/ - Diff - DockOnSurf - Forge du Centre Blaise Pascal

Révision e8bebcca

     def check_collision(slab_molec, slab_num_atoms, min_height, vect, nn_slab=0,
                         nn_molec=0, coll_coeff=0.9):
                         nn_molec=0, coll_coeff=1.2):
         """Checks whether a slab and a molecule collide or not.
         @param slab_molec: The system of adsorbate-slab for which to detect if there
-...
             colliding.
         @param vect: The vector perpendicular to the slab.
         @return: bool, whether the surface and the molecule collide.
         """  # TODO Enable both checks: 1st height, 2nd sphere collision
         """
         from ase.neighborlist import natural_cutoffs, neighbor_list
         # Check structure overlap by height
         if min_height is not False:
             cart_axes = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0],
                          [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, -1.0]]
             if vect.tolist() in cart_axes:
                 for atom in slab_molec[slab_num_atoms:]:
                     for i, coord in enumerate(vect):
                         if coord == 0:
                             continue
                         if atom.position[i] * coord < min_height:
                             return True
                 return False
         else:
             if vect.tolist() not in cart_axes:
                 err_msg = "'min_coll_height' option is only implemented for " \
                           "'surf_norm_vect' to be one of the x, y or z axes. "
                 logger.error(err_msg)
                 raise ValueError(err_msg)
             for atom in slab_molec[slab_num_atoms:]:
                 for i, coord in enumerate(vect):
                     if coord == 0:
                         continue
                     if atom.position[i] * coord < min_height * coord:
                         return True
         # Check structure overlap by sphere collision
         if coll_coeff is not 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
         return False
     def correct_coll(molec, slab, ctr_coord, site_coord, num_pts,
                      min_coll_height, norm_vect, slab_nghbs, molec_nghbs,
                      coll_coeff, height=2.5):
         # TODO Rethink this function
         """Tries to adsorb a molecule on a slab trying to avoid collisions by doing
         small rotations.
         @param molec: ase.Atoms object of the molecule to adsorb
         @param slab: ase.Atoms object of the surface on which to adsorb the
             molecule
         @param ctr_coord: The coordinates of the molecule to use as adsorption
             center.
         @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 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.
         @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
         @return collision: bool, whether the structure generated has collisions
             between slab and adsorbate.
         """
         from copy import deepcopy
         slab_num_atoms = len(slab)
         slab_molec = []
         collision = True
         max_corr = 6  # Should be an even number
         d_angle = 180 / ((max_corr / 2.0) * num_pts)
         num_corr = 0
         while collision and num_corr <= max_corr:
             k = num_corr * (-1) ** num_corr
             slab_molec = deepcopy(slab)
             molec.euler_rotate(k * d_angle, k * d_angle / 2, k * d_angle,
                                center=ctr_coord)
             add_adsorbate(slab_molec, molec, site_coord, ctr_coord, height,
                           norm_vect=norm_vect)
             collision = check_collision(slab_molec, slab_num_atoms, min_coll_height,
                                         norm_vect, slab_nghbs, molec_nghbs,
                                         coll_coeff)
             num_corr += 1
         return slab_molec, collision
     def dissociate_h(slab_molec_orig, h_idx, num_atoms_slab, h_acceptor,
-...
         return disso_structs
     def correct_coll(molec, slab, ctr_coord, site_coord, num_pts,
                      min_coll_height, norm_vect, slab_nghbs, molec_nghbs,
                      coll_coeff, height=2.5):
         # TODO Rethink this function
         """Tries to adsorb a molecule on a slab trying to avoid collisions by doing
         small rotations.
         @param molec: ase.Atoms object of the molecule to adsorb
         @param slab: ase.Atoms object of the surface on which to adsorb the
             molecule
         @param ctr_coord: The coordinates of the molecule to use as adsorption
             center.
         @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 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.
         @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
         @return collision: bool, whether the structure generated has collisions
             between slab and adsorbate.
         """
         from copy import deepcopy
         slab_num_atoms = len(slab)
         slab_molec = []
         collision = True
         max_corr = 6  # Should be an even number
         d_angle = 180 / ((max_corr / 2.0) * num_pts)
         num_corr = 0
         while collision and num_corr <= max_corr:
             k = num_corr * (-1) ** num_corr
             slab_molec = deepcopy(slab)
             molec.euler_rotate(k * d_angle, k * d_angle / 2, k * d_angle,
                                center=ctr_coord)
             add_adsorbate(slab_molec, molec, site_coord, ctr_coord, height,
                           norm_vect=norm_vect)
             collision = check_collision(slab_molec, slab_num_atoms, min_coll_height,
                                         norm_vect, slab_nghbs, molec_nghbs,
                                         coll_coeff)
             num_corr += 1
         return slab_molec, collision
     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):
-...
                                                          ctr_coords, site_coords,
                                                          num_pts, min_coll_height,
                                                          norm_vect, slab_nghbs,
                                                          molec_nghbs, coll_coeff,
 .5)
                                                          molec_nghbs, coll_coeff)
                     if not collision and \
                             not any([np.allclose(slab_molec.positions,
                                                  conf.positions)
-...
         surf_ads_list = []
         sites_coords = get_atom_coords(surf, sites)
         if min_coll_height is False:
         if coll_coeff is not False:
             surf_cutoffs = natural_cutoffs(surf, mult=coll_coeff)
             surf_nghbs = len(neighbor_list("i", surf, surf_cutoffs))
         else:
-...
             if inp_vars['pbc_cell'] is not False:
                 conf.set_pbc(True)
                 conf.set_cell(inp_vars['pbc_cell'])
             if min_coll_height is False:
             if coll_coeff is not False:
                 conf_cutoffs = natural_cutoffs(conf, mult=coll_coeff)
                 molec_nghbs = len(neighbor_list("i", conf, conf_cutoffs))
             else:

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Chimie Théorique » scripts_chimie4psmn » DockOnSurf

Révision e8bebcca