Every evaluation uploaded both copies of the atoms' densities (the gather's and the gradient's) and their
boxes, although in a positions-only minimisation no B changes between two Refits. The engine now keeps one
copy (the gradient kernel reads ModelDensityGPU's atoms and boxes), uploads it only where some atom's
density was made again, and sends the positions from a pinned buffer without waiting. The densities that
are made again (every atom in a B minimisation) and the grid positions are worked out on the refinement's
threads. Same bits.
9yl4: upload 3.29 -> 0.56 s, host side 1.29 -> 0.61 s, refinement 22.3 -> 17.7 s; 5reo 4.8 -> 4.4 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 46c3b67c91aee0aec3473b0fb1a4945c00bda070)
(cherry picked from commit 0aebc98110c8155932af647d6204891aec662294)
EstimateLikelihoodParameters fits each resolution bin on its own and writes only that bin's values, so
the bins run under ParallelFor; the result is the same, bit for bit. It was the largest single stage of
a refinement (107 calls, one core): 5reo 2.42 -> 0.56 s, 8dyz 2.46 -> 0.57 s, 9yl4 3.54 -> 0.88 s;
whole refinement 5reo 6.3 -> 4.8 s, 8dyz 6.9 -> 5.3 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 85aa34d3031c8e36be4462fca544bc801af45d5a)
(cherry picked from commit d84ba55252adf455d5b4ba62052dfbafa6290a64)
RefinementStage sums the time of each stage over a refinement (Refit and its parts, the evaluations and
their X-ray, restraint, host and upload shares, the repulsion build, the riding hydrogens, the rungs) and
logs it at debug level at the end; rugnux_refine_test -v shows it. No change to any result.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 9491f54e0beccf36c65ebcec9afff90d08485f86)
(cherry picked from commit 0ce206a88df960754476ce2f75ffaed90fbf3123)
On deposited models the per-residue B shift raised R-free at every resolution tried (2.56 A: 0.320 ->
0.327) and the rigid bodies rarely helped; each is now kept only where it lowers R-free by more than the
0.001 tie, otherwise the model goes on as it was. The positions' weight ladder runs from 1/1024 to 1/32 of
the gradient-balanced weight: the R-free optimum sat near 1/500 at 2.6 A and near 1/50 at 1.1-1.7 A.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit d444fb03f610db70903de04f53f0489a71540b37)
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)
leonarski_f