3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_f	001e61c1a4	Refinement: the repulsion search on the refinement's threads, hydrogens skipped before the neighbour walk ... BuildRepulsions walked the neighbours of every atom and only then dropped the pairs of a riding hydrogen; those atoms are now skipped before the walk. The atoms are searched in 64 blocks under ParallelFor and the blocks' pairs joined in atom order, so the restraint list is the same as before for any thread count. The model is no longer copied for the NeighborSearch. Same bits. 9yl4: repulsions 3.37 -> 1.09 s (91 calls), refinement 17.7 -> 14.2 s; 5reo 0.38 -> 0.12 s (RTX 5080, -N 8, loaded box). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit ded11388a18f5a4138a73150c4bb073570152727) (cherry picked from commit 9c96836a90c9f170008d343af2cd885a4e59b321)	2026-10-26 01:38:23 +01:00
leonarski_fandClaude Opus 5.5	f077320efa	Refinement restraints: n_slots, not slots - Qt defines slots as a macro, which broke the viewer's build through Rugnux.h ... Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu	2026-10-25 10:22:02 +01:00
leonarski_f	b4b68d368f	Restrained refinement on the GPU: ML amplitude target, FFT gradient, dictionary restraints, R1 + R2 driver, blobs ... RefineModel (Refinement.h) refines a placed model against the merge, reading and writing nothing: - placement stage (R1): every chain of 50+ atoms as a rigid body at once (L-BFGS on six parameters per chain, their gradient from the per-atom one through Ceres jets), then one B shift per residue; - restrained stage (R2): positions and isotropic B of every atom of a residue the embedded dictionary describes, the rest held fixed but kept in Fcalc and the mask; riding hydrogens added by gemmi's topology, moved with their parents, re-placed every macro-cycle. Macro-cycles refit the mask, the scale and bulk solvent (FitModelScale / ModelScaleGPUPool) and the likelihood's D and beta (ML on the free set in resolution bins), rebuild the repulsion pairs (symmetry mates included), then L-BFGS on positions and, where chosen, on B. - weights: a ladder of full refinements at multiples of the gradient-balanced X-ray weight, chosen by R-free within bond/angle bounds (ties to the tighter geometry), then the B refinement tried at its own weights and kept only where it beats B held by more than the tie. The target and its gradient (RefinementXray, RefinementGPU): the Rice/centric amplitude likelihood (RefinementMath.h, shared host/device code), the gradient by Agarwal's FFT method - the adjoint of the reciprocal-space symmetry composition into a half-l (CPU) or half-u (cuFFT) spectrum, one inverse real transform, then each atom's density derivatives (xyz and B) summed over its box. On the GPU everything per evaluation stays on the device: ModelDensityGPU's gather, r2c, a fused compose + likelihood kernel, a CSR gather for the adjoint (no atomics), c2r, one warp per atom for the gradient; the restraints are one kernel per restraint plus a per-atom gather of gradient slots; cub reductions. Deterministic. Restraints (RefinementRestraints): bonds, angles, torsions (with esd, no phi/psi, no alternative sugar puckers), chiral volumes, least-squares planes from gemmi's Topo; repulsions beyond 1-4 (vdW radii from the dictionary's energy library, 2.6 A for H-bond pairs, 1.9 A metal-N/O/S); B similarity of bonded and angle-related atoms. DensityBlobs (D1): gemmi's flood-fill blobs of mFo-DFc above 3 sigma peaking above 4 sigma, placed beside the model and labelled WATER / ION / LIGAND / MODEL_ERROR by distance, contacts, volume and the anomalous map. tools/rugnux_refine_test refines a model against a finished run's p.mtz (developer utility, not installed). Tests: likelihood derivative, the embedded library, restraint values on ideal residues and every restraint kind's gradient against finite differences (CPU, and the GPU against the CPU), the X-ray gradient against finite differences in P1, P212121, C2 and P6122 (CPU and GPU), and a synthetic refinement that recovers a shaken model. Credits in docs/ACKNOWLEDGEMENT.md and at the algorithms. Measured on the open arm's battery outputs against REFMAC 5.8, 10 cycles, same p.mtz, free set and start model (R-free): 5reo 0.2228 vs 0.2236, 8dyz 0.1733 vs 0.1651, 9chw 0.1995 vs 0.1969 (CPU engine). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 8efe6f2322b3bfdae580bb34f256e67730dfc3c2)	2026-10-25 07:20:32 +01:00