leonarski_fandClaude Opus 5
4ef6bd9952
Pass 1 searched for the space group on the geometry the run started with, stashed the answer, and reinstated it before pass 2's merge - so the decision was made on the worse of the two passes and then fed forward as a constraint. Four guards existed to reconcile it with what pass 2 later found. Now pass 1 does not search at all. It keeps its first merge, which is where mosaicity smoothing and geometry post-refinement already happen, and skips the in-symmetry re-merge that existed only to feed the search. prepass_merge_sg_, prepass_promoted_point_group_, the reinstatement, the primitive-to-conventional reindex it needed, and lattice_conflicts_with_prepass_sg all go. The obstacle was the pass-adoption guard, which compared completeness and CC1/2 across what could now be two different space groups. It compares each pass's FIRST merge instead - P1 on both sides, full range, before correction surfaces - which pass 2 produces anyway. One guard had to be replaced rather than removed. The index-time veto is re-keyed from pass 1's GROUP to its LATTICE and made one-directional: a centred pass-1 lattice against a primitive pass-2 one. Without it a C2 crystal fell to P1, and the obvious narrower fix - exempting a pass-1 P1 - would not have caught it, because that crystal's pass-2 lattice is monoclinic-P rather than triclinic. A centred lattice and its primitive sub-cell share a primitive volume, so the supercell arm cannot see that demotion. Corpus of 93 datasets, both arms at -N 6, every log validated: 78 comparable, 65 with a byte-identical p.hkl. Two crystals gain their reference point group, one gains its screw axis, one is lost. Per shell, over the 72 unchanged crystals, the median move is +0.25 points of R_meas and zero in <I/sigma>, CC1/2 and completeness. Load-matched compute is +0.4%, and the header-geometry fallback fires three times in the old arm against once in the new. What is lost is one crystal whose 222 the operator correlations still confirm: the merge chi-squared ratio moves 3% across a fixed bound at the refined geometry. A second crystal in the XDS harness crosses the H bound the same way. Both bounds are in SearchSpaceGroup and are recorded elsewhere as miscalibrated; recalibrating them is deliberately left to its own change. The comment at the long-axis rescue is corrected while here: the resolution setting only sizes the FFT histogram, and coarsening moves the true axis DOWN the direction ranking - 1996 to 16361 of 16384 - rather than making it more robust as the comment claimed. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Lc5JG6kJqZoCWaoZ43JGTW
Jungfraujoch
Application to receive data from the PSI JUNGFRAU and EIGER detectors.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.