Révision 1e9e784d

b/modules/refinement.py
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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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def select_confs(orig_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 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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    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 orig_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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    conf_list = deepcopy(orig_conf_list)


  		





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    selected_ids = []


  		





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    conf_enrgs = collect_energies(code, 'screening') * 27.2113845  # Ha to eV


  		





  
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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_list = collect_coords(inp_vars['code'], 'screening', 'ase',


  		





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                               inp_vars['special_atoms'])


  		





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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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    selected_confs = select_confs(conf_list, finished_calcs,


  		





  
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                                  inp_vars['energy_cutoff'], inp_vars['code'])


  		





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    run_calc('refinement', inp_vars, selected_confs)


  		





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    logger.info('Finished the procedures for the refinement of '


  		





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                'adsorbate-surface structures section.')


  		












  

    
      b/modules/screening.py
    
  






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    atoms.info[prop_name] = prop_val


  		





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def select_confs(orig_conf_list: list, magns: list, num_sel: int, code: str):


  		





  
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def select_confs(orig_conf_list: list, calc_dirs: list, magns: list, num_sel: int, code: str):


  		





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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 magns: list of str with the names of the magnitudes to use for the


  		





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        conformer selection.


  		





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        Supported magnitudes: 'energy', 'moi'.


  		





  
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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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    # Read properties


  		





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    if 'energy' in magns:


  		





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        conf_enrgs = collect_energies(code, 'isolated')


  		





  
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        conf_enrgs = collect_energies(calc_dirs, code, 'isolated')


  		





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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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    conformer_atoms_list = collect_coords(finished_calcs, inp_vars['code'],


  		





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                                          'isolated', inp_vars['special_atoms'])


  		





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    selected_confs = select_confs(conformer_atoms_list,


  		





  
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    selected_confs = select_confs(conformer_atoms_list, finished_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'])


  		












Formats disponibles :
  Unified diff