def test_positive_intensity(self):
""" Test that potential_synthesis raises an error if diffraction intensity is not positive """
aR1, aR2, aR3 = self.crystal.lattice_vectors
extent = np.arange(0, 5, 0.1)
with suppress_warnings():
plane = plane_mesh(aR3, aR1 + aR2, x1=extent)
self.intensities[0] = self.intensities[0] * -1
with self.assertRaises(ValueError):
potmap = potential_synthesis(self.reflections, self.intensities,
self.crystal, plane)
def test_trivial(self):
""" Test that potential_synthesis calculated from zero intensity is zero everywhere """
aR1, aR2, aR3 = self.crystal.lattice_vectors
extent = np.arange(0, 10, 0.1)
with suppress_warnings():
plane = plane_mesh(aR3, aR1 + aR2, x1=extent)
potmap = potential_synthesis(self.reflections,
np.zeros_like(self.intensities),
self.crystal, plane)
self.assertTrue(np.allclose(potmap, 0))
def test_shape(self):
""" Test that potential_synthesis returns a map with the same shape as the mesh """
aR1, aR2, aR3 = self.crystal.lattice_vectors
extent = np.arange(0, 5, 0.1)
with suppress_warnings():
plane = plane_mesh(aR3, aR1 + aR2, x1=extent)
potmap = potential_synthesis(self.reflections, self.intensities,
self.crystal, plane)
xx, yy, zz = plane
for arr in plane:
self.assertTupleEqual(potmap.shape, arr.shape)
def test_potential_synthesis_positive_intensity():
""" Test that potential_synthesis raises an error if diffraction intensity is not positive """
crystal = Crystal.from_database("C")
reflections = list(combinations_with_replacement(range(-3, 4), 3))
intensities = [
np.abs(structure_factor(crystal, *reflection))**2
for reflection in reflections
]
aR1, aR2, aR3 = crystal.lattice_vectors
extent = np.arange(0, 5, 0.1)
with suppress_warnings():
plane = plane_mesh(aR3, aR1 + aR2, x1=extent)
intensities[0] = intensities[0] * -1
with pytest.raises(ValueError):
potmap = potential_synthesis(reflections, intensities, crystal, plane)
def test_potential_synthesis_trivial():
""" Test that potential_synthesis calculated from zero intensity is zero everywhere """
crystal = Crystal.from_database("C")
reflections = list(combinations_with_replacement(range(-3, 4), 3))
intensities = [
np.abs(structure_factor(crystal, *reflection))**2
for reflection in reflections
]
aR1, aR2, aR3 = crystal.lattice_vectors
extent = np.arange(0, 10, 0.1)
with suppress_warnings():
plane = plane_mesh(aR3, aR1 + aR2, x1=extent)
potmap = potential_synthesis(reflections, np.zeros_like(intensities),
crystal, plane)
assert np.allclose(potmap, 0)
def test_potential_synthesis_shape():
""" Test that potential_synthesis returns a map with the same shape as the mesh """
crystal = Crystal.from_database("C")
reflections = list(combinations_with_replacement(range(-3, 4), 3))
intensities = [
np.abs(structure_factor(crystal, *reflection))**2
for reflection in reflections
]
aR1, aR2, aR3 = crystal.lattice_vectors
extent = np.arange(0, 5, 0.1)
with suppress_warnings():
plane = plane_mesh(aR3, aR1 + aR2, x1=extent)
potmap = potential_synthesis(reflections, intensities, crystal, plane)
xx, yy, zz = plane
for arr in plane:
assert potmap.shape == arr.shape