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Fix MPSOCSet raising ValueError on structure=None #3310

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Sep 10, 2023
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Fix MPSOCSet raising ValueError on structure=None #3310

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70 changes: 22 additions & 48 deletions pymatgen/io/vasp/sets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.core.periodic_table import Element, Species
from pymatgen.core.sites import PeriodicSite
from pymatgen.core.structure import Structure
from pymatgen.core.structure import SiteCollection, Structure
from pymatgen.io.vasp.inputs import Incar, Kpoints, Poscar, Potcar, VaspInput
from pymatgen.io.vasp.outputs import Outcar, Vasprun
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
Expand Down Expand Up @@ -254,7 +254,7 @@ class DictSet(VaspInputSet):

def __init__(
self,
structure: Structure = None,
structure: Structure | None = None,
config_dict: dict[str, Any] | None = None,
files_to_transfer=None,
user_incar_settings=None,
Expand Down Expand Up @@ -386,17 +386,17 @@ def __init__(
"the subclass to be explicit on the differences.",
BadInputSetWarning,
)
for k, v in self.user_potcar_settings.items():
self._config_dict["POTCAR"][k] = v
for key, val in self.user_potcar_settings.items():
self._config_dict["POTCAR"][key] = val

@property
def structure(self) -> Structure:
"""Structure"""
return self._structure
return self._structure # type: ignore

@structure.setter
def structure(self, structure):
if structure is not None:
def structure(self, structure: Structure | None) -> None:
if isinstance(structure, SiteCollection): # could be Structure or Molecule
if self.user_potcar_functional == "PBE_54" and "W" in structure.symbol_set:
# when using 5.4 POTCARs, default Tungsten POTCAR to W_Sv but still allow user to override
self.user_potcar_settings = {"W": "W_sv", **(self.user_potcar_settings or {})}
Expand Down Expand Up @@ -524,10 +524,8 @@ def incar(self) -> Incar:
or incar.get("LDAU", False)
or incar.get("LUSE_VDW", False)
):
warnings.warn(
"LASPH = True should be set for +U, meta-GGAs, hybrids, and vdW-DFT",
BadInputSetWarning,
)
warn_msg = "LASPH = True should be set for +U, meta-GGAs, hybrids, and vdW-DFT"
warnings.warn(warn_msg, BadInputSetWarning)

if self.constrain_total_magmom:
n_up_down = sum(mag if abs(mag) > 0.6 else 0 for mag in incar["MAGMOM"])
Expand Down Expand Up @@ -1030,7 +1028,7 @@ class MPStaticSet(DictSet):

def __init__(
self,
structure,
structure: Structure | None = None,
prev_incar=None,
prev_kpoints=None,
lepsilon=False,
Expand Down Expand Up @@ -1454,16 +1452,7 @@ def __init__(
"""
super().__init__(structure, **kwargs)
self.user_incar_settings = user_incar_settings or {}
self._config_dict["INCAR"].update(
{
"NSW": 0,
"ISMEAR": 0,
"SIGMA": 0.05,
"ISYM": 3,
"LCHARG": False,
"NELMIN": 5,
}
)
self._config_dict["INCAR"].update(NSW=0, ISMEAR=0, SIGMA=0.05, ISYM=3, LCHARG=False, NELMIN=5)
self.added_kpoints = added_kpoints if added_kpoints is not None else []
self.mode = mode

Expand Down Expand Up @@ -1539,10 +1528,8 @@ def override_from_prev_calc(self, prev_calc_dir="."):
# k-points
if self.standardize:
warnings.warn(
"Use of standardize=True with from_prev_calc is not "
"recommended as there is no guarantee the copied "
"files will be appropriate for the standardized "
"structure."
"Use of standardize=True with from_prev_calc is not recommended as there "
"is no guarantee the copied files will be appropriate for the standardized structure."
)

if self.mode.lower() == "gap":
Expand Down Expand Up @@ -1659,17 +1646,7 @@ def incar(self) -> Incar:
incar.update(self.prev_incar.items())

# Overwrite necessary INCAR parameters from previous runs
incar.update(
{
"IBRION": -1,
"LCHARG": False,
"LORBIT": 11,
"LWAVE": False,
"NSW": 0,
"ISYM": 0,
"ICHARG": 11,
}
)
incar.update(IBRION=-1, LCHARG=False, LORBIT=11, LWAVE=False, NSW=0, ISYM=0, ICHARG=11)

if self.mode.lower() == "uniform":
# use tetrahedron method for DOS and optics calculations
Expand Down Expand Up @@ -1824,8 +1801,8 @@ class MPSOCSet(MPStaticSet):

def __init__(
self,
structure,
saxis=(0, 0, 1),
structure: Structure | None = None,
saxis: tuple[int, int, int] = (0, 0, 1),
copy_chgcar=True,
nbands_factor=1.2,
reciprocal_density=100,
Expand All @@ -1849,7 +1826,7 @@ def __init__(
magmom (list[list[float]]): Override for the structure magmoms.
**kwargs: kwargs supported by MPStaticSet.
"""
if not hasattr(structure[0], "magmom") and not isinstance(structure[0].magmom, list):
if structure and not hasattr(structure[0], "magmom") and not isinstance(structure[0].magmom, list):
raise ValueError(
"The structure must have the 'magmom' site "
"property and each magnetic moment value must have 3 "
Expand Down Expand Up @@ -2403,9 +2380,7 @@ def incar(self) -> Incar:

# The default incar setting is used for metallic system, for
# insulator or semiconductor, ISMEAR need to be changed.
incar.update(
{"LCHARG": False, "NELM": 60, "PREC": "Normal", "EDIFFG": -0.02, "ICHARG": 0, "NSW": 200, "EDIFF": 0.0001}
)
incar.update(LCHARG=False, NELM=60, PREC="Normal", EDIFFG=-0.02, ICHARG=0, NSW=200, EDIFF=0.0001)

if self.is_metal:
incar["ISMEAR"] = 1
Expand Down Expand Up @@ -3042,15 +3017,15 @@ def standardize_structure(structure, sym_prec=0.1, international_monoclinic=True
if abs(vpa_old - vpa_new) / vpa_old > 0.02:
raise ValueError(f"Standardizing cell failed! VPA old: {vpa_old}, VPA new: {vpa_new}")

sm = StructureMatcher()
if not sm.fit(structure, new_structure):
matcher = StructureMatcher()
if not matcher.fit(structure, new_structure):
raise ValueError("Standardizing cell failed! Old structure doesn't match new.")

return new_structure


class BadInputSetWarning(UserWarning):
"""Warning class for bad but legal inputs."""
"""Warning class for bad but legal VASP inputs."""


def batch_write_input(
Expand Down Expand Up @@ -3274,8 +3249,7 @@ def incar(self) -> Incar:
if self.prev_incar is not None:
incar = Incar(self.prev_incar)
# Default parameters for diagonalization calculation.
incar.update({"ALGO": "Exact", "LOPTICS": True, "CSHIFT": 0.1, "LWAVE": "True"})
incar.update({"NEDOS": self.nedos or 2001})
incar.update(ALGO="Exact", LOPTICS=True, CSHIFT=0.1, LWAVE=True, NEDOS=self.nedos or 2001)
else:
incar = Incar(parent_incar)

Expand Down