def incar(self):
parent_incar = super(PRLRoughStaticSet, self).incar
incar = Incar(self.prev_incar) if self.prev_incar is not None else \
Incar(parent_incar)
for k in ["MAGMOM", "NUPDOWN"] + list(
self.kwargs.get("user_incar_settings", {}).keys()):
# For these parameters as well as user specified settings, override
# the incar settings.
if parent_incar.get(k, None) is not None:
incar[k] = parent_incar[k]
else:
incar.pop(k, None)
# use new LDAUU when possible b/c the Poscar might have changed
# representation
if incar.get('LDAU'):
u = incar.get('LDAUU', [])
j = incar.get('LDAUJ', [])
if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
incar.update({tag: parent_incar[tag]})
# ensure to have LMAXMIX for GGA+U static run
if "LMAXMIX" not in incar:
incar.update({"LMAXMIX": parent_incar["LMAXMIX"]})
# Compare ediff between previous and staticinputset values,
# choose the tighter ediff
incar["EDIFF"] = min(incar.get("EDIFF", 1), parent_incar["EDIFF"])
return incar
def incar(self):
parent_incar = super(PRLStaticSet, self).incar
incar = Incar(self.prev_incar) if self.prev_incar is not None else \
Incar(parent_incar)
incar.update({
"IBRION": -1,
"ISMEAR": -5,
"LAECHG": True,
"LCHARG": True,
"LORBIT": 11,
"LVHAR": True,
"LWAVE": False,
"NSW": 0,
"ICHARG": 0,
"ALGO": "Normal"
})
if self.lepsilon:
incar["IBRION"] = 8
incar["LEPSILON"] = True
# LPEAD=T: numerical evaluation of overlap integral prevents
# LRF_COMMUTATOR errors and can lead to better expt. agreement
# but produces slightly different results
incar["LPEAD"] = True
# Note that DFPT calculations MUST unset NSW. NSW = 0 will fail
# to output ionic.
incar.pop("NSW", None)
incar.pop("NPAR", None)
if self.lcalcpol:
incar["LCALCPOL"] = True
for k in ["MAGMOM", "NUPDOWN"] + list(
self.kwargs.get("user_incar_settings", {}).keys()):
# For these parameters as well as user specified settings, override
# the incar settings.
if parent_incar.get(k, None) is not None:
incar[k] = parent_incar[k]
else:
incar.pop(k, None)
# use new LDAUU when possible b/c the Poscar might have changed
# representation
if incar.get('LDAU'):
u = incar.get('LDAUU', [])
j = incar.get('LDAUJ', [])
if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
incar.update({tag: parent_incar[tag]})
# ensure to have LMAXMIX for GGA+U static run
if "LMAXMIX" not in incar:
incar.update({"LMAXMIX": parent_incar["LMAXMIX"]})
# Compare ediff between previous and staticinputset values,
# choose the tighter ediff
incar["EDIFF"] = min(incar.get("EDIFF", 1), parent_incar["EDIFF"])
return incar
def get_defect_charge_state(poscar: Poscar, potcar: Potcar, incar: Incar):
"""Get defect charge state from structure, potcar, and NELECT in INCAR. """
nelect = incar.get("NELECT", None)
if nelect is None:
logger.info("Since NELECT is not written in INCAR, so 0 is returned.")
return 0
potcar_elements = [symbol.split("_")[0] for symbol in potcar.symbols]
if poscar.site_symbols != potcar_elements:
raise ValueError(
f"Sequence of elements in POSCAR {poscar.site_symbols}"
f" and that in POTCAR {potcar.symbols} is different.")
num_elect_neutral = sum([
num_atom * pot.nelectrons
for num_atom, pot in zip(poscar.natoms, potcar)
])
excess_num_electrons = int(nelect - num_elect_neutral)
return -excess_num_electrons