feat: pbc in neighbour lists, fix duplicate pairs in the RDF fallback, and speed up get_neighbors ~2.x+ - #423
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…, and speed up get_neighbors ~2.x+ ## Why `get_neighbors` and `build_distances` never read `atoms.pbc` — periodicity was applied in all three directions unconditionally. Reachable in production: `load_lammps_dump` doesn't force pbc, so a slab dump written with `ITEM: BOX BOUNDS ff ff pp` was silently analysed as fully periodic. This had no effect on the analysis so far, but I could imagine it leads to some in the future when the user base grows and workflows as well. ## Fixes - **`pbc` honoured per lattice vector**: non-periodic vectors are padded by `2 * cutoff` so no wrapped image can reach; the kernels are unchanged. - **`rdf._compute_distances` non-numba fallback emitted duplicate pairs** when a box edge spanned fewer than three cells. Deleted in favour of the shared path, removing a third copy of the cell-list loop. - Degenerate cells / molecules with no cell raised `SystemError`; `build_distances` raised on 0 atoms and zero volume; NaN coordinates silently vanished under `fastmath`. - Minimum-image warning used perpendicular height (a lower bound), so it fired spuriously on every slab and skewed cell. ## Performance `get_neighbors` **2x+ faster** , from replacing the per-atom Python output loops with one vectorised gather. `build_distances` unchanged (~1.2x). ## Behaviour changes No signature or return-type changes. Fully periodic bulk results are bit-identical. Non- or partially-periodic structures now return different, correct neighbour lists, and NaN coordinates / zero-volume periodic cells raise `ValueError` instead of silently dropping atoms or crashing.
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Changing this to 0.0 to make it more physically motivated
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Why
get_neighborsandbuild_distancesnever readatoms.pbc— periodicity was applied in all three directions unconditionally. Reachable in production:load_lammps_dumpdoesn't force pbc, so a slab dump written withITEM: BOX BOUNDS ff ff ppwas silently analysed as fully periodic. This had no effect on the analysis so far, but I could imagine it leads to some in the future when the user base grows and workflows as well.Fixes
pbchonoured per lattice vector: non-periodic vectors are padded by2 * cutoffso no wrapped image can reach; the kernels are unchanged.rdf._compute_distancesnon-numba fallback emitted duplicate pairs when a box edge spanned fewer than three cells. Deleted in favour of the shared path, removing a third copy of the cell-list loop.SystemError;build_distancesraised on 0 atoms and zero volume; NaN coordinates silently vanished underfastmath.Performance
get_neighbors2x+ faster , from replacing the per-atom Python output loops with one vectorised gather.build_distancesunchanged (~1.2x).Behaviour changes
No signature or return-type changes. Fully periodic bulk results are bit-identical. Non- or partially-periodic structures now return different, correct neighbour lists, and NaN coordinates / zero-volume periodic cells raise
ValueErrorinstead of silently dropping atoms or crashing.