BCC diffraction pattern only shows first reflections and structure factors are reported as NaN

[diegodeasantana]

Title

BCC diffraction pattern only shows first reflections and structure factors are reported as NaN

Description

I am trying to simulate an electron diffraction pattern for a BCC Fe structure. However, only the first allowed reflections are appearing in the diffraction pattern.

For example, when using the zone axis [0, 0, 1], only the 110 and 200 reflections (and their symmetry-equivalent reflections) are present. Higher-order reflections that should also satisfy the BCC selection rules do not appear.

I also tried increasing the reciprocal_radius value, but the behavior remains unchanged and no additional reflections are generated.

Another issue is that the structure factor values reported by sim.coordinates.print_table() are returned as NaN:

 h k l      d     |F|_hkl   |F|^2   |F|^2_rel   Mult
 1 1 0    2.027     nan      nan       nan       12
 2 0 0    1.433     nan      nan       nan       6

Because of this, I am not sure whether the missing reflections are related to the structure factor calculation or to the diffraction pattern generation itself.

Minimal Reproducible Example

from orix.crystal_map import Phase
from orix.vector import Vector3d
from orix.quaternion import Rotation
from diffpy.structure import Atom, Lattice, Structure
from diffsims.generators.simulation_generator import SimulationGenerator
import numpy as np
import matplotlib.pyplot as plt

a = 2.866

latt = Lattice(a, a, a, 90, 90, 90)

motif = [
    Atom("Fe", [0, 0, 0], lattice=latt),
    Atom("Fe", [0.5, 0.5, 0.5], lattice=latt),
]

structure = Structure(atoms=motif, lattice=latt)

ferrite = Phase(
    name="Ferrite",
    structure=structure,
    space_group=229,
)

zone_axis = Vector3d([[0, 0, 1]])
rot = Rotation.from_align_vectors(zone_axis, Vector3d.zvector())

gen = SimulationGenerator(accelerating_voltage=200)

sim = gen.calculate_diffraction2d(
    phase=ferrite,
    rotation=rot,
)

sim.coordinates.print_table()

coordinates = sim.coordinates.data
intensity = sim.coordinates.intensity
indices = sim.coordinates.hkl

fig, ax = plt.subplots()

ax.scatter(
    coordinates[:, 0],
    coordinates[:, 1],
    s=100 * np.log10(intensity + 1),
    color="tab:blue",
)

ax.set_aspect("equal")
ax.set_xlabel(r"$\AA^{-1}$")
ax.set_ylabel(r"$\AA^{-1}$")

ax.set_xlim(-1, 1)
ax.set_ylim(-1, 1)

plt.show()

Expected Behavior
For a BCC structure viewed along the [001] zone axis, I would expect higher-order allowed reflections to appear when the reciprocal-space radius is sufficiently large. I would also expect valid structure factor values instead of NaN.

Questions

• Is it possible to include the higher-order reflections in the calculation?
• Why are the structure factor values (|F|_hkl, |F|^2, |F|^2_rel) returned as NaN for this structure?

Version:
diffsims: 0.7.0
diffpy: 3.4.0
orix: 0.14.3