Révision 1e9e784d modules/refinement.py

b/modules/refinement.py
3 3 
logger = logging.getLogger('DockOnSurf')
4 4 

  		





  5
  5
  
    

  		





  6
  
  
    
def select_confs(orig_conf_list, energy_cutoff, code):


  		





  
  6
  
    
def select_confs(orig_conf_list, calc_dirs, energy_cutoff, code):


  		





  7
  7
  
    
    """From a list of atomic configurations selects the most stable ones.


  		





  8
  8
  
    

  		





  9
  9
  
    
    Given a list of ase.Atoms configurations and an energy cutoff, selects all


  		





  10
  
  
    
    the structures that have an energy at most the value of energy cutoff larger


  		





  11
  
  
    
    than the most stable one.


  		





  12
  
  
    
    @param orig_conf_list: The original list of atomic configurations


  		





  
  10
  
    
    the structures that have an energy lower than, the energy of the most stable


  		





  
  11
  
    
    conformer plus the cutoff.


  		





  
  12
  
    

  		





  
  13
  
    
    @param orig_conf_list: List of ase.Atoms objects of the conformers


  		





  
  14
  
    
    @param calc_dirs: List of the directories of the finished calculations


  		





  13
  15
  
    
    @param energy_cutoff: The maximum energy above the most stable configuration


  		





  14
  16
  
    
    @param code: the code used to carry out the screening of structures.


  		





  15
  17
  
    
    @return: list of the the most stable configurations within the energy cutoff


  		





  ......




  19
  21
  
    

  		





  20
  22
  
    
    conf_list = deepcopy(orig_conf_list)


  		





  21
  23
  
    
    selected_ids = []


  		





  22
  
  
    
    conf_enrgs = collect_energies(code, 'screening') * 27.2113845  # Ha to eV


  		





  
  24
  
    
    conf_enrgs = collect_energies(calc_dirs, code, 'screening')


  		





  23
  25
  
    

  		





  24
  26
  
    
    for i, conf in enumerate(conf_list):


  		





  25
  27
  
    
        conf.info['energy'] = conf_enrgs[i]


  		





  ......




  64
  66
  
    
    conf_list = collect_coords(inp_vars['code'], 'screening', 'ase',


  		





  65
  67
  
    
                               inp_vars['special_atoms'])


  		





  66
  68
  
    
    logger.info(f"Found {len(conf_list)} structures on screening directory.")


  		





  67
  
  
    
    selected_confs = select_confs(conf_list, inp_vars['energy_cutoff'],


  		





  68
  
  
    
                                  inp_vars['code'])


  		





  
  69
  
    
    selected_confs = select_confs(conf_list, finished_calcs,


  		





  
  70
  
    
                                  inp_vars['energy_cutoff'], inp_vars['code'])


  		





  69
  71
  
    
    run_calc('refinement', inp_vars, selected_confs)


  		





  70
  72
  
    
    logger.info('Finished the procedures for the refinement of '


  		





  71
  73
  
    
                'adsorbate-surface structures section.')


  		












Formats disponibles :
  Unified diff