[Code scan] Allow scalar-cutoff AtomicData.from_points without atomic numbers

[njzjz]

This issue comes from a Codex global repository scan.

Problem

The neighbor-list helper unconditionally requires atomic_numbers:

dftio/dftio/data/AtomicData.py

Line 994 in c9d128f

assert atomic_numbers is not None

That breaks scalar-cutoff construction where species are not needed. AtomicData.from_points(pos=..., r_max=2.0) should be able to build a graph from positions and a scalar cutoff, but it fails before the cutoff is used.

Suggested fix

Require atomic_numbers only when r_max is species-dependent, such as a dict keyed by atom type. Scalar cutoff paths should not assert atomic numbers are present.