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
--model validation (battery-only for users) was 18% of the battery's time. Every
number it produces is unchanged to the bit (p.mtz, maps, placed model and every
model-validation line of the report md5/diff-identical on 11 open sets); only
when and where the work runs changes:
- The bulk-solvent grid fit (FitModelScale, most of the CPU time) fits each
solvent pair on a copy of gemmi::Scaling's target that takes
|Fcalc + k_sol exp(-b_sol s^2) Fmask| once per pair instead of at every
solver evaluation; same expressions, same types (new test checks a grid
point against gemmi's own Scaling fit with ==).
- Fcalc density and the solvent mask are made on two threads; the model's
structure factors beside the GPU engine reservation.
- The indexing probe fits the relabellings concurrently.
- The null's replicates run beside the real model's placement (they start
from a snapshot of the model as read); one GPU engine per replicate plus
one for the real fit instead of a cap of 4 (engines are interchangeable
and deterministic).
- The 2mFo-DFc, mFo-DFc and anomalous maps are made and written
concurrently; the placed model is written beside the reflection files.
- A rigid-body zone whose solvent-mask grid needs gemmi's shrink is sent to
the CPU when the engines are reserved (ModelMaskGPU::ShrinkIsNoOp), instead
of failing on the GPU and validating everything again on the CPU - the
same CPU result, without the wasted first attempt.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
A pure move. ModelValidation, RigidBodyRefine, RigidBodyGPU, ModelFFT, ModelGrid,
ModelScaling, ModelMaskGPU, ModelScaleGPU and SigmaA - everything that works on an
atomic model - become the JFJochStructureRefinement library, linked by
JFJochImageAnalysis. WriteModel (the placed-model mmCIF/PDB writer) goes to writer/
as its own small JFJochModelWriter target, so JFJochWriter, which a writer-only build
compiles, does not gain a gemmi dependency. Only include paths and CMake lists change.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
leonarski_fandClaude Opus 5.5