def setUpClass(cls):
cls.bcc = CrystalStructure("Fe",
bravais_basis="bcc",
lattice_constants=[2.7])
cls.fcc = CrystalStructure("Fe",
bravais_basis="fcc",
lattice_constants=[3.6])
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_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_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_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_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_set_empty_states(self):
atoms = CrystalStructure("Pt", BravaisBasis="fcc", a=3.98)
self.job.structure = atoms
self.job.set_empty_states(n_empty_states=10)
self.assertEqual(self.job.input.incar["NBANDS"], 15)
self.job.structure = atoms.repeat([3, 1, 1])
self.job.set_empty_states(n_empty_states=10)
self.assertEqual(self.job.input.incar["NBANDS"], 25)
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_get_layers_across_pbc(self):
structure = CrystalStructure('Fe',
bravais_basis='bcc',
lattice_constants=2.8).repeat(2)
layers = structure.analyse.get_layers()
structure.cell[1, 0] += 0.01
structure.center_coordinates_in_unit_cell()
self.assertEqual(
len(np.unique(layers[structure.analyse.get_layers()[:, 0] == 0,
0])), 1)
def test_get_layers_with_strain(self):
structure = CrystalStructure('Fe',
bravais_basis='bcc',
lattice_constants=2.8).repeat(2)
layers = structure.analyse.get_layers().tolist()
structure.apply_strain(0.1 * (np.random.random((3, 3)) - 0.5))
self.assertEqual(
layers,
structure.analyse.get_layers(
planes=np.linalg.inv(structure.cell).T).tolist())
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_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_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_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_neighborhood_single(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc')
neigh = struct.get_neighborhood(np.random.random(3), cutoff_radius=3)
distances = neigh.distances.copy()
neigh.allow_ragged = False
self.assertTrue(np.array_equal(neigh.distances, distances))
neigh.allow_ragged = True
self.assertTrue(np.array_equal(neigh.distances, distances))
neigh.allow_ragged = False
self.assertTrue(np.array_equal(neigh.distances, distances))
def test_getter_and_ragged(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc').repeat(2)
del struct[0]
neigh = struct.get_neighbors_by_distance(cutoff_radius=3,
mode='filled')
vecs = neigh.filled.vecs
distances = neigh.filled.distances
indices = neigh.filled.indices
self.assertTrue(np.array_equal(neigh.distances, distances))
self.assertTrue(np.array_equal(neigh.indices, indices))
self.assertTrue(np.array_equal(neigh.vecs, vecs))
def test_getter_and_ragged(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc').repeat(2)
del struct[0]
neigh = struct.get_neighbors_by_distance(cutoff_radius=3)
vecs = neigh.get_vectors(allow_ragged=False)
distances = neigh.get_distances(allow_ragged=False)
indices = neigh.get_indices(allow_ragged=False)
neigh.allow_ragged = False
self.assertTrue(np.array_equal(neigh.distances, distances))
self.assertTrue(np.array_equal(neigh.indices, indices))
self.assertTrue(np.array_equal(neigh.vecs, vecs))
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_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_run(self):
job = self.project.create_job('HessianJob', "job_test")
basis = CrystalStructure(element="Fe",
bravais_basis="bcc",
lattice_constant=2.85)
basis.set_initial_magnetic_moments([2] * len(basis))
job.set_reference_structure(basis)
phono = job.create_job("PhonopyJob", "phono")
structure = phono.list_structures()[0]
magmoms = structure.get_initial_magnetic_moments()
self.assertAlmostEqual(sum(magmoms - 2), 0)
rep = phono._phonopy_supercell_matrix().diagonal().astype(int)
job._reference_structure.set_repeat(rep)
job.structure.set_repeat(rep)
job.set_force_constants(1)
def setUpClass(cls):
state.update({
'resource_paths':
os.path.join(os.path.dirname(os.path.abspath(__file__)),
"../static")
})
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, "test_vasp"))
cls.job = cls.project.create_job("Vasp", "trial")
cls.job_spin = cls.project.create_job("Vasp", "spin")
cls.job_spin.structure = CrystalStructure("Fe",
BravaisBasis="bcc",
a=2.83)
cls.job_spin.structure = cls.job_spin.structure.repeat(2)
cls.job_spin.structure[2] = "Se"
cls.job_spin.structure[3] = "O"
cls.job_metadyn = cls.project.create_job("VaspMetadyn",
"trial_metadyn")
cls.job_complete = Vasp(
project=ProjectHDFio(project=cls.project,
file_name="vasp_complete"),
job_name="vasp_complete",
)
poscar_file = posixpath.join(
cls.execution_path,
"../static/vasp_test_files/full_job_sample/POSCAR")
cls.job_complete.structure = read_atoms(poscar_file,
species_from_potcar=True)
poscar_file = posixpath.join(
cls.execution_path,
"../static/vasp_test_files/poscar_samples/POSCAR_metadyn")
cls.job_metadyn.structure = read_atoms(poscar_file)
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.file_location, "test_elast"))
cls.basis = CrystalStructure(element="Fe",
bravais_basis="bcc",
lattice_constant=2.83)
cls.project.remove_jobs_silently(recursive=True)
def test_get_voronoi_vertices(self):
basis = CrystalStructure('Al',
bravais_basis='fcc',
lattice_constants=4)
self.assertEqual(len(basis.analyse.get_voronoi_vertices()), 12)
self.assertEqual(
len(basis.analyse.get_voronoi_vertices(distance_threshold=2)), 1)
def setUp(self) -> None:
self.job = ToyAtomisticJob(
project=ProjectHDFio(project=self.project, file_name="test_job"),
job_name="test_job",
)
self.job.structure = CrystalStructure(element="Al",
bravais_basis="fcc",
lattice_constants=4).repeat(4)
self.job.run()
def setUpClass(cls):
cls.al_fcc = ase_to_pyiron(bulk("Al", cubic=True))
cls.fe_bcc = ase_to_pyiron(bulk("Fe", cubic=True))
cls.ti_hcp = ase_to_pyiron(bulk("Ti", orthorhombic=True))
cls.si_dia = ase_to_pyiron(bulk("Si", cubic=True))
cls.al_fcc_4 = CrystalStructure(element="Al",
bravais_basis="fcc",
lattice_constants=4
).repeat(4)
def test_pyscal_centro_symmetry(self):
basis = CrystalStructure('Fe',
bravais_basis='bcc',
lattice_constants=2.8)
self.assertTrue(
all([
np.isclose(v, 0.0)
for v in basis.analyse.pyscal_centro_symmetry(num_neighbors=8)
]))
def test_get_neighborhood(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc')
struct.positions += 0.01 * (
2 * np.random.random(struct.positions.shape) - 1)
struct = struct.center_coordinates_in_unit_cell()
positions = np.random.random((2, 3)).dot(struct.cell)
neigh = struct.get_neighborhood(positions)
positions = np.random.random((2, 3)).dot(struct.cell)
new_neigh = neigh.get_neighborhood(positions)
self.assertTrue(
np.array_equal(new_neigh.distances,
neigh.get_distances(positions)))
self.assertTrue(
np.array_equal(new_neigh.vecs, neigh.get_vectors(positions)))
self.assertTrue(
np.array_equal(new_neigh.indices, neigh.get_indices(positions)))
def test_set_structure(self):
self.assertEqual(self.job.structure, None)
atoms = CrystalStructure("Pt", BravaisBasis="fcc", a=3.98)
self.job.structure = atoms
self.assertEqual(self.job.structure, atoms)
self.job.structure = None
self.assertEqual(self.job.structure, None)
self.job.structure = atoms
self.assertEqual(self.job.structure, atoms)
def setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, "test_job"))
cls.job = AtomisticGenericJob(
project=ProjectHDFio(project=cls.project, file_name="test_job"),
job_name="test_job",
)
cls.job.structure = CrystalStructure(element="Al",
bravais_basis="fcc",
lattice_constants=4).repeat(4)
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()))