Révision cf8fe0e3 modules/screening.py
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import os |
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import random |
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from modules.formats import read_coords, adapt_format |
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from modules.calculation import run_calc |
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from modules.calculation import run_calc, check_finished_calcs
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if not os.path.isdir("isolated"):
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err = "'isolated' directory not found. It is needed in order to carry " |
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"out the screening of structures to be adsorbed" |
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logger.error(err) |
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raise ValueError(err)
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raise FileNotFoundError(err)
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logger.info('Carrying out procedures for the screening of adsorbate-surface'
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' structures.') |
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conf_list = read_coords(inp_vars['code'], 'isolated', 'ase', |
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finished_calcs, unfinished_calcs = check_finished_calcs('isolated',
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inp_vars['code']) |
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if len(unfinished_calcs) == 0: |
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logger.info(f"Found {len(finished_calcs)} structures of isolated "
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f"conformers.") |
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else: |
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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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logger.warning(f"Found {len(unfinished_calcs)} calculations more that "
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f"did not finish normally: {unfinished_calcs}. Using "
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f"only the {len(finished_calcs)} ones who finished "
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f"normally") |
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conf_list = read_coords(finished_calcs, inp_vars['code'], 'isolated', |
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inp_vars['special_atoms']) |
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logger.info(f"Found {len(conf_list)} structures of isolated conformers.")
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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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inp_vars['code']) |
| ... | ... | |
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surf_ads_list = random.sample(surf_ads_list, inp_vars['max_structures']) |
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logger.info(f'Generated {len(surf_ads_list)} adsorbate-surface atomic '
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f'configurations to carry out a calculation of.') |
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for i in range(len(surf_ads_list)): |
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for j in range(i): |
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if (surf_ads_list[i].positions == surf_ads_list[j].positions).all(): |
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logger.warning(i, j, 'Same') |
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run_calc('screening', inp_vars, surf_ads_list)
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logger.info('Finished the procedures for the screening of adsorbate-surface'
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