Chimie Théorique » scripts_chimie4psmn » DockOnSurf

def check_collision(slab_molec, slab_num_atoms, min_height, vect, nn_slab,

                    nn_molec, coll_coeff):

    """Checks whether a slab and a molecule collide or not.

    @param slab_molec: The system of adsorbate-slab for which to detect if there

        are collisions.

    @param nn_slab: Number of neigbors in the surface.

    @param nn_molec: 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 slab_num_atoms: Number of atoms of the bare slab.

    @param min_height: The minimum height atoms can have to not be considered as

        colliding.

    @param vect: The vector perpendicular to the slab.

    @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

    else:

        return False