def run_task(self, fw_spec):
#workdir=fw_spec['workdir']
vasp_cmd = fw_spec['vasp_cmd']
#with cd(workdir):
incar = Incar.from_file('INCAR')
kpoints = Kpoints.from_file('KPOINTS')
poscar = Poscar.from_file('POSCAR')
potcar = Potcar.from_file('POTCAR')
try:
out = Outcar(work_dir + '/OUTCAR')
if len(out.run_stats) != 7:
raise VaspDoneError()
except:
try:
contcar = Structure.from_file('CONTCAR')
os.rename('CONTCAR', 'POSCAR')
except:
pass
job = VaspJob(vasp_cmd)
handlers=[VaspErrorHandler(),UnconvergedErrorHandler(),FrozenJobErrorHandler(),\
NonConvergingErrorHandler(nionic_steps=2, change_algo=True),MeshSymmetryErrorHandler()]
c = Custodian(handlers, [job], max_errors=10)
c.run()
else:
print 'Vasp job was already done well. No need to rerun!'
def run_task(self, fw_spec):
task_id = fw_spec['task_id']
initial_struct = fw_spec['initial_struct']
charge = fw_spec['charge']
site = fw_spec['site']
s = fw_spec['s']
hse = fw_spec['hse']
####----------------initialization over-------------
dict_transf = {
'history': [{
'source': task_id
}],
'compo': initial_struct.composition.as_dict(),
'defect_type': site['short_name'],
'defect_site': site['unique_sites'].as_dict(),
'charge': charge,
'supercell': s['size']
}
dict_params = MPRelaxSet(s['structure']).all_input
incar = dict_params['INCAR']
incar['IBRION'] = 2
incar['ISIF'] = 0
incar['ISPIN'] = 2
incar['LWAVE'] = False
incar['LCHARG'] = False
incar['EDIFF'] = 0.0001
incar['EDIFFG'] = 0.001
incar['ISMEAR'] = 0
incar['SIGMA'] = 0.05
incar['LVHAR'] = True
incar['LORBIT'] = 11
incar['ALGO'] = "Normal"
if hse == True:
incar['LHFCALC'] = True
incar["ALGO"] = "All"
incar["HFSCREEN"] = 0.2
incar["PRECFOCK"] = "Fast"
kpoint = Kpoints.monkhorst_automatic()
f = open("transformations.json", 'w')
f.write(json.dumps(jsanitize(dict_transf)))
f.close()
comp = s['structure'].composition
sum_elec = 0
elts = set()
for p in dict_params['POTCAR']:
if p.element not in elts:
sum_elec += comp.as_dict()[p.element] * p.nelectrons
elts.add(p.element)
#print p.element
#print comp.as_dict[p.element]
#print p.valence
if charge != 0:
incar['NELECT'] = sum_elec - charge
dict_params['POTCAR'].write_file("POTCAR")
incar.write_file("INCAR")
kpoint.write_file("KPOINTS")
dict_params['POSCAR'].write_file("POSCAR")
def _add_weighted_kpts(self, irreducible_kpoints):
kpts = [k[0] for k in irreducible_kpoints]
weights = [k[1] for k in irreducible_kpoints]
labels = [None] * len(irreducible_kpoints)
self._kpoints = Kpoints(comment=self.comment,
style=Kpoints.supported_modes.Reciprocal,
num_kpts=len(kpts),
kpts=kpts,
kpts_weights=weights,
labels=labels)
def _set_kpoints(self):
# symmetrizer must be recreated since the fractional coordinates are
# different in different lattices.
# Symmetrized structure doesn't need the symprec and angle_tolerance
symmetrizer = StructureSymmetrizer(self._structure)
irreducible_kpoints = symmetrizer.irreducible_kpoints(
self._num_kpt_list, self._kpt_shift)
self.comment = ""
if self._kpt_mode is KpointsMode.band:
self._add_weighted_kpts(irreducible_kpoints)
self._add_band_path_kpts()
self._num_kpts = len(self._kpoints.kpts)
else:
self._kpoints = Kpoints(comment=self.comment,
kpts=(self._num_kpt_list, ),
kpts_shift=self._kpt_shift)
self._num_kpts = len(irreducible_kpoints)
self.kpoints.comment += f"Num irrep kpoints: {self._num_kpts}"
def run_task(self, fw_spec):
from pymongo import MongoClient
clt = MongoClient('marilyn.pcpm.ucl.ac.be', 27017)
db = clt.results_GY
db.authenticate('gyu', 'pulco')
hse_gap = db.HSE_gaps_ICSD
pbe_bs = fw_spec['pbe_bs']
job_info_array = fw_spec['_job_info']
prev_job_info = job_info_array[-1]
result = {}
icsd_id = fw_spec['icsd_id']
xml = Vasprun(prev_job_info['launch_dir'] + '/vasprun.xml')
ks = Kpoints.from_file(prev_job_info['launch_dir'] + '/KPOINTS')
is_converged = xml.converged
bs = xml.get_band_structure()
formula = xml.final_structure.composition.reduced_formula
material = {
'icsd_id': icsd_id,
'formula': formula,
'is_spin_polarized': bs.is_spin_polarized
}
input = {}
incar = xml.incar.as_dict()
potcar = xml.potcar_spec
crystal = xml.final_structure.as_dict()
kpoints = ks.as_dict()
input['incar'] = incar
input['potcar'] = potcar
input['crystal'] = crystal
input['kpoints'] = kpoints
gap_info = {}
######### HSE #####################
gap_info['HSE'] = {}
gap_info['HSE']['gap'] = bs.get_band_gap()['energy']
cbm = {}
cbm['energy'] = bs.get_cbm()['energy']
cbm_kpoint = {}
cbm_kpoint['coordinate'] = list(bs.get_cbm()['kpoint']._fcoords)
cbm_kpoint['label'] = bs.get_cbm()['kpoint'].label
cbm['kpoint'] = cbm_kpoint
vbm = {}
vbm['energy'] = bs.get_vbm()['energy']
vbm_kpoint = {}
vbm_kpoint['coordiante'] = list(bs.get_vbm()['kpoint']._fcoords)
vbm_kpoint['label'] = bs.get_vbm()['kpoint'].label
vbm['kpoint'] = vbm_kpoint
gap_info['HSE']['cbm'] = cbm
gap_info['HSE']['vbm'] = vbm
########### PBE from ICSD############
gap_info['PBE_icsd'] = {}
gap_info['PBE_icsd']['gap'] = pbe_bs.get_band_gap()['energy']
pbe_cbm = {}
pbe_cbm['energy'] = pbe_bs.get_cbm()['energy']
pbe_cbm_kpoint = {}
pbe_cbm_kpoint['coordinate'] = list(
pbe_bs.get_cbm()['kpoint']._fcoords)
pbe_cbm_kpoint['label'] = pbe_bs.get_cbm()['kpoint'].label
pbe_cbm['kpoint'] = pbe_cbm_kpoint
pbe_vbm = {}
pbe_vbm['energy'] = pbe_bs.get_vbm()['energy']
pbe_vbm_kpoint = {}
pbe_vbm_kpoint['coordiante'] = list(
pbe_bs.get_vbm()['kpoint']._fcoords)
pbe_vbm_kpoint['label'] = pbe_bs.get_vbm()['kpoint'].label
pbe_vbm['kpoint'] = pbe_vbm_kpoint
gap_info['PBE_icsd']['cbm'] = pbe_cbm
gap_info['PBE_icsd']['vbm'] = pbe_vbm
#############################################################################
result['material'] = material
result['input'] = input
result['gap_info'] = gap_info
result['is_converged'] = is_converged
##################################################################################
hse_gap.insert(result)