def test_surface(self):
"""Test the helper surface generator."""
slab = surface('Pd', size=(2, 2, 4), vacuum=10)
# Slab should have 16 Pd atoms
assert (len(slab) == 16)
correct_connectivity = np.array(
[[0, 2, 2, 2, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0],
[2, 0, 2, 2, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0],
[2, 2, 0, 2, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
[2, 2, 2, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 1, 1, 0, 2, 2, 2, 1, 1, 1, 0, 0, 0, 0, 0],
[1, 0, 1, 1, 2, 0, 2, 2, 1, 1, 0, 1, 0, 0, 0, 0],
[1, 1, 0, 1, 2, 2, 0, 2, 1, 0, 1, 1, 0, 0, 0, 0],
[1, 1, 1, 0, 2, 2, 2, 0, 0, 1, 1, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 1, 1, 1, 0, 0, 2, 2, 2, 1, 1, 1, 0],
[0, 0, 0, 0, 1, 1, 0, 1, 2, 0, 2, 2, 1, 1, 0, 1],
[0, 0, 0, 0, 1, 0, 1, 1, 2, 2, 0, 2, 1, 0, 1, 1],
[0, 0, 0, 0, 0, 1, 1, 1, 2, 2, 2, 0, 0, 1, 1, 1],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 2, 2, 2],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 2, 0, 2, 2],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 2, 2, 0, 2],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 2, 2, 2, 0]])
assert_array_equal(slab.connectivity, correct_connectivity)
correct_surf_atoms = np.array([12, 13, 14, 15])
assert_array_equal(slab.get_surface_atoms(), correct_surf_atoms)
# Test the ability to pass an atoms object
atoms = bulk('Pd', cubic=True)
slab = surface(atoms, size=(2, 2, 4), vacuum=10)
def test_nonlocal_fingerprinting(self):
"""Test the non-local fingerprint example"""
atoms = bulk('Pd', cubic=True)
atoms[3].symbol = 'Pt'
slab = surface('Al', size=(2, 2, 3), a=3.8, vacuum=10)
images = [atoms, slab]
parameters = [
'atomic_number',
'atomic_radius',
'atomic_volume',
]
operations = [
'periodic_convolution',
['periodic_convolution', {'d': 1}]
]
fp = Fingerprinter(images)
fingerprints = fp.get_fp(parameters, operations)
truth = np.array([
[12432.0, 7.562800000000001, 320.44, 136896.0, 90.7488, 3844.8],
[2028.0, 24.53879999999999, 1200.0, 20280.0, 245.388, 12000.0]])
np.testing.assert_allclose(fingerprints, truth)
def test_surface(self):
"""Test catkit.build.surface generator."""
slab = surface('Pd', size=(2, 2, 4), vacuum=10)
# Slab should have 16 Pd atoms
assert (len(slab) == 16)
degree = slab.degree
test_degree = np.array(
[9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9, 9])
assert_array_equal(degree, test_degree)
correct_surf_atoms = np.array([12, 13, 14, 15])
assert_array_equal(slab.get_surface_atoms(), correct_surf_atoms)
# Test the ability to pass an atoms object
atoms = bulk('Pd', cubic=True)
slab = surface(atoms, size=(2, 2, 4), vacuum=10)
# Test orthogonalization search
slab = surface(atoms, size=(1, 4), vacuum=10)
def test_surface_examples(self):
"""Test surface construction examples."""
atoms = bulk('Pd', 'fcc', a=4, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(
atoms, miller_index=(2, 1, 1), layers=6, 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) == 16)
atoms = surface('Pd', size=(3, 3), miller=(1, 1, 1), vacuum=4)
con_matrix = atoms.connectivity
test_con_matrix = np.array([
[0, 3, 3, 1, 1, 1, 0, 0, 0],
[3, 0, 3, 1, 1, 1, 0, 0, 0],
[3, 3, 0, 1, 1, 1, 0, 0, 0],
[1, 1, 1, 0, 3, 3, 1, 1, 1],
[1, 1, 1, 3, 0, 3, 1, 1, 1],
[1, 1, 1, 3, 3, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1, 0, 3, 3],
[0, 0, 0, 1, 1, 1, 3, 0, 3],
[0, 0, 0, 1, 1, 1, 3, 3, 0]])
np.testing.assert_allclose(con_matrix, test_con_matrix)
test_surf_atoms = np.array([6, 7, 8])
np.testing.assert_allclose(atoms.get_surface_atoms(), 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, layer_type='trim',
fixed=2, vacuum=10)
atoms = gen.get_slab()
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)