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Cleanup input sets with linting.
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Shyue Ping Ong committed Sep 1, 2023
1 parent fabdd27 commit 28f9309
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Showing 2 changed files with 57 additions and 42 deletions.
92 changes: 53 additions & 39 deletions pymatgen/io/vasp/sets.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -340,11 +340,7 @@ def __init__(
if (valid_potcars := self._valid_potcars) and user_potcar_functional not in valid_potcars:
raise ValueError(f"Invalid {user_potcar_functional=}, must be one of {valid_potcars}")

if 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
user_potcar_settings = {"W": "W_sv", **(user_potcar_settings or {})}

self._config_dict = deepcopy(config_dict)
self._config_dict = deepcopy(config_dict) if config_dict is not None else {}
self.files_to_transfer = files_to_transfer or {}
self.constrain_total_magmom = constrain_total_magmom
self.sort_structure = sort_structure
Expand All @@ -359,7 +355,6 @@ def __init__(
self.sym_prec = sym_prec
self.international_monoclinic = international_monoclinic
self.validate_magmom = validate_magmom
self.structure = structure

if self.user_incar_settings.get("KSPACING") and user_kpoints_settings is not None:
warnings.warn(
Expand Down Expand Up @@ -396,6 +391,8 @@ def __init__(
BadInputSetWarning,
)

self.structure = structure # type: ignore

if self.user_potcar_settings:
warnings.warn(
"Overriding POTCARs is generally not recommended as it "
Expand All @@ -419,6 +416,9 @@ def structure(self) -> Structure:
@structure.setter
def structure(self, structure):
if structure is not None:
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 {})}
if self.reduce_structure:
structure = structure.get_reduced_structure(self.reduce_structure)
if self.sort_structure:
Expand Down Expand Up @@ -2259,10 +2259,7 @@ def __init__(
:param sort_structure:
:param kwargs: Other kwargs supported by :class:`DictSet`.
"""
super().__init__(structure, **kwargs)

if sort_structure:
structure = structure.get_sorted_structure()
super().__init__(structure, sort_structure=sort_structure, **kwargs)

self.k_product = k_product
self.bulk = bulk
Expand All @@ -2271,6 +2268,10 @@ def __init__(
self.set_mix = set_mix
self.kpt_calc = None

@property
def incar(self) -> Incar:
structure = self.structure

slab_incar = {
"EDIFF": 1e-4,
"EDIFFG": -0.02,
Expand All @@ -2294,8 +2295,8 @@ def __init__(
slab_incar["IDIPOL"] = 3
slab_incar["LDIPOL"] = True
slab_incar["DIPOL"] = center_of_mass

self._config_dict["INCAR"].update(slab_incar)
return super().incar

@property
def kpoints(self):
Expand Down Expand Up @@ -2701,17 +2702,13 @@ def __init__(
"NBLOCK": 1,
"KBLOCK": 100,
"SMASS": 0,
"POTIM": 2,
"POTIM": time_step,
"PREC": "Normal",
"ISPIN": 2 if spin_polarized else 1,
"LDAU": False,
"ADDGRID": True,
}

if Element("H") in structure.species:
defaults["POTIM"] = 0.5
defaults["NSW"] = defaults["NSW"] * 4

super().__init__(structure, **kwargs)

self.start_temp = start_temp
Expand All @@ -2727,6 +2724,14 @@ def __init__(
self._config_dict["INCAR"].pop("MAGMOM", None)
self._config_dict["INCAR"].update(defaults)

@property
def incar(self) -> Incar:
incar = super().incar
if Element("H") in self.structure.species:
incar["POTIM"] = 0.5
incar["NSW"] = incar["NSW"] * 4
return incar

@property
def kpoints(self) -> Kpoints:
"""Kpoints"""
Expand Down Expand Up @@ -2764,30 +2769,36 @@ def __init__(
The ISPIN parameter. Defaults to False.
**kwargs: Other kwargs supported by :class:`DictSet`.
"""
user_incar_settings = kwargs.get("user_incar_settings", {})
super().__init__(structure, start_temp, end_temp, nsteps, time_step, spin_polarized, **kwargs)

@property
def incar(self) -> Incar:
"""
Special processing of incar.
"""

# NPT-AIMD default settings
defaults = {
"ALGO": "Fast",
"ISIF": 3,
"LANGEVIN_GAMMA": [10] * structure.ntypesp,
"LANGEVIN_GAMMA": [10] * self.structure.ntypesp,
"LANGEVIN_GAMMA_L": 1,
"MDALGO": 3,
"PMASS": 10,
"PSTRESS": 0,
"SMASS": 0,
}

defaults.update(user_incar_settings)
kwargs["user_incar_settings"] = defaults

super().__init__(structure, start_temp, end_temp, nsteps, time_step, spin_polarized, **kwargs)
defaults.update(self.user_incar_settings)
self.user_incar_settings = defaults

# Set NPT-AIMD ENCUT = 1.5 * VASP_default
enmax = [self.potcar[i].keywords["ENMAX"] for i in range(structure.ntypesp)]
enmax = [self.potcar[i].keywords["ENMAX"] for i in range(self.structure.ntypesp)]
encut = max(enmax) * 1.5
self._config_dict["INCAR"]["ENCUT"] = encut

return super().incar


class MVLScanRelaxSet(MPRelaxSet):
"""
Expand Down Expand Up @@ -2873,7 +2884,6 @@ def __init__(
e.g. {"Fe": "Fe_pv", "O": "O"}; if not supplied, a standard basis is used.
**kwargs: Other kwargs supported by :class:`DictSet`.
"""
from pymatgen.io.lobster import Lobsterin

warnings.warn("Make sure that all parameters are okay! This is a brand new implementation.")

Expand All @@ -2887,7 +2897,6 @@ def __init__(
kwargs.setdefault("user_potcar_functional", "PBE_54")

super().__init__(structure, **kwargs)

# reciprocal density
if self.user_kpoints_settings is not None:
if not reciprocal_density or "reciprocal_density" not in self.user_kpoints_settings:
Expand All @@ -2900,46 +2909,51 @@ def __init__(
self.reciprocal_density = 310
else:
self.reciprocal_density = reciprocal_density

self._config_dict["POTCAR"]["W"] = "W_sv"
self.isym = isym
self.ismear = ismear
self.user_supplied_basis = user_supplied_basis
self.address_basis_file = address_basis_file
self._config_dict["KPOINTS"]["reciprocal_density"] = self.reciprocal_density

@property
def incar(self) -> Incar:
from pymatgen.io.lobster import Lobsterin

# predefined basis! Check if the basis is okay! (charge spilling and bandoverlaps!)
if user_supplied_basis is None and address_basis_file is None:
basis = Lobsterin.get_basis(structure=structure, potcar_symbols=self.potcar_symbols)
elif address_basis_file is not None:
if self.user_supplied_basis is None and self.address_basis_file is None:
basis = Lobsterin.get_basis(structure=self.structure, potcar_symbols=self.potcar_symbols)
elif self.address_basis_file is not None:
basis = Lobsterin.get_basis(
structure=structure,
structure=self.structure,
potcar_symbols=self.potcar_symbols,
address_basis_file=address_basis_file,
address_basis_file=self.address_basis_file,
)
elif user_supplied_basis is not None:
elif self.user_supplied_basis is not None:
# test if all elements from structure are in user_supplied_basis
for atom_type in structure.symbol_set:
if atom_type not in user_supplied_basis:
for atom_type in self.structure.symbol_set:
if atom_type not in self.user_supplied_basis:
raise ValueError(f"There are no basis functions for the atom type {atom_type}")
basis = [f"{key} {value}" for key, value in user_supplied_basis.items()]
basis = [f"{key} {value}" for key, value in self.user_supplied_basis.items()]

lobsterin = Lobsterin(settingsdict={"basisfunctions": basis})
nbands = lobsterin._get_nbands(structure=structure)
nbands = lobsterin._get_nbands(structure=self.structure)

update_dict = {
"EDIFF": 1e-6,
"NSW": 0,
"LWAVE": True,
"ISYM": isym,
"ISYM": self.isym,
"NBANDS": nbands,
"IBRION": -1,
"ISMEAR": ismear,
"ISMEAR": self.ismear,
"LORBIT": 11,
"ICHARG": 0,
"ALGO": "Normal",
}

self._config_dict["INCAR"].update(update_dict)
self._config_dict["KPOINTS"]["reciprocal_density"] = self.reciprocal_density
return super().incar


def get_vasprun_outcar(path, parse_dos=True, parse_eigen=True):
Expand Down
7 changes: 4 additions & 3 deletions tests/io/vasp/test_sets.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,7 @@ def test_no_structure_init(self):
# basic test of initialization with no structure.
vis = MPRelaxSet()
with pytest.raises(RuntimeError, match="No structure is associated with the input set!"):
vis.incar
_ = vis.incar
vis.structure = self.structure
assert vis.incar["LDAUU"] == [5.3, 0, 0]

Expand Down Expand Up @@ -587,7 +587,8 @@ def test_valid_magmom_struct(self):
struct.insert(0, "Li", [0, 0, 0])

# vis = MPRelaxSet(struct, user_potcar_settings={"Fe": "Fe"}, validate_magmom=False)
# with pytest.raises(TypeError, match=r"float\(\) argument must be a string or a (real )?number, not 'NoneType'"):
# with pytest.raises(TypeError, match=r"float\(\) argument must be a string or a (real )?number,
# not 'NoneType'"):
# vis.get_vasp_input()

vis = MPRelaxSet(struct, user_potcar_settings={"Fe": "Fe"}, validate_magmom=True)
Expand Down Expand Up @@ -1764,7 +1765,7 @@ def setUp(self):
user_supplied_basis={"Fe": "3d 3p 4s", "P": "3p 3s", "O": "2p 2s"},
)
with pytest.raises(ValueError, match="There are no basis functions for the atom type O"):
self.lobsterset6 = self.set(self.struct, user_supplied_basis={"Fe": "3d 3p 4s", "P": "3p 3s"})
self.lobsterset6 = self.set(self.struct, user_supplied_basis={"Fe": "3d 3p 4s", "P": "3p 3s"}).incar
self.lobsterset7 = self.set(
self.struct,
address_basis_file=f"{MODULE_DIR}/../lobster/lobster_basis/BASIS_PBE_54_standard.yaml",
Expand Down

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