def from_dict(d):
path = d['path']
inputs = {}
inputs["structures"] = [
Structure.from_dict(s) for s in d['inputs']['structures']
]
inputs["INCAR"] = Incar.from_dict(d['inputs']['INCAR'])
inputs["KPOINTS"] = Kpoints.from_dict(d['inputs']['KPOINTS'])
inputs["POTCAR"] = Potcar.from_dict(d['inputs']['POTCAR'])
job_settings = d['job_settings']
job_script_filename = d['job_script_filename']
name = d['name']
outputs = {}
vaspNEBjob = VaspNEBJob(path, inputs, job_settings, outputs,
job_script_filename, name)
vaspNEBjob._is_step_limit_reached = d['is_step_limit_reached']
vaspNEBjob._is_converged = d['is_converged']
vaspNEBjob._r = np.array(d['r'])
vaspNEBjob._energies = np.array(d['energies'])
vaspNEBjob._forces = np.array(d['forces'])
return vaspNEBjob
def __init__(self, name, incar, poscar, potcar, kpoints,
qadapter=None, **kwargs ):
"""
default INCAR from config_dict
"""
self.name = name
self.incar = Incar.from_dict(incar.as_dict())
self.poscar = Poscar.from_dict(poscar.as_dict())
self.potcar = Potcar.from_dict(potcar.as_dict())
self.kpoints = Kpoints.from_dict(kpoints.as_dict())
self.extra = kwargs
if qadapter is not None:
self.qadapter = qadapter.from_dict(qadapter.to_dict())
else:
self.qadapter = None
config_dict = {}
config_dict['INCAR'] = self.incar.as_dict()
config_dict['POSCAR'] = self.poscar.as_dict()
#caution the key and the value are not always the same
config_dict['POTCAR'] = self.potcar.as_dict()
#dict(zip(self.potcar.as_dict()['symbols'],
#self.potcar.as_dict()['symbols']))
config_dict['KPOINTS'] = self.kpoints.as_dict()
#self.user_incar_settings = self.incar.as_dict()
DictVaspInputSet.__init__(self, name, config_dict,
ediff_per_atom=False, **kwargs)
def __init__(self, name, incar, poscar, potcar, kpoints,
qadapter=None, script_name='submit_script',
vis_logger=None, **kwargs):
"""
default INCAR from config_dict
"""
self.name = name
self.incar = Incar.from_dict(incar.as_dict())
self.poscar = Poscar.from_dict(poscar.as_dict())
self.potcar = Potcar.from_dict(potcar.as_dict())
self.kpoints = Kpoints.from_dict(kpoints.as_dict())
self.extra = kwargs
if qadapter is not None:
self.qadapter = qadapter.from_dict(qadapter.to_dict())
else:
self.qadapter = None
self.script_name = script_name
config_dict = {}
config_dict['INCAR'] = self.incar.as_dict()
config_dict['POSCAR'] = self.poscar.as_dict()
# caution the key and the value are not always the same
config_dict['POTCAR'] = self.potcar.as_dict()
# dict(zip(self.potcar.as_dict()['symbols'],
# self.potcar.as_dict()['symbols']))
config_dict['KPOINTS'] = self.kpoints.as_dict()
# self.user_incar_settings = self.incar.as_dict()
DictVaspInputSet.__init__(self, name, config_dict,
ediff_per_atom=False, **kwargs)
if vis_logger:
self.logger = vis_logger
else:
self.logger = logger
def __init__(self,
name,
incar,
poscar,
kpoints,
potcar=None,
qadapter=None,
script_name='submit_script',
vis_logger=None,
reuse_path=None,
test=False,
**kwargs):
"""
default INCAR from config_dict
"""
self.name = name
self.test = test
#print (test)
self.incar_init = Incar.from_dict(incar.as_dict())
self.poscar_init = Poscar.from_dict(poscar.as_dict())
if not self.test:
self.potcar_init = Potcar.from_dict(potcar.as_dict())
if not isinstance(kpoints, str):
self.kpoints_init = Kpoints.from_dict(kpoints.as_dict())
#print (kpoints)
else:
self.kpoints_init = kpoints
self.reuse_path = reuse_path # complete reuse paths
self.extra = kwargs
if qadapter is not None:
self.qadapter = qadapter.from_dict(qadapter.to_dict())
else:
self.qadapter = None
self.script_name = script_name
config_dict = {}
config_dict['INCAR'] = self.incar_init.as_dict()
config_dict['POSCAR'] = self.poscar_init.as_dict()
# caution the key and the value are not always the same
if not self.test:
config_dict['POTCAR'] = self.potcar_init.as_dict()
# dict(zip(self.potcar.as_dict()['symbols'],
# self.potcar.as_dict()['symbols']))
if not isinstance(kpoints, str):
#print (self.kpoints_init)
config_dict['KPOINTS'] = self.kpoints_init.as_dict()
else:
# need to find a way to dictify this kpoints string more
# appropriately
config_dict['KPOINTS'] = {'kpts_hse': self.kpoints_init}
# self.user_incar_settings = self.incar.as_dict()
DictSet.__init__(self, poscar.structure, config_dict)
#**kwargs)
if vis_logger:
self.logger = vis_logger
else:
self.logger = logger
def from_dict(cls, d):
incar = Incar.from_dict(d["incar"])
poscar = Poscar.from_dict(d["poscar"])
potcar = Potcar.from_dict(d["potcar"])
kpoints = Kpoints.from_dict(d["kpoints"])
qadapter = None
if d["qadapter"] is not None:
qadapter = CommonAdapter.from_dict(d["qadapter"])
return MPINTVaspInputSet(d["name"], incar, poscar, potcar,
kpoints, qadapter, **d["kwargs"])
def from_dict(cls, d):
incar = Incar.from_dict(d["incar"])
poscar = Poscar.from_dict(d["poscar"])
potcar = Potcar.from_dict(d["potcar"])
kpoints = Kpoints.from_dict(d["kpoints"])
qadapter = None
if d["qadapter"] is not None:
qadapter = CommonAdapter.from_dict(d["qadapter"])
script_name = d["script_name"]
return MPINTVaspInputSet(d["name"], incar, poscar, potcar,
kpoints, qadapter,
script_name=script_name,
vis_logger=logging.getLogger(d["logger"]),
**d["kwargs"])
def from_dict(cls, d):
incar = Incar.from_dict(d["incar"])
poscar = Poscar.from_dict(d["poscar"])
potcar = Potcar.from_dict(d["potcar"])
kpoints = Kpoints.from_dict(d["kpoints"])
cal = Calibrate(incar, poscar, potcar, kpoints,
system=d["system"], is_matrix = d["is_matrix"],
Grid_type = d["Grid_type"],
parent_job_dir=d["parent_job_dir"],
job_dir=d["job_dir"], qadapter=d.get("qadapter"),
job_cmd=d["job_cmd"], wait=d["wait"],
turn_knobs=d["turn_knobs"])
cal.job_dir_list = d["job_dir_list"]
cal.job_ids = d["job_ids"]
return cal
def from_dict(cls, d):
incar = Incar.from_dict(d["incar"])
poscar = Poscar.from_dict(d["poscar"])
potcar = Potcar.from_dict(d["potcar"])
kpoints = Kpoints.from_dict(d["kpoints"])
cal = Calibrate(incar, poscar, potcar, kpoints,
system=d["system"], is_matrix=d["is_matrix"],
Grid_type=d["Grid_type"],
parent_job_dir=d["parent_job_dir"],
job_dir=d["job_dir"], qadapter=d.get("qadapter"),
job_cmd=d["job_cmd"], wait=d["wait"],
turn_knobs=d["turn_knobs"])
cal.job_dir_list = d["job_dir_list"]
cal.job_ids = d["job_ids"]
return cal
def __init__(self, name, incar, poscar, kpoints, potcar=None,
qadapter=None, script_name='submit_script',
vis_logger=None, reuse_path=None, test=False,
**kwargs):
"""
default INCAR from config_dict
"""
self.name = name
self.test = test
self.incar_init = Incar.from_dict(incar.as_dict())
self.poscar_init = Poscar.from_dict(poscar.as_dict())
if not self.test:
self.potcar_init = Potcar.from_dict(potcar.as_dict())
if not isinstance(kpoints, str):
self.kpoints_init = Kpoints.from_dict(kpoints.as_dict())
else:
self.kpoints_init = kpoints
self.reuse_path = reuse_path # complete reuse paths
self.extra = kwargs
if qadapter is not None:
self.qadapter = qadapter.from_dict(qadapter.to_dict())
else:
self.qadapter = None
self.script_name = script_name
config_dict = {}
config_dict['INCAR'] = self.incar_init.as_dict()
config_dict['POSCAR'] = self.poscar_init.as_dict()
# caution the key and the value are not always the same
if not self.test:
config_dict['POTCAR'] = self.potcar_init.as_dict()
# dict(zip(self.potcar.as_dict()['symbols'],
# self.potcar.as_dict()['symbols']))
if not isinstance(kpoints, str):
config_dict['KPOINTS'] = self.kpoints_init.as_dict()
else:
# need to find a way to dictify this kpoints string more
# appropriately
config_dict['KPOINTS'] = {'kpts_hse':self.kpoints_init}
# self.user_incar_settings = self.incar.as_dict()
DictSet.__init__(self, poscar.structure, config_dict)
#**kwargs)
if vis_logger:
self.logger = vis_logger
else:
self.logger = logger
def test_to_from_dict(self):
d = self.potcar.as_dict()
potcar = Potcar.from_dict(d)
self.assertEqual(potcar.symbols, ["Fe", "P", "O"])
def test_to_from_dict(self):
d = self.potcar.as_dict()
potcar = Potcar.from_dict(d)
self.assertEqual(potcar.symbols, ["Fe", "P", "O"])
