def test_euclidian_lattice_equality():
""" Test equality between identical Lattice instances and copies """
lattice = Lattice(np.eye(3))
assert lattice == lattice
assert lattice == deepcopy(lattice)
assert lattice != Lattice(2 * np.eye(3))
def test_lattice_frac_mesh_two_arr():
""" Test that Lattice.frac_mesh is raising an exception for two input vectors """
lattice = Lattice(np.eye(3))
x = np.linspace(0, 1, num=2)
with pytest.raises(ValueError):
lattice.frac_mesh(x, x)
def test_lattice_frac_mesh():
""" Test that Lattice.frac_mesh is working as expected compared to numpy.meshgrid """
lattice = Lattice(np.eye(3))
x = np.linspace(0, 1, num=8)
for out, n in zip(lattice.frac_mesh(x), np.meshgrid(x, x, x)):
assert np.allclose(out, n)
def test_lattice_real_mesh_trivial():
""" Test that Lattice.mesh works identically to Lattice.frac_mesh for trivial lattice """
lattice = Lattice(np.eye(3))
x = np.linspace(0, 1, num=8)
for frac, real in zip(lattice.frac_mesh(x), lattice.mesh(x)):
assert np.allclose(frac, real)
def test_lattice_real_mesh():
""" Test that Lattice.mesh works as expected """
lattice = Lattice(2 * np.eye(3))
x = np.linspace(0, 1, num=8)
# since lattice is a stretched euclidian lattice, we expect
# a maximum length of 2
assert np.max(lattice.mesh(x)[0]) == 2
def test_back_and_forth():
"""Test that Lattice.miller_indices and Lattice.scattering_vector are
reciprocal to each other"""
lattice = Lattice(np.random.random((3, 3)))
h, k, l = np.random.randint(-10, 10, size=(3, ))
vector = lattice.scattering_vector((h, k, l))
hp, kp, lp = lattice.miller_indices(vector)
assert round(abs(h - float(hp)), 7) == 0
assert round(abs(k - float(kp)), 7) == 0
assert round(abs(l - float(lp)), 7) == 0
def test_atomic_distance_different_lattice():
"""Test that fractional and cartesian distances
between atoms in different lattices raises an error."""
lattice1 = Lattice(np.eye(3))
lattice2 = Lattice(2 * np.eye(3))
atm1 = Atom("He", [0, 0, 0], lattice=lattice1)
atm2 = Atom("He", [1, 0, 0], lattice=lattice2)
with pytest.raises(RuntimeError):
distance_fractional(atm1, atm2)
with pytest.raises(RuntimeError):
distance_cartesian(atm1, atm2)
def test_monoclinic_lattice_system():
"""Test that the Lattice.lattice_system attribute is working properly for monoclinic lattice
including all possible permutations."""
parameters = (1, 2, 3, 90, 115, 90)
l = Lattice.from_parameters(*parameters)
assert l.lattice_system == LatticeSystem.monoclinic
parameters = (2, 3, 1, 115, 90, 90)
l = Lattice.from_parameters(*parameters)
assert l.lattice_system == LatticeSystem.monoclinic
parameters = (3, 1, 2, 90, 90, 115)
l = Lattice.from_parameters(*parameters)
assert l.lattice_system == LatticeSystem.monoclinic
def test_euclidian_lattice():
lattice = Lattice(np.eye(3))
assert np.array_equal(lattice.a1, [1, 0, 0])
assert np.array_equal(lattice.a2, [0, 1, 0])
assert np.array_equal(lattice.a3, [0, 0, 1])
assert lattice.volume == 1
def test_distance_different_lattice(self):
""" Test that fractional and cartesian distances
between atoms in different lattices raises an error. """
lattice1 = Lattice(np.eye(3))
lattice2 = Lattice(2 * np.eye(3))
atm1 = Atom("He", [0, 0, 0], lattice=lattice1)
atm2 = Atom("He", [1, 0, 0], lattice=lattice2)
with self.subTest("Fractional distance"):
with self.assertRaises(RuntimeError):
distance_fractional(atm1, atm2)
with self.subTest("Cartesian distance"):
with self.assertRaises(RuntimeError):
distance_cartesian(atm1, atm2)
def test_lattice_parameters_reciprocal_and_back():
"""Create lattice from parameters, take reciprocal twice,
and see if the parameters have changed."""
triclinic = (3, 4, 20, 45, 90, 126)
triclinic2 = Lattice.from_parameters(
*triclinic).reciprocal.reciprocal.lattice_parameters
assert np.allclose(triclinic, triclinic2)
def test_distance_cartesian(self):
""" Test the cartesian distance between atom """
lattice = Lattice(4 * np.eye(3)) # Cubic lattice side length 4 angs
atm1 = Atom("He", [0, 0, 0], lattice=lattice)
atm2 = Atom("He", [1, 0, 0], lattice=lattice)
self.assertEqual(distance_cartesian(atm1, atm2), 4.0)
def test_atomic_distance_cartesian():
"""Test the cartesian distance between atom"""
lattice = Lattice(4 * np.eye(3)) # Cubic lattice side length 4 angs
atm1 = Atom("He", [0, 0, 0], lattice=lattice)
atm2 = Atom("He", [1, 0, 0], lattice=lattice)
assert distance_cartesian(atm1, atm2) == 4.0
def test_hexagonal_lattice_system():
"""Test that the Lattice.lattice_system attribute is working properly for hexagonal lattice,
including all possible permutations of lattice parameters."""
parameters = (2, 2, 3, 90, 90, 120)
l = Lattice.from_parameters(*parameters)
assert l.lattice_system == LatticeSystem.hexagonal
parameters = (3, 2, 2, 120, 90, 90)
l = Lattice.from_parameters(*parameters)
assert l.lattice_system == LatticeSystem.hexagonal
parameters = (2, 3, 2, 90, 120, 90)
l = Lattice.from_parameters(*parameters)
assert l.lattice_system == LatticeSystem.hexagonal
parameters = (2, 2, 2, 90, 120, 90)
l = Lattice.from_parameters(*parameters)
assert l.lattice_system == LatticeSystem.hexagonal
def test_lattice_parameters_triclinic():
""" alpha, beta, gama =/= 90 """
a1, a2, a3 = Lattice.from_parameters(1, 2, 3, 75, 40, 81).lattice_vectors
assert round(abs(norm(a1) - 1), 7) == 0
assert round(abs(norm(a2) - 2), 7) == 0
assert round(abs(norm(a3) - 3), 7) == 0
assert round(abs(angle_between(a2, a3) - 75), 7) == 0
assert round(abs(angle_between(a3, a1) - 40), 7) == 0
assert round(abs(angle_between(a1, a2) - 81), 7) == 0
def test_lattice_parameters_monoclinic():
""" beta =/= 90 """
a1, a2, a3 = Lattice.from_parameters(1, 2, 3, 90, 120, 90).lattice_vectors
assert round(abs(norm(a1) - 1), 7) == 0
assert round(abs(norm(a2) - 2), 7) == 0
assert round(abs(norm(a3) - 3), 7) == 0
assert round(abs(angle_between(a2, a3) - 90), 7) == 0
assert round(abs(angle_between(a3, a1) - 120), 7) == 0
assert round(abs(angle_between(a1, a2) - 90), 7) == 0
def _generate_unitcell_atoms(crystal: Crystal):
for atm in crystal:
for factors in product(range(-2, 2), range(-2, 2), range(-2, 2)):
coords = atm.coords_fractional + np.asarray(factors)
if np.all(coords <= 1.1) and np.all(coords >= -0.1):
yield Atom(
element=atm.element,
coords=coords,
lattice=Lattice(crystal.lattice_vectors),
displacement=atm.displacement,
magmom=atm.magmom,
occupancy=atm.occupancy,
)
def test_cubic_lattice_system():
""" Test that the Lattice.lattice_system attribute is working properly for cubic lattice """
assert Lattice(2 * np.eye(3)).lattice_system == LatticeSystem.cubic
def test_miller_indices_trivial():
""" Test that Lattice.miller_indices is working """
lattice = Lattice(np.random.random((3, 3)))
assert np.allclose(lattice.miller_indices((0, 0, 0)), ((0, 0, 0)))
def test_lattice_parameters_orthorombic():
""" alpha = beta = gamma = 90"""
a1, a2, a3 = Lattice.from_parameters(2, 1, 5, 90, 90, 90).lattice_vectors
assert np.allclose(a1, [2, 0, 0])
assert np.allclose(a2, [0, 1, 0])
assert np.allclose(a3, [0, 0, 5])
def test_tetragonal_lattice_system():
""" Test that the Lattice.lattice_system attribute is working properly for tetragonal lattice """
parameters = (2, 2, 3, 90, 90, 90)
l = Lattice.from_parameters(*parameters)
assert l.lattice_system == LatticeSystem.tetragonal
def test_triclinic_lattice_system():
""" Test that the Lattice.lattice_system attribute is working properly for triclinic lattice """
l = Lattice.from_parameters(1, 2, 3, 75, 40, 81)
assert l.lattice_system == LatticeSystem.triclinic
def test_rhombohedral_lattice_system():
""" Test that the Lattice.lattice_system attribute is working properly for rhombohedral lattice """
parameters = (1, 1, 1, 87, 87, 87)
l = Lattice.from_parameters(*parameters)
assert l.lattice_system == LatticeSystem.rhombohedral
def test_scattering_vector_trivial():
""" Test that Lattice.scattering_vectors is working """
lattice = Lattice(np.random.random((3, 3)))
assert np.allclose(lattice.scattering_vector((0, 0, 0)), ((0, 0, 0)))
def test_scattering_vector_table():
""" Test that Lattice.scattering_vector is working on tables of reflections """
lattice = Lattice(2 * np.pi * np.eye(3))
vectors = np.random.random(size=(10, 3))
assert np.allclose(lattice.scattering_vector(vectors), vectors)
def test_lattice_array_dtype():
""" Test that the data-type of array(Lattice(...)) is respected """
arr = np.random.random(size=(3, 3))
lattice = Lattice(arr)
assert np.array(lattice, dtype=np.int32).dtype, np.int32
def test_lattice_array_shape():
""" Test that array(Lattice(...)) is always 3x3 """
arr = np.random.random(size=(3, 3))
lattice = Lattice(arr)
assert np.allclose(arr, np.array(lattice))
def test_miller_indices_table():
""" Test that Lattice.miller_indices is working on tables of vectors """
lattice = Lattice(2 * np.pi * np.eye(3))
vectors = np.random.random(size=(10, 3))
assert np.allclose(lattice.miller_indices(vectors), vectors)
