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leonarski_f 2be88e11e3 Refinement restraints: contacts with lattice translates are kept, and an atom's own symmetry contact once 
Contacts() dropped every pair found in image 0 with a nonzero lattice shift ("the identity term
covers the contact"), but that pair is a contact with a translated copy of j, not with j itself:
in P1 no intermolecular repulsion or B-contact restraint was made at all, and in every group the
contacts along a, b and c were missing (MeasureGeometry's clash count with them). Such a pair is
now kept like a symmetry mate's, from the lower atom of the two.

An atom against its own image x -> T x is also met through T^-1 at the same distance (another
operator, or the same one at another lattice shift for a screw), and both were kept: atoms near
a 3-, 4- or 6-fold or a screw axis were repelled twice. For i == j the image first in fractional
coordinates of T x and T^-1 x is kept; an involution is kept once as before.

Test: in P1 two waters 2.4 A apart across a cell face get one repulsion and one B contact (none
before); a water 1.4 A from a 3-fold axis gets one repulsion with its images (two before).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 0d6e4d0491e655a49d59b709e1398843506d162a)
2026-10-26 15:38:59 +01:00
..
crystfel
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
data
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
test_data
Refinement: common cofactors and modified RNA nucleotides in the embedded dictionary; heme iron restrained from LINK records
2026-10-26 13:56:29 +01:00
xds
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
xds_durin
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
xds_neggia
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
AcquisitionCountersTest.cpp
v1.0.0-rc.36
2025-05-05 19:32:22 +02:00
AdaptiveSpotFinderCPUTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
AdaptiveSpotFinderGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
AdaptiveThresholdTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
AndersonMixingTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
AnisotropyAnalysisTest.cpp
v1.0.0-rc.177 (#87)
2026-10-19 16:07:31 +02:00
AutoIncrVectorTest.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
AzimuthalIntegrationTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
BackgroundApertureTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BackgroundGainTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BandwidthEstimateTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BeamCenterFFTGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
BeamCenterFFTTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
BeamCenterFromBackgroundTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BearerTokensTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
BraggIntegrationEngineCompressedImageTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
BraggIntegrationEngineCPUTest.cpp
Beam stop: a reflection whose signal disk reaches the shadow is not integrated; no-data pixels are dead, not shadow
2026-10-25 07:20:21 +01:00
BraggIntegrationEngineGPUTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BraggIntegrationEngineMetalTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BraggStencilTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
BrokerHttpAuthTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
BSLZ4DecoderGPUFuzzTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
BSLZ4DecoderGPUTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
CalcBraggPredictionTest.cpp
Stills prediction: every frame predicts through two rocking widths of the run, measured first and centred on its radial scale
2026-10-26 10:50:52 +01:00
CalibrationTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
CBORTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
CCTest.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
CellEsdTest.cpp
CellEsdTest: synthetic cells in place of cells that looked measured
2026-10-26 15:38:58 +01:00
CellPopulationTest.cpp
Stills geometry: fit only the given cell's crystal form; a stray frame is no cell population
2026-10-25 07:20:25 +01:00
CheckImageOutput.h
v1.0.0-rc.36
2025-05-05 19:32:22 +02:00
CMakeLists.txt
rugnux: unit-cell e.s.d.s - ZERR in a new SHELX .ins beside the .hkl, _cell.*_esd in the mmCIF, CELL_ESD_* in the report
2026-10-26 14:33:38 +01:00
CoordTest.cpp
v1.0.0-rc.41
2025-06-10 18:14:04 +02:00
CorrectionSurfaceGPUTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
CrystalLatticeTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
CrystalSettingTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
CrystFELGeometryTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
CudaHandledErrorTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
CUDAMemHelpersTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
DectrisSimplonClientTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
DetectorGeometryTest.cpp
v1.0.0-rc.103 (#8)
2025-11-19 09:40:50 +01:00
DetectorModulesTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
DetectorSettingsTest.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
DetectorSetupTest.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
DetGeomCalibTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DiagnosticOutputTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
DiffractionExperimentTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DiffractionGeometryTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DiffractionSpotTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
DirectHostReadGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
enospc_shim.c
SHIM library improvements from the HDF Group
2026-05-08 11:39:51 +02:00
FFBIDXIndexerCPUTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
FPGAFrameGeneratorTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
FPGAHLSModulesTest.cpp
v1.0.0-rc.91
2025-10-20 20:43:44 +02:00
FPGAHostWriterTest.cpp
v1.0.0-rc.34
2025-04-14 11:52:06 +02:00
FPGAIntegrationTest.cpp
v1.0.0-rc.97
2025-11-09 12:42:27 +01:00
FPGANetworkTest.cpp
v1.0.0-rc.72
2025-09-08 20:28:59 +02:00
FPGAPTPTest.cpp
v1.0.0-rc.72
2025-09-08 20:28:59 +02:00
FPGASpotFindingUnitTest.cpp
v.1.0.0-rc.32
2025-03-24 12:16:33 +01:00
FrameTransformationTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
FrenchWilsonTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
GoniometerAxisTest.cpp
v1.0.0-rc49
2025-06-18 15:19:18 +02:00
GridScanSettingsTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
HDF5WritingTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
HistogramTest.cpp
v1.0.0-rc.121 (#28)
2025-12-12 21:24:20 +01:00
HKLKeyTest.cpp
v1.0.0-rc.124 (#31)
2026-02-01 13:29:33 +01:00
HostMemoryTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
HotPixelFinderTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
ImageBufferTest.cpp
v1.0.0-rc.128 (#35)
2026-03-03 22:24:44 +01:00
ImageMetadataTest.cpp
v1.0.0-rc.103 (#8)
2025-11-19 09:40:50 +01:00
ImagePreprocessorGPUFusedTest.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
ImageSpotFinderCPUTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
ImageSpotFinderGPUTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
IndexingUnitTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
JFCalibrationTest.cpp
v1.0.0-rc.36
2025-05-05 19:32:22 +02:00
JFConversionTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
jfjoch_hdf5_enospc_test.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
JFJochImageBufferReaderTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
JFJochReaderTest.cpp
Tests: the stills rocking width - the window at a reflection's resolution, _process.h5 round trip
2026-10-26 14:09:32 +01:00
JFJochReceiverIntegrationTest.cpp
v1.0.0-rc.150 (#60)
2026-06-15 20:24:15 +02:00
JFJochReceiverLiteTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
JFJochReceiverPlotsTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
JFJochReceiverProcessingTest.cpp
v1.0.0-rc.160 (#70)
2026-07-19 09:39:28 +02:00
JFJochStateMachineTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
JFPedestalTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
JPEGTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
LatticeReductionTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
LatticeSearchTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
LePageLatticeTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
LiveCollectionTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
LoadReferenceMtzFreeFlagsTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
LoadReferenceSfCifTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
LossyFilterTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
MergeScaleTest.cpp
Tests: the stills rocking width - the window at a reflection's resolution, _process.h5 round trip
2026-10-26 14:09:32 +01:00
ModelDensityGPUTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
ModelDensityMetalTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
ModelMaskGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
ModelScaleGPUTest.cpp
Refinement GPU: the robust scale fit on the card, the pool back in every trial slot
2026-10-26 01:38:24 +01:00
ModelScalingTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
ModelValidationTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
ModuleRefinementTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
ModuleSummationTest.cpp
version 1.0.0-rc.27 minor fixes
2024-12-04 20:58:51 +01:00
MolecularReplacementMetalTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
MolecularReplacementTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
MovingAverageTest.cpp
v1.0.0-rc.31
2025-03-02 13:15:28 +01:00
MultiLatticeSearchTest.cpp
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
MultiReaderTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
nxmx_geometry_dials_test.py
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
PairSortGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
PanelLayoutTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
ParallelForTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
PedestalCalcTest.cpp
v1.0.0-rc.97
2025-11-09 12:42:27 +01:00
PixelMaskTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
PortableTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
PostRefineTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
PreflightTest.cpp
v1.0.0-rc.165 (#75)
2026-08-27 22:16:54 +02:00
PreviewCounterTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
RawToConvertedGeometryTest.cpp
v1.0.0-rc.97
2025-11-09 12:42:27 +01:00
ReceiveRingBufferTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
RefinementTest.cpp
Refinement restraints: contacts with lattice translates are kept, and an atom's own symmetry contact once
2026-10-26 15:38:59 +01:00
RefineOnlyTest.cpp
Refinement: an exception in a trial slot or in RefineModel no longer ends the run
2026-10-26 15:38:58 +01:00
RegressionTest.cpp
1.0.0-rc.89
2025-10-01 22:54:40 +02:00
ReindexAmbiguityTest.cpp
Serial stills with a reference or model: crystals their own cells anchor keep that indexing
2026-10-26 06:49:20 +01:00
ResolutionShellsTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
ResultReportTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
RfreeFlagsTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
RingsFromProfileTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
ROIIntegrationCPUTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROIIntegrationGPUTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
ROIMapTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
RotationIndexerTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
RotationIngestGPUTest.cpp
Scaling: the low-resolution limit bounds the scale fit, not the merge
2026-10-25 07:20:21 +01:00
RotationScaleWalkTest.cpp
rugnux: a rotation scale is integrated with pass 1's lattice refit at it, and walked to the refit's fixed point
2026-10-25 07:20:25 +01:00
RugnuxInputKindTest.cpp
rugnux: a model and a reference among the inputs, in any order, told by their contents
2026-10-26 01:38:25 +01:00
RugnuxLargeTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
RugnuxLiveStatusTest.cpp
rugnux live: a score that is not finite is left out of the status, not sent as null
2026-10-26 15:38:58 +01:00
RugnuxResultFilesTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
RugnuxStructureTest.cpp
Rugnux live: the uploaded model is refined after placement; refined scores, model, maps and blobs in the status, the viewer and the hero
2026-10-26 01:38:25 +01:00
RugnuxTest.cpp
rugnux: a placed model is refined by default - giving a model is the opt-in
2026-10-26 01:38:24 +01:00
SaturationCeilingTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
SearchSpaceGroupTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
SearchSpaceGroupTwinTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
ShadowFinderTest.cpp
Polarization plane: measured on the pooled background, refused beyond what a source can give, logged, and kept across passes
2026-10-25 07:20:25 +01:00
SphericalHarmonicSurfaceTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
SpindleBlindFractionTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
SpindleCuspLossTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
SpotExtractorGPUParityTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
SpotFootprintTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
SpotTilesTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
SpotUtilsTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
StatusVectorTest.cpp
v1.0.0-rc.127 (#34)
2026-03-02 15:57:12 +01:00
StoredImageDecodeGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
StreamWriterTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
StrongPixelSetTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
SweepLayoutTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
SyntheticMergedReflections.h
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
TCPImagePusherTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
TestData.h
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ThreadSafeFIFOSetTest.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
TIFFTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
TimeTest.cpp
v1.0.0-rc.96 (#1)
2025-11-02 13:45:57 +01:00
TopPixelsTest.cpp
v1.0.0-rc.121 (#28)
2025-12-12 21:24:20 +01:00
TranslationalNCSTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
TwinningAnalysisTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
UnitCellTest.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
WilsonOutliersTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
WriteReflectionsTest.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
XDSPluginTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
XFELReaderTest.cpp
v1.0.0-rc.179 (#90)
2026-10-24 14:52:29 +02:00
XtalOptimizerTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
XtalRefineCeres.h
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
XtalRefineTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
ZMQImagePusherTest.cpp
v1.0.0-rc.178 (#88)
2026-10-21 11:20:01 +02:00
ZMQMetadataSocketTest.cpp
v1.0.0-rc.133
2026-03-26 20:50:33 +01:00
ZMQPreviewSocketTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
ZSTDCompressorTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00