def test_adsorption_examples():
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms, miller_index=(1, 1, 1), layers=3, vacuum=4)
atoms = gen.get_slab(primitive=True)
atoms.set_surface_atoms([8, 9, 10, 11])
sites = AdsorptionSites(atoms)
sites.plot('./Pd3Cu-adsorption-sites.png')
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms, miller_index=(3, 2, 1), layers=13, vacuum=5)
atoms = gen.get_slab(primitive=True)
top, _ = gen.get_voronoi_surface_atoms(atoms)
atoms.set_surface_atoms(top)
sites = AdsorptionSites(atoms)
coordinates = sites.get_coordinates()
assert (len(coordinates) == 56)
connectivity = sites.get_connectivity()
test_connectivity = np.array([
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 4, 4
])
np.testing.assert_allclose(connectivity, test_connectivity)
topology = sites.get_topology()
assert (len(topology) == 56)
periodic = sites.get_periodic_sites()
symmetric = sites.get_symmetric_sites()
print(periodic)
np.testing.assert_allclose(symmetric, periodic)
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms, miller_index=(2, 1, 1), layers=10, vacuum=5)
atoms = gen.get_slab(primitive=True)
top, _ = gen.get_voronoi_surface_atoms(atoms, attach_graph=False)
atoms.set_surface_atoms(top)
sites = AdsorptionSites(atoms)
coordinates = sites.get_coordinates()
vectors = sites.get_adsorption_vectors(unique=False)
assert (len(vectors) == 32)
def test_surface_examples():
atoms = bulk('Pd', 'fcc', a=4, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms,
miller_index=(2, 1, 1),
layers=9,
fixed=5,
vacuum=4)
terminations = gen.get_unique_terminations()
assert (len(terminations) == 2)
for i, t in enumerate(terminations):
slab = gen.get_slab(iterm=i)
assert (len(slab) == 18)
atoms = bulk('Pd', 'hcp', a=3, cubic=True)
gen = SlabGenerator(atoms,
miller_index=(1, 1, 0),
layers=6,
fixed=2,
vacuum=4)
atoms = gen.get_slab()
con_matrix = gen.get_graph_from_bulk(atoms, attach=True)
test_con_matrix = np.array(
[[0.0, 2.0, 2.0, 2.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[2.0, 0.0, 2.0, 2.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[2.0, 2.0, 0.0, 2.0, 2.0, 2.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[2.0, 2.0, 2.0, 0.0, 2.0, 2.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
[1.0, 0.0, 2.0, 2.0, 0.0, 2.0, 2.0, 2.0, 1.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 2.0, 2.0, 2.0, 0.0, 2.0, 2.0, 0.0, 1.0, 0.0, 0.0],
[0.0, 0.0, 1.0, 0.0, 2.0, 2.0, 0.0, 2.0, 2.0, 2.0, 1.0, 0.0],
[0.0, 0.0, 0.0, 1.0, 2.0, 2.0, 2.0, 0.0, 2.0, 2.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 2.0, 2.0, 0.0, 2.0, 2.0, 2.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 2.0, 2.0, 2.0, 0.0, 2.0, 2.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 2.0, 2.0, 0.0, 2.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 2.0, 2.0, 2.0, 0.0]])
np.testing.assert_allclose(con_matrix, test_con_matrix)
# We can identify both top and bottom sites.
top, bottom = gen.get_voronoi_surface_atoms(atoms)
atoms.set_surface_atoms(top)
test_surf_atoms = np.array([8, 9, 10, 11])
np.testing.assert_allclose(top, test_surf_atoms)
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms,
miller_index=(1, 1, 1),
layers=3,
fixed=2,
vacuum=10)
atoms = gen.get_slab(primitive=True)
coordinates, connectivity = gen.adsorption_sites(atoms)
test_connectivity = np.array([1, 1, 2, 2, 2, 3, 3, 3, 3])
np.testing.assert_allclose(connectivity, test_connectivity)
