def test_get_global_shells(self):
structure = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc').repeat(2)
neigh = structure.get_neighbors()
self.assertTrue(np.array_equal(neigh.shells,
neigh.get_global_shells()))
structure += Atoms(elements='C', positions=[[0, 0, 0.5 * 4]])
neigh = structure.get_neighbors()
self.assertFalse(
np.array_equal(neigh.shells, neigh.get_global_shells()))
structure = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc').repeat(2)
neigh = structure.get_neighbors()
shells = neigh.get_global_shells()
structure.positions += 0.01 * (np.random.random(
(len(structure), 3)) - 0.5)
structure.center_coordinates_in_unit_cell()
neigh = structure.get_neighbors()
self.assertTrue(
np.array_equal(
shells,
neigh.get_global_shells(cluster_by_vecs=True,
cluster_by_distances=True)))
neigh.reset_clusters()
self.assertTrue(
np.array_equal(shells,
neigh.get_global_shells(cluster_by_vecs=True)))
self.assertFalse(np.array_equal(shells, neigh.get_global_shells()))
def test_get_distances_arbitrary_array(self):
basis = CrystalStructure("Al",
bravais_basis="fcc",
lattice_constants=4.2).repeat(3)
neigh = basis.get_neighbors(cutoff_radius=3.5, num_neighbors=None)
self.assertEqual(
len(neigh.get_indices(np.random.random(3), num_neighbors=12)), 12)
self.assertEqual(
len(
neigh.get_distances(np.random.random(3),
num_neighbors=12,
allow_ragged=True)), 12)
self.assertLessEqual(
len(
neigh.get_vectors(np.random.random(3),
num_neighbors=12,
allow_ragged=True,
cutoff_radius=3.5)), 12)
self.assertTrue(
neigh.get_vectors(np.random.random((
2, 3)), num_neighbors=12).shape == (2, 12, 3))
neigh = basis.get_neighbors(num_neighbors=50)
self.assertTrue(
neigh.get_distances(np.random.random(3)).shape == (50, ))
self.assertTrue(
neigh.get_indices(np.random.random((2, 3))).shape == (2, 50))
self.assertTrue(
neigh.get_vectors(np.random.random((2, 2, 3))).shape == (2, 2, 50,
3))
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
_ = neigh.get_neighborhood(np.random.random(3), num_neighbors=51)
self.assertEqual(len(w), 1)
_ = neigh.get_distances(np.random.random(3), num_neighbors=51)
self.assertEqual(len(w), 2)
def test_fe_small(self):
struct = CrystalStructure(elements='Fe',
lattice_constants=2.85,
bravais_basis='bcc')
neigh = struct.get_neighbors()
self.assertAlmostEqual(neigh.vecs[neigh.shells == 1].sum(), 0)
with self.assertRaises(ValueError):
_ = struct.get_neighbors(num_neighbors=None)
def test_al_small(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4.04,
bravais_basis='fcc')
neigh = struct.get_neighbors()
self.assertAlmostEqual(
np.absolute(neigh.distances -
np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
self.assertAlmostEqual(neigh.vecs[neigh.shells == 1].sum(), 0)
with self.assertRaises(ValueError):
struct.get_neighbors(num_neighbors=0)
def test_get_local_shells_ragged(self):
structure = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc').repeat(2)
del structure[0]
neigh = structure.get_neighbors(cutoff_radius=3.5, num_neighbors=None)
self.assertEqual(np.sum(neigh.shells == -1), 12)
self.assertEqual(
np.sum(neigh.get_local_shells(cluster_by_distances=True) == -1),
12)
self.assertEqual(
np.sum(neigh.get_local_shells(cluster_by_vecs=True) == -1), 12)
self.assertEqual(
np.sum(
neigh.get_local_shells(cluster_by_distances=True,
cluster_by_vecs=True) == -1), 12)
neigh.allow_ragged = True
self.assertEqual(np.sum([len(s) == 11 for s in neigh.shells]), 12)
self.assertEqual(
np.sum([
len(s) == 11
for s in neigh.get_local_shells(cluster_by_distances=True)
]), 12)
self.assertEqual(
np.sum([
len(s) == 11
for s in neigh.get_local_shells(cluster_by_vecs=True)
]), 12)
self.assertEqual(
np.sum([
len(s) == 11
for s in neigh.get_local_shells(cluster_by_distances=True,
cluster_by_vecs=True)
]), 12)
def test_get_neighbors(self):
struct = CrystalStructure(elements='Fe',
lattice_constants=2.85,
bravais_basis='bcc').repeat(10)
cell = struct.cell.copy()
cell += np.random.random((3, 3)) - 0.5
struct.positions += np.random.random((len(struct), 3)) - 0.5
struct.set_cell(cell, scale_atoms=True)
neigh = struct.get_neighbors()
self.assertAlmostEqual(
np.absolute(neigh.distances -
np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
myself = np.ones_like(neigh.indices)
myself = myself * np.arange(len(myself))[:, np.newaxis]
dist = struct.get_distances(myself.flatten(),
neigh.indices.flatten(),
mic=True)
self.assertAlmostEqual(
np.absolute(dist - neigh.distances.flatten()).max(), 0)
vecs = struct.get_distances(myself.flatten(),
neigh.indices.flatten(),
mic=True,
vector=True)
self.assertAlmostEqual(
np.absolute(vecs - neigh.vecs.reshape(-1, 3)).max(), 0)
dist = struct.get_scaled_positions()
dist = dist[:, np.newaxis, :] - dist[np.newaxis, :, :]
dist -= np.rint(dist)
dist = np.einsum('nmi,ij->nmj', dist, struct.cell)
dist = np.linalg.norm(dist, axis=-1).flatten()
dist = dist[dist > 0]
self.assertAlmostEqual(neigh.distances.min(), dist.min())
def test_getters(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc')
neigh = struct.get_neighbors()
self.assertTrue(np.array_equal(neigh.distances, neigh.get_distances()))
self.assertTrue(np.array_equal(neigh.vecs, neigh.get_vectors()))
self.assertTrue(np.array_equal(neigh.indices, neigh.get_indices()))
def test_get_bonds(self):
basis = CrystalStructure("Al",
bravais_basis="fcc",
lattice_constants=4.2).repeat(5)
neigh = basis.get_neighbors(num_neighbors=20)
bonds = neigh.get_bonds()
self.assertTrue(
np.array_equal(np.sort(bonds[0]['Al'][0]),
np.sort(neigh.indices[0, neigh.shells[0] == 1])))
def test_al_large(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4.04,
bravais_basis='fcc').repeat(10)
neigh = struct.get_neighbors()
self.assertAlmostEqual(
np.absolute(neigh.distances -
np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
self.assertAlmostEqual(neigh.vecs[neigh.shells == 1].sum(), 0)
self.assertAlmostEqual(neigh.vecs[0, neigh.shells[0] == 1].sum(), 0)
def test_get_local_shells(self):
structure = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc').repeat(2)
neigh = structure.get_neighbors()
shells = neigh.get_local_shells()
structure.positions += 0.01 * (np.random.random(
(len(structure), 3)) - 0.5)
neigh = structure.get_neighbors()
self.assertTrue(
np.array_equal(
shells,
neigh.get_local_shells(cluster_by_vecs=True,
cluster_by_distances=True)))
neigh.reset_clusters()
self.assertTrue(
np.array_equal(shells,
neigh.get_local_shells(cluster_by_vecs=True)))
self.assertFalse(np.array_equal(shells, neigh.get_local_shells()))
def test_norm_order(self):
a_0 = 2.8
basis = CrystalStructure("Fe",
bravais_basis="bcc",
lattice_constants=a_0).repeat(10)
neigh = basis.get_neighbors(num_neighbors=None,
norm_order=np.inf,
cutoff_radius=a_0 + 0.01)
self.assertEqual(len(neigh.indices[0]), 34)
with self.assertRaises(ValueError):
neigh.norm_order = 3
def test_get_shell_matrix(self):
structure = CrystalStructure(elements='Fe',
lattice_constants=2.83,
bravais_basis='bcc').repeat(2)
structure[0] = 'Ni'
neigh = structure.get_neighbors(num_neighbors=8)
mat = neigh.get_shell_matrix()
self.assertEqual(mat[0].sum(), 8 * len(structure))
mat = neigh.get_shell_matrix(chemical_pair=['Fe', 'Ni'])
self.assertEqual(mat[0].sum(), 16)
mat = neigh.get_shell_matrix(chemical_pair=['Ni', 'Ni'])
self.assertEqual(mat[0].sum(), 0)
def test_cluster_analysis(self):
basis = CrystalStructure("Al",
bravais_basis="fcc",
lattice_constants=4.2).repeat(10)
neigh = basis.get_neighbors(num_neighbors=100)
key, counts = neigh.cluster_analysis(id_list=[0, 1],
return_cluster_sizes=True)
self.assertTrue(np.array_equal(key[1], [0, 1]))
self.assertEqual(counts[0], 2)
key, counts = neigh.cluster_analysis(id_list=[0,
int(len(basis) / 2)],
return_cluster_sizes=True)
self.assertTrue(np.array_equal(key[1], [0]))
self.assertEqual(counts[0], 1)
def test_pbc_false(self):
struct = CrystalStructure(elements='Fe',
lattice_constants=2.85,
bravais_basis='bcc').repeat(10)
struct.pbc = False
cell = struct.cell.copy()
cell += np.random.random((3, 3)) - 0.5
struct.set_cell(cell, scale_atoms=True)
neigh = struct.get_neighbors()
self.assertAlmostEqual(
np.absolute(neigh.distances -
np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
myself = np.ones_like(neigh.indices)
myself = myself * np.arange(len(myself))[:, np.newaxis]
dist = np.linalg.norm(struct.positions[myself] -
struct.positions[neigh.indices],
axis=-1)
self.assertAlmostEqual(np.absolute(dist - neigh.distances).max(), 0)
def test_wrapped_positions(self):
structure = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc').repeat(2)
neigh = structure.get_neighbors()
distances = neigh.distances
new_positions = structure.positions + structure.cell.diagonal() * 2
self.assertFalse(
np.all(
np.isclose(
distances,
neigh.get_distances(new_positions, num_neighbors=13)[:,
1:])))
neigh.wrap_positions = True
self.assertTrue(
np.all(
np.isclose(
distances,
neigh.get_distances(new_positions, num_neighbors=13)[:,
1:])))
def test_allow_ragged(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc').repeat(10)
del struct[0]
neigh = struct.get_neighbors_by_distance(cutoff_radius=3)
self.assertTrue(neigh.allow_ragged)
self.assertTrue(isinstance(neigh.indices, list))
indices = neigh.indices.copy()
with self.assertRaises(ValueError):
neigh.allow_ragged = 'yes'
neigh.allow_ragged = False
self.assertTrue(isinstance(neigh.indices, np.ndarray))
self.assertGreater(len(neigh.indices[0]), len(indices[0]))
with self.assertRaises(IndexError):
struct.positions[neigh.indices] = struct.positions[neigh.indices]
neigh.allow_ragged = True
self.assertTrue(np.array_equal(neigh.indices[0], indices[0]))
neigh = struct.get_neighbors(cutoff_radius=3, num_neighbors=None)
self.assertFalse(neigh.allow_ragged)
self.assertTrue(isinstance(neigh.indices, np.ndarray))
def test_repr(self):
basis = CrystalStructure("Al",
bravais_basis="fcc",
lattice_constants=4.2).repeat(3)
neigh = basis.get_neighbors(cutoff_radius=3.5, num_neighbors=None)
self.assertTrue('each atom' in neigh.__repr__())