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_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_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_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())
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)
struct = CrystalStructure(elements='Fe', lattice_constants=2.85, bravais_basis='bcc').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)
struct = CrystalStructure(elements='Fe', lattice_constants=2.85, bravais_basis='bcc')
neigh = struct.get_neighbors()
self.assertAlmostEqual(neigh.vecs[neigh.shells==1].sum(), 0)
struct = CrystalStructure(elements='Al', lattice_constants=4.04, bravais_basis='bcc').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)
struct = CrystalStructure(elements='Al', lattice_constants=4.04, bravais_basis='bcc')
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_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])))