Chimie Théorique » scripts_chimie4psmn » DockOnSurf

    @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.

    @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,

    """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.

    @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,

                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,

    """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.

    @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,

                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']

    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,

                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,

    return surf_ads_list