def post_process(self, task_list):
cwd = os.getcwd()
poscar_start = os.path.abspath(
os.path.join(task_list[0], '..', 'POSCAR'))
os.chdir(os.path.join(task_list[0], '..'))
if os.path.isfile(os.path.join(task_list[0], 'INCAR')):
incar = incar_upper(
Incar.from_file(os.path.join(task_list[0], 'INCAR')))
kspacing = incar.get('KSPACING')
kgamma = incar.get('KGAMMA', False)
ret = vasp.make_kspacing_kpoints(poscar_start, kspacing, kgamma)
kp = Kpoints.from_string(ret)
if os.path.isfile('KPOINTS'):
os.remove('KPOINTS')
kp.write_file("KPOINTS")
os.chdir(cwd)
kpoints_universal = os.path.abspath(
os.path.join(task_list[0], '..', 'KPOINTS'))
for ii in task_list:
if os.path.isfile(os.path.join(ii, 'KPOINTS')):
os.remove(os.path.join(ii, 'KPOINTS'))
if os.path.islink(os.path.join(ii, 'KPOINTS')):
os.remove(os.path.join(ii, 'KPOINTS'))
os.chdir(ii)
os.symlink(os.path.relpath(kpoints_universal), 'KPOINTS')
os.chdir(cwd)
def make_vasp_kpoints_from_incar(work_dir, jdata):
cwd = os.getcwd()
fp_aniso_kspacing = jdata.get('fp_aniso_kspacing')
os.chdir(work_dir)
# get kspacing and kgamma from incar
assert (os.path.exists('INCAR'))
with open('INCAR') as fp:
incar = fp.read()
standard_incar = incar_upper(Incar.from_string(incar))
if fp_aniso_kspacing is None:
try:
kspacing = standard_incar['KSPACING']
except KeyError:
raise RuntimeError("KSPACING must be given in INCAR")
else:
kspacing = fp_aniso_kspacing
try:
gamma = standard_incar['KGAMMA']
if isinstance(gamma, bool):
pass
else:
if gamma[0].upper() == "T":
gamma = True
else:
gamma = False
except KeyError:
raise RuntimeError("KGAMMA must be given in INCAR")
# check poscar
assert (os.path.exists('POSCAR'))
# make kpoints
ret = make_kspacing_kpoints('POSCAR', kspacing, gamma)
kp = Kpoints.from_string(ret)
kp.write_file("KPOINTS")
os.chdir(cwd)
def _check_kpoints(testCase, idx) :
fp_path = os.path.join('iter.%06d' % idx, '02.fp')
tasks = glob.glob(os.path.join(fp_path, 'task.*'))
for ii in tasks :
kpoints=Kpoints.from_file(os.path.join(os.path.join(ii, 'KPOINTS')))
incar=Incar.from_file(os.path.join(os.path.join(ii, 'INCAR')))
kspacing = incar['KSPACING']
gamma = incar['KGAMMA']
if isinstance(gamma,bool):
pass
else:
if gamma[0].upper()=="T":
gamma=True
else:
gamma=False
ret=make_kspacing_kpoints(os.path.join(os.path.join(ii, 'POSCAR')), kspacing, gamma)
kpoints_ref=Kpoints.from_string(ret)
testCase.assertEqual(repr(kpoints), repr(kpoints_ref))
def make_input_file(self, output_dir, task_type, task_param):
sepline(ch=output_dir)
dumpfn(task_param, os.path.join(output_dir, 'task.json'), indent=4)
assert (os.path.exists(self.incar)), 'no INCAR file for relaxation'
relax_incar_path = os.path.abspath(self.incar)
incar_relax = incar_upper(Incar.from_file(relax_incar_path))
# deal with relaxation
cal_type = task_param['cal_type']
cal_setting = task_param['cal_setting']
# user input INCAR for property calculation
if 'input_prop' in cal_setting and os.path.isfile(
cal_setting['input_prop']):
incar_prop = os.path.abspath(cal_setting['input_prop'])
incar = incar_upper(Incar.from_file(incar_prop))
# revise INCAR based on the INCAR provided in the "interaction"
else:
incar = incar_relax
if cal_type == 'relaxation':
relax_pos = cal_setting['relax_pos']
relax_shape = cal_setting['relax_shape']
relax_vol = cal_setting['relax_vol']
if [relax_pos, relax_shape, relax_vol] == [True, False, False]:
isif = 2
elif [relax_pos, relax_shape, relax_vol] == [True, True, True]:
isif = 3
elif [relax_pos, relax_shape,
relax_vol] == [True, True, False]:
isif = 4
elif [relax_pos, relax_shape,
relax_vol] == [False, True, False]:
isif = 5
elif [relax_pos, relax_shape,
relax_vol] == [False, True, True]:
isif = 6
elif [relax_pos, relax_shape,
relax_vol] == [False, False, True]:
isif = 7
elif [relax_pos, relax_shape,
relax_vol] == [False, False, False]:
nsw = 0
isif = 2
if not ('NSW' in incar and incar.get('NSW') == nsw):
dlog.info("%s setting NSW to %d" %
(self.make_input_file.__name__, nsw))
incar['NSW'] = nsw
else:
raise RuntimeError(
"not supported calculation setting for VASP")
if not ('ISIF' in incar and incar.get('ISIF') == isif):
dlog.info("%s setting ISIF to %d" %
(self.make_input_file.__name__, isif))
incar['ISIF'] = isif
elif cal_type == 'static':
nsw = 0
if not ('NSW' in incar and incar.get('NSW') == nsw):
dlog.info("%s setting NSW to %d" %
(self.make_input_file.__name__, nsw))
incar['NSW'] = nsw
else:
raise RuntimeError("not supported calculation type for VASP")
if 'ediff' in cal_setting:
dlog.info(
"%s setting EDIFF to %s" %
(self.make_input_file.__name__, cal_setting['ediff']))
incar['EDIFF'] = cal_setting['ediff']
if 'ediffg' in cal_setting:
dlog.info(
"%s setting EDIFFG to %s" %
(self.make_input_file.__name__, cal_setting['ediffg']))
incar['EDIFFG'] = cal_setting['ediffg']
if 'encut' in cal_setting:
dlog.info(
"%s setting ENCUT to %s" %
(self.make_input_file.__name__, cal_setting['encut']))
incar['ENCUT'] = cal_setting['encut']
if 'kspacing' in cal_setting:
dlog.info(
"%s setting KSAPCING to %s" %
(self.make_input_file.__name__, cal_setting['kspacing']))
incar['KSAPCING'] = cal_setting['kspacing']
if 'kgamma' in cal_setting:
dlog.info(
"%s setting KGAMMA to %s" %
(self.make_input_file.__name__, cal_setting['kgamma']))
incar['KGAMMA'] = cal_setting['kgamma']
try:
kspacing = incar.get('KSPACING')
except KeyError:
raise RuntimeError("KSPACING must be given in INCAR")
if 'KGAMMA' in incar:
kgamma = incar.get('KGAMMA')
else:
kgamma = False
incar.write_file(os.path.join(output_dir, '../INCAR'))
cwd = os.getcwd()
os.chdir(output_dir)
if not os.path.islink('INCAR'):
os.symlink('../INCAR', 'INCAR')
elif not '../INCAR' == os.readlink('INCAR'):
os.remove('INCAR')
os.symlink('../INCAR', 'INCAR')
os.chdir(cwd)
ret = vasp.make_kspacing_kpoints(self.path_to_poscar, kspacing, kgamma)
kp = Kpoints.from_string(ret)
kp.write_file(os.path.join(output_dir, "KPOINTS"))