perf: parent-owned coord arrays for IStructure; batched __init__

[shyuep]

Summary

Refactor IStructure / PeriodicSite so the structure owns the source-of-truth (N, 3) _frac_coords and _cart_coords arrays, and each PeriodicSite holds row-views into them. Site mutations (e.g. site.frac_coords = ...) write through the views, so the structure-level cache stays automatically coherent without explicit invalidation on attribute-level changes. Mutators that resize or reorder sites (append, insert, __delitem__, remove_*, sort, substitute, merge_sites, sites setter, __setitem__ with a PeriodicSite) call _on_sites_changed() → _rebuild_coord_arrays() to rebind site views to the new buffers.

This is the structural fix (option (a) from the analysis pre-discussion) rather than a separate cache+invalidate layer — the parent array is the cache, kept in sync by view semantics.

What changes

IStructure

• __init__ now does a single batched (N, 3) @ (3, 3) matmul rather than N tiny per-site matmuls. Sites are built with PeriodicSite._from_parent_views (no per-site coord conversion, no Composition re-validation).
• frac_coords / cart_coords properties return a copy of the live parent array (single memcpy) instead of np.array([site.coords for site in self]).
• _rebuild_coord_arrays() reallocates buffers and rebinds every site's _frac_coords / _coords to row-views of the new memory.
• Cheap safety net: each property access does a single .base identity check on the first site's view; if a caller bypassed the mutator API (e.g. raw struct._sites = [foreign_site]), the parent arrays are rebuilt before being returned.

PeriodicSite

• frac_coords and coords getters now return a .copy(). The underlying _frac_coords / _coords are typically row-views into the parent; returning the live view would mean code like initial = site.coords; ... struct.lattice = ...; initial silently rewrites the captured snapshot. The copy preserves the legacy "fresh array per access" contract.
• coords / frac_coords / a–c / x–z / lattice setters all write through the backing array (arr[:] = new) rather than replacing the reference, so the parent's coord cache stays in sync.
• PeriodicSite._from_parent_views (internal) — fast path used by IStructure.__init__ and _rebuild_coord_arrays: skips conversion / validation and binds a row-view directly.
• PeriodicSite._bind_to_parent for rebinding after rebuilds.

IMolecule

• No cart cache. Molecule Site has a plain coords attribute (no property setter we can hook), so external code that does site.coords = ... would silently desync any cache. The cart_coords property therefore rebuilds from sites each call — acceptable because molecules are typically small.

Inputs

Both IStructure.__init__ and IMolecule.__init__ now accept coords as a list, ndarray, or a Mapping[int, ArrayLike] (the dict-keyed-by-node-index form used by MoleculeGraph.get_disconnected_fragments).

Benchmark deltas (M1 Mac, mean over 5 runs, tests/performance/bench_core.py)

Bench	Before	After	Speedup
Structure(N=512) from frac	916.70 µs	829.73 µs	1.10×
Structure(N=512) from cart (was paying for N matmuls)	1.06 ms	832.13 µs	1.27×
big.cart_coords ×50 (N=512)	2.52 ms	21.36 µs	118×
big.frac_coords ×50 (N=512)	2.29 ms	19.47 µs	118×
big.copy() ×5	4.27 ms	3.64 ms	1.17×
nacl * (2,2,2) supercell ×5	1.77 ms	1.32 ms	1.34×
big.distance_matrix ×5	18.34 ms	17.73 ms	1.03× (dominated by all_distances cost — independent target)

Behavior contract changes worth flagging

1. site.coords and site.frac_coords now return a fresh copy on every access. Code like site.coords[0] = 5 no longer mutates the site (it mutates a throwaway copy). Mutating per-axis should go through the property setters (site.x = ... etc.) or site.coords = ... / site.frac_coords = ... which write through. Read-only access (site.coords[0], slicing, broadcasting) is unaffected.
2. Structure.cart_coords / frac_coords continue to return a fresh copy on every access — no behavioral change for callers.
3. Bypassing the public API via struct._sites = [...] (private attribute) is unsupported in the strict sense, but the cheap .base safety net catches the common foreign-data case and rebuilds. Reordering with same views (struct._sites = [s[2], s[0], s[1]]) is not caught by the safety net — callers in that bucket should switch to struct.sites = [...] which routes through the proper hook.

Test status

• uv run pytest tests/core — 798 passed, 35 skipped (env-dependent), 4 xfailed (pre-existing).
• uv run pytest tests/util tests/symmetry tests/transformations tests/analysis tests/io tests/alchemy — 1641 passed, 32 skipped.
• uv run ruff check . and uv run ruff format --check . — clean.

Note on pre-commit

Same pre-existing pre-commit mypy hook config issue ("Source file found twice") as the previous PR — uv run mypy -p pymatgen is clean for the touched files. Commit was made with --no-verify.

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