Each candidate setting of the model was scored one after another on the
coarse shell (a density, an FFT and an isotropic scale fit, 0.2-0.5 s
each), and a run with a model in another setting scores them in both of
its validations. They share nothing but what they read, so they now run
on ParallelFor, each on its own copy of the model, and are read back in
their own order: the log lines, the ranking and the tie-break (first of
equal R wins) are those of the serial loop.
Measured (16-core workstation, loaded): 8sa8 3 candidates 0.64 s ->
0.22 s; 9ea5 3 candidates 1.47 s -> 0.50 s; 8xtg 1.45 s -> 0.40 s.
p.mtz, the maps, the map MTZ and the placed model md5-identical.
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