4 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	6025d51a48	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	2026-10-09 12:38:37 +02:00
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