3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	f956eb25e8	rugnux: model validation does the same work in less time ... --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	2026-10-09 00:01:14 +02:00
leonarski_fandClaude Opus 5.5	9ad92b6bfe	Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/ ... 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	2026-10-07 14:05:37 +02:00
leonarski_f	84228bf8be	v1.0.0-rc.173 (#83) ... * jfjoch_broker: Optional per-dataset authentication - statistics, images and plots can require a bearer token, which jfjoch_viewer supports. * jfjoch_viewer: Dark mode and a theme-matched colour scheme, a magnifier panel, and simpler contrast and background controls. * Rugnux: Multiple performance improvements on GPU and CPU (CPU-only processing up to 40% faster, faster image decoding on ARM), with unchanged results. * Rugnux: `--model` rigid-body refinement runs on the GPU, and the model-validation check is faster and more reliable. * Rugnux: Improved scaling and merging - error model, outlier rejection, absorption correction and French-Wilson amplitudes now agree more closely with XDS and ctruncate. * Rugnux: Improved integration - radial background on powder and ice rings, crowded rotation data keep their reflections, and CPU-only builds integrate large unit cells as GPU builds do. * Rugnux: More robust detector geometry - measured beam centre, X-ray bandwidth and goniometer rate, and geometry refinement accepted only on significant evidence. * Rugnux: Merged files are written in the standard setting, or in the setting of a reference MTZ, structure-factor mmCIF or model, with its free-R flags. * Rugnux: Richer report - ice and powder rings, further lattices, superstructure candidates and mosaicity, with warnings worded as prompts to check. * Rugnux: Clear error messages when a data set needs more GPU or host memory than is available. Reviewed-on: #83 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-29 15:57:32 +02:00