Chimie Théorique » scripts_chimie4psmn » DockOnSurf

import logging

logger = logging.getLogger('DockOnSurf')

def select_confs(orig_conf_list, calc_dirs, energy_cutoff, code):

    """From a list of atomic configurations selects the most stable ones.

    Given a list of ase.Atoms configurations and an energy cutoff, selects all

    the structures that have an energy lower than, the energy of the most stable

    conformer plus the cutoff.

    @param orig_conf_list: List of ase.Atoms objects of the conformers

    @param calc_dirs: List of the directories of the finished calculations

    @param energy_cutoff: The maximum energy above the most stable configuration

    @param code: the code used to carry out the screening of structures.

    @return: list of the the most stable configurations within the energy cutoff

    """

    from copy import deepcopy

    from modules.formats import collect_energies

    conf_list = deepcopy(orig_conf_list)

    selected_ids = []

    conf_enrgs = collect_energies(calc_dirs, code, 'screening')

    for i, conf in enumerate(conf_list):

        conf.info['energy'] = conf_enrgs[i]

    sorted_list = sorted(conf_list, key=lambda conf: conf.info['energy'])

    lowest_e = sorted_list[0].info['energy']

    return [conf for conf in sorted_list

            if conf.info['energy'] < lowest_e + energy_cutoff]

def run_refinement(inp_vars):

    """Carries out the refinement of adsorbate-slab structures after screening.

    @param inp_vars: Calculation parameters from input file.

    """

    import os

    from modules.formats import collect_coords

    from modules.calculation import run_calc, check_finished_calcs

    if not os.path.isdir("screening"):

        err = "'screening' directory not found. It is needed in order to carry "

        "out the refinement of structures to be adsorbed"

        logger.error(err)

        raise FileNotFoundError(err)

    logger.info('Carrying out procedures for the refinement of '

                'adsorbate-surface structures.')

    finished_calcs, unfinished_calcs = check_finished_calcs('screening',

                                                            inp_vars['code'])

    if len(unfinished_calcs) == 0:

        logger.info(f"Found {len(finished_calcs)} structures of "

                    f"adsorbate-surface atomic configurations.")

    else:

        logger.info(f"Found {len(finished_calcs)} structures of "

                    f"adsorbate-surface atomic configurations whose calculation"

                    f" finished normally.")

        logger.warning(f"Found {len(unfinished_calcs)} calculations more that "

                       f"did not finish normally: {unfinished_calcs}. Using "

                       f"only the {len(finished_calcs)} ones who finished "

                       f"normally")

    conf_list = collect_coords(inp_vars['code'], 'screening', 'ase',

                               inp_vars['special_atoms'])

    logger.info(f"Found {len(conf_list)} structures on screening directory.")

    selected_confs = select_confs(conf_list, finished_calcs,

                                  inp_vars['energy_cutoff'], inp_vars['code'])

    run_calc('refinement', inp_vars, selected_confs)

    logger.info('Finished the procedures for the refinement of '

                'adsorbate-surface structures section.')