[pull] develop from lammps:develop#157
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When running with the KOKKOS package and per-atom data residing on a device (e.g. a GPU), the library function lammps_extract_atom() (and the Python and Fortran wrappers built on it) returned a pointer to host data that could be stale. The host copy is only guaranteed current at output steps and at the end of a run, but extract_atom() may be called at arbitrary times -- e.g. from the LAMMPS GUI (which runs the simulation in a separate thread) or from a "python" command during a run. Make Atom::extract() virtual and override it in AtomKokkos: map the property name to the KOKKOS data mask of the dual view that holds it and sync(Host, mask) before delegating to Atom::extract(). Custom per-atom double vectors/arrays (d_*/d2_*) sync via DVECTOR_MASK. Names whose data is not device-resident fall through unchanged (their host copy is always current). The sync is a no-op when the host copy is already current, and atom->extract() is only called from the library interface, so there is no impact on hot code paths. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Builds on PR #5014. Its custom-data fallback matched "^d2?_" and synced DVECTOR_MASK for both d_ (dvector) and d2_ (darray), which syncs the wrong storage for d2_ and never handles i_/i2_. extract() sees four kinds of custom per-atom data (fix property/atom): i_ (ivector), d_ (dvector), i2_ (iarray), d2_ (darray). The fallback now matches the full "^[id]2?_" pattern (same as Atom::extract) and decodes the prefix to the matching mask: i_ -> IVECTOR_MASK d_ -> DVECTOR_MASK i2_ -> IARRAY_MASK d2_ -> DARRAY_MASK Groups all four custom masks together in atom_masks.h: moves DVECTOR_MASK out of the DPD section into a new "custom per-atom vectors and arrays" section alongside the new IVECTOR_MASK / IARRAY_MASK / DARRAY_MASK, and renumbers so the bit values stay contiguous and gap-free. Only dvector is currently device-resident, so the three new masks are no-ops for now, but using all four means extract() needs no change once that custom data is ported to the device. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Co-Authored-By: Stan Moore <stanmoore1@gmail.com> Claude-Session: https://claude.ai/code/session_01WvmBeBBxFmEGbgGo4eDZxu
KOKKOS: make extract_atom device-aware (sync to host before returning, #3945)
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