layer.add_site(Site(name='hollow1', pos=pos1)) pos2 = np.array([positions[2, 0], positions[2, 1], 0.672]) #slab += ase.atoms.Atoms('H', cell=slab.cell, scaled_positions=[pos1]) #slab += ase.atoms.Atoms('H', cell=slab.cell, scaled_positions=[pos2]) #ase.visualize.view(slab, repeat=(1,1,1)) rpos = np.linalg.solve(slab.cell, np.array(pos2)) layer.add_site(Site(name='hollow2', pos=pos2)) pt.add_layer(layer) pt.lattice.representation = '[%s]' % get_ase_constructor(slab) # Add species pt.add_species(name='empty', color='#ffffff') pt.add_species(name='H', representation="Atoms('H')", color='#ffff00') #Add Processes pt.parse_and_add_process('H_adsorption_hollow1; ->H@hollow1; 100000') pt.parse_and_add_process('H_adsorption_hollow2; ->H@hollow2; 100000') pt.parse_and_add_process('H_desorption_hollow1; H@hollow1->; 100000') pt.parse_and_add_process('H_desorption_hollow2; H@hollow2->; 100000') pt.parse_and_add_process('H_diff_h1h2; H@hollow1 -> H@hollow2; 1000000000') pt.parse_and_add_process('H_diff_h2h1; H@hollow2 -> H@hollow1; 1000000000')