Source code for atomate2.lobster.jobs

"""Module defining lobster jobs."""

from __future__ import annotations

import logging
from dataclasses import dataclass, field
from pathlib import Path

from jobflow import Maker, job
from pymatgen.electronic_structure.cohp import CompleteCohp
from pymatgen.electronic_structure.dos import LobsterCompleteDos
from pymatgen.io.lobster import Lobsterin

from atomate2 import SETTINGS
from atomate2.common.files import gzip_output_folder
from atomate2.lobster.files import LOBSTEROUTPUT_FILES, copy_lobster_files
from atomate2.lobster.run import run_lobster
from atomate2.lobster.schemas import LobsterTaskDocument

__all__ = ["LobsterMaker"]

logger = logging.getLogger(__name__)


_FILES_TO_ZIP = [*LOBSTEROUTPUT_FILES, "lobsterin"]




@dataclass
class LobsterMaker(Maker):
    """
    LOBSTER job maker.

    The maker copies DFT output files necessary for the LOBSTER run. It will create all
    lobsterin files, run LOBSTER, zip the outputs and parse the LOBSTER outputs.

    Parameters
    ----------
    name : str
        Name of jobs produced by this maker.
    task_document_kwargs : dict
        Keyword arguments passed to :obj:`.LobsterTaskDocument.from_directory`.
    user_lobsterin_settings : dict
        Dict including additional information on the Lobster settings.
    run_lobster_kwargs : dict
        Keyword arguments that will get passed to :obj:`.run_lobster`.
    calculation_type : str
        Type of calculation for the Lobster run that will get passed to
        :obj:`.Lobsterin.standard_calculations_from_vasp_files`.
    """

    name: str = "lobster"
    task_document_kwargs: dict = field(default_factory=dict)
    user_lobsterin_settings: dict | None = None
    run_lobster_kwargs: dict = field(default_factory=dict)
    calculation_type: str = "standard"



    @job(output_schema=LobsterTaskDocument, data=[CompleteCohp, LobsterCompleteDos])
    def make(
        self,
        wavefunction_dir: str | Path = None,
        basis_dict: dict | None = None,
    ):
        """
        Run a LOBSTER calculation.

        Parameters
        ----------
        wavefunction_dir : str or Path
            A directory containing a WAVEFUNCTION and other outputs needed for Lobster
        basis_dict: dict
            A dict including information on the basis set
        """
        # copy previous inputs # VASP for example
        copy_lobster_files(wavefunction_dir)

        # write lobster settings
        lobsterin = Lobsterin.standard_calculations_from_vasp_files(
            "POSCAR", "INCAR", dict_for_basis=basis_dict, option=self.calculation_type
        )

        if self.user_lobsterin_settings:
            for key, parameter in self.user_lobsterin_settings.items():
                # basis function can only be changed with the help of a yaml file
                if key != "basisfunctions":
                    lobsterin[key] = parameter

        lobsterin.write_lobsterin("lobsterin")

        # run lobster
        logger.info("Running LOBSTER")
        run_lobster(**self.run_lobster_kwargs)

        # gzip folder
        gzip_output_folder(
            directory=Path.cwd(),
            setting=SETTINGS.LOBSTER_ZIP_FILES,
            files_list=_FILES_TO_ZIP,
        )

        # parse lobster outputs
        return LobsterTaskDocument.from_directory(
            Path.cwd(),
            **self.task_document_kwargs,
        )