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import logging
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logger = logging.getLogger('DockOnSurf')
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def select_confs(orig_conf_list, 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 at most the value of energy cutoff larger
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than the most stable one.
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@param orig_conf_list: The original list of atomic configurations
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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 read_energies
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conf_list = deepcopy(orig_conf_list)
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selected_ids = []
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conf_enrgs = read_energies(code, 'screening') * 27.2113845 # Ha to eV
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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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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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pass
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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 read_coords
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from modules.calculation import run_calc
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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 ValueError(err)
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conf_list = read_coords(inp_vars['code'], 'screening', 'ase')
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logger.info(f"Found {len(conf_list)} structures on screening directory.")
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selected_confs = select_confs(conf_list, inp_vars['energy_cutoff'],
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inp_vars['code'])
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run_calc('refinement', inp_vars, selected_confs)
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