# # ChangeLog for src/Fragmentation/Automation # # Generated by Trac 1.4.4 # Mar 17, 2025, 3:07:12 PM Thu, 19 Sep 2013 20:10:24 GMT Frederik Heber [f6c19d] * src/Fragmentation/Automation/VMGDebugGridFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGDebugGridJob.hpp (modified) * src/Jobs/VMGJob.hpp (modified) InterfaceVMGDebugJob now also uses optionally open boundary (FAS ... Thu, 15 Aug 2013 08:41:17 GMT Frederik Heber [ee9018] * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) InterfaceVMGJob now may also use open boundary (FAS instead of CS). ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [a953c4] * configure.ac (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) Using priorizing of jobs. - we now require JobMarket 1.1.4. - ... Wed, 12 Jun 2013 10:11:59 GMT Frederik Heber [5aaa43] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (modified) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/parseKeySetFile.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/Parameters/Validators/Specific/PotentialTypeValidator.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FilesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RealSpaceMatrixCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/cleanUp.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) * tests/regression/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Graph/CreateAdjacency/testsuite-graph-create-adjacency.at (modified) * tests/regression/Graph/DestroyAdjacency/testsuite-graph-destroy-adjacency.at (modified) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) * tests/regression/testsuite.at (modified) FIX: Fixed new copyright line since start of 2013 in CodeChecks test. ... Fri, 03 May 2013 09:46:45 GMT Frederik Heber [e2925fd] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Eigenhistogram.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Eigenvalues.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Energy.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Forces.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_LongRangeEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Times.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_VMGEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Eigenhistogram.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Eigenvalues.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Energy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Forces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Times.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentShortRangeResults.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Split long-range calculations into two parts to overcome ... Wed, 01 May 2013 07:53:26 GMT Frederik Heber [b6b21a] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added option DoPrintDebug to FragmentationAutomationAction. - this ... Wed, 01 May 2013 07:52:55 GMT Frederik Heber [6ff62c] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenhistogram.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenvalues.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Energy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Forces.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentResults.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Added DoValenceOnly has new option to FragmentationAutomationAction. ... Thu, 18 Apr 2013 16:23:48 GMT Frederik Heber [53c579] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) Removed fragment as parameter from ... Tue, 16 Apr 2013 06:30:39 GMT Frederik Heber [214240] * src/Actions/Makefile.am (modified) * src/Analysis/Makefile.am (modified) * src/Atom/Makefile.am (modified) * src/Element/Makefile.am (modified) * src/Filling/Makefile.am (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/Makefile.am (modified) * src/Fragmentation/Summation/Converter/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/FunctionApproximation/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Helpers/Makefile.am (modified) * src/LinkedCell/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Potentials/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/UIElements/Makefile.am (modified) FIX: Most of the includedirs were wrongly set. - each just needs to ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [fbf143] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/SetValues/unittests/Makefile.am (deleted) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp (moved) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (moved) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCData.cpp (moved) * src/Fragmentation/Summation/Containers/MPQCData.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCDataFused.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCDataMap.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCData_printKeyNames.hpp (moved) * src/Fragmentation/Summation/Containers/Makefile.am (moved) * src/Fragmentation/Summation/Containers/VMGData.cpp (moved) * src/Fragmentation/Summation/Containers/VMGData.hpp (moved) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (moved) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (moved) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (moved) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (moved) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.hpp (moved) * src/Fragmentation/Summation/Containers/extractJobIds.hpp (moved) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp (moved) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.hpp (moved) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (moved) * src/Fragmentation/Summation/Converter/DataConverter.hpp (moved) * src/Fragmentation/Summation/Converter/Makefile.am (moved) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (moved) * src/Fragmentation/Summation/SetValues/Fragment.hpp (moved) * src/Fragmentation/Summation/SetValues/Histogram.cpp (moved) * src/Fragmentation/Summation/SetValues/Histogram.hpp (moved) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (moved) * src/Fragmentation/Summation/SetValues/IndexedVectors.hpp (moved) * src/Fragmentation/Summation/SetValues/Makefile.am (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid_inline.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (added) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (moved) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) * src/Fragmentation/parseKeySetFile.cpp (moved) * src/Fragmentation/parseKeySetFile.hpp (moved) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob.hpp (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LevMartester.cpp (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/unittests/Makefile.am (modified) Placed Containers, Converter, and SetValues as subfolders into ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [8e84fe] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/SpecificFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Containers/FragmentationChargeDensity.cpp (moved) * src/Fragmentation/Containers/FragmentationChargeDensity.hpp (moved) * src/Fragmentation/Containers/FragmentationLongRangeResults.cpp (moved) * src/Fragmentation/Containers/FragmentationLongRangeResults.hpp (moved) * src/Fragmentation/Containers/FragmentationShortRangeResults.cpp (moved) * src/Fragmentation/Containers/FragmentationShortRangeResults.hpp (moved) * src/Fragmentation/Containers/MPQCData.cpp (moved) * src/Fragmentation/Containers/MPQCData.hpp (moved) * src/Fragmentation/Containers/MPQCDataFused.hpp (moved) * src/Fragmentation/Containers/MPQCDataMap.hpp (moved) * src/Fragmentation/Containers/MPQCData_printKeyNames.hpp (moved) * src/Fragmentation/Containers/Makefile.am (added) * src/Fragmentation/Containers/VMGData.cpp (moved) * src/Fragmentation/Containers/VMGData.hpp (moved) * src/Fragmentation/Containers/VMGDataFused.hpp (moved) * src/Fragmentation/Containers/VMGDataMap.hpp (moved) * src/Fragmentation/Containers/VMGData_printKeyNames.hpp (moved) * src/Fragmentation/Containers/createMatrixNrLookup.cpp (moved) * src/Fragmentation/Containers/createMatrixNrLookup.hpp (moved) * src/Fragmentation/Containers/extractJobIds.hpp (moved) * src/Fragmentation/Containers/parseKeySetFile.cpp (moved) * src/Fragmentation/Containers/parseKeySetFile.hpp (moved) * src/Fragmentation/Containers/unittests/MPQCDataUnitTest.cpp (moved) * src/Fragmentation/Containers/unittests/MPQCDataUnitTest.hpp (moved) * src/Fragmentation/Containers/unittests/Makefile.am (added) * src/Fragmentation/Converter/DataConverter.hpp (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/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/unittests/Makefile.am (modified) Moved ...Data and all related classes into new subfolder Containers. ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [7b0494] * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Automation/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/SetValues/Makefile.am (modified) * src/Fragmentation/SetValues/SamplingGrid.cpp (moved) * src/Fragmentation/SetValues/SamplingGrid.hpp (moved) * src/Fragmentation/SetValues/SamplingGridProperties.cpp (moved) * src/Fragmentation/SetValues/SamplingGridProperties.hpp (moved) * src/Fragmentation/SetValues/SamplingGrid_inline.hpp (moved) * src/Fragmentation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (moved) * src/Fragmentation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp (moved) * src/Fragmentation/SetValues/unittests/SamplingGridUnitTest.cpp (moved) * src/Fragmentation/SetValues/unittests/SamplingGridUnitTest.hpp (moved) * src/Jobs/Grid/Makefile.am (deleted) * src/Jobs/Grid/unittests/Makefile.am (deleted) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCData.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGData.hpp (modified) * src/Jobs/VMGDebugGridJob.hpp (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved SamplingGrid... over to Fragmentation/SetValues. - adapted ... Mon, 15 Apr 2013 10:30:31 GMT Frederik Heber [0cd8cf] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationLongRangeResults.cpp (moved) * src/Fragmentation/Automation/FragmentationLongRangeResults.hpp (moved) * src/Fragmentation/Automation/FragmentationShortRangeResults.cpp (added) * src/Fragmentation/Automation/FragmentationShortRangeResults.hpp (added) * src/Fragmentation/Automation/Makefile.am (modified) Split FragmentationResults into ..ShortRange.. and ..LongRange... - ... Mon, 15 Apr 2013 10:30:31 GMT Frederik Heber [503acc1] * configure.ac (modified) * m4/boost.m4 (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Jobs/MPQCData.cpp (modified) * src/Jobs/MPQCData.hpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob.hpp (modified) MPQCJob and MPQCData now have bool to decide whether to sample ... Mon, 15 Apr 2013 10:28:25 GMT Frederik Heber [bae7bc] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (added) * src/Actions/FragmentationAction/ParseFragmentJobsAction.def (added) * src/Actions/FragmentationAction/ParseFragmentJobsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) Outsourced parsing of fragment files into ParseFragmentJobsAction ... Mon, 15 Apr 2013 10:28:22 GMT Frederik Heber [ac9ca4] * configure.ac (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (added) * src/Fragmentation/Automation/FragmentJobQueue.hpp (added) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/KeySetsContainer.hpp (modified) * src/Fragmentation/Makefile.am (modified) FragmentAction creates FragmentJobs if no output-types are given. - ... Sun, 24 Feb 2013 12:59:34 GMT Frederik Heber [c91572] * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) DOCUFIX: Replaced \text by \mathrm in some formulas. Thu, 14 Feb 2013 13:29:24 GMT Frederik Heber [3d9a8d] * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGridProperties.cpp (modified) * src/Jobs/Grid/SamplingGridProperties.hpp (modified) * src/Jobs/Grid/unittests/Makefile.am (modified) * src/Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/MPQCJob_binding.hpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) SamplingGrid has no more size parameter but an end array. - this ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [79398d] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) Extended map in FragmentResults to a pair of ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [2dd305] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) Split FragmentResults functionality in cstor into cstor and ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [17c03f] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/parseKeySetFile.cpp (added) * src/Fragmentation/Automation/parseKeySetFile.hpp (added) Extracted parseKeySetFile from FragmentationResults, ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [b8f0b25] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) Extended FragmentResults and FragmentationChargeDensity to contain ... Mon, 10 Dec 2012 10:11:00 GMT Frederik Heber [cd2591] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added interpolation-degree as parameter to ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [67fec1] * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Jobs/VMGDataFused.hpp (modified) * src/Jobs/VMGDataMap.hpp (modified) * src/Jobs/VMGData_printKeyNames.hpp (modified) Changed VMGDataMap to contain entries for electron, nuclei, and total ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [5a5196] * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) FIX: Now we OrthogonalSumPerLevel potential * charge per fragment. ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [d4f31f] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) FIX: FragmentResults now sums up long-range correction only for level ... Mon, 10 Dec 2012 10:10:58 GMT Frederik Heber [19c50e] * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.hpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalFullSummator.hpp (deleted) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/SortedVector.hpp (modified) * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/Summation/SubsetMap.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/unittests/SubsetMapUnitTest.cpp (modified) * src/Fragmentation/Summation/unittests/SubsetMapUnitTest.hpp (modified) IndexSetContainer now treats super set specially. - The super set ... Mon, 10 Dec 2012 10:10:58 GMT Frederik Heber [27594e] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.cpp (added) * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (added) * src/Fragmentation/Automation/Makefile.am (modified) Added FragmentationChargeDensity to contain summed up charge density. Mon, 10 Dec 2012 10:10:58 GMT Frederik Heber [376a3b] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (added) * src/Fragmentation/Automation/FragmentationResults.hpp (added) * src/Fragmentation/Automation/Makefile.am (modified) Added FragmentationResults as a container to hold final fragmentation ... Mon, 10 Dec 2012 10:10:58 GMT Frederik Heber [184615] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/createMatrixNrLookup.cpp (added) * src/Fragmentation/Automation/createMatrixNrLookup.hpp (added) Extracted createMatrixNrLookup() into own header file. Mon, 10 Dec 2012 10:10:57 GMT Frederik Heber [447481] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/extractJobIds.hpp (added) * src/Jobs/Makefile.am (modified) Extracted template function extractJobIds() into own header file. Mon, 10 Dec 2012 10:10:57 GMT Frederik Heber [a2295a] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Summation/OrthogonalFullSummator.hpp (modified) * src/Jobs/VMGDataFused.hpp (modified) * src/Jobs/VMGDataMap.hpp (modified) * src/Jobs/VMGData_printKeyNames.hpp (modified) We now create one full potential VMGJob of each summed up grid per ... Mon, 10 Dec 2012 10:10:57 GMT Frederik Heber [238868] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.cpp (added) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (added) * src/Jobs/InterfaceVMGDebugGridJob.cpp (added) * src/Jobs/InterfaceVMGDebugGridJob.hpp (added) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob.cpp (added) * src/Jobs/VMGDebugGridJob.hpp (added) Added VMGDebugGridJob that just prints given sampled grid as VTK ... Mon, 10 Dec 2012 10:10:56 GMT Frederik Heber [de84ef] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) FIX: Poisson problem is now calculated in atomic length units. - as ... Mon, 10 Dec 2012 10:10:56 GMT Frederik Heber [065574] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added level and near_field_cells as options to ... Mon, 10 Dec 2012 10:10:56 GMT Frederik Heber [c44322] * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) Using operator<<(SamplingGrid&) to give debug info in ... Mon, 10 Dec 2012 10:10:19 GMT Frederik Heber [ffe057] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (added) * src/Fragmentation/Automation/MPQCFragmentController.hpp (added) * src/Fragmentation/Automation/Makefile.am (added) * src/Fragmentation/Automation/SpecificFragmentController.cpp (added) * src/Fragmentation/Automation/SpecificFragmentController.hpp (added) * src/Fragmentation/Automation/SpecificFragmentController_impl.hpp (added) * src/Fragmentation/Automation/VMGFragmentController.cpp (added) * src/Fragmentation/Automation/VMGFragmentController.hpp (added) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Added SpecificFragmentController and subclasses that contain ...