Source code for atomate2.vasp.sets.eos
"""
Module defining equation of state (EOS) parameter sets.
Three families of sets: default atomate2 params,
MP GGA compatible, and MP meta-GGA compatible
"""
from __future__ import annotations
from dataclasses import dataclass, field
from importlib.resources import files as import_files
from typing import TYPE_CHECKING
from monty.serialization import loadfn
from atomate2.vasp.sets.base import VaspInputGenerator
if TYPE_CHECKING:
from pymatgen.core import Structure
from pymatgen.io.vasp import Outcar, Vasprun
_BASE_MP_GGA_RELAX_SET = loadfn(
import_files("atomate2.vasp.sets") / "BaseMPGGASet.yaml"
)
_BASE_MP_R2SCAN_RELAX_SET = loadfn(
import_files("atomate2.vasp.sets") / "BaseMPR2SCANRelaxSet.yaml"
)
[docs]
@dataclass
class EosSetGenerator(VaspInputGenerator):
"""Class to generate VASP EOS deformation + relax input sets."""
force_gamma: bool = True
auto_ismear: bool = False
auto_kspacing: bool = False
inherit_incar: bool = False
[docs]
def get_incar_updates(
self,
structure: Structure,
prev_incar: dict = None,
bandgap: float = None,
vasprun: Vasprun = None,
outcar: Outcar = None,
) -> dict:
"""
Get updates to the INCAR for a relaxation job.
Parameters
----------
structure
A structure.
prev_incar
An incar from a previous calculation.
bandgap
The band gap.
vasprun
A vasprun from a previous calculation.
outcar
An outcar from a previous calculation.
Returns
-------
dict
A dictionary of updates to apply.
"""
return {
"NSW": 99,
"LCHARG": False,
"ISIF": 3,
"IBRION": 2,
"EDIFF": 1e-6,
"ENCUT": 680,
"ENAUG": 1360,
"LREAL": False,
"LWAVE": True,
"ISMEAR": 0,
"SIGMA": 0.05,
"KSPACING": 0.22,
}
# MPLegacy prefix = MP PBE-GGA compatible with atomate implementation
[docs]
@dataclass
class MPLegacyEosRelaxSetGenerator(VaspInputGenerator):
"""Class to generate atomate1-MP-compatible VASP GGA EOS relax input sets."""
config_dict: dict = field(default_factory=lambda: _BASE_MP_GGA_RELAX_SET)
auto_ismear: bool = False
auto_kspacing: bool = False
inherit_incar: bool = False
[docs]
def get_incar_updates(
self,
structure: Structure,
prev_incar: dict = None,
bandgap: float = None,
vasprun: Vasprun = None,
outcar: Outcar = None,
) -> dict:
"""
Get updates to the INCAR for a relaxation job.
Parameters
----------
structure
A structure.
prev_incar
An incar from a previous calculation.
bandgap
The band gap.
vasprun
A vasprun from a previous calculation.
outcar
An outcar from a previous calculation.
Returns
-------
dict
A dictionary of updates to apply.
"""
return {
"NSW": 99,
"LCHARG": False,
"ISIF": 3,
"IBRION": 2,
"EDIFF": 1e-6,
"ENCUT": 600,
"LREAL": False,
"LWAVE": True,
}
[docs]
def get_kpoints_updates(
self,
structure: Structure,
prev_incar: dict = None,
bandgap: float = 0.0,
vasprun: Vasprun = None,
outcar: Outcar = None,
) -> dict:
"""
Get updates to the kpoints configuration for a non-self consistent VASP job.
Note, these updates will be ignored if the user has set user_kpoint_settings.
Parameters
----------
structure
A structure.
prev_incar
An incar from a previous calculation.
bandgap
The band gap.
vasprun
A vasprun from a previous calculation.
outcar
An outcar from a previous calculation.
Returns
-------
dict
A dictionary of updates to apply to the KPOINTS config.
"""
return {"grid_density": 7000}
[docs]
@dataclass
class MPLegacyEosStaticSetGenerator(EosSetGenerator):
"""Class to generate atomate1-MP-compatible VASP GGA EOS relax input sets."""
config_dict: dict = field(default_factory=lambda: _BASE_MP_GGA_RELAX_SET)
auto_ismear: bool = False
auto_kspacing: bool = False
inherit_incar: bool = False
[docs]
def get_incar_updates(
self,
structure: Structure,
prev_incar: dict = None,
bandgap: float = None,
vasprun: Vasprun = None,
outcar: Outcar = None,
) -> dict:
"""
Get updates to the INCAR for a relaxation job.
Parameters
----------
structure
A structure.
prev_incar
An incar from a previous calculation.
bandgap
The band gap.
vasprun
A vasprun from a previous calculation.
outcar
An outcar from a previous calculation.
Returns
-------
dict
A dictionary of updates to apply.
"""
# Original atomate wf_bulk_modulus had 600 eV cutoff
# and k-point grid_density = 7,000
return {
"NSW": 0,
"LCHARG": False,
"EDIFF": 1e-6,
"ENCUT": 600,
"LREAL": False,
"LWAVE": False,
"IBRION": -1,
"ISMEAR": -5,
"LORBIT": 11,
"ALGO": "Normal",
}
# MPGGA prefix = MP GGA compatible
[docs]
@dataclass
class MPGGAEosRelaxSetGenerator(VaspInputGenerator):
"""Class to generate MP-compatible VASP GGA EOS relax input sets."""
config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET)
auto_ismear: bool = False
auto_kspacing: bool = False
inherit_incar: bool = False
[docs]
def get_incar_updates(
self,
structure: Structure,
prev_incar: dict = None,
bandgap: float = None,
vasprun: Vasprun = None,
outcar: Outcar = None,
) -> dict:
"""
Get updates to the INCAR for a relaxation job.
Parameters
----------
structure
A structure.
prev_incar
An incar from a previous calculation.
bandgap
The band gap.
vasprun
A vasprun from a previous calculation.
outcar
An outcar from a previous calculation.
Returns
-------
dict
A dictionary of updates to apply.
"""
return {
"NSW": 99,
"LCHARG": False,
"ISIF": 3,
"IBRION": 2,
"EDIFF": 1e-6,
"ALGO": "FAST",
"LREAL": False,
"LWAVE": True,
"ISMEAR": 0,
"SIGMA": 0.05,
"LMAXMIX": 6,
"KSPACING": 0.22,
"METAGGA": None,
}
[docs]
@dataclass
class MPGGAEosStaticSetGenerator(EosSetGenerator):
"""Class to generate MP-compatible VASP GGA EOS relax input sets."""
config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET)
auto_ismear: bool = False
auto_kspacing: bool = False
inherit_incar: bool = False
[docs]
def get_incar_updates(
self,
structure: Structure,
prev_incar: dict = None,
bandgap: float = None,
vasprun: Vasprun = None,
outcar: Outcar = None,
) -> dict:
"""
Get updates to the INCAR for a relaxation job.
Parameters
----------
structure
A structure.
prev_incar
An incar from a previous calculation.
bandgap
The band gap.
vasprun
A vasprun from a previous calculation.
outcar
An outcar from a previous calculation.
Returns
-------
dict
A dictionary of updates to apply.
"""
return {
"NSW": 0,
"LCHARG": False,
"IBRION": -1,
"EDIFF": 1e-6,
"ALGO": "NORMAL",
"LREAL": False,
"LWAVE": False,
"ISMEAR": -5,
"LMAXMIX": 6,
"KSPACING": 0.22,
"METAGGA": None,
}
# MPMetaGGA prefix = MP r2SCAN meta-GGA compatible
[docs]
@dataclass
class MPMetaGGAEosStaticSetGenerator(VaspInputGenerator):
"""Class to generate MP-compatible VASP Meta-GGA static input sets."""
config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET)
auto_ismear: bool = False
auto_kspacing: bool = False
inherit_incar: bool = False
[docs]
def get_incar_updates(
self,
structure: Structure,
prev_incar: dict = None,
bandgap: float = None,
vasprun: Vasprun = None,
outcar: Outcar = None,
) -> dict:
"""
Get updates to the INCAR for this calculation type.
Parameters
----------
structure
A structure.
prev_incar
An incar from a previous calculation.
bandgap
The band gap.
vasprun
A vasprun from a previous calculation.
outcar
An outcar from a previous calculation.
Returns
-------
dict
A dictionary of updates to apply.
"""
return {
"EDIFF": 1e-6,
"ALGO": "NORMAL",
"GGA": None, # unset GGA, shouldn't be set anyway but best be sure
"NSW": 0,
"LCHARG": True,
"LWAVE": False,
"LREAL": False,
"ISMEAR": -5,
"IBRION": -1,
"LMAXMIX": 6,
"KSPACING": 0.22,
}
[docs]
@dataclass
class MPMetaGGAEosRelaxSetGenerator(VaspInputGenerator):
"""Class to generate MP-compatible VASP meta-GGA relaxation input sets.
Parameters
----------
config_dict: dict
The config dict.
bandgap_tol: float
Tolerance for metallic bandgap. If bandgap < bandgap_tol, KSPACING will be 0.22,
otherwise it will increase with bandgap up to a max of 0.44.
"""
config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET)
bandgap_tol: float = 1e-4
auto_ismear: bool = False
auto_kspacing: bool = False
inherit_incar: bool = False
[docs]
def get_incar_updates(
self,
structure: Structure,
prev_incar: dict = None,
bandgap: float = None,
vasprun: Vasprun = None,
outcar: Outcar = None,
) -> dict:
"""
Get updates to the INCAR for this calculation type.
Parameters
----------
structure
A structure.
prev_incar
An incar from a previous calculation.
bandgap
The band gap.
vasprun
A vasprun from a previous calculation.
outcar
An outcar from a previous calculation.
Returns
-------
dict
A dictionary of updates to apply.
"""
# unset GGA, shouldn't be set anyway but doesn't hurt to be sure
return {
"LCHARG": True,
"LWAVE": True,
"GGA": None,
"LMAXMIX": 6,
"KSPACING": 0.22,
"NSW": 99,
"ISIF": 3,
"IBRION": 2,
"EDIFF": 1e-6,
"LREAL": False,
"ISMEAR": 0,
"SIGMA": 0.05,
}
[docs]
@dataclass
class MPMetaGGAEosPreRelaxSetGenerator(VaspInputGenerator):
"""Class to generate MP-compatible VASP meta-GGA pre-relaxation input sets.
Parameters
----------
config_dict: dict
The config dict.
bandgap_tol: float
Tolerance for metallic bandgap. If bandgap < bandgap_tol, KSPACING will be 0.22,
otherwise it will increase with bandgap up to a max of 0.44.
"""
config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET)
bandgap_tol: float = 1e-4
auto_ismear: bool = False
auto_kspacing: bool = False
inherit_incar: bool = False
[docs]
def get_incar_updates(
self,
structure: Structure,
prev_incar: dict = None,
bandgap: float = None,
vasprun: Vasprun = None,
outcar: Outcar = None,
) -> dict:
"""
Get updates to the INCAR for this calculation type.
Parameters
----------
structure
A structure.
prev_incar
An incar from a previous calculation.
bandgap
The band gap.
vasprun
A vasprun from a previous calculation.
outcar
An outcar from a previous calculation.
Returns
-------
dict
A dictionary of updates to apply.
"""
# unset METAGGA, shouldn't be set anyway but doesn't hurt to be sure
return {
"LCHARG": True,
"LWAVE": True,
"GGA": "PS",
"METAGGA": None,
"NSW": 99,
"ISIF": 3,
"IBRION": 2,
"EDIFF": 1e-6,
"EDIFFG": -0.05,
"LREAL": False,
"ISMEAR": 0,
"SIGMA": 0.05,
"KSPACING": 0.22,
}