Improve `Atoms.index` usability

[tfrederiksen]

Currently, geom.atoms.index("H") raises a KeyError("Could not find atom in the list of atoms.") if no atoms of that species exist. This makes workflows like subsetting by element more cumbersome, since users must wrap calls in try/except.

It would be more intuitive if:

• Atoms.index(symbol) returned an empty array [] when no atoms are found.
• Atoms.index accepted multiple species in one call, e.g.:

geom.atoms.index("H", "C")
geom.atoms.index(["H", "C"])

returning the combined indices.

Both changes would simplify common tasks like extracting subsets (CH, CN, etc.) while remaining backwards-compatible.

Happy to open a PR if this direction is welcome.

[zerothi]

Agreed, I have done it like this because list behaves the same, but I can see the use-case.

Please open a PR ;)

And, could you add a Note saying that it won't raise a KeyError like list because of the cases you mention. E.g. if one wishes to know if a species exist, one should check if the list has len(idx)>0.

Thanks!