# # ChangeLog for src/Parser/unittests # # Generated by Trac 1.4.4 # Dec 28, 2024, 10:37:46 PM Wed, 18 May 2016 22:03:03 GMT Frederik Heber [ed8a68] * src/Parser/Makefile.am (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/TremoloParser_ElementKeys.cpp (deleted) * src/Parser/TremoloParser_ElementKeys.hpp (deleted) * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.cpp (deleted) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.hpp (deleted) Removed TremoloParser's ElementKeys, superceded by ParticleRegistry. Wed, 18 May 2016 22:03:03 GMT Frederik Heber [045228] * src/Parser/TremoloParser_ElementKeys.cpp (modified) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.cpp (modified) TremoloParser's ElementKeys now registers types also with ... Sun, 11 Oct 2015 07:11:38 GMT Frederik Heber [e3c4c5] * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (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) MpqcParser additionally allows to save optimization jobs. - this is ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [fac58f] * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/Parser/FormatParserInterface.hpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XmlParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (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/moleculelist.cpp (modified) Converted FormatParser::save() to using vector of const atom ptrs. ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [a58c16] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/GraphAction/CorrectBondDegreeAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.def (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.def (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (modified) * src/Descriptors/AtomNameDescriptor.cpp (added) * src/Descriptors/AtomNameDescriptor.hpp (added) * src/Descriptors/AtomNameDescriptor_impl.hpp (added) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Filling/unittests/ClusterUnitTest.cpp (modified) * src/Filling/unittests/FillerUnitTest.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Makefile.am (modified) * src/Parameters/Specifics/Value_atom.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.cpp (modified) Replaced World::getAllAtoms() by const version where possible. Fri, 24 Jul 2015 16:44:34 GMT Frederik Heber [f01769] * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FillAction/SuspendInMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/RemoveAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Atom/AtomSet.hpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/AtomIdSet.cpp (modified) * src/AtomIdSet.hpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Filling/unittests/ClusterUnitTest.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Graph/AdjacencyList.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/BuildInducedSubgraph.hpp (modified) * src/Parameters/Specifics/Value_molecule.cpp (modified) * src/Parameters/StreamOperators.hpp (modified) * src/Parameters/Validators/Specific/AtomIdValidator.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.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/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.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/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AtomIdSetUnitTest.cpp (modified) Replaced World::getAtom() wherever possible by const version. - ... Thu, 21 Aug 2014 06:43:46 GMT Frederik Heber [748fc7] * src/Actions/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/builder_init.cpp (modified) * src/unittests/Makefile.am (modified) libMolecuilder is now a shared library. - linking error ... Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [e9e86f] * src/Actions/unittests/Makefile.am (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) FIX: UnitTestMain placed into convenience libUnitTest. - removed ... Wed, 20 Aug 2014 12:58:30 GMT Frederik Heber [4e65af] * src/Parser/PdbParser.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) FIX: PdbParser would write coordinates 4.1000 instead of 5.000. - ... 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. ... Wed, 17 Apr 2013 18:56:32 GMT Frederik Heber [708277] * configure.ac (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomObserver.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.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/ShapeRegistry.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/cleanUp.cpp (modified) * src/molecule.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) FIX: Using fixed Observer in CodePatterns 1.2.6. - we now require ... Mon, 18 Mar 2013 13:31:46 GMT Frederik Heber [105b72] * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.hpp (modified) FIX: PdbParser skipped when coordinate exceeded 9999.999. - the ... Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber [a2f5e5] * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/Psi3Parser.hpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) FIX: Cleaned up includes in Psi3Parser_Parameters. Fri, 14 Dec 2012 14:29:34 GMT Frederik Heber [7ace68] * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser.hpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * tests/regression/Parser/Psi3/pre/testtwocon.psi (modified) * tests/regression/Parser/Psi3/pre/testuhf.psi (modified) Added multiplicity guesser for Psi3Parser's UHF. - TESTFIX: changed ... Fri, 14 Dec 2012 13:02:50 GMT Frederik Heber [05e2ed] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo/pre/bio.data (added) * tests/regression/Parser/Tremolo/pre/bio.potentials (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-improper.at (added) * tests/regression/Parser/testsuite-parser.at (modified) FIX: TremoloParser did not load/save imprData or torsion correctly. ... Wed, 26 Sep 2012 17:24:47 GMT Frederik Heber [94d5ac6] * LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Line.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LinePoint.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Plane.cpp (modified) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Space.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Vector.cpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (modified) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (modified) * LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (modified) * LinearAlgebra/src/unittests/LineUnitTest.cpp (modified) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (modified) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (modified) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (modified) * LinearAlgebra/src/unittests/PlaneUnitTest.cpp (modified) * LinearAlgebra/src/unittests/RealSpaceMatrixUnitTest.cpp (modified) * LinearAlgebra/src/unittests/TestRunnerMain.cpp (modified) * LinearAlgebra/src/unittests/UnitTestMain.cpp (modified) * LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (modified) * LinearAlgebra/src/unittests/VectorSetUnitTest.cpp (modified) * LinearAlgebra/src/unittests/VectorUnitTest.cpp (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpRedistributeAction.cpp (added) * src/Actions/CommandAction/HelpRedistributeAction.def (added) * src/Actions/CommandAction/HelpRedistributeAction.hpp (added) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSphericalSurfaceAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_SaturateDanglingBonds.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_graphnode.cpp (modified) * src/Atom/atom_graphnodeinfo.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_particleinfo.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (modified) * src/AtomIdSet.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/Box_BoundaryConditions.cpp (modified) * src/ControllerOptions_MPQCCommandJob.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomOrderDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Filling/Cluster.cpp (modified) * src/Filling/Filler.cpp (modified) * src/Filling/Generators/NodeGenerator.cpp (modified) * src/Filling/Inserter/Inserter.cpp (modified) * src/Filling/Inserter/RandomInserter.cpp (modified) * src/Filling/Inserter/SimpleInserter.cpp (modified) * src/Filling/Inserter/SurfaceInserter.cpp (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Filling/Mesh/Mesh.cpp (modified) * src/Filling/Predicates/AnyFillPredicate.cpp (modified) * src/Filling/Predicates/FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideSurface_FillPredicate.cpp (modified) * src/Filling/Predicates/IsValidInDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsVoidNode_FillPredicate.cpp (modified) * src/Filling/Predicates/Ops_FillPredicate.cpp (modified) * src/Filling/unittests/ClusterUnitTest.cpp (modified) * src/Filling/unittests/FillerUnitTest.cpp (modified) * src/Filling/unittests/IsInsideDomain_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsInsideSurface_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsValidInDomain_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsVoidNode_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/Ops_FillPredicateUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCCommandJob_MPQCData.cpp (modified) * src/Jobs/unittests/MPQCCommandJobUnitTest.cpp (modified) * src/Jobs/unittests/MPQCDataUnitTest.cpp (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp (modified) * src/LinkedCell/LinkedCell_Model_Update.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/tripleIndex.cpp (modified) * src/LinkedCell/unittests/LinkedCellUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomDataValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomIdValidator.cpp (modified) * src/Parameters/Validators/Specific/BoundaryConditionValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxLengthValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxVectorValidator.cpp (modified) * src/Parameters/Validators/Specific/FileSuffixValidator.cpp (modified) * src/Parameters/Validators/Specific/FormulaValidator.cpp (modified) * src/Parameters/Validators/Specific/KeyValueValidator.cpp (modified) * src/Parameters/Validators/Specific/MoleculeIdValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserFileValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/RandomNumberValidators.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixInvertibleValidator.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixSymmetricValidator.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorNotZeroValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorPositiveComponentsValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorZeroOneComponentsValidator.cpp (modified) * src/Parameters/unittests/ContinuousParameterTest.cpp (modified) * src/Parameters/unittests/ContinuousValueTest.cpp (modified) * src/Parameters/unittests/DiscreteParameterTest.cpp (modified) * src/Parameters/unittests/DiscreteValueTest.cpp (modified) * src/Parameters/unittests/Ops_ValidatorTest.cpp (modified) * src/Parameters/unittests/stubs/ActionNameValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxLengthValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxVectorValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/TimeStepPresentValidatorStub.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser_ElementKeys.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/ParserTremolo_ElementKeysUnitTest.cpp (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Server.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/BaseShapesUnitTest.cpp (modified) * src/Shapes/unittests/ShapeOpsUnitTest.cpp (modified) * src/Shapes/unittests/Shape_HomogeneousPointsUnitTest.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp (modified) * src/Tesselation/ApproximateShapeArea.cpp (modified) * src/Tesselation/ApproximateShapeVolume.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.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/EmptyCommandLineQuery.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/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FilesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQueryList.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RealSpaceMatrixQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FilesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RealSpaceMatrixTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.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/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/controller.cpp (modified) * src/controller_AddOn_MPQCCommandJob.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/poolworker.cpp (modified) * src/unittests/AtomIdSetUnitTest.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/Box_BoundaryConditionsUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/MoleculeUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * src/unittests/stubs/AtomStub.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) * tests/JobMarket/mpqc.cpp (modified) FIX: As we use GSL internally, we are as of now required to use GPL ... Wed, 26 Sep 2012 17:24:47 GMT Frederik Heber [eb0d77] * src/Actions/unittests/Makefile.am (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: Shared library libMolecuilderJobs needs to be given explicitly ... Wed, 26 Sep 2012 17:24:47 GMT Frederik Heber [e9dc19] * src/Parser/MpqcParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * tests/regression/Atoms/Add/post/test.in (modified) * tests/regression/Parser/Mpqc/post/doublewater.in (modified) * tests/regression/Parser/Mpqc/post/test.in (modified) FIX: MpqcParser now does not center the written set of atoms anymore. ... Wed, 26 Sep 2012 17:24:47 GMT Frederik Heber [e6e4a0] * src/Parser/TremoloParser.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * tests/regression/Atoms/Add/post/test.data (modified) * tests/regression/Parser/Tremolo-Potentials/post/test.data (modified) * tests/regression/Parser/Tremolo/post/test.data (modified) * tests/regression/Parser/Tremolo/pre/test.data (modified) FIX: TremoloParser did not treat key F properly in saveLine() and ... Mon, 18 Jun 2012 10:53:30 GMT Frederik Heber [ca331c] * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.def (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/output.data (added) * tests/regression/Parser/Tremolo-SetAtomdata/post/undo.data (added) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-resetatomdata.at (added) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at (modified) * tests/regression/Parser/Tremolo/post/water-neighbors.data (added) * tests/regression/Parser/testsuite-parser.at (modified) Added Undo/Redo capability to SetTremoloAtomdataAction. - ... Thu, 14 Jun 2012 09:02:58 GMT Frederik Heber [5a667d] * src/Parameters/Validators/Specific/AtomDataValidator.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) AtomDataValidator implemented, uses static ... Fri, 06 Apr 2012 11:46:15 GMT Frederik Heber [006e1e] * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ChangeTracker.hpp (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/UIElements/TextUI/TextWindow.cpp (modified) FIX: ChangeTracker has not been observing AtomObserver so far. - ... Fri, 06 Apr 2012 11:45:54 GMT Frederik Heber [23fd43] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) FIX: TremoloParser now contains usedFields_load and _save to allow ... Thu, 05 Apr 2012 15:55:48 GMT Frederik Heber [2034f3] * src/Atom/AtomicInfo.cpp (modified) * src/Atom/AtomicInfo.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (modified) * tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.potentials (added) * tests/regression/Molecules/Copy/post/tensid-undo.data (deleted) * tests/regression/Molecules/Copy/post/tensid.data (modified) * tests/regression/Molecules/Copy/pre/tensid.data (modified) * tests/regression/Molecules/Copy/pre/tensid.potentials (modified) * tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) * tests/regression/Molecules/CreateMicelle/post/tensid.data (modified) * tests/regression/Molecules/CreateMicelle/pre/tensid.data (modified) * tests/regression/Molecules/CreateMicelle/pre/tensid.potentials (modified) Added AtomInfo::charge along with getter and setter. - charge is ... Wed, 04 Apr 2012 11:32:30 GMT Frederik Heber [d2596b] * README (modified) * src/Parser/Makefile.am (modified) * src/Parser/ParserTypes.def (modified) * src/Parser/XmlParser.cpp (added) * src/Parser/XmlParser.hpp (added) * src/Parser/pugixml/pugiconfig.hpp (added) * src/Parser/pugixml/pugixml.cpp (added) * src/Parser/pugixml/pugixml.hpp (added) * src/Parser/pugixml/readme.txt (added) * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (added) * src/Parser/unittests/ParserXmlUnitTest.hpp (added) * tests/CodeChecks/testsuite-config_h.at (modified) * tests/CodeChecks/testsuite-memdebug.at (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) Added XmlParser for parsing configurations for ScaFaCoS generic test ... Tue, 03 Apr 2012 07:58:43 GMT Frederik Heber [ccb487] * src/Parser/TremoloParser.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * tests/regression/Domain/RepeatBox/post/ec.data (modified) * tests/regression/Domain/RepeatBox/pre/ec.data (modified) * tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/Copy/post/tensid-undo.data (modified) * tests/regression/Molecules/Copy/post/tensid.data (modified) * tests/regression/Molecules/Copy/pre/tensid.data (modified) * tests/regression/Molecules/CreateMicelle/post/tensid.data (modified) * tests/regression/Molecules/CreateMicelle/pre/tensid.data (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data (modified) TremoloParser now always writes current domain as "# Box ..." into ... Tue, 03 Apr 2012 07:58:43 GMT Frederik Heber [d9005c1] * src/Parser/Exceptions.hpp (added) * src/Parser/Makefile.am (modified) * src/Parser/TremoloParser_ElementKeys.cpp (added) * src/Parser/TremoloParser_ElementKeys.hpp (added) * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.cpp (added) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.hpp (added) Extracted TremoloParser::knownTypes into distinct class ElementKeys, ... Fri, 06 Jan 2012 14:02:08 GMT Frederik Heber [c0e28c] * src/Parser/FormatParser_common.cpp (modified) * src/Parser/FormatParser_common.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Mpqc/post/doublewater.in (added) * tests/regression/Parser/Mpqc/pre/water.in (added) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at (added) * tests/regression/Parser/Pcp/post/doubletest.conf (added) * tests/regression/Parser/Pcp/post/doublewater.conf (added) * tests/regression/Parser/Pcp/pre/water.conf (added) * tests/regression/Parser/Pcp/testsuite-parser-pcp-load-multiply.at (added) * tests/regression/Parser/Pdb/post/doublewater.pdb (added) * tests/regression/Parser/Pdb/pre/water.pdb (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load-multiply.at (added) * tests/regression/Parser/Psi3/post/doublewater.psi (added) * tests/regression/Parser/Psi3/pre/water.psi (added) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load-multiply.at (added) * tests/regression/Parser/Tremolo/post/doublewater.data (added) * tests/regression/Parser/Tremolo/pre/water.data (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at (added) * tests/regression/Parser/Xyz/post/doublewater.xyz (added) * tests/regression/Parser/Xyz/pre/water.xyz (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load-multiply.at (added) * tests/regression/Parser/testsuite-parser.at (modified) FIX: One could not load another pdb file due to local ids messing up. ... Wed, 04 Jan 2012 14:28:40 GMT Frederik Heber [0aa122] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_graphnode.cpp (modified) * src/Atom/atom_graphnodeinfo.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_particleinfo.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp (modified) * src/LinkedCell/LinkedCell_Model_Update.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/tripleIndex.cpp (modified) * src/LinkedCell/unittests/LinkedCellUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/AtomStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldStub.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/StringParameter.cpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.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/ParserXyzUnitTest.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/ShapeUnitTest.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.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/BoxCommandLineQuery.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/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.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/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/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/AtomQuery.cpp (modified) * src/UIElements/Query/AtomsQuery.cpp (modified) * src/UIElements/Query/BooleanQuery.cpp (modified) * src/UIElements/Query/BoxQuery.cpp (modified) * src/UIElements/Query/DoubleQuery.cpp (modified) * src/UIElements/Query/DoublesQuery.cpp (modified) * src/UIElements/Query/ElementQuery.cpp (modified) * src/UIElements/Query/ElementsQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/FileQuery.cpp (modified) * src/UIElements/Query/IntQuery.cpp (modified) * src/UIElements/Query/IntsQuery.cpp (modified) * src/UIElements/Query/MoleculeQuery.cpp (modified) * src/UIElements/Query/MoleculesQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp (modified) * src/UIElements/Query/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.cpp (modified) * src/UIElements/Query/UnsignedIntQuery.cpp (modified) * src/UIElements/Query/UnsignedIntsQuery.cpp (modified) * src/UIElements/Query/VectorQuery.cpp (modified) * src/UIElements/Query/VectorsQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.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/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) Updated all source files's copyright note to current year 2012. Wed, 28 Dec 2011 15:30:06 GMT Frederik Heber [6f0841] * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Atom/AtomSet.hpp (moved) * src/Atom/AtomicInfo.cpp (moved) * src/Atom/AtomicInfo.hpp (moved) * src/Atom/Makefile.am (added) * src/Atom/TesselPoint.cpp (moved) * src/Atom/TesselPoint.hpp (moved) * src/Atom/atom.cpp (moved) * src/Atom/atom.hpp (moved) * src/Atom/atom_atominfo.cpp (moved) * src/Atom/atom_atominfo.hpp (moved) * src/Atom/atom_bondedparticle.cpp (moved) * src/Atom/atom_bondedparticle.hpp (moved) * src/Atom/atom_bondedparticleinfo.cpp (moved) * src/Atom/atom_bondedparticleinfo.hpp (moved) * src/Atom/atom_graphnode.cpp (moved) * src/Atom/atom_graphnode.hpp (moved) * src/Atom/atom_graphnodeinfo.cpp (moved) * src/Atom/atom_graphnodeinfo.hpp (moved) * src/Atom/atom_observable.cpp (moved) * src/Atom/atom_observable.hpp (moved) * src/Atom/atom_particleinfo.cpp (moved) * src/Atom/atom_particleinfo.hpp (moved) * src/Bond/bond.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/LinkedCell/PointCloudAdaptor.hpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/Makefile.am (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/TremoloParser.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/ParserXyzUnitTest.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Thermostat.hpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) Shifted all modules related to atoms into own subfolder src/Atom/ - ... Wed, 28 Dec 2011 15:24:58 GMT Frederik Heber [d103d3] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/AtomicInfo.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/StringParameter.cpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.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/ParserXyzUnitTest.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/ShapeUnitTest.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/TesselPoint.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.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/BoxCommandLineQuery.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/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.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/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/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/AtomQuery.cpp (modified) * src/UIElements/Query/AtomsQuery.cpp (modified) * src/UIElements/Query/BooleanQuery.cpp (modified) * src/UIElements/Query/BoxQuery.cpp (modified) * src/UIElements/Query/DoubleQuery.cpp (modified) * src/UIElements/Query/DoublesQuery.cpp (modified) * src/UIElements/Query/ElementQuery.cpp (modified) * src/UIElements/Query/ElementsQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/FileQuery.cpp (modified) * src/UIElements/Query/IntQuery.cpp (modified) * src/UIElements/Query/IntsQuery.cpp (modified) * src/UIElements/Query/MoleculeQuery.cpp (modified) * src/UIElements/Query/MoleculesQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp (modified) * src/UIElements/Query/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.cpp (modified) * src/UIElements/Query/UnsignedIntQuery.cpp (modified) * src/UIElements/Query/UnsignedIntsQuery.cpp (modified) * src/UIElements/Query/VectorQuery.cpp (modified) * src/UIElements/Query/VectorsQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.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/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_observable.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) Added additional check in CodeCheck's project disclaimer for current ... Thu, 20 Oct 2011 22:42:16 GMT Frederik Heber [360c8b] * configure.ac (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/Parser/FormatParserInterface.hpp (added) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/FormatParserTrait.hpp (added) * src/Parser/FormatParserTrait_specializations_header.hpp (added) * src/Parser/FormatParser_Parameters.cpp (added) * src/Parser/FormatParser_Parameters.hpp (modified) * src/Parser/FormatParser_common.cpp (moved) * src/Parser/FormatParser_common.hpp (added) * src/Parser/FormatParser_specializations_header.hpp (added) * src/Parser/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/Parameters/ContinuousParameter.hpp (added) * src/Parser/Parameters/ContinuousParameter_impl.hpp (added) * src/Parser/Parameters/ContinuousValue.hpp (added) * src/Parser/Parameters/ContinuousValue_impl.hpp (added) * src/Parser/Parameters/DiscreteParameter.hpp (added) * src/Parser/Parameters/DiscreteParameter_impl.hpp (added) * src/Parser/Parameters/DiscreteValue.hpp (added) * src/Parser/Parameters/DiscreteValue_impl.hpp (added) * src/Parser/Parameters/Parameter.hpp (added) * src/Parser/Parameters/ParameterStorage.cpp (added) * src/Parser/Parameters/ParameterStorage.hpp (added) * src/Parser/Parameters/StringParameter.cpp (added) * src/Parser/Parameters/StringParameter.hpp (added) * src/Parser/Parameters/ValueInterface.hpp (added) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (added) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.hpp (added) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (added) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.hpp (added) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (added) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.hpp (added) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (added) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.hpp (added) * src/Parser/Parameters/unittests/Makefile.am (added) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (added) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.hpp (added) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (added) * src/Parser/Parameters/unittests/StringParameterUnitTest.hpp (added) * src/Parser/ParserTypes.cpp (added) * src/Parser/ParserTypes.def (added) * src/Parser/ParserTypes.hpp (added) * src/Parser/ParserTypes.undef (added) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Parser/PdbAtomInfoContainer.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/Psi3Parser.cpp (added) * src/Parser/Psi3Parser.hpp (added) * src/Parser/Psi3Parser_Parameters.cpp (added) * src/Parser/Psi3Parser_Parameters.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.hpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.hpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.hpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (added) * src/Parser/unittests/ParserPsi3UnitTest.hpp (added) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.hpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/moleculelist.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Psi3/post/empty.psi (added) * tests/regression/Parser/Psi3/post/test.psi (added) * tests/regression/Parser/Psi3/pre/empty.psi (added) * tests/regression/Parser/Psi3/pre/test.xyz (added) * tests/regression/Parser/Psi3/pre/testrhf.psi (added) * tests/regression/Parser/Psi3/pre/testrohf.psi (added) * tests/regression/Parser/Psi3/pre/testtwocon.psi (added) * tests/regression/Parser/Psi3/pre/testuhf.psi (added) * tests/regression/Parser/Psi3/testsuite-parser-psi3-empty.at (added) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load.at (added) * tests/regression/Parser/Psi3/testsuite-parser-psi3-save.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Merge branch 'Adding_Psi3Parser' into stable Conflicts: ... Tue, 18 Oct 2011 08:23:11 GMT Frederik Heber [d640ea] * src/Parser/Psi3Parser.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) Implemented Psi3Parser::save(). - also we now have working unit ... Tue, 18 Oct 2011 08:22:49 GMT Frederik Heber [120a86] * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) TESTFIX: Added check whether streams are empty to ... Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber [a67cf0] * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) Renamed Psi3Parser_Parameters::multipParam to ::multiplicityParam. Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber [032f31] * src/Parser/Psi3Parser.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) Implemented Psi3Parser::load(). - also we now have working unit ... Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber [f758dd] * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) ParserPsi3UnitTest::ParameterSetterTest() is working. Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber [154a45] * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.hpp (modified) ParserPsi3UnitTest::ParameterCloneTest() is working. Mon, 17 Oct 2011 16:56:36 GMT Frederik Heber [1bef07] * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/Makefile.am (modified) * src/Parser/ParserTypes.def (modified) * src/Parser/Psi3Parser.cpp (added) * src/Parser/Psi3Parser.hpp (added) * src/Parser/Psi3Parser_Parameters.cpp (added) * src/Parser/Psi3Parser_Parameters.hpp (added) * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (added) * src/Parser/unittests/ParserPsi3UnitTest.hpp (added) Added first working version of a Psi3Parser. - is so far mostly ... Mon, 17 Oct 2011 16:56:36 GMT Frederik Heber [ee50c1] * src/Parser/FormatParser_Parameters.cpp (added) * src/Parser/FormatParser_Parameters.hpp (modified) * src/Parser/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.hpp (modified) Complete rewrite of MpqcParser_Parameters to incorporate new ... Mon, 17 Oct 2011 16:18:54 GMT Frederik Heber [3bdb6d] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/AtomicInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/Hbondangle.db (moved) * src/Element/Hbonddistance.db (moved) * src/Element/Makefile.am (added) * src/Element/element.cpp (moved) * src/Element/element.hpp (moved) * src/Element/elements.db (moved) * src/Element/elements_db.cpp (moved) * src/Element/elements_db.hpp (moved) * src/Element/orbitals.db (moved) * src/Element/periodentafel.cpp (moved) * src/Element/periodentafel.hpp (moved) * src/Element/valence.db (moved) * src/Formula.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.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/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/TextWindow.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/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ElementUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/PeriodentafelUnitTest.cpp (modified) Moved all stuff related to elements into own subfolder and has its ... Mon, 17 Oct 2011 14:36:56 GMT Frederik Heber [84e752] * src/Parser/Makefile.am (modified) * src/Parser/Parameters/ContinuousValue.hpp (moved) * src/Parser/Parameters/ContinuousValue_impl.hpp (moved) * src/Parser/Parameters/DiscreteValue.hpp (moved) * src/Parser/Parameters/DiscreteValue_impl.hpp (moved) * src/Parser/Parameters/ValueInterface.hpp (moved) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (moved) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.hpp (moved) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (moved) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.hpp (moved) * src/Parser/Parameters/unittests/Makefile.am (added) * src/Parser/unittests/Makefile.am (modified) Moved Continuous- and DiscreteValue into subfolder Parameters. - ... Mon, 17 Oct 2011 14:36:47 GMT Frederik Heber [a7d753] * src/Parser/ContinuousValue.hpp (added) * src/Parser/ContinuousValue_impl.hpp (added) * src/Parser/DiscreteValue.hpp (modified) * src/Parser/DiscreteValue_impl.hpp (modified) * src/Parser/ValueInterface.hpp (added) * src/Parser/unittests/ContinuousValueUnitTest.cpp (added) * src/Parser/unittests/ContinuousValueUnitTest.hpp (added) * src/Parser/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/unittests/DiscreteValueUnitTest.hpp (modified) * src/Parser/unittests/Makefile.am (modified) Extended DiscreteValue to ContinuousValue and added ValueInterface ... Mon, 17 Oct 2011 14:31:00 GMT Frederik Heber [3308b6] * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) FIX: 3 out of 4 unit tests have not been told to throw ... Mon, 17 Oct 2011 14:30:55 GMT Frederik Heber [e09d67] * src/Parser/DiscreteValue.hpp (added) * src/Parser/DiscreteValue_impl.hpp (added) * src/Parser/unittests/DiscreteValueUnitTest.cpp (added) * src/Parser/unittests/DiscreteValueUnitTest.hpp (added) * src/Parser/unittests/Makefile.am (modified) Added class DiscreteValue that contains enums. - class has ... Fri, 14 Oct 2011 15:15:30 GMT Frederik Heber [765f16] * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/Parser/FormatParserInterface.hpp (added) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/FormatParserTrait.hpp (added) * src/Parser/FormatParserTrait_specializations_header.hpp (added) * src/Parser/FormatParser_common.cpp (moved) * src/Parser/FormatParser_common.hpp (added) * src/Parser/FormatParser_specializations_header.hpp (added) * src/Parser/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/ParserTypes.cpp (added) * src/Parser/ParserTypes.def (added) * src/Parser/ParserTypes.hpp (modified) * src/Parser/ParserTypes.undef (added) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Parser/PdbAtomInfoContainer.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.hpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.hpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.hpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.hpp (modified) * src/moleculelist.cpp (modified) Huge Refactoring of FormatParserStorage and all FormatParser's. ... Mon, 10 Oct 2011 14:27:06 GMT Frederik Heber [c1db05] * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/Parser/FormatParser_Parameters.hpp (added) * src/Parser/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.hpp (modified) Abstracted FormatParser_Parameters and made it "Clone"able. - this ... Fri, 30 Sep 2011 08:19:37 GMT Frederik Heber [79de12] * LinearAlgebra/configure.ac (modified) * LinearAlgebra/src/unittests/Makefile.am (modified) * configure.ac (modified) * m4/ax_boost_base.m4 (deleted) * m4/ax_boost_filesystem.m4 (deleted) * m4/ax_boost_program_options.m4 (deleted) * m4/ax_boost_system.m4 (deleted) * m4/ax_codepatterns.m4 (modified) * m4/boost.m4 (added) * m4/m4_ax_boost_thread.m4 (deleted) * src/Descriptors/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Replaced *_boost_*.m4 by boost.m4 from tsuna. - ... Mon, 18 Apr 2011 12:45:06 GMT Frederik Heber [305e7e] * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloAtomInfoContainer.hpp (modified) * src/Parser/TremoloKey.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * tests/regression/Atoms/Add/post/test.data (modified) * tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/pre/water.data (modified) * tests/regression/Molecules/Copy/post/tensid.data (modified) * tests/regression/Molecules/Copy/pre/tensid.data (modified) * tests/regression/Parser/Tremolo-Potentials/post/argon.data (modified) * tests/regression/Parser/Tremolo-Potentials/post/test.data (modified) * tests/regression/Parser/Tremolo-Potentials/pre/argon.data (modified) * tests/regression/Parser/Tremolo/post/argon.data (modified) * tests/regression/Parser/Tremolo/post/test.data (modified) * tests/regression/Parser/Tremolo/pre/argon.data (modified) * tests/regression/Parser/Tremolo/pre/test.data (modified) FIX: Type is actually spelled type with TREMOLO. - corrected in ... Mon, 18 Apr 2011 12:45:06 GMT Frederik Heber [455573] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Large Commit: SUBDIRS in src/Makefile.am replaced by include. - ... Fri, 08 Apr 2011 15:48:50 GMT Frederik Heber [bf4b9f] * LinearAlgebra/.gitignore (added) * LinearAlgebra/AUTHORS (added) * LinearAlgebra/COPYING (added) * LinearAlgebra/ChangeLog (added) * LinearAlgebra/INSTALL (added) * LinearAlgebra/LinearAlgebra-debug.pc.in (added) * LinearAlgebra/LinearAlgebra.pc.in (moved) * LinearAlgebra/Makefile.am (added) * LinearAlgebra/NEWS (added) * LinearAlgebra/README (added) * LinearAlgebra/bootstrap (added) * LinearAlgebra/build-aux/README (added) * LinearAlgebra/configure.ac (added) * LinearAlgebra/doc/Doxyfile (added) * LinearAlgebra/doc/Makefile.am (added) * LinearAlgebra/libLinearAlgebra_config.h.in (added) * LinearAlgebra/m4 (added) * LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (moved) * LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Exceptions.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Makefile.am (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.hpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Vector.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Vector.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorContent.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorInterface.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (moved) * LinearAlgebra/src/LinearAlgebra/defs.hpp (moved) * LinearAlgebra/src/LinearAlgebra/fast_functions.hpp (moved) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (moved) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.hpp (moved) * LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (moved) * LinearAlgebra/src/LinearAlgebra/vector_ops.hpp (moved) * LinearAlgebra/src/unittests/LineUnitTest.cpp (moved) * LinearAlgebra/src/unittests/LineUnitTest.hpp (moved) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (moved) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.hpp (moved) * LinearAlgebra/src/unittests/Makefile.am (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.hpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.cpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.hpp (moved) * LinearAlgebra/src/unittests/TestRunnerMain.cpp (added) * LinearAlgebra/src/unittests/UnitTestMain.cpp (added) * LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.hpp (moved) * LinearAlgebra/tests/CodeChecks/Makefile.am (added) * LinearAlgebra/tests/CodeChecks/atlocal.in (added) * LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (added) * LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (added) * LinearAlgebra/tests/CodeChecks/testsuite.at (added) * Makefile.am (modified) * bootstrap (modified) * build-aux/README (added) * config/depcomp (deleted) * config/install-sh (deleted) * config/ltmain.sh (deleted) * config/missing (deleted) * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved LinearAlgebra from folder src/ into distinct sub-package. - ... Wed, 06 Apr 2011 13:50:42 GMT Frederik Heber [3e2225f] * configure.ac (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Exceptions/CustomException.cpp (deleted) * src/Exceptions/CustomException.hpp (deleted) * src/Exceptions/Makefile.am (deleted) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Removed subdir Exceptions and libMolecuilderExceptions. - changes ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [255829] * configure.ac (modified) * src/BoundaryPolygonSet.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/OutputTemperature.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Formula.hpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Helpers/Makefile.am (deleted) * src/Helpers/defs.hpp (modified) * src/Helpers/helpers.cpp (deleted) * src/Helpers/helpers.hpp (modified) * src/Makefile.am (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.hpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/TesselationUnitTest.cpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) Removed Helpers.hpp, deleted Helpers.cpp and libMoleCuilderHelpers.la ... Tue, 01 Mar 2011 10:16:37 GMT Frederik Heber [0180d6] * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.hpp (modified) * tests/regression/Parser/Xyz/post/testmulti.xyz (added) * tests/regression/Parser/Xyz/pre/testmulti.xyz (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz.at (modified) Enhanced XyzParser to load and save multiple time steps. - Extended ... Thu, 24 Feb 2011 19:47:41 GMT Frederik Heber [6a465e] * src/ConfigFileBuffer.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/config.cpp (modified) * tests/regression/Molecules/SaveTemperature/post/test.ekin (modified) Rewrote LoadMolecule() for PcpParser. - LoadMolecule() rewritten as ... Thu, 24 Feb 2011 19:26:14 GMT Frederik Heber [073a9e4] * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/molecule.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) BondedParticle::(Un)RegisterBond,AddBond,IsBondedTo with step. - ... Thu, 24 Feb 2011 16:30:56 GMT Frederik Heber [bce72c] * src/AtomicInfo.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) AtomicInfo::AtomicVelocity and ::AtomicForce are now private. - ... Thu, 10 Feb 2011 19:08:22 GMT Frederik Heber [b6b3b2] * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) Merge branch 'MpqcParser_fixes' into stable Thu, 10 Feb 2011 18:58:48 GMT Frederik Heber [311da7b] * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) FIX: Changed MpqcParser. - some ASSERTs were missing and showed up ... Wed, 09 Feb 2011 17:25:13 GMT Frederik Heber [4d4d33] * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (added) * src/Actions/ParserAction/ParseTremoloPotentialsAction.def (added) * src/Actions/ParserAction/ParseTremoloPotentialsAction.hpp (added) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloAtomInfoContainer.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) Added tremolo's potential file parsing, reported by Daniel Dueck. ... Mon, 07 Feb 2011 10:43:41 GMT Frederik Heber [44fce5] * src/Parser/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (added) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.hpp (modified) Extended MpqcParser_Parameters, can set and get all values. - new ... Mon, 07 Feb 2011 10:43:35 GMT Frederik Heber [61d69a4] * src/Parser/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/MpqcParser_Parameters.cpp (added) * src/Parser/MpqcParser_Parameters.hpp (added) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.hpp (modified) * tests/regression/Atoms/Add/post/test.in (modified) * tests/regression/Atoms/Remove/post/test.in (modified) * tests/regression/Parser/Mpqc/post/test.in (modified) Added MpqcParser_Parameter class to MpqcParser. - contains all ... Mon, 07 Feb 2011 10:27:23 GMT Frederik Heber [aa8ef2] * src/Parser/MpqcParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.hpp (modified) Implemented MpqcParser::load(). - extended ParserMpqcUnitTest to ... Mon, 07 Feb 2011 10:27:23 GMT Frederik Heber [f31edc] * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) Extended MpqcParser to write config files for all possible theory ... Mon, 07 Feb 2011 10:27:18 GMT Frederik Heber [bb74ba] * 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/test.in (modified) * tests/regression/Parser/Mpqc/pre/test.in (modified) MpqcParser now writes correct MP2 configuration. - while the ... Mon, 07 Feb 2011 10:25:52 GMT Frederik Heber [9e4fd1] * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserCommonUnitTest.hpp (deleted) * src/Parser/unittests/ParserMpqcUnitTest.cpp (added) * src/Parser/unittests/ParserMpqcUnitTest.hpp (added) * src/Parser/unittests/ParserPcpUnitTest.cpp (moved) * src/Parser/unittests/ParserPcpUnitTest.hpp (added) * src/Parser/unittests/ParserPdbUnitTest.cpp (added) * src/Parser/unittests/ParserPdbUnitTest.hpp (added) * src/Parser/unittests/ParserXyzUnitTest.cpp (added) * src/Parser/unittests/ParserXyzUnitTest.hpp (added) * src/unittests/Makefile.am (modified) Split up ParserCommonUnitTest into a UnitTest for each Parser. Thu, 03 Feb 2011 09:59:28 GMT Frederik Heber [1ee3b8d] * configure.ac (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/LinearAlgebra/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (added) * src/RandomNumbers/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Made RandomNumbers sources into its own library ... Thu, 23 Dec 2010 17:41:54 GMT Frederik Heber [6d2207] * configure.ac (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (added) * src/Shapes/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: Forgot Shapes/unittests and made Shapes into own library. - ... Thu, 23 Dec 2010 17:41:54 GMT Frederik Heber [acbe1b] * MoleCuilder.pc.in (added) * configure.ac (modified) * molecuilder.pc.in (deleted) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Exceptions/Makefile.am (modified) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/unittests/Makefile.am (modified) All libraries don't have version in name anymore. - we used gained ... Thu, 23 Dec 2010 17:40:13 GMT Frederik Heber [56f73b] * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp (modified) * src/Actions/AtomAction/TranslateAction.hpp (modified) * src/Actions/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/BondLengthTableAction.hpp (modified) * src/Actions/CommandAction/ElementDbAction.hpp (modified) * src/Actions/CommandAction/FastParsingAction.hpp (modified) * src/Actions/CommandAction/HelpAction.hpp (modified) * src/Actions/CommandAction/VerboseAction.hpp (modified) * src/Actions/CommandAction/VersionAction.hpp (modified) * src/Actions/CommandAction/WarrantyAction.hpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.hpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.hpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/CopyAction.hpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified) * src/Actions/MoleculeAction/LoadAction.hpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Actions/MoleculeAction/SaveAction.hpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/OptionRegistry.hpp (modified) * src/Actions/OptionTrait.hpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.hpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.hpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.hpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.hpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.hpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.hpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.hpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.hpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.hpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.hpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.hpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.hpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.hpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.hpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.hpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.hpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.hpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.hpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.hpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/ValueStorage.hpp (modified) * src/Actions/Values.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.hpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.hpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.hpp (modified) * src/AtomSet.hpp (modified) * src/AtomicInfo.hpp (modified) * src/BoundaryLineSet.hpp (modified) * src/BoundaryMaps.hpp (modified) * src/BoundaryPointSet.hpp (modified) * src/BoundaryPolygonSet.hpp (modified) * src/BoundaryTriangleSet.hpp (modified) * src/Box.hpp (modified) * src/CandidateForTesselation.hpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/AtomIdDescriptor.hpp (modified) * src/Descriptors/AtomIdDescriptor_impl.hpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.hpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp (modified) * src/Descriptors/AtomSelectionDescriptor.hpp (modified) * src/Descriptors/AtomSelectionDescriptor_impl.hpp (modified) * src/Descriptors/AtomShapeDescriptor.hpp (modified) * src/Descriptors/AtomShapeDescriptor_impl.hpp (modified) * src/Descriptors/AtomTypeDescriptor.hpp (modified) * src/Descriptors/AtomTypeDescriptor_impl.hpp (modified) * src/Descriptors/DescriptorBase.hpp (modified) * src/Descriptors/DescriptorBase_impl.hpp (modified) * src/Descriptors/MoleculeDescriptor.hpp (modified) * src/Descriptors/MoleculeDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.hpp (modified) * src/Descriptors/MoleculeFormulaDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeIdDescriptor.hpp (modified) * src/Descriptors/MoleculeIdDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeNameDescriptor.hpp (modified) * src/Descriptors/MoleculeNameDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.hpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeOrderDescriptor.hpp (modified) * src/Descriptors/MoleculeOrderDescriptor_impl.hpp (modified) * src/Descriptors/MoleculePtrDescriptor.hpp (modified) * src/Descriptors/MoleculePtrDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.hpp (modified) * src/Descriptors/MoleculeSelectionDescriptor_impl.hpp (modified) * src/Descriptors/SelectiveIterator.hpp (modified) * src/Descriptors/SelectiveIterator_impl.hpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.hpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.hpp (modified) * src/Exceptions/CustomException.hpp (modified) * src/Exceptions/IllegalTypeException.hpp (modified) * src/Exceptions/LinearDependenceException.hpp (modified) * src/Exceptions/MathException.hpp (modified) * src/Exceptions/MissingValueException.hpp (modified) * src/Exceptions/MultipleSolutionsException.hpp (modified) * src/Exceptions/NotInvertibleException.hpp (modified) * src/Exceptions/NotOnSurfaceException.hpp (modified) * src/Exceptions/ParseError.hpp (modified) * src/Exceptions/ShapeException.hpp (modified) * src/Exceptions/SkewException.hpp (modified) * src/Exceptions/ZeroVectorException.hpp (modified) * src/Formula.hpp (modified) * src/Helpers/defs.hpp (modified) * src/Helpers/fast_functions.hpp (modified) * src/LinearAlgebra/BoxVector.hpp (modified) * src/LinearAlgebra/Eigenspace.hpp (modified) * src/LinearAlgebra/Line.hpp (modified) * src/LinearAlgebra/LineSegment.hpp (modified) * src/LinearAlgebra/LineSegmentSet.hpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/MatrixVector_ops.hpp (modified) * src/LinearAlgebra/Plane.hpp (modified) * src/LinearAlgebra/RealSpaceMatrix.hpp (modified) * src/LinearAlgebra/Space.hpp (modified) * src/LinearAlgebra/Subspace.hpp (modified) * src/LinearAlgebra/VectorContent.hpp (modified) * src/LinearAlgebra/VectorInterface.hpp (modified) * src/LinearAlgebra/VectorSet.hpp (modified) * src/LinearAlgebra/unittests/LineUnitTest.hpp (modified) * src/LinearAlgebra/unittests/LinearSystemOfEquationsUnitTest.hpp (modified) * src/LinearAlgebra/unittests/MatrixContentSymmetricUnitTest.hpp (modified) * src/LinearAlgebra/unittests/MatrixContentUnitTest.hpp (modified) * src/LinearAlgebra/unittests/MatrixUnitTest.hpp (modified) * src/LinearAlgebra/unittests/PlaneUnitTest.hpp (modified) * src/LinearAlgebra/unittests/VectorContentUnitTest.hpp (modified) * src/LinearAlgebra/unittests/VectorUnitTest.hpp (modified) * src/LinearAlgebra/vector_ops.hpp (modified) * src/Parser/ChangeTracker.hpp (modified) * src/Parser/FormatParser.hpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Parser/PdbAtomInfoContainer.hpp (modified) * src/Parser/PdbKey.hpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/TremoloAtomInfoContainer.hpp (modified) * src/Parser/TremoloKey.hpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.hpp (modified) * src/Parser/unittests/ParserCommonUnitTest.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.hpp (modified) * src/PointCloud.hpp (modified) * src/Shapes/BaseShapes.hpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.hpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/Shape_impl.hpp (modified) * src/Shapes/unittests/ShapeUnitTest.hpp (modified) * src/SubspaceFactorizer.cpp (modified) * src/TesselPoint.hpp (modified) * src/Thermostats/Berendsen.hpp (modified) * src/Thermostats/GaussianThermostat.hpp (modified) * src/Thermostats/Langevin.hpp (modified) * src/Thermostats/NoThermostat.hpp (modified) * src/Thermostats/NoseHoover.hpp (modified) * src/Thermostats/Thermostat.hpp (modified) * src/Thermostats/Woodcock.hpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.hpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.hpp (modified) * src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.hpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/MainWindow.hpp (modified) * src/UIElements/Menu/Menu.hpp (modified) * src/UIElements/Menu/MenuDescription.hpp (modified) * src/UIElements/Menu/MenuInterface.hpp (modified) * src/UIElements/Menu/Qt4/QtMenu.hpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.hpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.hpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/QtQueryListPipe.hpp (modified) * src/UIElements/Qt4/Pipe/QtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.hpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Qt4/QtUIFactory.hpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/TextUI/Query/TextQuery.hpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/TextUI/TextStatusIndicator.hpp (modified) * src/UIElements/TextUI/TextUIFactory.hpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/UIElements/Views/MethodStringView.hpp (modified) * src/UIElements/Views/Qt4/GLMoleculeView.hpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.hpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.hpp (modified) * src/UIElements/Views/Qt4/QtWorldView.hpp (modified) * src/UIElements/Views/StreamStringView.hpp (modified) * src/UIElements/Views/StringView.hpp (modified) * src/UIElements/Views/View.hpp (modified) * src/World_calculations.hpp (modified) * src/builder_init.hpp (modified) * src/datacreator.hpp (modified) * src/elements_db.hpp (modified) * src/lists.hpp (modified) * src/types.hpp (modified) * src/unittests/AnalysisBondsUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * src/unittests/BondGraphUnitTest.hpp (modified) * src/unittests/BoxUnitTest.hpp (modified) * src/unittests/CountBondsUnitTest.hpp (modified) * src/unittests/DummyUI.hpp (modified) * src/unittests/FormulaUnitTest.hpp (modified) * src/unittests/LinkedCellUnitTest.hpp (modified) * src/unittests/ListOfBondsUnitTest.hpp (modified) * src/unittests/PeriodentafelUnitTest.hpp (modified) * src/unittests/SubspaceFactorizerUnitTest.hpp (modified) * src/unittests/TesselationUnitTest.hpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified) * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-config_h.at (added) * tests/CodeChecks/testsuite-memdebug.at (added) * tests/CodeChecks/testsuite.at (modified) Added config.h also to all header files, code check test ascertain ... Thu, 23 Dec 2010 17:40:04 GMT Frederik Heber [a0064e] * configure.ac (modified) * m4/ax_codepatterns.m4 (added) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Exceptions/Makefile.am (modified) * src/Formula.hpp (modified) * src/Helpers/Assert.cpp (deleted) * src/Helpers/Assert.hpp (deleted) * src/Helpers/Info.cpp (deleted) * src/Helpers/Info.hpp (deleted) * src/Helpers/Log.cpp (deleted) * src/Helpers/Log.hpp (deleted) * src/Helpers/Makefile.am (deleted) * src/Helpers/MemDebug.cpp (deleted) * src/Helpers/MemDebug.hpp (deleted) * src/Helpers/Range.hpp (deleted) * src/Helpers/Verbose.cpp (deleted) * src/Helpers/Verbose.hpp (deleted) * src/Helpers/errorlogger.cpp (deleted) * src/Helpers/errorlogger.hpp (deleted) * src/Helpers/fast_functions.hpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/helpers.hpp (modified) * src/Helpers/logger.cpp (deleted) * src/Helpers/logger.hpp (deleted) * src/Helpers/toString.hpp (deleted) * src/Helpers/unittests/InfoUnitTest.cpp (deleted) * src/Helpers/unittests/InfoUnitTest.hpp (deleted) * src/Helpers/unittests/LogUnitTest.cpp (deleted) * src/Helpers/unittests/LogUnitTest.hpp (deleted) * src/Helpers/unittests/Makefile.am (deleted) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Patterns/Cacheable.hpp (deleted) * src/Patterns/ObservedContainer.hpp (deleted) * src/Patterns/ObservedContainer_impl.hpp (deleted) * src/Patterns/ObservedIterator.hpp (deleted) * src/Patterns/Observer.cpp (deleted) * src/Patterns/Observer.hpp (deleted) * src/Patterns/Registry.hpp (deleted) * src/Patterns/Registry_impl.hpp (deleted) * src/Patterns/Singleton.hpp (deleted) * src/Patterns/Singleton_impl.hpp (deleted) * src/Patterns/unittests/CacheableUnitTest.cpp (deleted) * src/Patterns/unittests/CacheableUnitTest.hpp (deleted) * src/Patterns/unittests/Makefile.am (deleted) * src/Patterns/unittests/ObserverUnitTest.cpp (deleted) * src/Patterns/unittests/ObserverUnitTest.hpp (deleted) * src/Patterns/unittests/RegistryUnitTest.cpp (deleted) * src/Patterns/unittests/RegistryUnitTest.hpp (deleted) * src/Patterns/unittests/SingletonUnitTest.cpp (deleted) * src/Patterns/unittests/SingletonUnitTest.hpp (deleted) * src/Shapes/unittests/Makefile.am (modified) * src/SubspaceFactorizer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/SubspaceFactorizerUnitTest.cpp (modified) Moved stuff in src/Helpers and src/Patterns out to stand-alone ... Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [41396a] * configure.ac (modified) * src/Parser/unittests/Makefile.am (added) * src/Parser/unittests/ParserCommonUnitTest.cpp (moved) * src/Parser/unittests/ParserCommonUnitTest.hpp (moved) * src/Parser/unittests/ParserTremoloUnitTest.cpp (moved) * src/Parser/unittests/ParserTremoloUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved Parser...UnitTest to Parser/unittests/Parser...UnitTest.