Chimie Théorique » scripts_chimie4psmn » DockOnSurf

import os

import logging

logger = logging.getLogger('DockOnSurf')

def create_bak_calc_dir(run_type):

    """Checks if calculations directory already exists, backs it up if so and

    creates an empty one.

    @param run_type: Type of calculation. 'isolated', 'screening' or

    'refinement'

    """

    dir_name = run_type

    bak_num = 0

    while dir_name in os.listdir("."):

        bak_num += 1

        dir_name = dir_name.split(".")[0] + f".bak{bak_num}"

    if bak_num > 0:

        os.rename(run_type, dir_name)

        logger.warning(f"'{run_type}' directory already present. Moved former "

                       f"directory to {dir_name}")

    os.mkdir(run_type)

def prep_cp2k(inp_file, run_type, atms_list):

    """Prepares the directories to run isolated calculation with CP2K.

    @param inp_file: CP2K Input file to run the calculations with.

    @param run_type: Type of calculation. 'isolated', 'screening' or

        'refinement'

    @param atms_list: list of ase.Atoms objects to run the calculation of.

    @return: None

    """

    from shutil import copy

    import ase.io

    from pycp2k import CP2K

    cp2k = CP2K()

    cp2k.parse(inp_file)

    force_eval = cp2k.CP2K_INPUT.FORCE_EVAL_list[0]

    coord_file = force_eval.SUBSYS.TOPOLOGY.Coord_file_name

    # Creating and setting up directories for every atoms configuration.

    for i, conf in enumerate(atms_list):

        os.mkdir(f'{run_type}/conf_{i}')

        copy(inp_file, f'{run_type}/conf_{i}/')

        ase.io.write(f'{run_type}/conf_{i}/{coord_file}', conf)

def run_calc(run_type, inp_vars, atms_list):

    """Directs the calculation run according to the provided arguments.

    @param run_type: Type of calculation. 'isolated', 'screening' or

    'refinement'

    @param inp_vars: Calculation parameters from input file.

    @param atms_list: List of ase.Atoms objects containing the sets of atoms

    aimed to run the calculations of.

    """

    run_types = ['isolated', 'screening', 'refinement']

    run_type_err = f"'run_type' should be one of the following: {run_types}"

    if not isinstance(run_type, str) or run_type.lower() not in run_types:

        logger.error(run_type_err)

        raise ValueError(run_type_err)

    logger.info(f"Running {run_type} calculation with {inp_vars['code']} on "

                f"{inp_vars['batch_q_sys']}")

    create_bak_calc_dir(run_type)

    if run_type == 'isolated':

        if inp_vars['code'] == 'cp2k':

            prep_cp2k(inp_vars['isol_inp_file'], run_type, atms_list)