Source code for

"""Jobs for performing electron phonon calculations in VASP."""

from __future__ import annotations

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

import numpy as np
from jobflow import Flow, Response, job

from import BaseVaspMaker, vasp_job
from import TransmuterMaker
from atomate2.vasp.schemas.elph import ElectronPhononRenormalisationDoc
from atomate2.vasp.sets.core import ElectronPhononSetGenerator

    from pathlib import Path

    from pymatgen.core import Structure
    from pymatgen.electronic_structure.bandstructure import BandStructure

DEFAULT_ELPH_TEMPERATURES = (0, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000)
logger = logging.getLogger(__name__)

[docs] @dataclass class SupercellElectronPhononDisplacedStructureMaker(TransmuterMaker): """ Maker to run electron phonon VASP jobs to generate displaced structures. This job: 1. Generates a close to cubic supercell with cell lengths > 15 Å. 2. Performs an IBRION = 6 finite-displacement calculation to calculate the phonon eigenvalues and eigenvectors. 3. Displaces the atoms to simulate a range of temperatures. .. warning:: Electron phonon properties should be converged with respect to supercell size. Typically, cells with all lattice vectors greater than 15 Å should be a reasonable starting point. .. note:: The input structure should be well relaxed to avoid imaginary modes. For example, using :obj:`TightRelaxMaker`. .. note:: Requires VASP 6.0 and higher. See phonon_interactions_from_Monte-Carlo_sampling for more details. 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 = "supercell electron phonon displacements" input_set_generator: ElectronPhononSetGenerator = field( default_factory=ElectronPhononSetGenerator ) transformations: tuple[str, ...] = ("SupercellTransformation",) transformation_params: tuple[dict, ...] = None temperatures: tuple[float, ...] = DEFAULT_ELPH_TEMPERATURES min_supercell_length: float = DEFAULT_MIN_SUPERCELL_LENGTH
[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. """ dim = self.min_supercell_length / np.array( scaling_matrix = np.diag(np.ceil(dim).astype(int)).tolist() if self.transformation_params is None: # only overwrite transformation params if it is not set self.transformation_params = ({"scaling_matrix": scaling_matrix},) # update temperatures self.input_set_generator.temperatures = self.temperatures return super().make.original(self, structure, prev_dir)
[docs] @job def run_elph_displacements( temperatures: list[float], structures: list[Structure], vasp_maker: BaseVaspMaker, prev_dir: str | Path | None = None, original_structure: Structure = None, supercell_structure: Structure = None, ) -> Response: """ Run electron phonon displaced structures. Note, this job will replace itself with N displacement calculations. Parameters ---------- temperatures : list of float Temperatures at which electron phonon structures were generated. structures : list of Structure Electron phonon displaced structures for each temperature. vasp_maker : BaseVaspMaker A maker to generate VASP calculations on the displaced structures. prev_dir : str or Path or None A previous VASP directory to use for copying VASP outputs. original_structure : Structure The original structure before supercell is made and before electron phonon displacements. """ if len(temperatures) != len(structures): raise ValueError( f"Number of temperatures ({len(temperatures)}) does not equal number of " f"structures ({len(structures)})." ) jobs = [] outputs: dict[str, list] = { "temperatures": [], "band_structures": [], "structures": [], "uuids": [], "dirs": [], } for temp, structure in zip(temperatures, structures): # create the job elph_job = vasp_maker.make(structure, prev_dir=prev_dir) elph_job.append_name(f" T={temp}") # write details of the electron phonon temperature and structure elph_info.json # file. this file will automatically get added to the task document and allow # the elph builder to reconstruct the elph document. note the ":" is # automatically converted to a "." in the filename. info = { "temperature": temp, "original_structure": original_structure, "supercell_structure": supercell_structure, } elph_job.update_maker_kwargs( {"_set": {"write_additional_data->elph_info:json": info}}, dict_mod=True ) jobs.append(elph_job) # extract the outputs we want outputs["temperatures"].append(temp) outputs["band_structures"].append(elph_job.output.vasp_objects["bandstructure"]) outputs["structures"].append(elph_job.output.structure) outputs["dirs"].append(elph_job.output.dir_name) outputs["uuids"].append(elph_job.output.uuid) disp_flow = Flow(jobs, outputs) return Response(replace=disp_flow)
[docs] @job(output_schema=ElectronPhononRenormalisationDoc) def calculate_electron_phonon_renormalisation( temperatures: list[float], displacement_band_structures: list[BandStructure], displacement_structures: list[Structure], displacement_uuids: list[str], displacement_dirs: list[str], bulk_band_structure: BandStructure, bulk_structure: Structure, bulk_uuid: str, bulk_dir: str, elph_uuid: str, elph_dir: str, original_structure: Structure, ) -> ElectronPhononRenormalisationDoc: """ Calculate the electron-phonon renormalisation of the band gap. Parameters ---------- temperatures : list of float The temperatures at which electron phonon properties were calculated. displacement_band_structures : list of BandStructure The electron-phonon displaced band structures. displacement_structures : list of Structure The electron-phonon displaced structures. displacement_uuids : list of str The UUIDs of the electron-phonon displaced band structure calculations. displacement_dirs : list of str The calculation directories of the electron-phonon displaced band structure calculations. bulk_band_structure : BandStructure The band structure of the bulk undisplaced supercell calculation. bulk_structure : Structure The structure of the bulk undisplaced supercell. bulk_uuid : str The UUID of the bulk undisplaced supercell band structure calculation. bulk_dir : str The directory of the bulk undisplaced supercell band structure calculation. elph_uuid : str The UUID of electron-phonon calculation that generated the displaced structures. elph_dir : str The directory of electron-phonon calculation that generated the displaced structures. original_structure : Structure The original primitive structure for which electron-phonon calculations were performed. """ if bulk_structure is None: raise ValueError( "Bulk (undisplaced) supercell band structure calculation failed. Cannot " "calculate electron-phonon renormalisation." ) # filter band structures that are None (i.e., the displacement calculation failed) keep = [idx for idx, b in enumerate(displacement_band_structures) if b is not None] temperatures = [temperatures[i] for i in keep] displacement_band_structures = [displacement_band_structures[i] for i in keep] displacement_structures = [displacement_structures[i] for i in keep] displacement_uuids = [displacement_uuids[i] for i in keep] displacement_dirs = [displacement_dirs[i] for i in keep]"Calculating electron-phonon renormalisation") return ElectronPhononRenormalisationDoc.from_band_structures( temperatures, displacement_band_structures, displacement_structures, displacement_uuids, displacement_dirs, bulk_band_structure, bulk_structure, bulk_uuid, bulk_dir, elph_uuid, elph_dir, original_structure, )