Révision 1d8c374e modules/screening.py
| b/modules/screening.py | ||
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logger = logging.getLogger('DockOnSurf')
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def assign_prop(atoms: ase.Atoms, prop_name: str, prop_val): # TODO Needed? |
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atoms.info[prop_name] = prop_val |
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def select_confs(orig_conf_list: list, calc_dirs: list, magns: list, |
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num_sel: int, code: str): |
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def select_confs(conf_list: list, magns: list, num_sel: int): |
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"""Takes a list ase.Atoms and selects the most different magnitude-wise. |
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Given a list of ase.Atoms objects and a list of magnitudes, it selects a |
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number of the most different conformers according to every magnitude |
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specified. |
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@param orig_conf_list: list of ase.Atoms objects to select among. |
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@param calc_dirs: List of directories where to read the energies from. |
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@param conf_list: list of ase.Atoms objects to select among. |
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@param magns: list of str with the names of the magnitudes to use for the |
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conformer selection. Supported magnitudes: 'energy', 'moi'. |
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@param num_sel: number of conformers to select for every of the magnitudes. |
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@param code: The code that generated the magnitude information. |
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Supported codes: See formats.py |
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@return: list of the selected ase.Atoms objects. |
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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_list = deepcopy(orig_conf_list) |
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conf_enrgs, mois, selected_ids = [], [], [] |
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selected_ids = [] |
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if num_sel >= len(conf_list): |
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logger.warning('Number of conformers per magnitude is equal or larger '
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'than the total number of conformers. Using all ' |
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f'available conformers: {len(conf_list)}.')
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return conf_list |
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# Read properties |
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if 'energy' in magns: |
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if code == 'cp2k': |
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conf_enrgs = collect_energies(calc_dirs, code, 'isolated') |
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elif code == 'vasp': |
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conf_enrgs = np.array([conf.get_total_energy() |
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for conf in orig_conf_list]) |
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# Assign mois |
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if 'moi' in magns: |
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mois = np.array([conf.get_moments_of_inertia() for conf in conf_list]) |
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# Assign values |
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for i, conf in enumerate(conf_list): |
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assign_prop(conf, 'idx', i) |
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assign_prop(conf, 'iso', calc_dirs[i]) |
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if 'energy' in magns: |
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assign_prop(conf, 'energy', conf_enrgs[i]) |
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if 'moi' in magns: |
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assign_prop(conf, 'moi', mois[i, 2]) |
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for conf in conf_list: |
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conf.info["moi"] = conf.get_moments_of_inertia()[2] |
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# pick ids |
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for magn in magns: |
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sorted_list = sorted(conf_list, key=lambda conf: abs(conf.info[magn])) |
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if sorted_list[-1].info['idx'] not in selected_ids:
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selected_ids.append(sorted_list[-1].info['idx'])
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if sorted_list[-1].info['iso'] not in selected_ids:
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selected_ids.append(sorted_list[-1].info['iso'])
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if num_sel > 1: |
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for i in range(0, len(sorted_list) - 1, |
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len(conf_list) // (num_sel - 1)): |
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if sorted_list[i].info['idx'] not in selected_ids:
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selected_ids.append(sorted_list[i].info['idx'])
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if sorted_list[i].info['iso'] not in selected_ids:
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selected_ids.append(sorted_list[i].info['iso'])
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logger.info(f'Selected {len(selected_ids)} conformers for adsorption.')
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return [conf_list[idx] for idx in selected_ids]
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return [conf for conf in conf_list if conf.info["iso"] in selected_ids]
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def get_vect_angle(v1: list, v2: list, ref=None, degrees=True): |
| ... | ... | |
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""" |
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import os |
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import random |
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from modules.formats import collect_coords, adapt_format
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from modules.formats import collect_confs, adapt_format
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from modules.calculation import run_calc, check_finished_calcs |
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logger.info('Carrying out procedures for the screening of adsorbate-surface'
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| ... | ... | |
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logger.error(err) |
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raise FileNotFoundError(err) |
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correct_calcs, failed_calcs = check_finished_calcs('isolated',
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inp_vars['code']) |
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if not correct_calcs:
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finished_calcs, failed_calcs = check_finished_calcs('isolated',
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inp_vars['code'])
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if not finished_calcs:
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err_msg = "No calculations on 'isolated' 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(correct_calcs)} structures of isolated "
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logger.info(f"Found {len(finished_calcs)} structures of isolated "
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f"conformers whose calculation finished normally.") |
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if len(failed_calcs) != 0: |
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logger.warning( |
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f"Found {len(failed_calcs)} calculations more that "
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f"did not finish normally: {failed_calcs}. \n"
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f"Using only the ones that finished normally: " |
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f"{correct_calcs}.")
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conformer_atoms_list = collect_coords(correct_calcs, inp_vars['code'], |
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'isolated', |
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inp_vars['special_atoms']) |
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selected_confs = select_confs(conformer_atoms_list, correct_calcs, |
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inp_vars['select_magns'], |
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inp_vars['confs_per_magn'], |
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inp_vars['code']) |
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f"{finished_calcs}.")
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conf_list = collect_confs(finished_calcs, inp_vars['code'], 'isolated', |
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inp_vars['special_atoms']) |
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selected_confs = select_confs(conf_list, inp_vars['select_magns'], |
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inp_vars['confs_per_magn']) |
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surf = adapt_format('ase', inp_vars['surf_file'], inp_vars['special_atoms'])
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surf.info = {}
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surf_ads_list = adsorb_confs(selected_confs, surf, inp_vars) |
Formats disponibles : Unified diff