def test_appropriate_scaling(self, diffraction_calculator: DiffractionGenerator):
"""Tests that doubling the unit cell halves the pattern spacing."""
si = pmg.Element("Si")
lattice = pmg.Lattice.cubic(5.431)
big_lattice = pmg.Lattice.cubic(10.862)
silicon = pmg.Structure.from_spacegroup("Fd-3m", lattice, [si], [[0, 0, 0]])
big_silicon = pmg.Structure.from_spacegroup("Fd-3m", big_lattice, [si], [[0, 0, 0]])
diffraction = diffraction_calculator.calculate_ed_data(structure=silicon, reciprocal_radius=5.)
big_diffraction = diffraction_calculator.calculate_ed_data(structure=big_silicon, reciprocal_radius=5.)
indices = [tuple(i) for i in diffraction.indices]
big_indices = [tuple(i) for i in big_diffraction.indices]
assert (2, 2, 0) in indices
assert (2, 2, 0) in big_indices
coordinates = diffraction.coordinates[indices.index((2, 2, 0))]
big_coordinates = big_diffraction.coordinates[big_indices.index((2, 2, 0))]
assert np.allclose(coordinates, big_coordinates * 2)
def test_appropriate_scaling(self,
diffraction_calculator: DiffractionGenerator):
"""Tests that doubling the unit cell halves the pattern spacing."""
silicon = make_structure(5)
big_silicon = make_structure(10)
diffraction = diffraction_calculator.calculate_ed_data(
structure=silicon, reciprocal_radius=5.)
big_diffraction = diffraction_calculator.calculate_ed_data(
structure=big_silicon, reciprocal_radius=5.)
indices = [tuple(i) for i in diffraction.indices]
big_indices = [tuple(i) for i in big_diffraction.indices]
assert (2, 2, 0) in indices
assert (2, 2, 0) in big_indices
coordinates = diffraction.coordinates[indices.index((2, 2, 0))]
big_coordinates = big_diffraction.coordinates[big_indices.index(
(2, 2, 0))]
assert np.allclose(coordinates, big_coordinates * 2)
def test_strain_mapping_affine_transform():
latt = diffpy.structure.lattice.Lattice(3, 3, 3, 90, 90, 90)
atom = diffpy.structure.atom.Atom(atype='Zn', xyz=[0, 0, 0], lattice=latt)
structure = diffpy.structure.Structure(atoms=[atom], lattice=latt)
ediff = DiffractionGenerator(300., 0.025)
affines = [[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
[[1.04, 0, 0], [0, 1, 0], [0, 0, 1]],
[[1.08, 0, 0], [0, 1, 0], [0, 0, 1]],
[[1.12, 0, 0], [0, 1, 0], [0, 0, 1]]]
data = []
for affine in affines:
# same coords as used for latt above
latt_rot = diffpy.structure.lattice.Lattice(3,
3,
3,
90,
90,
90,
baserot=affine)
structure.placeInLattice(latt_rot)
diff_dat = ediff.calculate_ed_data(structure, 2.5)
dpi = diff_dat.as_signal(64, 0.02, 2.5)
data.append(dpi.data)
data = np.array(data)
dp = ElectronDiffraction(data.reshape((2, 2, 64, 64)))
m = dp.create_model()
ref = ScalableReferencePattern(dp.inav[0, 0])
m.append(ref)
m.multifit()
disp_grad = ref.construct_displacement_gradient()
assert disp_grad.data.shape == np.asarray(affines).reshape(2, 2, 3,
3).shape
def diffraction_calculator():
return DiffractionGenerator(300., 0.02)
def diffraction_calculator(request):
return DiffractionGenerator(*request.param)
def check_pattern_equivilance(p1, p2, coords_only=False):
assert np.allclose(p1.coordinates, p2.coordinates)
if not coords_only:
assert np.allclose(p1.indices, p2.indices)
assert np.allclose(p1.intensities, p2.intensities)
# Becuase of the slight differences between each of the structures, the
# explictily named, ugly pathway has been taken
Cl = pmg.Element("Cl")
Ar = pmg.Element("Ar")
cubic_lattice = pmg.Lattice.cubic(5)
Mscope = DiffractionGenerator(300, 5e-2) #a 300kev EM
formal_cubic_I = pmg.Structure.from_spacegroup("I23", cubic_lattice, [Cl],
[[0, 0, 0]])
casual_cubic_I = pmg.Structure.from_spacegroup(195, cubic_lattice, [Cl, Cl],
[[0, 0, 0], [0.5, 0.5, 0.5]])
fake_cubic_I = pmg.Structure.from_spacegroup(195, cubic_lattice, [Cl, Ar],
[[0, 0, 0], [0.5, 0.5, 0.5]])
larger_cubic_I = pmg.Structure.from_spacegroup("I23", cubic_lattice, [Cl],
[[0, 0, 0]])
larger_cubic_I.make_supercell([2, 4, 2])
formal_pattern = get_pattern(Mscope, formal_cubic_I)
casual_pattern = get_pattern(Mscope, casual_cubic_I)
fake_pattern = get_pattern(Mscope, fake_cubic_I)
larger_pattern = get_pattern(Mscope, larger_cubic_I)
def test_invalid_scattering_params():
scattering_param = '_empty'
generator = DiffractionGenerator(300,
0.2,
None,
scattering_params=scattering_param)
def test_param_check(scattering_param):
generator = DiffractionGenerator(300,
0.2,
None,
scattering_params=scattering_param)