def test_kinematic_intensities_error_raise(structure, rotation):
"""Test that kinematically forbidden diffraction spots gets zero intensity also after rotation."""
rotated_lattice = diffpy.structure.lattice.Lattice(structure.lattice)
rotated_lattice.setLatPar(baserot=rotation)
structure.placeInLattice(rotated_lattice)
reciprocal_lattice = structure.lattice.reciprocal()
g_indices = [(0, 0, 1)]
g_hkls = reciprocal_lattice.dist(g_indices, [0, 0, 0])
intensities = get_kinematical_intensities(structure,
g_indices,
g_hkls,
excitation_error=0,
maximum_excitation_error=1,
debye_waller_factors={},
scattering_params='_empty')
def test_kinematic_intensities_rotation(structure, rotation):
"""Test that kinematically forbidden diffraction spots gets zero intensity also after rotation."""
rotated_lattice = diffpy.structure.lattice.Lattice(structure.lattice)
rotated_lattice.setLatPar(baserot=rotation)
structure.placeInLattice(rotated_lattice)
reciprocal_lattice = structure.lattice.reciprocal()
g_indices = [(0, 0, 1)]
g_hkls = reciprocal_lattice.dist(g_indices, [0, 0, 0])
scattering_params_list = ['lobato', 'xtables']
for scattering_params in scattering_params_list:
intensities = get_kinematical_intensities(
structure,
g_indices,
g_hkls,
excitation_error=0,
maximum_excitation_error=1,
debye_waller_factors={},
scattering_params=scattering_params)
np.testing.assert_almost_equal(intensities, [0])
def calculate_ed_data(self,
structure,
reciprocal_radius,
with_direct_beam=True):
"""Calculates the Electron Diffraction data for a structure.
Parameters
----------
structure : Structure
The structure for which to derive the diffraction pattern. Note that
the structure must be rotated to the appropriate orientation and
that testing is conducted on unit cells (rather than supercells).
reciprocal_radius : float
The maximum radius of the sphere of reciprocal space to sample, in
reciprocal angstroms.
Returns
-------
pyxem.DiffractionSimulation
The data associated with this structure and diffraction setup.
"""
# Specify variables used in calculation
wavelength = self.wavelength
max_excitation_error = self.max_excitation_error
debye_waller_factors = self.debye_waller_factors
latt = structure.lattice
scattering_params = self.scattering_params
# Obtain crystallographic reciprocal lattice points within `max_r` and
# g-vector magnitudes for intensity calculations.
recip_latt = latt.reciprocal()
spot_indicies, cartesian_coordinates, spot_distances = get_points_in_sphere(
recip_latt, reciprocal_radius)
# Identify points intersecting the Ewald sphere within maximum
# excitation error and store the magnitude of their excitation error.
r_sphere = 1 / wavelength
r_spot = np.sqrt(np.sum(np.square(cartesian_coordinates[:, :2]), axis=1))
z_sphere = -np.sqrt(r_sphere**2 - r_spot**2) + r_sphere
proximity = np.absolute(z_sphere - cartesian_coordinates[:, 2])
intersection = proximity < max_excitation_error
# Mask parameters corresponding to excited reflections.
intersection_coordinates = cartesian_coordinates[intersection]
intersection_indices = spot_indicies[intersection]
proximity = proximity[intersection]
g_hkls = spot_distances[intersection]
# Calculate diffracted intensities based on a kinematical model.
intensities = get_kinematical_intensities(structure,
intersection_indices,
g_hkls,
proximity,
max_excitation_error,
debye_waller_factors,
scattering_params)
# Threshold peaks included in simulation based on minimum intensity.
peak_mask = intensities > 1e-20
intensities = intensities[peak_mask]
intersection_coordinates = intersection_coordinates[peak_mask]
intersection_indices = intersection_indices[peak_mask]
return DiffractionSimulation(coordinates=intersection_coordinates,
indices=intersection_indices,
intensities=intensities,
with_direct_beam=with_direct_beam)
