v1.0.0-rc.172 (#82)

* Fixed `jfjoch_broker` cancelling every data collection with a CUDA "out of memory" error after long operation: GPU memory no longer leaks with each collection. * Rugnux scales a rotation sweep until the per-frame scales settle instead of for a fixed three rounds, and says so when they did not - merged intensities, and the space group, resolution cut and frame rejection read off them, change accordingly; `--scaling-iterations` is now the cap on that loop (default 100). * Rugnux places every frame of a marCCD, SMV or miniCBF series at the spindle angle its own header states, so a series with missing frames, or with angles written modulo 360, is no longer read at the wrong geometry or refused. * Every rotation run writes two diagnostic files beside its reflections: `<prefix>_detector.jpg`, the detector projection with the pixel mask and the detected beam-stop shadow drawn on it, and `<prefix>_plot.txt`, one row per image. Reviewed-on: #82 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-09-22 06:48:37 +02:00
parent 30b6800289
commit 6dfe065365
285 changed files with 12194 additions and 2588 deletions
@@ -272,6 +272,23 @@ void WriteMmcifReflections(const std::vector<MergedReflection> &reflections,
        if (twinning.moment_reflections > 0)
            out << "_reflns.jfjoch_second_moment_I        " << Fmt(twinning.second_moment, 3)
                << "   # <I^2>/<I>^2 (untwinned 2.00, perfect twin 1.50)\n";
+        // A twin law the run identified (TwinningAnalysisResult::twin_law_operator): the standard
+        // PDBx loop, one row per domain, the second domain related by the operator. Only meaningful
+        // in the true (sub)group's file, which is the one this is - in the higher group the operator
+        // is a symmetry element. Merohedral: the law is a lattice operation of the crystal system.
+        if (!twinning.twin_law_operator.empty()) {
+            out << "#\n";
+            out << "loop_\n";
+            out << "_pdbx_reflns_twin.domain_id\n";
+            out << "_pdbx_reflns_twin.crystal_id\n";
+            out << "_pdbx_reflns_twin.diffrn_id\n";
+            out << "_pdbx_reflns_twin.operator\n";
+            out << "_pdbx_reflns_twin.fraction\n";
+            out << "_pdbx_reflns_twin.type\n";
+            out << "1 1 1 'h,k,l' " << Fmt(1.0 - twinning.twin_law_fraction, 3) << " merohedral\n";
+            out << "2 1 1 " << CifStr(twinning.twin_law_operator) << " " << Fmt(twinning.twin_law_fraction, 3)
+                << " merohedral\n";
+        }
        // Radiation-damage monitor (rotation): the relative Debye-Waller B change from the first to the last
        // frame (A^2). A large magnitude flags a dose-dependent resolution-scale change = radiation damage;
        // positive is the typical direction (high-resolution intensity fades with dose). No standard mmCIF item.