Révision 61f71e3c
| b/modules/refinement.py | ||
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logger = logging.getLogger('DockOnSurf')
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def select_confs(orig_conf_list, calc_dirs, energy_cutoff, code):
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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 |
| 11 | 11 |
conformer plus the cutoff. |
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@param orig_conf_list: List of ase.Atoms objects of the conformers
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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. |
| ... | ... | |
| 19 | 19 |
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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selected_ids = [] |
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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']) |
| 30 | 29 |
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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if conf.info['energy'] <= lowest_e + energy_cutoff]
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def run_refinement(inp_vars): |
| ... | ... | |
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inp_vars['energy_cutoff'], inp_vars['code']) |
| 72 | 71 |
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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# 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, |
| 76 | 79 |
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}')
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f"is {most_stable_conf.info['id']}")
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