ModelDensityGPU's gather had arithmetic of its own: per-thread offsets in Cartesian, the atom's
nearest image to the brick, r2 = x x + y y + z z, the radius squared in float. It now does what
UseDensityBoxesByPlane + AtomDensity (ModelGrid.cpp) and ModelDensityMetal.metal do, in their order:
- each brick's atoms carry their box (c - d, wrapped start, 2 d); a point is in the box by a
subtraction, and f = centre - (u, v, w) in the box's own unwrapped index;
- x = m00 fx + (m01 fy + m02 fz), y = m11 fy + m12 fz, z = m22 fz with gemmi's orth_n
(orth * (1/n), as Grid sets it) in float; r2 = (y y + z z) + x x against max_r2 = float(r^2)
rounded from the double radius (new ModelDensityAtom field);
- gemmi's expapprox, the five Gaussians in order, atoms in model order per point. Device code is
already compiled with --fmad=false (top-level CMakeLists), so nothing is contracted.
- The centres are no longer wrapped into the cell (ModelStructureFactorsGPU, RigidBodyGPU's
place_kernel): float(fractional * n), as MakeDensityBox holds them; the mask keeps wrapped
fractional coordinates. The 'narrow' nearest-image branch is gone: Supports() already leaves
only boxes narrower than the cell.
The target is PutModelDensityOnGrid() with no orbits to symmetrize (one copy of the content, which
is what the gather grids; symmetry stays composed in reciprocal space). A rounding tie in the box
centre c (float on the GPU, double on the CPU) changes no point: either box covers the sphere with
half a spacing to spare. New ModelDensityGPU_BitIdenticalToCPU ([ModelValidation][gpu]) memcmps the
grids: triclinic P1 and P 21 21 21 cells, 3000 atoms over -0.5..1.5 of the cell, a quarter
anisotropic - 0 points differ.
RTX 5080, alternating base (8d199cceb) / this, under the GPU lock:
- gather kernel (nsys): 4nwv --model median 2.06 -> 2.55 ms, total 0.79 -> 0.97 s;
9s02 --mr median 0.30 -> 0.37 ms, total 0.94 -> 1.17 s (+~25%, the box test and per-point
index arithmetic).
- wall, two each: 4nwv --model 76.0/68.9 -> 74.4/71.0 s, --mr 71.3/71.1 -> 70.9/71.6 s;
9s02 --model 25.1/22.6 -> 23.3/23.5 s, --mr 23.3/23.6 -> 23.3/23.2 s; 5reo --model
6.2/5.5 -> 5.5/5.7 s. Model validation 4nwv 12.4/12.3 -> 12.3/11.7 s; MR 4nwv 15.4/15.2 ->
15.4/15.1 s, 9s02 2.3/2.4 -> 2.4/2.4 s: no change beyond noise.
- outputs (each build run-to-run identical): p.hkl identical on all; R-work/R-free and every
decision unchanged (4nwv validation 0.2982/0.2969, 9s02 MR AGREES P 21 21 2 0.2503/0.2517,
4nwv MR UNDECIDED I 2 2 2 / I 21 21 21). Moved: MODEL_FIT_SIGMA 9s02 99.21 -> 101.68, 5reo
103.96 -> 104.98; MR placement Z 9s02 142.1 -> 145.6, 4nwv 46.7 -> 46.2; 4nwv anomalous site
4.01 -> 4.02 sigma; 4nwv placed model 1322/125462 lines in the last digit (2fo-fc max |d| 0.04
rms, CC 0.99999994); 9s02/5reo models identical, maps to 2e-5 rms.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4
leonarski_fandClaude Opus 5.5
b6392a3f58