Source code for atomate2.amset.files

"""Module defining functions for manipulating amset files."""

from __future__ import annotations

import logging
from typing import TYPE_CHECKING

from monty.serialization import loadfn

from atomate2 import SETTINGS
from atomate2.common.files import copy_files, get_zfile, gunzip_files, rename_files
from atomate2.utils.file_client import FileClient, auto_fileclient
from atomate2.utils.path import strip_hostname

    from pathlib import Path

logger = logging.getLogger(__name__)

[docs] @auto_fileclient def copy_amset_files( src_dir: Path | str, src_host: str | None = None, file_client: FileClient = None, ) -> None: """ Copy AMSET files to current directory. This function will gunzip any gzipped files. Parameters ---------- src_dir : Path or str The source directory. src_host : str or None The source hostname used to specify a remote filesystem. Can be given as either "username@remote_host" or just "remote_host" in which case the username will be inferred from the current user. If ``None``, the local filesystem will be used as the source. file_client : FileClient A file client to use for performing file operations. """ src_dir = strip_hostname(src_dir) # TODO: Handle hostnames properly."Copying AMSET inputs from {src_dir}") directory_listing = file_client.listdir(src_dir, host=src_host) # find optional files files = [] for file in ( "settings.yaml", "vasprun.xml", "band_structure_data.json", "wavefunction.h5", "deformation.h5", "transport.json", ): found_file = get_zfile(directory_listing, file, allow_missing=True) if found_file is not None: files.append(found_file) copy_files( src_dir, src_host=src_host, include_files=files, file_client=file_client, ) gunzip_files( include_files=files, allow_missing=True, file_client=file_client, ) rename_files({"transport.json": "transport.prev.json"}, allow_missing=True)"Finished copying inputs")
[docs] def write_amset_settings(settings_updates: dict, from_prev: bool = False) -> None: """ Write AMSET settings to file. This function will also apply any settings specified in :obj:`.Atomate2Settings.AMSET_SETTINGS_UPDATE`. Parameters ---------- settings_updates : dict A dictionary of settings to write. from_prev : bool Whether apply the settings on top of an existing settings.yaml file in the current directory. """ from import write_settings if from_prev: settings = loadfn("settings.yaml") settings.update(settings_updates) else: settings = settings_updates if SETTINGS.AMSET_SETTINGS_UPDATE is not None: settings.update(SETTINGS.AMSET_SETTINGS_UPDATE) write_settings(settings, "settings.yaml")