wf = get_wf_neb_from_endpoints(
value[0],
value[0:2],
user_incar_settings=[{
'ICHARG': 2,
'EDIFF': 5E-5,
'EDIFFG': -0.01,
'IBRION': 2
}, {
'ICHARG': 2,
'EDIFF': 5E-5,
'EDIFFG': -0.01,
'IBRION': 2
}, {
'IMAGES': 5,
'EDIFF': 1E-4,
'EDIFFG': -0.03,
'IBRION': 3,
'IOPT': 2,
'ENCUT': 520,
'ISYM': 1,
'ICHAIN': 0,
'SPRING': -5,
'LCLIMB': 'TRUE',
'NSW': 200,
'PREC': 'Accurate',
'IALGO': 48,
'ALGO': 'Fast',
'LREAL': 'Auto',
'ISIF': 2,
'ISMEAR': 1,
'SIGMA': 0.1
}],
user_kpoints_settings=[{
"grid_density": kpoint
}, {
"grid_density": kpoint
}, {
"grid_density": kpoint
}],
additional_spec={
'wf_name':
'%s_%s_%d_%d_GSFE_NEB_Calcualtion_%s' %
(formula, key.replace(" ", ""), kpoint, layer,
datetime.datetime.today().strftime("%Y%m%d")),
'delta_coords':
value[-1]
})
def wf_nudged_elastic_band(structures, parent, c=None):
"""
Nudged elastic band (NEB) workflow from the given structures and config dict.
'is_optimized' default False
'neb_round' default 1
Notes:
Length of Structure list and "is_optimized" are used to determine the workflow:
1 structure # The parent structure & two endpoint indexes provided; need relaxation.
# The parent structure & two endpoint indexes provided; no need to relax.
2 structures # Two endpoints provided; need to relax two endpoints.
# Two relaxed endpoints provided; no need to relax two endpoints.
>=3 structures # All images including two endpoints are provided.
Args:
structures ([Structure]):
1) The parent structure
2) Two endpoint structures
3) An initial NEB path that comprises both images and endpoints
parent (Structure): parent structure used to get two endpoints.
c (dict): workflow config dict, basic format:
{"fireworks": [], "common_params": {}, "additional_ep_params": {},
"additional_neb_params": {}}. When the length of structures is 1, "site_indices" key
must be included in c. Note that "fireworks" is a list corresponding to the order of
execution.
Returns:
Workflow
"""
if not (isinstance(structures, list) and len(structures) > 0):
raise ValueError("structures must be a list of Structure objects!")
# config initialization
c = c or {}
# TODO: @shyuep - config dict params are typically capitalized and intended to be global
# params unless namespaced. e.g. NEB.COMMON_PARAMS if it's only settings for NEB
# workflows. -computron
spec = c.get("common_params", {})
is_optimized = spec.get("is_optimized", False)
# TODO: @shyuep: the whole point of preset workflows is that they are supposed to be simple.
# e.g., give a structure or a list of structures, and forget about the rest. Here it looks like
# one needs to construct some kind of complicated configuration dictionary. Pretty sure no one
# apart from the people in your group have any idea how to use these functions or set up this
# config dict (which should not be necessary in the first place). -computron
if c.get("fireworks"): # Check config dict file
fw_list = [f['fw'] for f in c.get("fireworks")]
neb_round = len([f for f in fw_list if "NEBFW" in f])
if neb_round < 1:
raise ValueError(
"At least one NEB Fireworks (NEBFW) is needed in the config dict!"
)
if len(structures) == 1:
assert "site_indices" in spec, "Site indices not provided in config dict!"
assert len(spec["site_indices"]
) == 2, "Only two site indices should be provided!"
if is_optimized:
assert len(fw_list) == neb_round + 1
else:
assert len(fw_list) == neb_round + 2
elif len(structures) == 2:
if is_optimized:
assert len(fw_list) == neb_round
else:
assert len(fw_list) == neb_round + 1
else: # Default settings if config dict is not provided.
neb_round = 1
# Get user_incar_settings, user_kpoints_settings & additional_cust_args
user_incar_settings = [{}] * (neb_round + 2)
user_kpoints_settings = [{"grid_density": 1000}] * (neb_round + 2)
additional_cust_args = [{}] * (neb_round + 2)
# TODO: @shyuep - I have no idea what's going on here -computron
if "fireworks" in c:
for i in range(1, len(c["fireworks"]) + 1):
user_incar_settings[-i] = c["fireworks"][-i].get(
"user_incar_settings", {})
user_kpoints_settings[-i] = c["fireworks"][-i].get(
"user_kpoints_settings", {"grid_density": 1000})
additional_cust_args[-i] = c["fireworks"][-i].get(
"additional_cust_args", {})
kwargs = {
"user_incar_settings": user_incar_settings,
"user_kpoints_settings": user_kpoints_settings,
"additional_cust_args": additional_cust_args
}
# Assign workflow using the number of given structures
if len(structures) == 1:
wf = get_wf_neb_from_structure(structure=structures[0],
additional_spec=spec,
**kwargs)
elif len(structures) == 2:
wf = get_wf_neb_from_endpoints(parent=parent,
endpoints=structures,
additional_spec=spec,
**kwargs)
else: # len(structures) >= 3
wf = get_wf_neb_from_images(parent=parent,
images=structures,
additional_spec=spec,
**kwargs)
return wf