ModelMaskGPU: gemmi's shrink step, so fine rigid-body zones stay on the GPU

The GPU bulk-solvent mask had no shrink step (SolventMasker::shrink(),
set_margin_around() with Refmac's r_shrink = 0.8 A), so every rigid-body
zone whose grid has an offset within 0.8 A was sent to the CPU. That is
not only fine grids: in an oblique setting (P2_1, beta ~141 deg) the
3.5 A zone's lattice-plane spacing is 0.69 A, and on such a set the real
fit and all nine null replicates ran their rigid bodies on the CPU.

The shrink is now two passes over the grid: mark the solvent points with
a macromolecule point among gemmi's near offsets, then turn into solvent
every macromolecule point with such an edge point at any stencil offset
(near or far, gemmi's split at the coarsest grid step). That is gemmi's
rule in both of its branches, and the stencil is built on the host in
double exactly as gemmi builds it. ModelMaskGPU::ShrinkIsNoOp() and
RigidBodyGPUEngine::MaskSupports() are gone; the rigid body no longer
refuses such zones.

Verified (ModelMaskGPU_ShrinkMatchesGemmi): the shrink alone on gemmi's
post-island mask is bit-identical, and the whole GPU mask equals gemmi's
put_mask_on_grid() bit for bit (0 differing points) on the five test
groups at 1.5 A and an oblique P2_1 cell at 3.5 A; repeats are identical.

Measured on the oblique-setting set of the open arm (P2_1, 14k atoms,
1.66 A): model validation 17.2 s -> 5.2 s with the GPU structure factors
of the next commit in place (the first validation's ten rigid bodies,
~12 s on the CPU, now take well under a second). p.mtz md5-identical;
the null moves from +73.1 to +86.1 sigma (the replicates are refined on
the GPU, which agrees with the CPU to rounding), verdict unchanged.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
This commit is contained in:
2026-10-09 12:38:37 +02:00
co-authored by Claude Opus 5.5
parent 91e63b6f52
commit 6025d51a48
7 changed files with 184 additions and 69 deletions
@@ -224,7 +224,7 @@ void PutModelDensityOnGrid(gemmi::DensityCalculator<Table, float> &dc, const gem
// symmetry spread over the threads as above - the same mask, bit for bit. The island removal and the
// shrink that follow are gemmi's own, except that the shrink is skipped where it cannot change a point:
// it looks at the grid offsets within rshrink of each point (set_margin_around), and on a grid whose
// spacing is coarser than rshrink along all three axes there are none - which is every rigid-body zone -
// spacing is coarser than rshrink along all three axes there are none - which is most rigid-body zones -
// yet it still walks the whole grid.
void PutMaskOnGrid(gemmi::Grid<float> &grid, const gemmi::Model &model, const std::vector<size_t> &orbit_leaders,
size_t nthreads) {