def from_dict(cls, d):
lattice = Lattice.from_dict(d["lattice"])
sites = [PeriodicSite.from_dict(sd, lattice) for sd in d["sites"]]
s = Structure.from_sites(sites)
return cls(
lattice=lattice,
species=s.species_and_occu, coords=s.frac_coords,
miller_index=d["miller_index"],
oriented_unit_cell=Structure.from_dict(d["oriented_unit_cell"]),
shift=d["shift"],
scale_factor=MontyDecoder().process_decoded(d["scale_factor"]),
site_properties=s.site_properties, energy=d["energy"]
)
def end_point_wf(mp_id, pair_index, image_num, moving_cation, col):
"""
:param col: collection name
:param mp_id: mp_id in the db_scripts
:param pair_index: pair_index in the db_scripts
:param image_num: index number of the image on the path from the db_scripts
:param moving_cation: pymatgen.Element object, represeting the moving cation, e.g. Element('Mg')
:return:
"""
MyDB.db_access().connect()
collection = MyDB.db_access().collection(col)
doc = collection.find_one({'mp-id': mp_id, 'pair_index': pair_index})
# Calculation that is already successful
if 'MEP_energy' in doc.keys() and ("image_{}".format(image_num)
in doc['MEP_energy']):
if doc['MEP_energy']['image_{}'.format(
image_num)]['status'] == 'success':
return
else:
# Calculation that has halted halfway due to errors
if 'CONTCAR_struct' in doc['MEP_energy']['image_{}'.format(
image_num)].keys():
struct = Structure.from_dict(doc["MEP_energy"][
"image_{}".format(image_num)]["CONTCAR_struct"])
# Calculation that has not been run before
else:
struct = Structure.from_dict(doc['gamma_structure'])
cation_site = PeriodicSite.from_dict(doc['path'][image_num])
struct.insert(0,
cation_site.specie,
cation_site.frac_coords,
properties=doc['path'][image_num]['properties'])
else:
struct = Structure.from_dict(doc['gamma_structure'])
cation_site = PeriodicSite.from_dict(doc['path'][image_num])
struct.insert(0,
cation_site.specie,
cation_site.frac_coords,
properties=doc['path'][image_num]['properties'])
task1 = WritePointRunInput(structure=struct.as_dict(),
moving_cation=moving_cation.as_dict())
task2 = PointCustodianRun(handlers='all')
task3 = PointRunAnalyze()
fw = Firework(
[task1, task2, task3],
spec={
"mp_id": mp_id,
"pair_index": pair_index,
"image_num": image_num,
"collection": col,
"_queueadapter": {
'nnodes': 128,
'walltime': '10:00:00',
'queue': 'Q.JCESR',
'job_name': "{}_{}".format(doc["pretty_formula"], image_num)
}
})
wf_list = [fw]
wf_depend = {}
wf = Workflow(wf_list, wf_depend)
MyDB.db_access().close()
return wf
