/ - Diff - DockOnSurf - Forge du Centre Blaise Pascal

Révision fe91ddb2

         return np.array(surf_norm_vect) / np.linalg.norm(surf_norm_vect)
     def get_adsorption_height():
         err_msg = num_error % ('adsorption_height', 'positive number')
         ads_height = try_command(dos_inp.getfloat, [(ValueError, err_msg)],
                                  'Screening', 'adsorption_height', fallback=2.5)
         if ads_height <= 0:
             logger.error(err_msg)
             raise ValueError(err_msg)
         return ads_height
     def get_set_angles():
         set_vals = ['euler', 'internal']
         check_expect_val(dos_inp.get('Screening', 'set_angles').lower(), set_vals)
-...
     def get_coll_thrsld():
         err_msg = num_error % ('collision_threshold',
                                'positive number')
         err_msg = num_error % ('collision_threshold', 'positive number')
         coll_thrsld_str = dos_inp.get('Screening', 'collision_threshold',
                                       fallback="1.3")
         if coll_thrsld_str.lower() in turn_false_answers:
-...
     # Refinement
     def get_refine_inp_file():  # TODO if not specified try isol_inp_file.
     def get_refine_inp_file():
         refine_inp_file = dos_inp.get('Refinement', 'refine_inp_file')
         if not os.path.isfile(refine_inp_file):
             logger.error(f'File {refine_inp_file} not found.')
-...
             inp_vars['select_magns'] = get_select_magns()
             inp_vars['confs_per_magn'] = get_confs_per_magn()
             inp_vars['surf_norm_vect'] = get_surf_norm_vect()
             inp_vars['adsorption_height'] = get_adsorption_height()
             inp_vars['set_angles'] = get_set_angles()
             inp_vars['sample_points_per_angle'] = get_pts_per_angle()
             inp_vars['pbc_cell'] = get_pbc_cell()

         @param coll_coeff: The coefficient that multiplies the covalent radius of
             atoms resulting in a distance that two atoms being closer to that is
             considered as atomic collision.
         @param height: Height on which to try adsorption
         @param height: Height on which to try adsorption.
         @return collision: bool, whether the structure generated has collisions
             between slab and adsorbate.
         """
-...
     def ads_euler(orig_molec, slab, ctr_coord, site_coord, num_pts,
                   min_coll_height, coll_coeff, norm_vect, slab_nghbs, molec_nghbs,
                   h_donor, h_acceptor):
                   h_donor, h_acceptor, height):
         """Generates adsorbate-surface structures by sampling over Euler angles.
         This function generates a number of adsorbate-surface structures at
-...
         @param molec_nghbs: Number of neighbors in the molecule.
         @param h_donor: List of atom types or atom numbers that are H-donors.
         @param h_acceptor: List of atom types or atom numbers that are H-acceptors.
         @param height: Height on which to try adsorption.
         @return: list of ase.Atoms object conatining all the orientations of a given
             conformer.
         """
-...
                                                          num_pts, min_coll_height,
                                                          norm_vect,
                                                          slab_nghbs, molec_nghbs,
                                                          coll_coeff)
                                                          coll_coeff, height)
                     if not collision and not any([np.allclose(slab_molec.positions,
                                                               conf.positions)
                                                   for conf in slab_ads_list]):
-...
     def ads_internal(orig_molec, slab, ctr1_mol, ctr2_mol, ctr3_mol, ctr1_surf,
                      ctr2_surf, num_pts, min_coll_height, coll_coeff, norm_vect,
                      slab_nghbs, molec_nghbs, h_donor, h_acceptor, max_hel):
                      slab_nghbs, molec_nghbs, h_donor, h_acceptor, max_hel, height):
         """Generates adsorbate-surface structures by sampling over internal angles.
         @param orig_molec: ase.Atoms object of the molecule to adsorb (adsorbate).
-...
         @param h_acceptor: List of atom types or atom numbers that are H-acceptors.
         @param max_hel: Maximum value for sampling the helicopter
             (surf-adsorbate dihedral) angle.
         @param height: Height on which to try adsorption.
         @return: list of ase.Atoms object conatining all the orientations of a given
             conformer.
         """
-...
                                                          ctr_coords, site_coords,
                                                          num_pts, min_coll_height,
                                                          norm_vect, slab_nghbs,
                                                          molec_nghbs, coll_coeff)
                                                          molec_nghbs, coll_coeff,
                                                          height)
                     if not collision and \
                             not any([np.allclose(slab_molec.positions,
                                                  conf.positions)
-...
         coll_coeff = inp_vars['collision_threshold']
         h_donor = inp_vars['h_donor']
         h_acceptor = inp_vars['h_acceptor']
         height = inp_vars['adsorption_height']
         if inp_vars['pbc_cell'] is not False:
             surf.set_pbc(True)
-...
                                                        num_pts, min_coll_height,
                                                        coll_coeff, norm_vect,
                                                        surf_nghbs, molec_nghbs,
                                                        h_donor, h_acceptor))
                                                        h_donor, h_acceptor, height))
                     elif angles == 'internal':
                         mol_ctr1 = molec_ctrs[c]
                         mol_ctr2 = inp_vars["molec_ctrs2"][c]
-...
                                                           coll_coeff, norm_vect,
                                                           surf_nghbs, molec_nghbs,
                                                           h_donor, h_acceptor,
                                                           max_h))
                                                           max_h, height))
         return surf_ads_list

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Chimie Théorique » scripts_chimie4psmn » DockOnSurf

Révision fe91ddb2