def test_get_intensities_params(default_structure):
latt = default_structure.lattice
reciprocal_lattice = latt.reciprocal()
reciprocal_radius = 0.2
unique_hkls, multiplicites, g_hkls = get_intensities_params(
reciprocal_lattice, reciprocal_radius)
np.testing.assert_equal(multiplicites, ([1.0]))
np.testing.assert_equal(g_hkls, [0.0])
np.testing.assert_array_equal(unique_hkls, [[-0.0, -0.0, 0.0]])
def test_get_kinematical_intensities(default_structure):
latt = default_structure.lattice
reciprocal_lattice = latt.reciprocal()
reciprocal_radius = 0.2
unique_hkls, multiplicites, g_hkls = get_intensities_params(
reciprocal_lattice, reciprocal_radius)
g_hkls_array = np.asarray(g_hkls)
i_hkls = get_kinematical_intensities(
default_structure,
g_indices=unique_hkls,
g_hkls_array=g_hkls_array,
debye_waller_factors={"Al": 1},
prefactor=multiplicites,
scattering_params="lobato",
)
np.testing.assert_array_almost_equal(i_hkls, ([43.0979]), decimal=4)
def calculate_profile_data(
self,
structure,
reciprocal_radius=1.0,
minimum_intensity=1e-3,
debye_waller_factors={},
):
"""Calculates a one dimensional diffraction profile for a
structure.
Parameters
----------
structure : diffpy.structure.structure.Structure
The structure for which to calculate the diffraction profile.
reciprocal_radius : float
The maximum radius of the sphere of reciprocal space to
sample, in reciprocal angstroms.
minimum_intensity : float
The minimum intensity required for a diffraction peak to be
considered real. Deals with numerical precision issues.
debye_waller_factors : dict of str:value pairs
Maps element names to their temperature-dependent Debye-Waller factors.
Returns
-------
diffsims.sims.diffraction_simulation.ProfileSimulation
The diffraction profile corresponding to this structure and
experimental conditions.
"""
wavelength = self.wavelength
latt = structure.lattice
# Obtain crystallographic reciprocal lattice points within range
recip_latt = latt.reciprocal()
spot_indices, _, spot_distances = get_points_in_sphere(
recip_latt, reciprocal_radius
)
##spot_indicies is a numpy.array of the hkls allowd in the recip radius
g_indices, multiplicities, g_hkls = get_intensities_params(
recip_latt, reciprocal_radius
)
i_hkl = get_kinematical_intensities(
structure,
g_indices,
np.asarray(g_hkls),
prefactor=multiplicities,
scattering_params=self.scattering_params,
debye_waller_factors=debye_waller_factors,
)
if is_lattice_hexagonal(latt):
# Use Miller-Bravais indices for hexagonal lattices.
g_indices = (
g_indices[0],
g_indices[1],
-g_indices[0] - g_indices[1],
g_indices[2],
)
hkls_labels = ["".join([str(int(x)) for x in xs]) for xs in g_indices]
peaks = {}
for l, i, g in zip(hkls_labels, i_hkl, g_hkls):
peaks[l] = [i, g]
# Scale intensities so that the max intensity is 100.
max_intensity = max([v[0] for v in peaks.values()])
x = []
y = []
hkls = []
for k in peaks.keys():
v = peaks[k]
if v[0] / max_intensity * 100 > minimum_intensity and (k != "000"):
x.append(v[1])
y.append(v[0])
hkls.append(k)
y = np.asarray(y) / max(y) * 100
return ProfileSimulation(x, y, hkls)