def __init__(self, spec, neb_label, from_images=True,
user_incar_settings=None,
user_kpoints_settings=None, additional_cust_args=None,
**kwargs):
"""
Args:
spec (dict): Specification of the job to run.
neb_label (str): "1", "2"..., label neb run.
from_images (bool): Set True to initialize from image structures, False starting
from relaxed endpoint structures.
user_incar_settings (dict): Additional INCAR settings.
user_kpoints_settings (dict): Additional KPOINTS settings.
additional_cust_args (dict): Other kwargs that are passed to RunVaspCustodian.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
assert neb_label.isdigit() and int(neb_label) >= 1
label = "neb{}".format(neb_label)
sort_tol = spec["sort_tol"]
d_img = spec["d_img"]
interpolation_type = spec["interpolation_type"]
# Task 1: Write NEB input sets
user_incar_settings = user_incar_settings or {}
user_kpoints_settings = user_kpoints_settings or {}
additional_cust_args = additional_cust_args or {}
if from_images:
write_neb_task = WriteNEBFromImages(neb_label=neb_label,
user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings)
else: # from endpoints
write_neb_task = WriteNEBFromEndpoints(
user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings,
sort_tol=sort_tol, d_img=d_img,
interpolation_type=interpolation_type)
# Task 2: Run NEB using Custodian
cust_args = {"job_type": "neb", "gzip_output": False,
"handler_group": "no_handler"}
cust_args.update(additional_cust_args)
run_neb_task = RunVaspCustodian(vasp_cmd=">>vasp_cmd<<",
gamma_vasp_cmd=">>gamma_vasp_cmd<<",
**cust_args)
# Task 3, 4: Transfer and PassCalcLocs
tasks = [write_neb_task, run_neb_task, TransferNEBTask(label=label),
PassCalcLocs(name=label)]
super(NEBFW, self).__init__(tasks, spec=spec, name=label, **kwargs)
def __init__(self, spec, label, user_incar_settings=None,
user_kpoints_settings=None,
additional_cust_args=None, **kwargs):
"""
Args:
spec (dict): Specification of the job to run.
label (str): "parent", "ep0" or "ep1"
vasp_input_set (VaspInputSet): Input set to use.
user_kpoints_settings (dict): Additional KPOINTS settings.
additional_cust_args (dict): Other kwargs that are passed to RunVaspCustodian.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
# Get structure from spec
assert label in ["parent", "ep0", "ep1"]
structure_dict = spec[label]
structure = Structure.from_dict(structure_dict)
user_incar_settings = user_incar_settings or {}
user_kpoints_settings = user_kpoints_settings or {}
additional_cust_args = additional_cust_args or {}
# Task 1: Write input sets
if label == 'parent':
vasp_input_set = MITRelaxSet(structure,
user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings)
else: # label == "ep0" or "ep1"
from pymatgen_diffusion.neb.io import MVLCINEBEndPointSet
vasp_input_set = MVLCINEBEndPointSet(structure,
user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings)
write_ep_task = WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set)
# Task 2: Run VASP using Custodian
cust_args = {"job_type": "normal", "gzip_output": False,
"handler_group": "no_handler"}
cust_args.update(additional_cust_args)
run_vasp = RunVaspCustodian(vasp_cmd=">>vasp_cmd<<",
gamma_vasp_cmd=">>gamma_vasp_cmd<<",
**cust_args)
# Task 3, 4: Transfer and PassCalLocs
tasks = [write_ep_task, run_vasp, TransferNEBTask(label=label),
PassCalcLocs(name=label)]
super(NEBRelaxationFW, self).__init__(tasks, spec=spec, name=label,
**kwargs)