Chimie Théorique » scripts_chimie4psmn » DockOnSurf

    """

    # Checks

                "numbers separated by ',' ';' or ' '." \

                "\nThey can be grouped in parentheses-like enclosers: '()', " \

                "'[]' or {}. Nested groups are not allowed. \n" \

    return max_helic_angle

def get_select_magns():

    select_magns_vals = ['energy', 'moi']

    select_magns_str = dos_inp.get('Screening', 'select_magns',

def get_set_angles():

    set_vals = ['euler', 'chemcat']

    check_expect_val(dos_inp.get('Screening', 'set_angles').lower(), set_vals)

    return set_angles

        inp_vars['min_coll_height'] = get_min_coll_height()

        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]]

            logger.warning("'min_coll_height' option is only implemented for "

                           "'surf_norm_vect' to be one of the x, y or z axes.")

                    if atom.position[i] * coord < min_height:

                        return True

            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 atom.symbol.lower() == el.lower():

                    for neigh_idx in nl.get_neighbors(atom.index)[0]:

                        if molec[neigh_idx].symbol == 'H':

                                                        + num_atoms_slab,

                                                        num_atoms_slab)

                            if disso_struct is not None:

    """

    from copy import deepcopy

    slab_num_atoms = len(slab)

    collision = True

    max_corr = 6  # Should be an even number

    d_angle = 180 / ((max_corr / 2.0) * num_pts)

    This function generates a number of adsorbate-surface structures at

    different orientations of the adsorbate sampled at multiple Euler (zxz)

    angles.

    @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

    @param num_pts: Number on which to sample Euler angles.

    @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 molec_nghbs: Number of neighbors in the molecule.

    @param disso_atoms: List of atom types or atom numbers to try to dissociate.

    @return: list of ase.Atoms object conatining all the orientations of a given

    """

    from copy import deepcopy

    slab_ads_list = []

                                                     norm_vect,

                                                     slab_nghbs, molec_nghbs,

                                                     coll_coeff)

                    slab_ads_list.append(slab_molec)

                    slab_ads_list.extend(dissociation(slab_molec, disso_atoms,

                                                      len(slab)))

        # Check bond rotation is unmodified

        bond_angle = get_vect_angle(-vect_inter, vect_mol)

        if np.isclose((dihedral_angle - dihedral_angle_target + 90) % 180 - 90,

                                                                    ctr1_mol)

                                                    - get_atom_coords(surf,

                                                                      ctr1_surf),

        # vect_mol)

        vect_mol_inner = np.dot(vect_mol, vect_mol)

        bond_inter_reject = -vect_inter - np.dot(-vect_inter, vect_mol) / \

        bond2_mol_reject = vect2_mol - np.dot(vect2_mol, vect_mol) / \

        dihedral_angle_ini = get_vect_angle(bond_inter_reject,

                                            bond2_mol_reject, vect_mol)

        # Update molecular bonds

        vect_mol = get_atom_coords(molecule, ctr2_mol) \

        vect2_mol = get_atom_coords(molecule, ctr3_mol) \

        # Check if rotation was successful

        # Check adsorbate dihedral rotation

        vect_mol_inner = np.dot(vect_mol, vect_mol)

        bond2_mol_reject = vect2_mol - np.dot(vect2_mol, vect_mol) / \

        mol_dihedral_angle = get_vect_angle(bond_inter_reject,

                                            bond2_mol_reject, vect_mol)

        # Check dihedral rotation

        vect_inter_inner = np.dot(vect_inter, vect_inter)

        vect_surf_reject = vect_surf - np.dot(vect_surf, vect_inter) / \

        vect_mol_reject = vect_mol - np.dot(vect_mol, vect_inter) / \

        dihedral_angle = get_vect_angle(vect_surf_reject, vect_mol_reject,

                                        vect_inter)

        # Check bond rotation is unmodified

def ads_chemcat(orig_molec, slab, ctr1_mol, ctr2_mol, ctr3_mol, ctr1_surf,

                ctr2_surf, num_pts, min_coll_height, coll_coeff, norm_vect,

                slab_nghbs, molec_nghbs, disso_atoms, max_h):

    from copy import deepcopy

    slab_ads_list = []

    # Rotation over bond angle

    for alpha in np.arange(90, 180, 90 / min(num_pts, 2)):

        # Rotation over surf-adsorbate dihedral angle

            # Rotation over adsorbate bond dihedral angle

            for gamma in np.arange(0, 360, 360 / num_pts):

                new_molec = deepcopy(orig_molec)

                                                     molec_nghbs, coll_coeff,

                                                     2.5)

                if not collision and \

                                 for conf in slab_ads_list]):

                    slab_ads_list.append(slab_molec)

                    slab_ads_list.extend(dissociation(slab_molec, disso_atoms,