Basis intensities and phase ambiguity

Keep the cubic translations above, but attach an atomic basis with A at fractional crystal coordinates $(0,0,0)$ and B at $(u,0,0)$. Stipulate real, angle-independent relative scattering amplitudes $f_A=1$ and $f_B=0.6$. Neglect wave absorption, repeated crystal scattering and thermal motion. This is a point-scatterer model under the Born approximation, not a claim about the scattering strengths of named elements. Its crystal basis structure factor isHere $J$ is a dimensionless squared motif amplitude. Comparing it with measured integrated wave intensities requires the experimental geometry and detector response as well. The algebra follows directly by multiplying $F$ by its complex conjugate; the cross term records wave interference between the two sites.

With $u=1/2$, reflections with even $h$ have $J=2.56$, whereas odd $h$ gives $J=0.16$, a ratio of $16:1$. With $u=1/4$, the first four $(h00)$ values instead are $1.36,0.16,1.36,2.56$. Their geometrically possible positions are unchanged, although their strengths change. For equal stipulated amplitudes $f_A=f_B=1$ and $u=1/2$, the odd-$h$ amplitude vanishes exactly: an example of a systematic absence. Different motif weights can thus expose a repeat that equal weights conceal.

The same formula also proves an ambiguity: $u=1/4$ and $u=3/4$ give identical $J_{hkl}$ for every integer $h,k,l$, because $\cos (2\pi h(1-u))=\cos (2\pi hu)$. Yet $F_{100}$ changes from $1+0.6i$ to $1-0.6i$, reversing its wave phase. This particular ambiguity is inversion of the motif; it does not prove that these two simple motifs are distinct chemical substances. The conclusion is conditional on the stipulated real scattering amplitudes.