/modules/screening.py - Diff - DockOnSurf - Forge du Centre Blaise Pascal

Révision 5fb01677 modules/screening.py

         @return: bool, whether the surface and the molecule collide.
         """
         from ase.neighborlist import natural_cutoffs, neighbor_list
         if (vect == np.array([1.0, 0.0, 0.0])).all \
                 or (vect == np.array([0.0, 1.0, 0.0])).all \
                 or (vect == np.array([0.0, 0.0, 1.0])).all:
             for atom in slab_molec[slab_num_atoms:]:
                 if np.linalg.norm(atom.position * vect) < min_height:
                     return True
         slab_molec_cutoffs = natural_cutoffs(slab_molec, mult=coll_coeff)
         slab_molec_nghbs = len(neighbor_list("i", slab_molec, slab_molec_cutoffs))
         if slab_molec_nghbs > nn_slab + nn_molec:
             return True
         if min_height is not False:
             cart_coords = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]
             if list(map(abs, vect.tolist())) in cart_coords:
                 for atom in slab_molec[slab_num_atoms:]:
                     if np.linalg.norm(atom.position * vect) < min_height:
                         #  TODO Check norm when there are negative values
                         return True
         else:
             return False
             slab_molec_cutoffs = natural_cutoffs(slab_molec, mult=coll_coeff)
             slab_molec_nghbs = len(neighbor_list("i", slab_molec, slab_molec_cutoffs))
             if slab_molec_nghbs > nn_slab + nn_molec:
                 return True
             else:
                 return False
     def correct_coll(molec, slab, ctr_coord, site_coord, num_pts,
                      coll_bttm, norm_vect, slab_nghbs, molec_nghbs, coll_coeff):
                      min_coll_height, norm_vect, slab_nghbs, molec_nghbs,
                      coll_coeff):
         # TODO Rethink this function
         """Tries to adsorb a molecule on a slab trying to avoid collisions by doing
         small rotations.
-...
         @param site_coord: The coordinates of the surface on which to adsorb the
             molecule
         @param num_pts: Number on which to sample Euler angles.
         @param coll_bttm: The lowermost height for which to detect a collision
         @param min_coll_height: The lowermost height for which to detect a collision
         @param norm_vect: The vector perpendicular to the surface.
         @param slab_nghbs: Number of neigbors in the surface.
         @param molec_nghbs: Number of neighbors in the molecule.
-...
                                center=ctr_coord)
             add_adsorbate(slab_molec, molec, site_coord, ctr_coord, 2.5,
                           norm_vect=norm_vect)
             collision = check_collision(slab_molec, slab_num_atoms, coll_bttm,
             collision = check_collision(slab_molec, slab_num_atoms, min_coll_height,
                                         norm_vect, slab_nghbs, molec_nghbs,
                                         coll_coeff)
             num_corr += 1
-...
     def ads_euler(orig_molec, slab, ctr_coord, site_coord, num_pts,
                   coll_bttm, coll_coeff, norm_vect, slab_nghbs, molec_nghbs):
                   min_coll_height, coll_coeff, norm_vect, slab_nghbs, molec_nghbs):
         """Generates adsorbate-surface structures by sampling over Euler angles.
         This function generates a number of adsorbate-surface structures at
-...
         @param site_coord: The coordinates of the surface on which to adsorb the
             molecule
         @param num_pts: Number on which to sample Euler angles.
         @param coll_bttm: The lowermost height for which to detect a collision
         @param min_coll_height: The lowermost height for which to detect a collision
         @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.
-...
                     molec = deepcopy(orig_molec)
                     molec.euler_rotate(alpha, beta, gamma, center=ctr_coord)
                     slab_molec, collision = correct_coll(molec, slab,
                         ctr_coord, site_coord, num_pts, coll_bttm, norm_vect,
                         slab_nghbs, molec_nghbs, coll_coeff)
                                                          ctr_coord, site_coord,
                                                          num_pts, min_coll_height,
                                                          norm_vect,
                                                          slab_nghbs, molec_nghbs,
                                                          coll_coeff)
                     if not collision:
                         slab_ads_list.append(slab_molec)
-...
     def adsorb_confs(conf_list, surf, molec_ctrs, sites, algo, num_pts, neigh_ctrs,
                      norm_vect, coll_bttm, coll_coeff):
                      norm_vect, min_coll_height, coll_coeff):
         """Generates a number of adsorbate-surface structure coordinates.
         Given a list of conformers, a surface, a list of atom indices (or list of
-...
         @param neigh_ctrs: the indices of the neighboring atoms to the adsorption
             atoms.
         @param norm_vect: The vector perpendicular to the surface.
         @param coll_bttm: The lowermost height for which to detect a collision
         @param min_coll_height: The lowermost height for which to detect a collision
         @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.
-...
         from ase.neighborlist import natural_cutoffs, neighbor_list
         surf_ads_list = []
         sites_coords = get_atom_coords(surf, sites)
         surf_cutoffs = natural_cutoffs(surf, mult=coll_coeff)
         surf_nghbs = len(neighbor_list("i", surf, surf_cutoffs))
         if min_coll_height is not False:
             surf_cutoffs = natural_cutoffs(surf, mult=coll_coeff)
             surf_nghbs = len(neighbor_list("i", surf, surf_cutoffs))
         else:
             surf_nghbs = 0
         for conf in conf_list:
             molec_ctr_coords = get_atom_coords(conf, molec_ctrs)
             molec_neigh_coords = get_atom_coords(conf, neigh_ctrs)
             conf_cutoffs = natural_cutoffs(conf, mult=coll_coeff)
             molec_nghbs = len(neighbor_list("i", conf, conf_cutoffs))
             if min_coll_height is not False:
                 conf_cutoffs = natural_cutoffs(conf, mult=coll_coeff)
                 molec_nghbs = len(neighbor_list("i", conf, conf_cutoffs))
             else:
                 molec_nghbs = 0
             for site in sites_coords:
                 for ctr in molec_ctr_coords:
                     if algo == 'euler':
                         surf_ads_list.extend(ads_euler(conf, surf, ctr, site,
                                                        num_pts, coll_bttm,
                                                        num_pts, min_coll_height,
                                                        coll_coeff, norm_vect,
                                                        surf_nghbs, molec_nghbs))
                     elif algo == 'chemcat':
-...
                                      inp_vars['sample_points_per_angle'],
                                      inp_vars['molec_neigh_ctrs'],
                                      inp_vars['surf_norm_vect'],
                                      inp_vars['collision_bottom'],
                                      inp_vars['min_coll_height'],
                                      inp_vars['collision_threshold'])
         run_calc('screening', inp_vars, surf_ads_list)

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Chimie Théorique » scripts_chimie4psmn » DockOnSurf

Révision 5fb01677 modules/screening.py