Reflectors (RuntimeWarning: invalid value encountered in divide)

[EffettiCollaterali]

Dear all,
I was wondering if the following way of building the reflectors, reported in discussion #664, it is OK or not, and if there are better ways to do it.

Thank you in advance,
Andrea

phase_list = PhaseList(
    names=["Ferrite", "Austenite"],
    space_groups=[229, 225],
    structures=[
        Structure(
            atoms=[Atom("fe", [0] * 3)],
            lattice=Lattice(0.287, 0.287, 0.287, 90, 90, 90)
        ),
        Structure(
            atoms=[Atom("fe", [0] * 3)],
            lattice=Lattice(0.356, 0.356, 0.356, 90, 90, 90)
        ),
    ]
)

reflectors = []
for indx, ph in phase_list:
    if indx != -1:
        lattice = ph.structure.lattice
        lattice.setLatPar(lattice.a * 10, lattice.b * 10, lattice.c * 10)

        rlv = ReciprocalLatticeVector.from_min_dspacing(ph, 0.5)
        rlv.sanitise_phase()
        rlv = rlv.unique(use_symmetry=True)
        rlv.calculate_structure_factor("lobato")
        structure_factor = abs(rlv.structure_factor)
        order = np.argsort(structure_factor)[::-1]
        rlv = rlv[order[0:7]]    # I workaround: slice the array because it contains values giving ValueError: negative dimensions are not allowed
        rlv = rlv.symmetrise()
        rlv.print_table()
        reflectors.append(rlv)

[EffettiCollaterali]

Dear all,
I'm still trying to get the correct set of reflectors.

I'm now using the code below to keep the reflectors with the highest structure factors. However, I got the following error, and it seems that the calculation of the structure factors it is incorrect as they pass from nan to 0.0.
How could I overcome this error?

Thank you in advance,
Andrea

/home/effetticollaterali/.local/lib/python3.8/site-packages/diffsims/crystallography/reciprocal_lattice_vector.py:885: RuntimeWarning: invalid value encountered in divide

INPUT

phase_list = PhaseList(
    names=["Ferrite", "Austenite"],
    space_groups=[229, 225],
    structures=[
        Structure(
            atoms=[Atom("fe", [0] * 3)],
            lattice=Lattice(0.287, 0.287, 0.287, 90, 90, 90)
        ),
        Structure(
            atoms=[Atom("fe", [0] * 3)],
            lattice=Lattice(0.356, 0.356, 0.356, 90, 90, 90)
        ),
    ]
)



reflectors = []
for indx, ph in phase_list:
    if indx != -1:
        lattice = ph.structure.lattice
        lattice.setLatPar(lattice.a * 10, lattice.b * 10, lattice.c * 10)
        rlv = ReciprocalLatticeVector.from_min_dspacing(ph, 0.5) 
        rlv = rlv[rlv.allowed]
        rlv = rlv.unique(use_symmetry=True).symmetrise()
        print(rlv.phase.structure)
        rlv.print_table()
        rlv.sanitise_phase()
        print(rlv.phase.structure)
        rlv = rlv.unique(use_symmetry=True)
        rlv.print_table()
        rlv.calculate_structure_factor("lobato")
        rlv.structure_factor 
        structure_factor = abs(rlv.structure_factor)
        F = abs(rlv.structure_factor)
        print(F)
        rlv = rlv[F > 0.05 * F.max()]
        rlv = rlv.symmetrise()
        rlv.print_table()
        reflectors.append(rlv)

OUTPUT

lattice=Lattice(a=2.87, b=2.87, c=2.87, alpha=90, beta=90, gamma=90)
fe 0.000000 0.000000 0.000000 1.0000
h k l d |F|_hkl |F|^2 |F|^2_rel Mult
3 3 2 0.612 nan nan nan 24
3 3 0 0.676 nan nan nan 12
4 0 0 0.717 nan nan nan 6
1 1 0 2.029 nan nan nan 12
3 1 0 0.908 nan nan nan 24
5 1 0 0.563 nan nan nan 24
2 2 0 1.015 nan nan nan 12
4 2 0 0.642 nan nan nan 24
4 4 0 0.507 nan nan nan 12
4 2 2 0.586 nan nan nan 24
2 1 1 1.172 nan nan nan 24
4 1 1 0.676 nan nan nan 24
3 2 1 0.767 nan nan nan 48
5 2 1 0.524 nan nan nan 48
4 3 1 0.563 nan nan nan 48
2 2 2 0.828 nan nan nan 8
2 0 0 1.435 nan nan nan 6
lattice=Lattice(a=2.87, b=2.87, c=2.87, alpha=90, beta=90, gamma=90)
fe 0.000000 0.000000 0.000000 1.0000
fe 0.500000 0.500000 0.500000 1.0000
/home/effetticollaterali/.local/lib/python3.8/site-packages/diffsims/crystallography/reciprocal_lattice_vector.py:885: RuntimeWarning: invalid value encountered in divide
f2_hkl_rel = (f2_hkl / f2_hkl[0]) * 100
h k l d |F|_hkl |F|^2 |F|^2_rel Mult
3 3 2 0.612 0.0 0.0 nan 24
3 3 0 0.676 0.0 0.0 nan 12
4 0 0 0.717 0.0 0.0 nan 6
1 1 0 2.029 0.0 0.0 nan 12
3 1 0 0.908 0.0 0.0 nan 24
5 1 0 0.563 0.0 0.0 nan 24
2 2 0 1.015 0.0 0.0 nan 12
4 2 0 0.642 0.0 0.0 nan 24
4 4 0 0.507 0.0 0.0 nan 12
4 2 2 0.586 0.0 0.0 nan 24
2 1 1 1.172 0.0 0.0 nan 24
4 1 1 0.676 0.0 0.0 nan 24
3 2 1 0.767 0.0 0.0 nan 48
5 2 1 0.524 0.0 0.0 nan 48
4 3 1 0.563 0.0 0.0 nan 48
2 2 2 0.828 0.0 0.0 nan 8
2 0 0 1.435 0.0 0.0 nan 6
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]

[EffettiCollaterali]

Dear all, I solved the problem, that was in the atom definition, I was using "fe" instead of "Fe".