def test_mos2(i):
size = 2
atoms = mx2(formula='MoS2', size=(size, size, 1))
permutation = np.roll(np.arange(3), i)
atoms = permute_axes(atoms, permutation)
result = find_inversion_symmetry(atoms)
check_result(atoms, result)
def test_nanotube(i):
size = 4
atoms = nanotube(3, 3, length=size)
permutation = np.roll(np.arange(3), i)
atoms = permute_axes(atoms, permutation)
result = find_inversion_symmetry(atoms)
assert result.rmsd < TOL
check_result(atoms, result)
atoms.rattle()
result = find_inversion_symmetry(atoms)
check_result(atoms, result)
def test_nanotube(seed, i):
size = 4
atoms = nanotube(3, 3, length=size)
permutation = np.roll(np.arange(3), i)
atoms = permute_axes(atoms, permutation)
rng = np.random.RandomState(seed=seed)
atoms = randomize(rng, atoms)
result = find_crystal_reductions(atoms)[:3]
factors = [reduced.factor for reduced in result]
assert tuple(factors) == (1, 2, 4)
assert all([reduced.rmsd < TOL for reduced in result])
check_components(atoms, result)
def test_permute_axes(seed):
rng = np.random.RandomState(seed)
n = 10
atoms = Atoms(numbers=[1] * n,
scaled_positions=rng.uniform(0, 1, (n, 3)),
pbc=rng.randint(0, 2, 3),
cell=rng.uniform(-1, 1, (3, 3)))
permutation = rng.permutation(3)
permuted = permute_axes(atoms, permutation)
invperm = np.argsort(permutation)
original = permute_axes(permuted, invperm)
assert (original.pbc == atoms.pbc).all()
assert_allclose(original.cell, atoms.cell, atol=TOL)
assert_allclose(original.get_positions(), atoms.get_positions(), atol=TOL)
assert_allclose(atoms.get_positions()[:, permutation],
permuted.get_positions(),
atol=TOL)
assert_allclose(atoms.cell.volume, permuted.cell.volume, atol=TOL)
assert_allclose(atoms.cell.volume, original.cell.volume, atol=TOL)
assert (permuted.pbc == atoms.pbc[permutation]).all()
def test_mos2(seed, i):
size = 4
atoms = mx2(formula='MoS2', size=(size, size, 1))
permutation = np.roll(np.arange(3), i)
atoms = permute_axes(atoms, permutation)
rng = np.random.RandomState(seed=seed)
atoms = randomize(rng, atoms)
result = find_crystal_reductions(atoms)
assert len(result) == size + 1
assert all([reduced.rmsd < TOL for reduced in result])
factors = [reduced.factor for reduced in result]
assert tuple(factors) == (1, 2, 4, 8, 16)
check_components(atoms, result)
def prepare(seed, i, translate, atoms):
rng = np.random.RandomState(seed=seed)
atoms = standardize(atoms).atoms
permutation = np.roll(np.arange(3), i)
atoms = permute_axes(atoms, permutation)
if translate:
atoms.positions += rng.uniform(-1, 1, atoms.positions.shape)
atoms.wrap(eps=0)
positions = atoms.get_positions(wrap=False)
offset = rng.randint(-5, 6, positions.shape)
for i in range(3):
if not atoms.pbc[i]:
offset[:, i] = 0
scattered = positions.copy() + offset @ atoms.cell
wrapped = wrap_positions(scattered, atoms.cell, atoms.pbc)
check_result(atoms, positions, wrapped, translate)