# # ChangeLog for / # # Generated by Trac 1.6 # May 23, 2025, 4:43:28 PM Thu, 20 Oct 2016 20:54:48 GMT Frederik Heber [72e40d0] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.cpp (added) * src/Actions/WorldAction/StepWorldTimeAction.def (added) * src/Actions/WorldAction/StepWorldTimeAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/testsuite-options.at (modified) * tests/regression/WorldTime/SetWorldTime/testsuite-worldtime-set-world-time.at (moved) * tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (added) * tests/regression/WorldTime/testsuite-worldtime.at (added) * tests/regression/testsuite.at (modified) Added single action to step backward and forward through time. - ... Thu, 20 Oct 2016 20:54:23 GMT Frederik Heber [a1c8fa] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) FIX: BondedParticleInfo::MaxOrder and ::AdapativeOrder are now stored ... Thu, 20 Oct 2016 20:54:23 GMT Frederik Heber [064b34] * src/Actions/WorldAction/OutputAction.cpp (modified) FIX: OutputAction gives a more helpful error message on fail. Thu, 20 Oct 2016 20:54:23 GMT Frederik Heber [180b5f] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FragmentationAction does not give error on adjacencyfile when not ... Fri, 30 Sep 2016 15:47:43 GMT Frederik Heber [097535] * debian/changelog (modified) Added version to debian changelog. Tue, 20 Sep 2016 09:02:32 GMT Frederik Heber [4b5bd2] * configure.ac (modified) Set version to 1.5.4. - MoleCuilder library is now 17:0:0. - ... Tue, 20 Sep 2016 09:02:32 GMT Frederik Heber [b85145] * src/Tesselation/tesselation.cpp (modified) FIX: Tesselation::GetCircleOfSetOfPoints() did not check for ... Tue, 20 Sep 2016 09:02:32 GMT Frederik Heber [67645e] * src/Tesselation/tesselation.cpp (modified) WARNINGFIX: unused variable in NDEBUG case in Tesselation::operator(). Tue, 20 Sep 2016 09:02:32 GMT Frederik Heber [d00441] * src/Filling/Cluster.cpp (modified) WARNINGFIX: Cluster::insert() unused variable in NDEBUG case. Mon, 19 Sep 2016 18:12:01 GMT Frederik Heber [72b467] * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) ParseFragmentResultsAction warns when parsing container with grids ... Mon, 19 Sep 2016 18:12:01 GMT Frederik Heber [059833] * tests/regression/Fragmentation/ParseSaveFragmentResults/post/results_empty_longrange_disabled.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/post/results_empty_longrange_enabled.dat (moved) * tests/regression/Fragmentation/ParseSaveFragmentResults/post/results_longrange_disabled.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/post/results_longrange_enabled.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (modified) ENABLEFIX: FragmentResultsContainer serialization differs with no ... Sun, 18 Sep 2016 19:52:09 GMT Frederik Heber [25f5b66] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) WARNINGFIX: Commented-out unused ... Sun, 18 Sep 2016 19:52:09 GMT Frederik Heber [42715d] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillVolumeAction.cpp (modified) * src/Actions/FillAction/SuspendInMoleculeAction.cpp (modified) WARNINGFIX: Removed AtomVector typedef in some Fill..Actions. Sun, 18 Sep 2016 19:52:09 GMT Frederik Heber [bcf351] * src/Potentials/Particles/ParticleRegistry.hpp (modified) MEMFIX: ParticleRegistry did not cleanup on dstor. Sun, 18 Sep 2016 19:52:03 GMT Frederik Heber [34709f] * src/Fragmentation/Exporters/unittests/Makefile.am (modified) DISTFIX: SphericalPointDistribution_assistant.hpp missing in Makefile.am. Wed, 14 Sep 2016 18:43:53 GMT Frederik Heber [3fb9ab] * src/Parser/MpqcParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * tests/regression/Atoms/Add/post/test.in (modified) * tests/regression/Atoms/Remove/post/test.in (modified) * tests/regression/Parser/Mpqc/post/doublewater.in (modified) * tests/regression/Parser/Mpqc/post/empty.in (modified) * tests/regression/Parser/Mpqc/post/test.in (modified) * tests/regression/Parser/Mpqc/post/testCLHF.in (modified) * tests/regression/Parser/Mpqc/post/testCLKS.in (modified) * tests/regression/Parser/Mpqc/post/testMBPT2.in (modified) * tests/regression/Parser/Mpqc/post/testMBPT2_R12.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF_n.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF_n_ascend_ids.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF_n_mixed_ids.in (modified) * tests/regression/Parser/Mpqc/pre/testCLKS.in (modified) * tests/regression/Parser/Mpqc/pre/testMBPT2.in (modified) * tests/regression/Parser/Mpqc/pre/testMBPT2_R12.in (modified) * tests/regression/Parser/Mpqc/pre/water.in (modified) * tests/regression/Parser/SetParameters/Mpqc/post/testCLHF.in (modified) * tests/regression/Parser/SetParameters/Mpqc/pre/testCLHF.in (modified) FIX: Preventing MPQC from using old temp files for restart. - ... Wed, 14 Sep 2016 18:43:53 GMT Frederik Heber [703369] * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) FIX: FragmentationAutomation limited nfc to 20 and grid to 10 ... Wed, 14 Sep 2016 18:43:53 GMT Frederik Heber [291ad9] * src/Fragmentation/Summation/SetValues/FragmentForces.cpp (modified) * src/Fragmentation/Summation/SetValues/FragmentForces.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/FragmentForcesUnitTest.cpp (added) * src/Fragmentation/Summation/SetValues/unittests/FragmentForcesUnitTest.hpp (added) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) Added operator+=() to FragmentForces and unit test. - FIX: ... Wed, 14 Sep 2016 18:43:46 GMT Frederik Heber [82034f1] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) Added currently inactive alternative NN contribution calculation from ... Wed, 14 Sep 2016 18:43:46 GMT Frederik Heber [964c63] * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) Need to check given max-meshwidth for not being too large w.r.t delta. Wed, 14 Sep 2016 18:43:46 GMT Frederik Heber [dd9b90] * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/unittests/ExportGraph_ToJobsUnitTest.cpp (modified) FIX: Fragment grid may also become smaller than specified level. - ... Wed, 14 Sep 2016 18:43:46 GMT Frederik Heber [eaef9b] * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) Modying nfc by power of 2 for each additional level in fragment grid. Wed, 14 Sep 2016 18:43:46 GMT Frederik Heber [4c648a] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) UNBREAKS: No longer downsample all grids but enforce a coarser global ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [45f4b6b] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) FragmentationLongRangeResults requires additional zeroinstance in ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [ebadb4] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp (modified) FragmentationChargeDensity requires additional zeroinstance in cstor. Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [b5134a] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp (modified) Split operations in FragmentationChargeDensity into cstor and ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [409a05] * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) ..SumUpPerLevel are now functors that allow to set the zero instance ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [da098d2] * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) * src/Fragmentation/Summation/ZeroInstanceInitializer.hpp (added) ..Summators and AllLevel..Summators pass through ZeroInstance, added ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [3d444a] * src/Fragmentation/Summation/OrthogonalSummation_impl.hpp (modified) * src/Fragmentation/Summation/Summation_impl.hpp (modified) (Orthogonal)Summation's Sum() can be further simplified now. Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [ff7ac6] * src/Fragmentation/Summation/OrthogonalSummation.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummation_impl.hpp (modified) * src/Fragmentation/Summation/Summation.hpp (modified) * src/Fragmentation/Summation/Summation_impl.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) BREAKS: Summation and OrthogonalSummation both now allow to set a ... Wed, 14 Sep 2016 18:43:45 GMT Frederik Heber [f856ec] * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) Histogram uses copy instead of superposeOtherHistogram() when ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [760fa22] * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) FragmentationLongRangeResults::operator() does not need to calculate ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [52a789] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) AnalyseFragmentationResultsAction now uses downsampled charge grids ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [11edf0] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/GridDownsampler.cpp (added) * src/Fragmentation/Summation/Containers/GridDownsampler.hpp (added) * src/Fragmentation/Summation/Containers/Makefile.am (modified) Added GridDownsampler as static functor. - extracted function from ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [4a3df8] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * tests/Python/AllActions/options.dat (modified) Fragmentation.. and ..AutomationAction accept a desired maximum mesh- ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [2ebfd7] * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) MPQCData::assignWithDownsampledGrid() uses downsample(). - in order ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [ec1aae] * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob.hpp (modified) FIX: MPQCData now correctly checks sampled_grid to be cubic. Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [160ad7] * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) * src/Fragmentation/Exporters/unittests/ExportGraph_ToJobsUnitTest.cpp (added) * src/Fragmentation/Exporters/unittests/ExportGraph_ToJobsUnitTest.hpp (added) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) ExportGraph_ToJobs::operator() now calculates a specific level for ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [b839fb] * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) Extracted getDomainGrid from ExportGraph_ToJobs as static fct. Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [57fda0] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) SamplingGrid::operator*=(), ::superposeOtherGrids() and ::integral() ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [6a5eb2] * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) SamplingGrid::downsample() uses padWithZerosForEvenNumberedSamples(). ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [d56e21] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (modified) Added padWithZerosForEvenNumberedSamples(), required by downsample(). ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [91e7658] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (modified) SamplingGridUnitTest checks downsample on window. - FIX: ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [06653a] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (modified) SamplingGrid has downsample() function. - we need this when small ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [cb30d9] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (modified) Extended SamplingGridProperties::isCompatible() to allow more finely ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [ca4b372] * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) Added getSurplusLevel() to SamplingGridProperties. - FIX: ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [336da8] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) WindowGrid_converter's refactored a bit with ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [c1948c] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid_inline.hpp (modified) Added getDiscreteWindowIndices() and getDiscreteWindowLengthPerAxis() ... Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [c6da5e] * src/Jobs/InterfaceVMGJob.cpp (modified) FIX: InterfaceVMGJob used box_end as end point, not as length of ... Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [978234] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties_inline.hpp (modified) FIX: Made getGridPointsPerAxis() not use pow() in every call. Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [e51f2c] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Potentials/PartialNucleiChargeFitter.cpp (modified) Renamed SamplingGrid::getDiscreteWindowIndices() -> ... Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [5b1e5e] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties_inline.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid_inline.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) FIX: Replaced 3 by NDIM in SamplingGrid which avoids some confusion ... Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [028790] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) Moved getNearestLowerGridPoint and ..Higher:: from SamplingGrid to ... Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [c6ddcb] * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.hpp (modified) Added getRoughBoundingBox to SaturatedFragment. Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [c24071] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToAtomFragments.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToAtomFragments.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) ExportGraph::operator() now returns bool. - FragmentationAction ... Wed, 14 Sep 2016 13:36:04 GMT Frederik Heber [c4abf2] * tests/regression/Atoms/Saturate/post/saturated_cholesterol_H48_50_53_67_73.pdb (added) * tests/regression/Atoms/Saturate/post/saturated_water.pdb (added) * tests/regression/Atoms/Saturate/post/saturated_water_H1.pdb (added) * tests/regression/Atoms/Saturate/pre/cholesterol.pdb (added) * tests/regression/Atoms/Saturate/pre/water.pdb (added) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-bonded_atoms.at (added) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-carbon.at (moved) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-nitrogen.at (moved) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) TEST: Added regression tests on saturating partially bonded atoms. Wed, 14 Sep 2016 13:36:04 GMT Frederik Heber [3dadd5] * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at (modified) Revert "Removing SphericalPointDistribution::getSimplePolygon() to ... Wed, 14 Sep 2016 13:36:04 GMT Frederik Heber [1af2ae] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) FIX: SphericalPointDistribution::findBestMatching() does not assert ... Wed, 14 Sep 2016 07:02:33 GMT Frederik Heber [fe90ab] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) recurseMatching() now takes connections into account. - ... Wed, 14 Sep 2016 07:02:33 GMT Frederik Heber [36bd59] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) FIX: Need to check whether old and newcenter are not linear dependent. Wed, 14 Sep 2016 07:02:31 GMT Frederik Heber [2ccdf4] * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest_assistant.hpp (modified) Fixing getConnectionTest() due to ambiguous tesselation. - with N=8 ... Mon, 12 Sep 2016 23:58:11 GMT Frederik Heber [2d8c4e] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) Removed all IsZero() checking and special cases for the triangle idea. Mon, 12 Sep 2016 23:48:37 GMT Frederik Heber [6393ff] * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution_getConnections.cpp (added) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest_assistant.hpp (added) * src/Fragmentation/Makefile.am (modified) Added getConnections() to SphericalPointDistribution. - we use ... Mon, 12 Sep 2016 23:48:37 GMT Frederik Heber [3678eb] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Added calculation of center of minimum distance by bisection. - ... Mon, 12 Sep 2016 23:48:36 GMT Frederik Heber [0983e6] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) Refactoring SphericalPointDistribution to combine point list and ... Mon, 12 Sep 2016 23:48:36 GMT Frederik Heber [653cea] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) SphericalPointDistribution is now working with bond degree weights. ... Mon, 12 Sep 2016 23:48:36 GMT Frederik Heber [450adf] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Extracted joinPoints() function to make it accessible to tests. - ... Mon, 12 Sep 2016 23:48:36 GMT Frederik Heber [2199c2] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) Extended SphericalPointDistribution::Polygon_t to WeightedPolygon_t. ... Mon, 12 Sep 2016 23:48:34 GMT Frederik Heber [b67d89] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Using the idea of three points giving a triangle to find rotation ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [158ecb] * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) Extended SphericalPointDistributionUnitTest to two and three matching ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [b3c052] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Dropped quaternion rotation for simple arbitrary rotation axis and ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [8e4471] * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) Added "arbitrary" rotation for matchSphericalPointDistributionsTest_2(). Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [92bc5c] * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Adding QuaternionTest for SphericalPointDistributionUnitTest, fixed ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [f9d85f] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) Implemented rotations via boost::quaternions. Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [8d38e6] * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Added more unit test functions up to N=8 to ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [946948] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) FIX: SphericalPointDistribution succeeds with unit test. - removed ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [7e81ca] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) Added Logging to SphericalPointDistribution for debugging. Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [6cb1cd] * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at (modified) Removing SphericalPointDistribution::getSimplePolygon() to allow for ... Mon, 12 Sep 2016 14:03:11 GMT Frederik Heber [0c42f2] * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution_getPoints.cpp (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at (modified) Extended SaturateAction to be able to deal with bonded atoms. - ... Sat, 10 Sep 2016 16:01:20 GMT Frederik Heber [64cafb2] * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (added) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (added) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at (modified) Revert "Trimmed down SphericalPointDistribution to what is needed at ... Sat, 10 Sep 2016 16:01:20 GMT Frederik Heber [d32f60] * src/builder_init.cpp (modified) FIX: Corrected copyright year to current one. Sat, 10 Sep 2016 16:01:20 GMT Frederik Heber [1745b7] * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondAddAction.def (modified) * tests/Python/AllActions/options.dat (modified) AddBondAction also sets a desired bond degree. Sat, 10 Sep 2016 16:01:20 GMT Frederik Heber [2312fc6] * src/Fragmentation/Exporters/SaturatedBond.cpp (modified) SaturateBond now uses default angle and Bond length with warning when ... Sat, 10 Sep 2016 16:01:20 GMT Frederik Heber [f723fa] * src/LinkedCell/LinkedCell_Model.cpp (modified) FIX: In debug we asserted possible deleteNode() in LinkedCell_model. ... Fri, 09 Sep 2016 17:23:11 GMT Frederik Heber [2ae247] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) FIX: Clearing FragmentationResultsContainer before adding results in ... Fri, 09 Sep 2016 17:23:11 GMT Frederik Heber [f83e26] * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) FIX: FragmentationResultContainer did not clear cycles on clear(). Fri, 09 Sep 2016 17:23:11 GMT Frederik Heber [d20335] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Removed parsing and saving of fragment results in analyse-fragment- ... Fri, 09 Sep 2016 17:10:10 GMT Frederik Heber [73a5f7] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (added) * src/Actions/FragmentationAction/ParseFragmentResultsAction.def (added) * src/Actions/FragmentationAction/ParseFragmentResultsAction.hpp (added) * src/Actions/FragmentationAction/SaveFragmentResultsAction.cpp (added) * src/Actions/FragmentationAction/SaveFragmentResultsAction.def (added) * src/Actions/FragmentationAction/SaveFragmentResultsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/ParseSaveFragmentResults/post/results_empty.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/pre/create_results_dat.py (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/pre/results.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added parsing and saving of fragment results container state. - ... Fri, 09 Sep 2016 17:10:10 GMT Frederik Heber [ce0f63] * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) FIX: Clarified hint for FragmentationAutomationAction's resultfile. Fri, 09 Sep 2016 17:04:06 GMT Frederik Heber [e598f5] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) FIX: appendToHomologies() sorted force keysets which brough them out ... Fri, 09 Sep 2016 13:58:02 GMT Frederik Heber [4fa333] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.cpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.hpp (modified) FIX: AtomFragmentsMap::clear() did not clear fullkeysets. Fri, 09 Sep 2016 13:51:43 GMT Frederik Heber [61fc12] * src/Fragmentation/Fragmentation.cpp (modified) FIX: FragmentBOSSANOVA got full molecule as restricted keyset. - ... Fri, 09 Sep 2016 13:51:36 GMT Frederik Heber [34af97] * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.hpp (modified) FIX: KeySetsContainer::insert(KeySetsContainer&) was not fully ... Fri, 09 Sep 2016 10:09:47 GMT Frederik Heber [9bdbc7] * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.hpp (modified) FIX: QtFragmentList controls access to clear() and refill() via mutex. Fri, 09 Sep 2016 10:09:47 GMT Frederik Heber [546f7d] * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) FIX: Selections in QtFragmentList works even under resorting. Fri, 09 Sep 2016 10:09:47 GMT Frederik Heber [d88397] * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FIX: Skipping empty curves in QtHomologyList::refill(). - this does ... Fri, 09 Sep 2016 10:09:47 GMT Frederik Heber [4aed01] * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtNumericalItem.cpp (added) * src/UIElements/Views/Qt4/QtNumericalItem.hpp (added) FragmentList's and QtHomologyList's numerical columns are now ... Fri, 09 Sep 2016 10:09:47 GMT Frederik Heber [562b0a] * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FragmentList and HomologyList can be sorted by clicking column title. Fri, 09 Sep 2016 08:22:09 GMT Frederik Heber [d33f24] * src/Potentials/PotentialTrainer.cpp (modified) Added additional checks to training data sensibility of PotentialTrainer. Fri, 09 Sep 2016 08:22:09 GMT Frederik Heber [647148] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) FIX: HomologyGraph's getNodeFromSet() and getEdgesFromSet ignored ...