feat(state): make pbc a per-system attribute

[lil-lon]

Summary

• Make SimState.pbc a per-system attribute of shape (n_systems, 3); a bool, list[bool], or (3,) tensor is broadcast to all systems. Moving it from _global_attributes to _system_attributes lets slicing, splitting, popping, and concatenation handle it like cell.
• atoms_to_state / structures_to_state accept inputs with different pbc instead of raising, and state_to_atoms / state_to_structures / trajectory files store each system's own pbc row.
• Ewald and PME models evaluate the periodic systems of a mixed batch and zero-fill systems with no periodic axis.
• Add require_full_pbc; elastic tensor calculation now rejects systems that are not fully periodic.
• The orb / NequIP / metatomic / fairchem wrappers convert pbc back to the legacy (3,) row on a shallow copy (_to_legacy_pbc_state) before delegating, because those integrations broadcast state.pbc themselves assuming the old shape; mixed-pbc batches raise a clear error there.
• Declare pbc after system_idx so __setattr__ can broadcast a (3,) row already during __init__, leaving a single broadcast site (__post_init__ only validates the shape). Simplify pbc handling in autobatching and io now that pbc is always a tensor.

Related issue: #584

Compatibility

Breaking:

• External code reading state.pbc as a global (3,) tensor must index it per system. The bundled orb / NequIP / metatomic / fairchem wrappers already adjusted this.
• get_attrs_for_scope: pbc moved from "global" to "per-system".

Unchanged:

• bool / list[bool] / (3,) inputs are still accepted and broadcast to all systems.
• Trajectory files still store a (3,) pbc array; existing files stay readable.

Discussion points

• _to_legacy_pbc_state hands third-party forward() a SimState whose pbc temporarily violates the (n_systems, 3) invariant. The preferred fix is upstream support for per-system pbc in the integrations; until then the shim keeps the current orb / NequIP / metatomic / fairchem releases working unchanged, since they only read plain attributes off the state.
• state.pbc = <1-D value> after construction broadcasts any length without validation (__post_init__ runs only at construction). Missing validation is pre-existing, but should __setattr__ enforce a length-3 row?

Checklist

Before a pull request can be merged, the following items must be checked:

• Doc strings have been added in the Google docstring format.
• Run ruff on your code.
• Tests have been added for any new functionality or bug fixes.

[CompRhys]

is this ready to merge?

[lil-lon]

Yes, ready for review.

One thing I'd like your eyes on: some potentials don't support mixed pbc, so they won't benefit from this change until upstream adds support. To keep them working, _to_legacy_pbc_state feeds them a state whose pbc temporarily violates the (n_systems, 3) invariant, which I'm slightly uneasy about (see Discussion points; mixed-pbc batches raise a ValueError there).
For potentials that support mixed pbc, I'm also considering a test that compares a mixed-pbc batch against per-system results.

[CompRhys]

some potentials don't support mixed pbc, so they won't benefit from this change until upstream adds support. To keep them working, _to_legacy_pbc_state feeds them a state whose pbc temporarily violates the (n_systems, 3) invariant, which I'm slightly uneasy about (see Discussion points; mixed-pbc batches raise a ValueError there).

Yeah this is likely a reason to hold off merging this for the time being. I hope to have some more time to review soon but have been busy with an international move.

[lil-lon]

No rush at all, and good luck with the move!

I think the concern is reasonable, but the invariant break is confined to the wrapped forward calls and is meant to be temporary until the upstream integrations accept per-system pbc. I checked that this fix should be straightforward: the necessary change is only a 2-3 line shape check.

Overall I think the benefits outweigh this temporary cost. Besides improving batching efficiency for mixed datasets, storing pbc per system makes it behave like cell everywhere: slicing, splitting, popping, and concatenation handle it consistently. In particular, concatenate_states used to silently adopt the first state's pbc for mixed inputs.