Chimie Théorique » scripts_chimie4psmn » DockOnSurf

def add_adsorbate(slab, adsorbate, surf_pos, mol_pos, height, offset=None,

                  norm_vect=(0, 0, 1)):

    """Add an adsorbate to a surface.

    This function extends the functionality of ase.build.add_adsorbate

    (https://wiki.fysik.dtu.dk/ase/ase/build/surface.html#ase.build.add_adsorbate)

    by enabling to change the z coordinate and the axis perpendicular to the

    surface.

    @param slab: ase.Atoms object containing the coordinates of the surface

    @param adsorbate: ase.Atoms object containing the coordinates of the

        adsorbate.

    @param surf_pos: The coordinates of the adsorption site on the surface.

    @param mol_pos: The coordinates of the adsorption center in the molecule.

    @param height: The height above the surface

    @param offset: Offsets the adsorbate by a number of unit cells. Mostly

        useful when adding more than one adsorbate.

    @param norm_vect: The vector perpendicular to the surface.

    """

    info = slab.info.get('adsorbate_info', {})

    pos = np.array([0.0, 0.0, 0.0])  # (x, y, z) part

    spos = np.array([0.0, 0.0, 0.0])  # part relative to unit cell

    norm_vect = np.array(norm_vect) / np.linalg.norm(norm_vect)

    if offset is not None:

        spos += np.asarray(offset, float)

    if isinstance(surf_pos, str):

        # A site-name:

        if 'sites' not in info:

            raise TypeError('If the atoms are not made by an ase.build '

                            'function, position cannot be a name.')

        if surf_pos not in info['sites']:

            raise TypeError('Adsorption site %s not supported.' % surf_pos)

        spos += info['sites'][surf_pos]

    else:

        pos += surf_pos

    if 'cell' in info:

        cell = info['cell']

    else:

        cell = slab.get_cell()

    pos += np.dot(spos, cell)

    # Convert the adsorbate to an Atoms object

    if isinstance(adsorbate, ase.Atoms):

        ads = adsorbate

    elif isinstance(adsorbate, ase.Atom):

        ads = ase.Atoms([adsorbate])

    else:

        # Assume it is a string representing a single Atom

        ads = ase.Atoms([ase.Atom(adsorbate)])

    pos += height * norm_vect

    # Move adsorbate into position

    ads.translate(pos - mol_pos)

    # Attach the adsorbate

    slab.extend(ads)

def ads_euler(molec, surf, site, ctr, pts_angle, neigh_ctr, norm_vect):

    from random import random

    plane_vect = np.cross(norm_vect, [random() for i in range(3)])

    add_adsorbate()

    return

def adsorb_confs(conf_list, surf, ads_ctrs, sites, algo, num_pts, neigh_ctrs,

                 norm_vect):

    @param norm_vect: The vector perpendicular to the surface.

                    surf_ads_list.append(ads_euler(conf, surf, site, molec_ctr,

                                                   num_pts, norm_vect,

                                 inp_vars['molec_neigh_ctrs'],

                                 inp_vars['surf_norm_vect'])