Source code for atomate2.vasp.jobs.lobster

"""Module defining amset jobs."""

from __future__ import annotations

import logging
from dataclasses import dataclass, field
from typing import TYPE_CHECKING, Any

from jobflow import Flow, Response, job
from pymatgen.io.lobster import Lobsterin

from atomate2.common.files import delete_files
from atomate2.lobster.jobs import LobsterMaker
from atomate2.utils.path import strip_hostname
from atomate2.vasp.jobs.base import BaseVaspMaker
from atomate2.vasp.powerups import update_user_incar_settings
from atomate2.vasp.sets.core import StaticSetGenerator

if TYPE_CHECKING:
    from pathlib import Path

    from pymatgen.core import Structure

    from atomate2.vasp.sets.base import VaspInputGenerator


logger = logging.getLogger(__name__)


[docs] @dataclass class LobsterStaticMaker(BaseVaspMaker): """ Maker that performs a VASP computation with settings that are required for Lobster. 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_run" input_set_generator: VaspInputGenerator = field( default_factory=lambda: StaticSetGenerator( auto_ispin=True, user_kpoints_settings={"reciprocal_density": 400}, user_incar_settings={ "EDIFF": 1e-7, "LAECHG": False, "LREAL": False, "LVTOT": False, "ALGO": "Normal", "LCHARG": False, "LWAVE": True, "ISYM": 0, }, ) )
[docs] @job def get_basis_infos( structure: Structure, vasp_maker: BaseVaspMaker, address_max_basis: str = None, address_min_basis: str = None, ) -> dict: """ Compute all relevant basis sets and maximum number of bands. Parameters ---------- structure : .Structure A structure object. vasp_maker : .BaseVaspMaker Maker for Vasp job including a POTCAR. address_max_basis : str string to yaml file including basis set information. address_min_basis : str string to yaml file including basis set information. Returns ------- dict Dictionary including number of bands and basis set information. """ # this logic enables handling of a flow or a simple maker try: potcar_symbols = vasp_maker.static_maker.input_set_generator._get_potcar( # noqa: SLF001 structure=structure, potcar_spec=True ) except AttributeError: potcar_symbols = vasp_maker.input_set_generator._get_potcar( # noqa: SLF001 structure=structure, potcar_spec=True ) # get data from LobsterInput list_basis_dict = Lobsterin.get_all_possible_basis_functions( structure=structure, potcar_symbols=potcar_symbols, address_basis_file_max=address_max_basis, address_basis_file_min=address_min_basis, ) n_band_list: list[int] = [] for dict_for_basis in list_basis_dict: basis = [f"{key} {value}" for key, value in dict_for_basis.items()] lobsterin = Lobsterin(settingsdict={"basisfunctions": basis}) n_bands = lobsterin._get_nbands(structure=structure) # noqa: SLF001 n_band_list.append(n_bands) return {"nbands": max(n_band_list), "basis_dict": list_basis_dict}
[docs] @job def update_user_incar_settings_maker( vasp_maker: BaseVaspMaker, nbands: int, structure: Structure, prev_dir: Path | str, ) -> Response: """ Update the INCAR settings of a maker. Parameters ---------- vasp_maker : .BaseVaspMaker A maker for the static run with all parameters relevant for Lobster. nbands : int integer indicating the correct number of bands structure : .Structure Structure object. prev_dir : Path or str Path or string to vasp files. Returns ------- .BaseVaspMaker LobsterStaticMaker with correct number of bands. """ vasp_maker = update_user_incar_settings(vasp_maker, {"NBANDS": nbands}) vasp_job = vasp_maker.make(structure=structure, prev_dir=prev_dir) return Response(replace=vasp_job)
[docs] @job def get_lobster_jobs( lobster_maker: LobsterMaker | None, basis_dict: dict, optimization_dir: Path | str, optimization_uuid: str, static_dir: Path | str, static_uuid: str, ) -> Response: """ Create a list of Lobster jobs with different basis sets. Parameters ---------- lobster_maker : .LobsterMaker or None maker for the Lobster jobs basis_dict : dict dict including basis set information. optimization_dir : Path or str Path to optimization run. optimization_uuid : str uuid of optimization run. static_dir : Path or str Path to static VASP calculation containing the WAVECAR. static_uuid : str Uuid of static run. Returns ------- list List of Lobster jobs. """ jobs = [] outputs: dict[str, Any] = { "optimization_dir": optimization_dir, "optimization_uuid": optimization_uuid, "static_dir": static_dir, "static_uuid": static_uuid, "lobster_uuids": [], "lobster_dirs": [], "lobster_task_documents": [], } lobster_maker = lobster_maker or LobsterMaker() for idx, basis in enumerate(basis_dict): lobster_job = lobster_maker.make(wavefunction_dir=static_dir, basis_dict=basis) lobster_job.append_name(f"_run_{idx}") outputs["lobster_uuids"].append(lobster_job.output.uuid) outputs["lobster_dirs"].append(lobster_job.output.dir_name) outputs["lobster_task_documents"].append(lobster_job.output) jobs.append(lobster_job) flow = Flow(jobs, output=outputs) return Response(replace=flow)
[docs] @job def delete_lobster_wavecar( dirs: list[Path | str], lobster_static_dir: Path | str = None, ) -> None: """ Delete all WAVECARs. Parameters ---------- dirs : list of path or str Path to directories of lobster jobs. lobster_static_dir : Path or str Path to directory of static VASP run. """ if lobster_static_dir: dirs.append(lobster_static_dir) for dir_name in dirs: delete_files( strip_hostname(dir_name), include_files=["WAVECAR", "WAVECAR.gz"], allow_missing=True, )