def from_dict(cls, d):
h = QChemErrorHandler(input_file=d["input_file"],
output_file=d["output_file"],
ex_backup_list=d["ex_backup_list"],
rca_gdm_thresh=d["rca_gdm_thresh"],
scf_max_cycles=d["scf_max_cycles"],
geom_max_cycles=d["geom_max_cycles"])
h.outdata = d["outdata"]
h.qcinp = QcInput.from_dict(d["qcinp"]) if d["qcinp"] else None
h.error_step_id = d["error_step_id"]
h.errors = d["errors"]
h.fix_step = QcTask.from_dict(d["fix_step"]) if d["fix_step"] else None
return h
def from_dict(cls, d):
h = QChemErrorHandler(input_file=d["input_file"],
output_file=d["output_file"],
ex_backup_list=d["ex_backup_list"],
rca_gdm_thresh=d["rca_gdm_thresh"],
scf_max_cycles=d["scf_max_cycles"],
geom_max_cycles=d["geom_max_cycles"])
h.outdata = d["outdata"]
h.qcinp = QcInput.from_dict(d["qcinp"]) if d["qcinp"] else None
h.error_step_id = d["error_step_id"]
h.errors = d["errors"]
h.fix_step = QcTask.from_dict(d["fix_step"]) if d["fix_step"] else None
return h
def _get_qcinp_from_fw_spec(fw_spec):
if isinstance(fw_spec["qcinp"], dict):
qcinp = QcInput.from_dict(fw_spec["qcinp"])
else:
qcinp = fw_spec["qcinp"]
if 'mol' in fw_spec:
if isinstance(fw_spec["mol"], dict):
mol = Molecule.from_dict(fw_spec["mol"])
else:
mol = fw_spec["mol"]
for qj in qcinp.jobs:
if isinstance(qj.mol, Molecule):
qj.mol = copy.deepcopy(mol)
return qcinp
def spawn_opt_freq_wf(mol, molname, mission, additional_user_tags,
priority, update_spec, charge, spin_multiplicity,
grid, qm_method):
fw_creator = QChemFireWorkCreator(
mol=mol,
molname=molname,
mission=mission,
additional_user_tags=additional_user_tags,
priority=priority,
update_spec=update_spec)
geom_fwid_cal, geom_fwid_db = -1, -2
freq_fwid_cal, freq_fwid_db = -3, -4
geom_fw_cal, geom_fw_db = fw_creator.geom_fw(charge,
spin_multiplicity,
geom_fwid_cal,
geom_fwid_db,
method=qm_method)
geom_fw_cal.spec["run_tags"]["task_type_amend"] = "imaginary " \
"frequency elimination"
freq_fw_cal, freq_fw_db = fw_creator.freq_fw(charge,
spin_multiplicity,
freq_fwid_cal,
freq_fwid_db,
method=qm_method)
freq_fw_cal.spec["run_tags"]["task_type_amend"] = "imaginary " \
"frequency elimination"
if grid:
for fw in [geom_fw_cal, geom_fw_db, freq_fw_cal, freq_fw_db]:
if isinstance(fw.spec["qcinp"], dict):
qcinp = QcInput.from_dict(fw.spec["qcinp"])
else:
qcinp = fw.spec["qcinp"]
for j in qcinp.jobs:
j.set_dft_grid(*grid)
j.set_integral_threshold(12)
if j.params["rem"]["jobtype"] == "opt":
j.scale_geom_opt_threshold(0.1, 0.1, 0.1)
j.set_geom_max_iterations(100)
fw.spec["qcinp"] = qcinp.as_dict()
fw.spec["run_tags"]["grid"] = grid
wf = Workflow(
[geom_fw_cal, geom_fw_db, freq_fw_cal, freq_fw_db],
links_dict={
geom_fwid_db: freq_fwid_cal,
geom_fwid_cal: geom_fwid_db,
freq_fwid_cal: freq_fwid_db
})
return wf
