Python get_ase_constructor Examples

Example #1

File: model_Pt111_surface.py Project: zqhuang2014/kmos

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')