dockonsurf / modules / refinement.py @ cdc1edbe
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import logging |
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logger = logging.getLogger('DockOnSurf')
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def select_confs(conf_list, calc_dirs, energy_cutoff, code): |
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"""From a list of atomic configurations selects the most stable ones.
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Given a list of ase.Atoms configurations and an energy cutoff, selects all
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the structures that have an energy lower than, the energy of the most stable
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conformer plus the cutoff.
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@param conf_list: List of ase.Atoms objects of the conformers
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@param calc_dirs: List of the directories of the finished calculations
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@param energy_cutoff: The maximum energy above the most stable configuration
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@param code: the code used to carry out the screening of structures.
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@return: list of the the most stable configurations within the energy cutoff
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"""
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from copy import deepcopy |
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from modules.formats import collect_energies |
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conf_enrgs = collect_energies(calc_dirs, code, 'screening')
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for i, conf in enumerate(conf_list): |
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conf.info['energy'] = conf_enrgs[i]
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conf.info['id'] = calc_dirs[i]
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sorted_list = sorted(conf_list, key=lambda conf: conf.info['energy']) |
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lowest_e = sorted_list[0].info['energy'] |
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return [conf for conf in sorted_list |
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if conf.info['energy'] <= lowest_e + energy_cutoff] |
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def run_refinement(inp_vars): |
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"""Carries out the refinement of adsorbate-slab structures after screening.
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@param inp_vars: Calculation parameters from input file.
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"""
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import os |
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from modules.formats import collect_coords |
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from modules.calculation import run_calc, check_finished_calcs |
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logger.info('Carrying out procedures for the refinement of '
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'adsorbate-surface structures.')
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if not os.path.isdir("screening"): |
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err = "'screening' directory not found. It is needed in order to carry "
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"out the refinement of structures to be adsorbed"
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logger.error(err) |
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raise FileNotFoundError(err)
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finished_calcs, unfinished_calcs = check_finished_calcs('screening',
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inp_vars['code'])
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if not finished_calcs: |
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err_msg = "No calculations on 'screening' finished normally."
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logger.error(err_msg) |
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raise FileNotFoundError(err_msg)
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logger.info(f"Found {len(finished_calcs)} structures of "
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f"adsorbate-surface atomic configurations whose calculation"
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f" finished normally.")
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if len(unfinished_calcs) != 0: |
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logger.warning(f"Found {len(unfinished_calcs)} calculations more that "
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f"did not finish normally: {unfinished_calcs}. \n"
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f"Using only the ones that finished normally: "
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f"{finished_calcs}.")
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conf_list = collect_coords(finished_calcs, inp_vars['code'], 'screening', |
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inp_vars['special_atoms'])
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selected_confs = select_confs(conf_list, finished_calcs, |
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inp_vars['energy_cutoff'], inp_vars['code']) |
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logger.info(f"Selected {len(selected_confs)} structures to carry out the"
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f" refinement")
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run_calc('refinement', inp_vars, selected_confs)
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finished_calcs, unfinished_calcs = check_finished_calcs('refinement',
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inp_vars['code'])
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conf_list = collect_coords(finished_calcs, inp_vars['code'], 'refinement', |
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inp_vars['special_atoms'])
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most_stable_conf = select_confs(conf_list, finished_calcs, 0,
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inp_vars['code'])[0] |
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logger.info('Finished the procedures for the refinement of '
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'adsorbate-surface structures section. Most stable structure '
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f"is {most_stable_conf.info['id']}")
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