def test_structure_factor(self):
result = get_structure_factor(
np.asanyarray([
2.2551711385, 2.478038901, 2.7001518288, 2.9214422642,
3.1418428, 3.3612863, 3.5797059197, 3.7970351263
]), self.atom_data)
self.assertIsNotNone(result)
def get_structure_factors(self, stl_range):
"""
Get the atom's structure factor for a given range of 2*sin(θ) / λ values.
Expects λ to be in nanometers!
"""
if self.atom_type is not None:
return float(get_structure_factor(stl_range, self.data_object))
else:
return 0.0
def get_structure_factors(self, stl_range):
"""
Get the atom's structure factor for a given range of 2*sin(θ) / λ values.
Expects λ to be in nanometers!
"""
if self.atom_type is not None:
return float(get_structure_factor(stl_range, self.data_object))
else:
return 0.0
def get_factors(range_stl, component):
r"""
Returns a tuple containing the structure factor and phase difference for
- range_stl: numpy array of 2*sin(θ) / λ values
- component: a :class:`~pyxrd.calculations.data_objects.ComponentData`
instance containing two lists of layer and interlayer
:class:`~pyxrd.calculations.data_objects.Atom`'s.
This function calls
:meth:`~pyxrd.calculations.atoms.get_structure_factor` for each
atom in the layer and interlayer list of the component data object and
sums the result to obtain the component's structure factors.
The component's phase differences are calculated as follows:
.. math::
:nowrap:
\begin{flalign*}
& \psi = e^ { 2 \pi \cdot { \frac { 2 \cdot sin(\theta)} {\lambda} } \cdot \left( d_{001} \cdot i - \pi \cdot \delta d_{001} \cdot { \frac {2 \cdot sin(\theta)} {\lambda} } \right) }
\end{flalign*}
"""
z_factor = (component.d001 - component.lattice_d) / (component.default_c -
component.lattice_d)
num_layer_atoms = len(component.layer_atoms)
sf_tot = 0.0 + 0.0j
for i, atom in enumerate(
chain(component.layer_atoms, component.interlayer_atoms)):
atom.z = atom.default_z
if i >= num_layer_atoms:
atom.z = calculate_z(atom.z, component.lattice_d, z_factor)
sf_tot += get_structure_factor(range_stl, atom)
phi_tot = np.exp(
2. * pi * range_stl *
(component.d001 * 1j - pi * component.delta_c * range_stl))
return sf_tot, phi_tot
def get_factors(range_stl, component):
r"""
Returns a tuple containing the structure factor and phase difference for
- range_stl: numpy array of 2*sin(θ) / λ values
- component: a :class:`~pyxrd.calculations.data_objects.ComponentData`
instance containing two lists of layer and interlayer
:class:`~pyxrd.calculations.data_objects.Atom`'s.
This function calls
:meth:`~pyxrd.calculations.atoms.get_structure_factor` for each
atom in the layer and interlayer list of the component data object and
sums the result to obtain the component's structure factors.
The component's phase differences are calculated as follows:
.. math::
:nowrap:
\begin{flalign*}
& \psi = e^ { 2 \pi \cdot { \frac { 2 \cdot sin(\theta)} {\lambda} } \cdot \left( d_{001} \cdot i - \pi \cdot \delta d_{001} \cdot { \frac {2 \cdot sin(\theta)} {\lambda} } \right) }
\end{flalign*}
"""
z_factor = (component.d001 - component.lattice_d) / (component.default_c - component.lattice_d)
num_layer_atoms = len(component.layer_atoms)
sf_tot = 0.0 + 0.0j
for i, atom in enumerate(chain(component.layer_atoms, component.interlayer_atoms)):
atom.z = atom.default_z
if i >= num_layer_atoms:
atom.z = calculate_z(atom.z, component.lattice_d, z_factor)
sf_tot += get_structure_factor(range_stl, atom)
phi_tot = np.exp(2.*pi * range_stl * (component.d001 * 1j - pi * component.delta_c * range_stl))
return sf_tot, phi_tot
def test_structure_factor(self):
result = get_structure_factor(
np.asanyarray([2.2551711385, 2.478038901, 2.7001518288, 2.9214422642, 3.1418428, 3.3612863, 3.5797059197, 3.7970351263]),
self.atom_data
)
self.assertIsNotNone(result)