"""Core jobs for running VASP calculations."""
from __future__ import annotations
import logging
from dataclasses import dataclass, field
from typing import TYPE_CHECKING, Literal
from pymatgen.alchemy.materials import TransformedStructure
from pymatgen.alchemy.transmuters import StandardTransmuter
from atomate2.common.utils import get_transformations
from atomate2.vasp.jobs.base import BaseVaspMaker, vasp_job
from atomate2.vasp.sets.core import (
HSEBSSetGenerator,
HSERelaxSetGenerator,
HSEStaticSetGenerator,
HSETightRelaxSetGenerator,
NonSCFSetGenerator,
RelaxSetGenerator,
StaticSetGenerator,
TightRelaxSetGenerator,
)
if TYPE_CHECKING:
from pathlib import Path
from jobflow import Response
from pymatgen.core.structure import Structure
from atomate2.vasp.sets.base import VaspInputGenerator
logger = logging.getLogger(__name__)
[docs]
@dataclass
class StaticMaker(BaseVaspMaker):
"""
Maker to create VASP static jobs.
Parameters
----------
name : str
The job name.
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
copy_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
run_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.run_vasp`.
task_document_kwargs : dict
Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
stop_children_kwargs : dict
Keyword arguments that will get passed to :obj:`.should_stop_children`.
write_additional_data : dict
Additional data to write to the current directory. Given as a dict of
{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
the "." character which is typically used to denote file extensions. To avoid
this, use the ":" character, which will automatically be converted to ".". E.g.
``{"my_file:txt": "contents of the file"}``.
"""
name: str = "static"
input_set_generator: VaspInputGenerator = field(default_factory=StaticSetGenerator)
[docs]
@dataclass
class RelaxMaker(BaseVaspMaker):
"""
Maker to create VASP relaxation jobs.
Parameters
----------
name : str
The job name.
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
copy_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
run_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.run_vasp`.
task_document_kwargs : dict
Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
stop_children_kwargs : dict
Keyword arguments that will get passed to :obj:`.should_stop_children`.
write_additional_data : dict
Additional data to write to the current directory. Given as a dict of
{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
the "." character which is typically used to denote file extensions. To avoid
this, use the ":" character, which will automatically be converted to ".". E.g.
``{"my_file:txt": "contents of the file"}``.
"""
name: str = "relax"
input_set_generator: VaspInputGenerator = field(default_factory=RelaxSetGenerator)
[docs]
@dataclass
class TightRelaxMaker(BaseVaspMaker):
"""
Maker to create tight VASP relaxation jobs.
Parameters
----------
name : str
The job name.
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
copy_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
run_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.run_vasp`.
task_document_kwargs : dict
Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
stop_children_kwargs : dict
Keyword arguments that will get passed to :obj:`.should_stop_children`.
write_additional_data : dict
Additional data to write to the current directory. Given as a dict of
{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
the "." character which is typically used to denote file extensions. To avoid
this, use the ":" character, which will automatically be converted to ".". E.g.
``{"my_file:txt": "contents of the file"}``.
"""
name: str = "tight relax"
input_set_generator: VaspInputGenerator = field(
default_factory=TightRelaxSetGenerator
)
[docs]
@dataclass
class NonSCFMaker(BaseVaspMaker):
"""
Maker to create non self consistent field VASP jobs.
Parameters
----------
name : str
The job name.
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
copy_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
run_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.run_vasp`.
task_document_kwargs : dict
Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
stop_children_kwargs : dict
Keyword arguments that will get passed to :obj:`.should_stop_children`.
write_additional_data : dict
Additional data to write to the current directory. Given as a dict of
{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
the "." character which is typically used to denote file extensions. To avoid
this, use the ":" character, which will automatically be converted to ".". E.g.
``{"my_file:txt": "contents of the file"}``.
"""
name: str = "non-scf"
input_set_generator: VaspInputGenerator = field(default_factory=NonSCFSetGenerator)
[docs]
@vasp_job
def make(
self,
structure: Structure,
prev_dir: str | Path | None,
mode: str = "uniform",
) -> Response:
"""
Run a non-scf VASP job.
Parameters
----------
structure : .Structure
A pymatgen structure object.
prev_dir : str or Path or None
A previous VASP calculation directory to copy output files from.
mode : str
Type of band structure calculation. Options are:
- "line": Full band structure along symmetry lines.
- "uniform": Uniform mesh band structure.
"""
self.input_set_generator.mode = mode
# parse DOS only for uniform band structure
self.task_document_kwargs.setdefault("parse_dos", mode == "uniform")
self.task_document_kwargs.setdefault("parse_bandstructure", mode)
# copy previous inputs
self.copy_vasp_kwargs.setdefault("additional_vasp_files", ("CHGCAR",))
return super().make.original(self, structure, prev_dir)
[docs]
@dataclass
class HSERelaxMaker(BaseVaspMaker):
"""
Maker to create HSE06 relaxation jobs.
Parameters
----------
name : str
The job name.
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
copy_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
run_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.run_vasp`.
task_document_kwargs : dict
Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
stop_children_kwargs : dict
Keyword arguments that will get passed to :obj:`.should_stop_children`.
write_additional_data : dict
Additional data to write to the current directory. Given as a dict of
{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
the "." character which is typically used to denote file extensions. To avoid
this, use the ":" character, which will automatically be converted to ".". E.g.
``{"my_file:txt": "contents of the file"}``.
"""
name: str = "hse relax"
input_set_generator: VaspInputGenerator = field(
default_factory=HSERelaxSetGenerator
)
[docs]
@dataclass
class HSETightRelaxMaker(BaseVaspMaker):
"""
Maker to create tight VASP relaxation jobs.
Parameters
----------
name : str
The job name.
input_set_generator
A generator used to make the input set.
write_input_set_kwargs
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
run_vasp_kwargs
Keyword arguments that will get passed to :obj:`.run_vasp`.
task_document_kwargs
Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
stop_children_kwargs
Keyword arguments that will get passed to :obj:`.should_stop_children`.
write_additional_data : dict
Additional data to write to the current directory. Given as a dict of
{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
the "." character which is typically used to denote file extensions. To avoid
this, use the ":" character, which will automatically be converted to ".". E.g.
``{"my_file:txt": "contents of the file"}``.
"""
name: str = "hse tight relax"
input_set_generator: VaspInputGenerator = field(
default_factory=HSETightRelaxSetGenerator
)
[docs]
@dataclass
class HSEStaticMaker(BaseVaspMaker):
"""
Maker to create HSE06 static jobs.
Parameters
----------
name : str
The job name.
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
copy_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
run_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.run_vasp`.
task_document_kwargs : dict
Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
stop_children_kwargs : dict
Keyword arguments that will get passed to :obj:`.should_stop_children`.
write_additional_data : dict
Additional data to write to the current directory. Given as a dict of
{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
the "." character which is typically used to denote file extensions. To avoid
this, use the ":" character, which will automatically be converted to ".". E.g.
``{"my_file:txt": "contents of the file"}``.
"""
name: str = "hse static"
input_set_generator: VaspInputGenerator = field(
default_factory=HSEStaticSetGenerator
)
[docs]
@dataclass
class HSEBSMaker(BaseVaspMaker):
"""
Maker to create HSE06 band structure jobs.
.. warning::
The number of bands will automatically be adjusted based on the number of bands
in the previous calculation. Therefore, if starting from a previous structure
ensure you are starting from a static/relaxation calculation that has the same
number of atoms (i.e., not a smaller/larger cell), as otherwise the number of
bands may be set incorrectly.
Parameters
----------
name : str
The job name.
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
copy_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
run_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.run_vasp`.
task_document_kwargs : dict
Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
stop_children_kwargs : dict
Keyword arguments that will get passed to :obj:`.should_stop_children`.
write_additional_data : dict
Additional data to write to the current directory. Given as a dict of
{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
the "." character which is typically used to denote file extensions. To avoid
this, use the ":" character, which will automatically be converted to ".". E.g.
``{"my_file:txt": "contents of the file"}``.
"""
name: str = "hse band structure"
input_set_generator: VaspInputGenerator = field(default_factory=HSEBSSetGenerator)
[docs]
@vasp_job
def make(
self,
structure: Structure,
prev_dir: str | Path | None = None,
mode: Literal["line", "uniform", "gap"] = "uniform",
) -> Response:
"""
Run a HSE06 band structure VASP job.
Parameters
----------
structure : .Structure
A pymatgen structure object.
prev_dir : str or Path or None
A previous VASP calculation directory to copy output files from.
mode : str = "uniform"
Type of band structure calculation. Options are:
- "line": Full band structure along symmetry lines.
- "uniform": Uniform mesh band structure.
- "gap": Get the energy at the CBM and VBM.
"""
self.input_set_generator.mode = mode
if mode == "gap" and prev_dir is None:
logger.warning(
"HSE band structure in 'gap' mode requires a previous VASP calculation "
"directory from which to extract the VBM and CBM k-points. This "
"calculation will instead be a standard uniform calculation."
)
mode = "uniform"
# parse DOS only for uniform band structure
self.task_document_kwargs.setdefault("parse_dos", "uniform" in mode)
parse_bandstructure = "uniform" if mode == "gap" else mode
self.task_document_kwargs.setdefault("parse_bandstructure", parse_bandstructure)
# copy previous inputs
if prev_dir is not None:
self.copy_vasp_kwargs.setdefault("additional_vasp_files", ("CHGCAR",))
return super().make.original(self, structure, prev_dir)
[docs]
@dataclass
class DielectricMaker(BaseVaspMaker):
"""
Maker to create dielectric calculation VASP jobs.
.. Note::
The input structure should be well relaxed to avoid imaginary modes. For
example, using :obj:`TightRelaxMaker`.
.. Note::
If starting from a previous calculation, magnetism will be disabled if all
MAGMOMs are less than 0.02.
Parameters
----------
name : str
The job name.
input_set_generator : .StaticSetGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
copy_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
run_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.run_vasp`.
task_document_kwargs : dict
Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
stop_children_kwargs : dict
Keyword arguments that will get passed to :obj:`.should_stop_children`.
write_additional_data : dict
Additional data to write to the current directory. Given as a dict of
{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
the "." character which is typically used to denote file extensions. To avoid
this, use the ":" character, which will automatically be converted to ".". E.g.
``{"my_file:txt": "contents of the file"}``.
"""
name: str = "dielectric"
input_set_generator: StaticSetGenerator = field(
default_factory=lambda: StaticSetGenerator(lepsilon=True, auto_ispin=True)
)
[docs]
@dataclass
class TransmuterMaker(BaseVaspMaker):
"""
A maker to apply transformations to a structure before writing the input sets.
Note that if a transformation yields many structures, only the last structure in the
list is used.
Parameters
----------
name : str
The job name.
transformations : tuple of str
The transformations to apply. Given as a list of names of transformation classes
as defined in the modules in pymatgen.transformations. For example,
``['DeformStructureTransformation', 'SupercellTransformation']``.
transformation_params : tuple of dict or None
The parameters used to instantiate each transformation class. Given as a list of
dicts.
input_set_generator : StaticSetGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
copy_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
run_vasp_kwargs : dict
Keyword arguments that will get passed to :obj:`.run_vasp`.
task_document_kwargs : dict
Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
stop_children_kwargs : dict
Keyword arguments that will get passed to :obj:`.should_stop_children`.
write_additional_data : dict
Additional data to write to the current directory. Given as a dict of
{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
the "." character which is typically used to denote file extensions. To avoid
this, use the ":" character, which will automatically be converted to ".". E.g.
``{"my_file:txt": "contents of the file"}``.
"""
name: str = "transmuter"
transformations: tuple[str, ...] = field(default_factory=tuple)
transformation_params: tuple[dict, ...] | None = None
input_set_generator: VaspInputGenerator = field(default_factory=StaticSetGenerator)
[docs]
@vasp_job
def make(
self,
structure: Structure,
prev_dir: str | Path | None = None,
) -> Response:
"""
Run a transmuter VASP job.
Parameters
----------
structure : Structure
A pymatgen structure object.
prev_dir : str or Path or None
A previous VASP calculation directory to copy output files from.
"""
transformations = get_transformations(
self.transformations, self.transformation_params
)
ts = TransformedStructure(structure)
transmuter = StandardTransmuter([ts], transformations)
structure = transmuter.transformed_structures[-1].final_structure
# to avoid MongoDB errors, ":" is automatically converted to "."
tjson = transmuter.transformed_structures[-1]
self.write_additional_data.setdefault("transformations:json", tjson)
return super().make.original(self, structure, prev_dir)