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):
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)