def generate_nscf_soc_folders(structures, saxis, user_incar):
"""
Generate the non self-consistent calculation with the spin-orbit coupling
"""
for name in structures:
# add magmom as a site property for each atom
outcar = Outcar(filename=os.path.join(name, 'OUTCAR'))
for i, atom in enumerate(structures[name].sites):
atom.properties = {
"magmom": [0., 0.,
round(outcar.magnetization[i]['tot'], 2)]
}
# geterate calculation from the MPSOCSet
mpsoc = MPSOCSet(structures[name],
saxis=saxis,
user_incar_settings=user_incar,
user_kpoints_settings={"reciprocal_density": 500})
mpsoc.write_input(os.path.join(name, 'nscf_SOC'))
# walk around the bug in MPSICSet to introduce LDAUU and LDAUL into INCAR
dic = mpsoc.incar.as_dict()
dic["LDAUU"] = list(dic["LDAUU"].values())
dic["LDAUL"] = list(dic["LDAUL"].values())
Incar.from_dict(dic).write_file(os.path.join(name, 'nscf_SOC/INCAR'))
shutil.copy(os.path.join(name, 'CHGCAR'),
os.path.join(name, 'nscf_SOC'))
def __init__(self,
structure,
magmom,
name="spin-orbit coupling",
saxis=(0, 0, 1),
vasp_cmd="vasp_ncl",
copy_vasp_outputs=True,
db_file=None,
parents=None,
**kwargs):
"""
Firework for spin orbit coupling calculation.
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
name (str): Name for the Firework.
vasp_cmd (str): Command to run vasp.
copy_vasp_outputs (bool): Whether to copy outputs from previous
run. Defaults to True.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
if copy_vasp_outputs:
t.append(
CopyVaspOutputs(calc_loc=True,
additional_files=["CHGCAR"],
contcar_to_poscar=True))
t.append(
WriteVaspSOCFromPrev(prev_calc_dir=".",
magmom=magmom,
saxis=saxis))
else:
vasp_input_set = MPSOCSet(structure)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.extend([
RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<"),
PassCalcLocs(name=name),
VaspToDb(db_file=db_file, additional_fields={"task_label": name})
])
super(SOCFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
**kwargs)
def run_task(self, fw_spec):
vis = MPSOCSet.from_prev_calc(
prev_calc_dir=self["prev_calc_dir"],
magmom=self["magmom"],
saxis=self["saxis"],
copy_chgcar=self.get("copy_chgcar", False),
nbands_factor=self.get("nbands_factor", 1.2),
reciprocal_density=self.get("reciprocal_density", 100),
small_gap_multiply=self.get("small_gap_multiply", None),
standardize=self.get("standardize", False),
sym_prec=self.get("sym_prec", 0.1),
international_monoclinic=self.get("international_monoclinic", True),
**self.get("other_params", {}))
vis.write_input(".")
def run_task(self, fw_spec):
vis = MPSOCSet.from_prev_calc(
prev_calc_dir=self["prev_calc_dir"],
magmom=self["magmom"],
saxis=self["saxis"],
copy_chgcar=self.get("copy_chgcar", False),
nbands_factor=self.get("nbands_factor", 1.2),
reciprocal_density=self.get("reciprocal_density", 100),
small_gap_multiply=self.get("small_gap_multiply", None),
standardize=self.get("standardize", False),
sym_prec=self.get("sym_prec", 0.1),
international_monoclinic=self.get("international_monoclinic",
True),
**self.get("other_params", {}))
vis.write_input(".")
def run_task(self, fw_spec):
# TODO: @albalu - can saxis have a default value e.g. [001] and be an optional parameter?
# -computron
# TODO: @albalu - can magmom be auto-parsed from the previous calc? -computron
vis = MPSOCSet.from_prev_calc(
prev_calc_dir=self.get("prev_calc_dir", "."),
magmom=self["magmom"],
saxis=self["saxis"],
copy_chgcar=self.get("copy_chgcar", False),
nbands_factor=self.get("nbands_factor", 1.2),
reciprocal_density=self.get("reciprocal_density", 100),
small_gap_multiply=self.get("small_gap_multiply", None),
standardize=self.get("standardize", False),
sym_prec=self.get("sym_prec", 0.1),
international_monoclinic=self.get("international_monoclinic", True),
**self.get("other_params", {}))
vis.write_input(".")
def run_task(self, fw_spec):
# TODO: @albalu - can saxis have a default value e.g. [001] and be an optional parameter?
# -computron
# TODO: @albalu - can magmom be auto-parsed from the previous calc? -computron
vis = MPSOCSet.from_prev_calc(
prev_calc_dir=self.get("prev_calc_dir", "."),
magmom=self["magmom"],
saxis=self["saxis"],
copy_chgcar=self.get("copy_chgcar", False),
nbands_factor=self.get("nbands_factor", 1.2),
reciprocal_density=self.get("reciprocal_density", 100),
small_gap_multiply=self.get("small_gap_multiply", None),
standardize=self.get("standardize", False),
sym_prec=self.get("sym_prec", 0.1),
international_monoclinic=self.get("international_monoclinic", True),
**self.get("other_params", {}))
vis.write_input(".")
