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, 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 get_poscar(self):
"""
Create and return a :class:`pymatgen.io.vasp.inputs.Poscar` instance
initialized from the node's stored structure data contents.
:return: a pymatgen Poscar instance
:rtype: :class:`pymatgen.io.vasp.inputs.Poscar`
"""
return Poscar.from_dict(self.get_dict())
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 update_spec_force_convergence(spec, user_vasp_settings=None):
fw_spec = spec
update_set = {"ENCUT": 700, "EDIFF": 0.000001, "ALGO":"N", "NPAR":2}
if user_vasp_settings and user_vasp_settings.get("incar"):
update_set.update(user_vasp_settings["incar"])
fw_spec['vasp']['incar'].update(update_set)
old_struct=Poscar.from_dict(fw_spec["vasp"]["poscar"]).structure
if user_vasp_settings and user_vasp_settings.get("kpoints"):
kpoints_density = user_vasp_settings["kpoints"]["kpoints_density"]
else:
kpoints_density = 7000
k=Kpoints.automatic_density(old_struct, kpoints_density)
fw_spec['vasp']['kpoints'] = k.as_dict()
return fw_spec
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):
poscar_string = """Test3
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
Selective dynamics
direct
0.000000 0.000000 0.000000 T T T Si
0.750000 0.500000 0.750000 F F F O
"""
poscar = Poscar.from_string(poscar_string)
d = poscar.as_dict()
poscar2 = Poscar.from_dict(d)
self.assertEqual(poscar2.comment, "Test3")
self.assertTrue(all(poscar2.selective_dynamics[0]))
self.assertFalse(all(poscar2.selective_dynamics[1]))
def test_to_from_dict(self):
poscar_string = """Test3
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
Selective dynamics
direct
0.000000 0.000000 0.000000 T T T Si
0.750000 0.500000 0.750000 F F F O
"""
poscar = Poscar.from_string(poscar_string)
d = poscar.as_dict()
poscar2 = Poscar.from_dict(d)
self.assertEqual(poscar2.comment, "Test3")
self.assertTrue(all(poscar2.selective_dynamics[0]))
self.assertFalse(all(poscar2.selective_dynamics[1]))
def set_poscar(self, scale=None, poscar=None):
"""
perturbs given structure by volume scaling factor
or takes user defined variants of Poscar
Args:
scale : Volume Scaling parameter
poscar : Poscar object of user defined structure
set the poscar: volume scaled by the scale factor
"""
if scale is not None:
structure = Poscar.from_dict(self.poscar_orig).structure
volume = structure.volume
structure.scale_lattice(scale *volume)
self.poscar = Poscar(structure)
elif poscar is not None:
self.poscar = poscar
def set_poscar(self, scale=None, poscar=None):
"""
perturbs given structure by volume scaling factor
or takes user defined variants of Poscar
Args:
scale : Volume Scaling parameter
poscar : Poscar object of user defined structure
set the poscar: volume scaled by the scale factor
"""
if scale is not None:
structure = Poscar.from_dict(self.poscar_orig).structure
volume = structure.volume
structure.scale_lattice(scale * volume)
self.poscar = Poscar(structure)
elif poscar is not None:
self.poscar = poscar
