing the actual critical points because they
# can change order between runs. But comparing everything else is sufficient.
for key in cpreport:
if key in ["structure", "field"]:
self.assertEqual(cpreport_reference[key], cpreport[key])
for key in yt:
if key != "units":
self.assertEqual(yt_reference[key], yt[key])
def test_CubeAndCritic2FW_defaults(self):
firework = CubeAndCritic2FW(molecule=self.act_mol)
self.assertEqual(
firework.tasks[0].as_dict(),
WriteInputFromIOSet(molecule=self.act_mol,
qchem_input_set="SinglePointSet",
input_file="mol.qin",
qchem_input_params={
"plot_cubes": True
}).as_dict())
self.assertEqual(
firework.tasks[1].as_dict(),
RunQChemCustodian(qchem_cmd=">>qchem_cmd<<",
multimode=">>multimode<<",
input_file="mol.qin",
output_file="mol.qout",
max_cores=">>max_cores<<",
job_type="normal").as_dict())
self.assertEqual(
firework.tasks[2].as_dict(),
RunCritic2(molecule=self.act_mol,
cube_file="dens.0.cube.gz").as_dict())
self.assertEqual(firework.tasks[3].as_dict(),
ProcessCritic2(molecule=self.act_mol).as_dict())
self.assertEqual(
firework.tasks[4].as_dict(),
QChemToDb(db_file=None,
input_file="mol.qin",
output_file="mol.qout",
additional_fields={
"task_label": "cube and critic2"
}).as_dict())
self.assertEqual(firework.parents, [])
self.assertEqual(firework.name, "cube and critic2")
def test_CubeAndCritic2FW_not_defaults(self):
firework = CubeAndCritic2FW(
molecule=self.act_mol,
name="special cube and critic2",
qchem_cmd="qchem -slurm",
multimode="mpi",
max_cores=12,
qchem_input_params={"pcm_dielectric": 10.0},
db_file=os.path.join(db_dir, "db.json"),
parents=None,
)
self.assertEqual(
firework.tasks[0].as_dict(),
WriteInputFromIOSet(
molecule=self.act_mol,
qchem_input_set="SinglePointSet",
input_file="mol.qin",
qchem_input_params={
"pcm_dielectric": 10.0,
"plot_cubes": True
},
).as_dict(),
)
self.assertEqual(
firework.tasks[1].as_dict(),
RunQChemCustodian(
qchem_cmd="qchem -slurm",
multimode="mpi",
input_file="mol.qin",
output_file="mol.qout",
max_cores=12,
job_type="normal",
).as_dict(),
)
self.assertEqual(
firework.tasks[2].as_dict(),
RunCritic2(molecule=self.act_mol,
cube_file="dens.0.cube.gz").as_dict(),
)
self.assertEqual(firework.tasks[3].as_dict(),
ProcessCritic2(molecule=self.act_mol).as_dict())
self.assertEqual(
firework.tasks[4].as_dict(),
QChemToDb(
db_file=os.path.join(db_dir, "db.json"),
input_file="mol.qin",
output_file="mol.qout",
additional_fields={
"task_label": "special cube and critic2"
},
).as_dict(),
)
self.assertEqual(firework.parents, [])
self.assertEqual(firework.name, "special cube and critic2")
def __init__(self,
molecule=None,
name="cube and critic2",
qchem_cmd=">>qchem_cmd<<",
multimode=">>multimode<<",
max_cores=">>max_cores<<",
qchem_input_params=None,
db_file=None,
parents=None,
**kwargs):
"""
Args:
molecule (Molecule): Input molecule.
name (str): Name for the Firework.
qchem_cmd (str): Command to run QChem. Supports env_chk.
multimode (str): Parallelization scheme, either openmp or mpi. Supports env_chk.
max_cores (int): Maximum number of cores to parallelize over. Supports env_chk.
qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.
Basic uses would be to modify the default inputs of the set,
such as dft_rung, basis_set, pcm_dielectric, scf_algorithm,
or max_scf_cycles. See pymatgen/io/qchem/sets.py for default
values of all input parameters. For instance, if a user wanted
to use a more advanced DFT functional, include a pcm with a
dielectric of 30, and use a larger basis, the user would set
qchem_input_params = {"dft_rung": 5, "pcm_dielectric": 30,
"basis_set": "6-311++g**"}. However, more advanced customization
of the input is also possible through the overwrite_inputs key
which allows the user to directly modify the rem, pcm, smd, and
solvent dictionaries that QChemDictSet passes to inputs.py to
print an actual input file. For instance, if a user wanted to
set the sym_ignore flag in the rem section of the input file
to true, then they would set qchem_input_params = {"overwrite_inputs":
"rem": {"sym_ignore": "true"}}. Of course, overwrite_inputs
could be used in conjuction with more typical modifications,
as seen in the test_double_FF_opt workflow test.
db_file (str): Path to file specifying db credentials to place output parsing.
parents ([Firework]): Parents of this particular Firework.
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
qchem_input_params = copy.deepcopy(qchem_input_params) or {}
qchem_input_params["plot_cubes"] = True
input_file = "mol.qin"
output_file = "mol.qout"
t = []
t.append(
WriteInputFromIOSet(molecule=molecule,
qchem_input_set="SinglePointSet",
input_file=input_file,
qchem_input_params=qchem_input_params))
t.append(
RunQChemCustodian(qchem_cmd=qchem_cmd,
multimode=multimode,
input_file=input_file,
output_file=output_file,
max_cores=max_cores,
job_type="normal"))
t.append(RunCritic2(molecule=molecule, cube_file="dens.0.cube.gz"))
t.append(
QChemToDb(db_file=db_file,
input_file=input_file,
output_file=output_file,
additional_fields={"task_label": name}))
super(CubeAndCritic2FW, self).__init__(t,
parents=parents,
name=name,
**kwargs)