# # ChangeLog for src/molecule_fragmentation.cpp # # Generated by Trac 1.4.4 # Jan 1, 2025, 7:16:34 PM Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [7adf0f] * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) Removed molecule::BondDistance, replaced by ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [5309ba] * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPointSet.hpp (modified) * src/Helpers/helpers.hpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/bond.cpp (modified) * src/boundary.cpp (modified) * src/ellipsoid.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/tesselation.cpp (modified) Renamed ParticleInfo_nr back to Nr. - Note that this mostly ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [735b1c] * src/BoundaryPointSet.cpp (modified) * src/BoundaryPointSet.hpp (modified) * src/analysis_bonds.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/bond.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) ParticleInfo::ParticleInfo_nr is protected and accessed via ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [a479fa] * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPointSet.hpp (modified) * src/Helpers/helpers.hpp (modified) * src/analysis_bonds.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/bond.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/TesselationUnitTest.cpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) Renamed ParticleInfo::nr to ParticleInfo::ParticleInfo_nr for easier ... Thu, 24 Feb 2011 19:43:03 GMT Frederik Heber [03c77c] * src/ConfigFileBuffer.cpp (modified) * src/Makefile.am (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/bond.cpp (modified) * src/bond.hpp (modified) * src/config.cpp (modified) * src/graph.hpp (modified) * src/lists.hpp (deleted) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) bonds::previous and ::next removed, lists.hpp deleted. - the last ... Thu, 24 Feb 2011 18:51:32 GMT Frederik Heber [9d83b6] * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/WorldTime.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_bondedparticleinfo.hpp (modified) * src/boundary.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/ListOfBondsUnitTest.cpp (modified) BondedParticleInfo now has vector - vector ... Fri, 04 Feb 2011 18:56:38 GMT Frederik Heber [48d43f] * src/molecule_fragmentation.cpp (modified) molecule::FragmentMolecule() - Bond degree is now re-calculated by ... Fri, 04 Feb 2011 18:56:38 GMT Frederik Heber [3c58f8] * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) Changed molecule::ScanForPeriodicCorrection(). - it still used ... Fri, 04 Feb 2011 18:56:38 GMT Frederik Heber [00b59d5] * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) FIX: molecule::FragmentMolecule() did not remove copied atoms and ... Thu, 23 Dec 2010 17:40:13 GMT Frederik Heber [ad011c] * m4/ax_codepatterns.m4 (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTraits.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/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/ConstructBondGraphAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/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/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/SaveAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.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/OptionRegistry.hpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (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/ValueStorage.hpp (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/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/AtomicInfo.cpp (modified) * src/BoundaryLineSet.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPolygonSet.cpp (modified) * src/BoundaryTriangleSet.cpp (modified) * src/Box.cpp (modified) * src/CandidateForTesselation.cpp (modified) * src/ConfigFileBuffer.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/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MissingValueException.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (modified) * src/Exceptions/NotOnSurfaceException.cpp (modified) * src/Exceptions/ParseError.cpp (modified) * src/Exceptions/ShapeException.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Formula.cpp (modified) * src/Formula.hpp (modified) * src/Helpers/defs.cpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/helpers.hpp (modified) * src/LinearAlgebra/BoxVector.cpp (modified) * src/LinearAlgebra/Eigenspace.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/LineSegment.cpp (modified) * src/LinearAlgebra/LineSegmentSet.cpp (modified) * src/LinearAlgebra/LinearSystemOfEquations.cpp (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixVector_ops.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Subspace.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/VectorInterface.cpp (modified) * src/LinearAlgebra/leastsquaremin.cpp (modified) * src/LinearAlgebra/unittests/VectorUnitTest.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ChangeTracker.hpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/PointCloud.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/SubspaceFactorizer.cpp (modified) * src/TesselPoint.cpp (modified) * src/ThermoStatContainer.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/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (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/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.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/MenuDescription.hpp (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/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.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/QtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.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/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.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/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.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/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.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/TextStatusIndicator.hpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/GLMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.hpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.hpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.hpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (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_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/PeriodentafelUnitTest.cpp (modified) * src/unittests/SubspaceFactorizerUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) CodePatterns places all includes now in subfolder CodePatterns/. - ... 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 ... Mon, 06 Dec 2010 19:37:05 GMT Frederik Heber [a564be] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Makefile.am (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/stackclass.hpp (deleted) * src/unittests/Makefile.am (modified) * src/unittests/stackclassunittest.cpp (deleted) * src/unittests/stackclassunittest.hpp (deleted) Removed ancient StackClass, replaced by std::deque. - all PopLast ... Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber [cca9ef] * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * src/LinearAlgebra/Vector.hpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps.hpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/atom_atominfo.hpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.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/tesselationhelpers.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/BoxUnittest.hpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MatrixUnittest.hpp (modified) * src/unittests/vectorunittest.cpp (modified) Renamed Matrix to RealSpaceMatrix. - class Matrix only represents ... Thu, 26 Aug 2010 12:44:19 GMT Tillmann Crueger [32ea56] * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) Removed last occurences of molecule::SetIndexedArrayForEachAtomTo() Wed, 25 Aug 2010 12:25:28 GMT Tillmann Crueger [51c3e4] * AUTHORS (modified) * COPYING (modified) * README (modified) * autogen.sh (deleted) * bootstrap (added) * configure.ac (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.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/TranslateAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.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/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.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/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/AtomicInfo.cpp (modified) * src/BoundaryLineSet.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPolygonSet.cpp (modified) * src/BoundaryTriangleSet.cpp (modified) * src/Box.cpp (modified) * src/CandidateForTesselation.cpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.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/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MissingValueException.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (modified) * src/Exceptions/ParseError.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Formula.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/Info.cpp (modified) * src/Helpers/Log.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/Verbose.cpp (modified) * src/Helpers/errorlogger.cpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/logger.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Matrix.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorInterface.cpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/gslvector.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Makefile.am (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Observer.cpp (modified) * src/PointCloud.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/TesselPoint.cpp (modified) * src/ThermoStatContainer.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/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/QT4/QTMenu.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/QT4/QTUIFactory.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/GLMoleculeView.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/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.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_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.cpp (modified) * src/element.cpp (modified) * src/element.hpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/BaseShapesUnittest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/FormulaUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/MapofActionsTest.cpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/SingletonTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (modified) * src/unittests/gslmatrixunittest.cpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/memoryusageobserverunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/version.h (modified) * test_all.sh (modified) * tests/regression/Makefile.am (modified) * tests/regression/atlocal.in (modified) * tests/regression/molecuilder.in (modified) * tests/regression/testsuite.at (modified) Merge branch 'stable' into StructureRefactoring Conflicts: ... Thu, 19 Aug 2010 15:23:37 GMT Frederik Heber [83f176] * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/analysis_bonds.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/element.cpp (modified) * src/element.hpp (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/periodentafel.cpp (modified) Made all member variables of class element private, added accessor ... Wed, 18 Aug 2010 14:09:58 GMT Tillmann Crueger [c743f8] * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) Removed some more invocations of ActOnAllAtoms Tue, 17 Aug 2010 13:14:22 GMT Frederik Heber [bcf653] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.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/TranslateAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.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/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.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/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/AtomicInfo.cpp (modified) * src/BoundaryLineSet.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPolygonSet.cpp (modified) * src/BoundaryTriangleSet.cpp (modified) * src/Box.cpp (modified) * src/CandidateForTesselation.cpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.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/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MissingValueException.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (modified) * src/Exceptions/ParseError.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Formula.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/Info.cpp (modified) * src/Helpers/Log.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/Verbose.cpp (modified) * src/Helpers/errorlogger.cpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/logger.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Matrix.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorInterface.cpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/gslvector.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Observer.cpp (modified) * src/PointCloud.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/TesselPoint.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/QT4/QTMenu.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/QT4/QTUIFactory.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/GLMoleculeView.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/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.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_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/BaseShapesUnittest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/FormulaUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/MapofActionsTest.cpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/SingletonTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (modified) * src/unittests/gslmatrixunittest.cpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/memoryusageobserverunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Added copyright note to each .cpp file and an extensive one to ... Wed, 11 Aug 2010 09:27:47 GMT Frederik Heber [bf3817] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (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/TranslateAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.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/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.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/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/BoundaryLineSet.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPolygonSet.cpp (modified) * src/BoundaryTriangleSet.cpp (modified) * src/Box.cpp (modified) * src/CandidateForTesselation.cpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.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/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MissingValueException.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (modified) * src/Exceptions/ParseError.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Formula.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/Info.cpp (modified) * src/Helpers/Log.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/Verbose.cpp (modified) * src/Helpers/errorlogger.cpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/logger.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Matrix.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorInterface.cpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/gslvector.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Observer.cpp (modified) * src/PointCloud.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/TesselPoint.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/QT4/QTMenu.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.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/GLMoleculeView.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/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.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_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/FormulaUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/MapofActionsTest.cpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/SingletonTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (modified) * src/unittests/gslmatrixunittest.cpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/memoryusageobserverunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Added ifdef HAVE_CONFIG and config.h include to each and every cpp ... Sat, 07 Aug 2010 12:07:04 GMT Frederik Heber [8f4df1] * 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/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/AtomSet.hpp (modified) * src/BoundaryLineSet.cpp (added) * src/BoundaryLineSet.hpp (added) * src/BoundaryMaps.hpp (added) * src/BoundaryPointSet.cpp (added) * src/BoundaryPointSet.hpp (added) * src/BoundaryPolygonSet.cpp (added) * src/BoundaryPolygonSet.hpp (added) * src/BoundaryTriangleSet.cpp (added) * src/BoundaryTriangleSet.hpp (added) * src/CandidateForTesselation.cpp (added) * src/CandidateForTesselation.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/Vector.hpp (modified) * src/LinearAlgebra/VectorInterface.cpp (added) * src/LinearAlgebra/VectorInterface.hpp (added) * src/LinearAlgebra/vector_ops.cpp (moved) * src/LinearAlgebra/vector_ops.hpp (moved) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/PointCloud.cpp (added) * src/PointCloud.hpp (added) * src/TesselPoint.cpp (added) * src/TesselPoint.hpp (added) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_bondedparticleinfo.hpp (modified) * src/atom_graphnodeinfo.hpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/triangleintersectionlist.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) Merge branch 'AtomicPositionEncapsulation' into stable Conflicts: ... Thu, 05 Aug 2010 19:41:21 GMT Frederik Heber [952f38] * configure.ac (modified) * src/Actions/Action.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/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.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/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/SelectiveIterator_impl.hpp (modified) * src/Helpers/Info.cpp (moved) * src/Helpers/Info.hpp (moved) * src/Helpers/Log.cpp (moved) * src/Helpers/Log.hpp (moved) * src/Helpers/Makefile.am (added) * src/Helpers/Verbose.cpp (moved) * src/Helpers/Verbose.hpp (moved) * src/Helpers/errorlogger.cpp (moved) * src/Helpers/errorlogger.hpp (moved) * src/Helpers/helpers.cpp (moved) * src/Helpers/helpers.hpp (moved) * src/Helpers/logger.cpp (moved) * src/Helpers/logger.hpp (moved) * src/Legacy/oldmenu.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector_ops.cpp (modified) created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> ... Thu, 05 Aug 2010 19:28:52 GMT Frederik Heber [57f243] * configure.ac (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/LinearAlgebra/Line.cpp (moved) * src/LinearAlgebra/Line.hpp (moved) * src/LinearAlgebra/Makefile.am (added) * src/LinearAlgebra/Matrix.cpp (moved) * src/LinearAlgebra/Matrix.hpp (moved) * src/LinearAlgebra/MatrixContent.hpp (moved) * src/LinearAlgebra/Plane.cpp (moved) * src/LinearAlgebra/Plane.hpp (moved) * src/LinearAlgebra/Space.cpp (moved) * src/LinearAlgebra/Space.hpp (moved) * src/LinearAlgebra/Vector.cpp (moved) * src/LinearAlgebra/Vector.hpp (moved) * src/LinearAlgebra/VectorContent.hpp (moved) * src/LinearAlgebra/VectorSet.hpp (moved) * src/LinearAlgebra/gslmatrix.cpp (moved) * src/LinearAlgebra/gslmatrix.hpp (moved) * src/LinearAlgebra/gslvector.cpp (moved) * src/LinearAlgebra/gslvector.hpp (moved) * src/LinearAlgebra/linearsystemofequations.cpp (moved) * src/LinearAlgebra/linearsystemofequations.hpp (moved) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/World.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/ShapeUnittest.hpp (modified) * src/unittests/gslmatrixsymmetricunittest.hpp (modified) * src/unittests/gslmatrixunittest.hpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.hpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector_ops.cpp (modified) Created libMolecuilderLinearAlgebra. - is shared. - contains the ... Sat, 31 Jul 2010 15:23:10 GMT Frederik Heber [d74077] * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/BoundaryLineSet.cpp (added) * src/BoundaryLineSet.hpp (added) * src/BoundaryMaps.hpp (added) * src/BoundaryPointSet.cpp (added) * src/BoundaryPointSet.hpp (added) * src/BoundaryPolygonSet.cpp (added) * src/BoundaryPolygonSet.hpp (added) * src/BoundaryTriangleSet.cpp (added) * src/BoundaryTriangleSet.hpp (added) * src/CandidateForTesselation.cpp (added) * src/CandidateForTesselation.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/PointCloud.cpp (added) * src/PointCloud.hpp (added) * src/TesselPoint.cpp (added) * src/TesselPoint.hpp (added) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/VectorInterface.cpp (added) * src/VectorInterface.hpp (added) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_bondedparticleinfo.hpp (modified) * src/atom_graphnodeinfo.hpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/triangleintersectionlist.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Member variable Vector and element of class atom are now private. - ... Wed, 07 Jul 2010 16:08:32 GMT Tillmann Crueger [4e10f5] * COPYING (added) * INSTALL (added) * README (modified) * config/config.guess (added) * config/config.sub (added) * config/depcomp (added) * config/install-sh (added) * config/missing (added) * configure.ac (modified) * m4/ax_lang_compiler_ms.m4 (added) * m4/cppunit.m4 (added) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (added) * src/CommandLineParser.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * tests/Tesselations/defs.in (modified) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-filling.at (modified) * tests/regression/testsuite-fragmentation.at (modified) * tests/regression/testsuite-graph.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-specifics.at (modified) * tests/regression/testsuite-standard_options.at (modified) * tests/regression/testsuite-tesselation.at (modified) Merge branch 'stable' into StructureRefactoring Conflicts: ... Sat, 03 Jul 2010 14:02:26 GMT Frederik Heber [c27778] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) MEMFIXES: ListOfLocalAtoms in molecule::FragmentMolecule() was not ... Fri, 02 Jul 2010 13:09:37 GMT Tillmann Crueger [36166d] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/graph.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/memoryallocator.cpp (deleted) * src/memoryallocator.hpp (deleted) * src/memoryusageobserver.cpp (deleted) * src/memoryusageobserver.hpp (deleted) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Removed left over parts from old memory-tracker Wed, 30 Jun 2010 13:55:42 GMT Tillmann Crueger [84c494] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/boundary.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) Made the world store the cell_size within a Box object. Wed, 30 Jun 2010 09:00:19 GMT Tillmann Crueger [5108e1] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/ellipsoid.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Removed MatrixMultiplication() method from Vector class Sat, 26 Jun 2010 11:52:50 GMT Tillmann Crueger [d10eb6] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Matrix.cpp (modified) * src/Matrix.hpp (modified) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) Made the ReturnFullMatrixForSymmetric return a Matrix object ... Fri, 25 Jun 2010 15:27:35 GMT Tillmann Crueger [c94eeb] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/ellipsoid.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Replaced several double* that were used as Matrixes with actuall ... Wed, 23 Jun 2010 15:52:50 GMT Frederik Heber [35b698] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/Makefile.am (modified) * tests/regression/Domain/6/post/test-x.conf.xyz (modified) * tests/regression/Domain/6/post/test-y.conf.xyz (modified) * tests/regression/Domain/6/post/test-z.conf.xyz (modified) * tests/regression/Domain/6/post/test.conf.xyz (modified) * tests/regression/Filling/1/post/test.conf (modified) * tests/regression/Simple_configuration/2/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/3/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/4/post/test.conf (modified) * tests/regression/Simple_configuration/4/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/5/post/test.conf (modified) * tests/regression/Simple_configuration/8/post/test.conf.xyz (modified) * tests/regression/testsuite-fragmentation.at (modified) BIG CHANGE: config::load and config::save in ... Thu, 10 Jun 2010 13:11:28 GMT Tillmann Crueger [112b09] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.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/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/CommandLineParser.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Line.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Observer.cpp (modified) * src/Plane.cpp (modified) * src/Space.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.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/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.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_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/graph.cpp (modified) * src/gslmatrix.cpp (modified) * src/gslvector.cpp (modified) * src/helpers.cpp (modified) * src/info.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/log.cpp (modified) * src/logger.cpp (modified) * src/memoryallocator.cpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/vector.cpp (modified) * src/vector_ops.cpp (modified) * src/verbose.cpp (modified) Added #include "Helpers/MemDebug.hpp" to all .cpp files Tue, 01 Jun 2010 19:59:25 GMT Frederik Heber [0de7e8] * src/helpers.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * tests/regression/testsuite-fragmentation.at (modified) FIX: Test Fragmentation is at MaxOrder was broken. - BUGFIX: ... Mon, 31 May 2010 18:41:12 GMT Frederik Heber [e08c46] * src/Legacy/oldmenu.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) Removed molecule::first, molecule::last. - molecule does not have a ... Mon, 31 May 2010 17:32:27 GMT Frederik Heber [1024cb] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedIterator.hpp (added) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/Plane.cpp (modified) * src/Plane.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/lists.cpp (deleted) * src/lists.hpp (modified) * src/memoryallocator.cpp (added) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/listofbondsunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * tests/regression/Domain/5/post/test.conf (modified) * tests/regression/Domain/5/pre/test.conf (modified) * tests/regression/Domain/6/post/test-x.conf (deleted) * tests/regression/Domain/6/post/test-x.conf.xyz (added) * tests/regression/Domain/6/post/test-y.conf (deleted) * tests/regression/Domain/6/post/test-y.conf.xyz (added) * tests/regression/Domain/6/post/test-z.conf (deleted) * tests/regression/Domain/6/post/test-z.conf.xyz (added) * tests/regression/Domain/6/post/test.conf (deleted) * tests/regression/Domain/6/pre/test.conf (modified) * tests/regression/Simple_configuration/8/post/test.conf (deleted) * tests/regression/Simple_configuration/8/post/test.conf.xyz (added) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) Merge commit 'jupiter/MoleculeStartEndSwitch' into ... Mon, 31 May 2010 14:33:11 GMT Frederik Heber [42af9e] * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/periodentafel.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) MEMFIXES: no more default saving/loading of element's db, ... Mon, 31 May 2010 13:09:58 GMT Frederik Heber [920c70] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Makefile.am (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/stackclass.hpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and ... Thu, 27 May 2010 10:46:54 GMT Tillmann Crueger [a7b761b] * src/Helpers/Assert.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedIterator.hpp (added) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.hpp (modified) * src/lists.cpp (deleted) * src/lists.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/listofbondsunittest.hpp (modified) Merge branch 'MoleculeStartEndSwitch' into StructureRefactoring ... Thu, 20 May 2010 15:51:14 GMT Tillmann Crueger [d4c9ae] * src/Plane.cpp (modified) * src/Plane.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Removed the DistanceToPlane method in the Vector class in favor of a ... Wed, 19 May 2010 14:03:42 GMT Tillmann Crueger [bab12a] * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) FIX: Fix of bug introduced during Vector Refactoring Testsuite now ... Sat, 08 May 2010 12:47:57 GMT Tillmann Crueger [68f03d] * src/Helpers/MemDebug.cpp (modified) * src/analysis_bonds.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/bond.cpp (modified) * src/builder.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/parser.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) FIX: Memory corruption in particleInfo class Thu, 29 Apr 2010 13:55:21 GMT Tillmann Crueger [8cbb97] * src/Exceptions/CustomException.cpp (added) * src/Exceptions/CustomException.hpp (added) * src/Exceptions/LinearDependenceException.cpp (added) * src/Exceptions/LinearDependenceException.hpp (added) * src/Helpers/fast_functions.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Plane.cpp (added) * src/Plane.hpp (added) * src/UIElements/TextDialog.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/gslmatrix.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActOnAllUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (added) * src/vector_ops.hpp (added) Merge branch 'VectorRefactoring' into StructureRefactoring ... Tue, 27 Apr 2010 14:25:42 GMT Frederik Heber [5f612ee] * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_bonds.hpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.hpp (modified) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/graph.cpp (modified) * src/gslvector.cpp (modified) * src/gslvector.hpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/info.cpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/log.cpp (modified) * src/log.hpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (added) * src/triangleintersectionlist.hpp (added) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/CountBondsUnitTest.cpp (added) * src/unittests/CountBondsUnitTest.hpp (added) * src/unittests/LinkedCellUnitTest.cpp (added) * src/unittests/LinkedCellUnitTest.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.hpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/tesselationunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/verbose.cpp (modified) * src/verbose.hpp (modified) * tests/Tesselations/1_2-dimethylbenzene/tecplot.phy (deleted) * tests/Tesselations/defs.in (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) Merge branch 'Analysis_PairCorrelation' into StructureRefactoring ... Thu, 22 Apr 2010 14:00:03 GMT Frederik Heber [a67d19] * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/info.cpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/vector.cpp (modified) Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) ... Tue, 13 Apr 2010 13:22:42 GMT Tillmann Crueger [273382] * src/Legacy/oldmenu.cpp (modified) * src/Plane.cpp (modified) * src/SingleVector.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/ellipsoid.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) Prepared interface of Vector Class for transition to VectorComposites Wed, 07 Apr 2010 15:45:38 GMT Tillmann Crueger [0a4f7f] * src/Exceptions/CustomException.cpp (added) * src/Exceptions/CustomException.hpp (added) * src/Exceptions/LinearDependenceException.cpp (added) * src/Exceptions/LinearDependenceException.hpp (added) * src/Helpers/fast_functions.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Plane.cpp (added) * src/Plane.hpp (added) * src/UIElements/TextDialog.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/gslmatrix.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActOnAllUnitTest.hpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (added) * src/vector_ops.hpp (added) Made data internal data-structure of vector class private - ... Fri, 19 Mar 2010 13:29:01 GMT Tillmann Crueger [ea7176] * src/Legacy/oldmenu.cpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) FIX: Made AtomCount a Cacheable so that the number of atoms in a ... Thu, 18 Mar 2010 11:39:57 GMT Frederik Heber [c7b1e7] * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) Merge branch 'FixGeneralizeStoreAdjacencyToFile' into ... Thu, 18 Mar 2010 11:37:26 GMT Frederik Heber [8ab0407] * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) molecule::StoreAdjacencyToFile() and molecule::StoreBondsToFile() now ... Thu, 18 Mar 2010 11:33:54 GMT Frederik Heber [58ed4a] * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/helpers.hpp (modified) * src/linkedcell.cpp (modified) * src/log.cpp (modified) * src/log.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/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/vector.cpp (modified) Log() and eLog() are prepended by a DoLog()/DoeLog() construct. - ... Wed, 10 Mar 2010 17:51:48 GMT Tillmann Crueger [23b547] * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Patterns/Singleton.hpp (added) * src/Patterns/Singleton_impl.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/defs.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Added generic singleton Pattern that can be inherited to any class ... Fri, 05 Mar 2010 10:16:47 GMT Frederik Heber [9879f6] * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.hpp (modified) * src/lists.cpp (deleted) * src/lists.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/listofbondsunittest.hpp (modified) Huge Refactoring due to class molecule now being an STL container. ... Wed, 03 Mar 2010 10:13:19 GMT Frederik Heber [b34306] * src/Makefile.am (modified) * src/World.cpp (added) * src/World.hpp (added) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/vector.cpp (modified) singleton class World introduced, contains only cell_size from class ... Thu, 25 Feb 2010 16:43:02 GMT Tillmann Crueger [cbc5fb] * src/Legacy/oldmenu.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/defs.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) Made the world solely responsible for creating and erasing molecules. Sun, 10 Jan 2010 19:05:34 GMT Frederik Heber [49e1ae] * src/analyzer.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/joiner.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) cstring header was missing in files, supplying definition of strlen, ... Mon, 23 Nov 2009 18:51:50 GMT Frederik Heber [e359a8] * src/analysis_correlation.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.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/parser.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) Fixing ticket #18. - each eLog() << Verbose(0) is now followed by ... Mon, 23 Nov 2009 18:22:33 GMT Frederik Heber [717e0c] * src/analyzer.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/linkedcell.cpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/vector.cpp (modified) Verbosity corrected for ERROR and WARNING - present ERROR and ... Wed, 04 Nov 2009 19:56:04 GMT Frederik Heber [e138de] * src/Makefile.am (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnode.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/element.cpp (modified) * src/element.hpp (modified) * src/ellipsoid.cpp (modified) * src/ellipsoid.hpp (modified) * src/errorlogger.cpp (moved) * src/errorlogger.hpp (moved) * src/graph.cpp (modified) * src/graph.hpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/log.cpp (modified) * src/log.hpp (modified) * src/logger.cpp (modified) * src/memoryallocator.hpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/verbose.cpp (modified) Huge change from ofstream * (const) out --> Log(). - first shift ... Tue, 03 Nov 2009 16:34:31 GMT Frederik Heber [3c349b] * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/helpers.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) "not working parsed molecule into subgraph splitting"-BUG fixed, ... Tue, 03 Nov 2009 12:37:55 GMT Frederik Heber [7218f8] * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.hpp (modified) * src/memoryallocator.hpp (modified) * src/memoryusageobserver.cpp (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/stackclass.hpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) Several memory bugfixes (thx valgrind). - main() - shortened case ... Sun, 18 Oct 2009 14:51:38 GMT Frederik Heber [266237] * src/atom.cpp (modified) * src/atom.hpp (modified) * src/bond.cpp (modified) * src/bond.hpp (modified) * src/builder.cpp (modified) * src/linkedcell.cpp (modified) * src/lists.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/listofbondsunittest.cpp (added) * src/unittests/listofbondsunittest.hpp (added) Huge refactoring: molecule::ListOfBondsPerAtom and ... Tue, 13 Oct 2009 16:42:30 GMT Frederik Heber [93d120] * src/molecule_fragmentation.cpp (modified) Fixed broken test "Fragmentation - Fragmentation". - BUGFIX: Code ... Mon, 12 Oct 2009 13:26:12 GMT Frederik Heber [407536] * src/molecule_fragmentation.cpp (modified) Refactored molecule::FragmentBOSSANOVA(). - renamed functions: ... Mon, 12 Oct 2009 13:05:46 GMT Frederik Heber [14e73a] * src/molecule_fragmentation.cpp (modified) Refactored molecule::PowerSetGenerator(). - new functions are: ... Mon, 12 Oct 2009 12:49:19 GMT Frederik Heber [d2943b] * src/molecule_fragmentation.cpp (modified) Rewritten molecule::molecule::SPFragmentGenerator() - new functions ... Mon, 12 Oct 2009 12:10:43 GMT Frederik Heber [5034e1] * src/atom.cpp (modified) * src/atom.hpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_template.hpp (modified) First half of molecule_fragmentation.cpp refactoring. - new ... Fri, 09 Oct 2009 10:54:52 GMT Frederik Heber [f66195] * src/ActOnAllUnitTest.cpp (modified) * src/Makefile.am (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/bond.cpp (modified) * src/bond.hpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/datacreator.cpp (modified) * src/datacreator.hpp (modified) * src/element.hpp (modified) * src/ellipsoid.cpp (modified) * src/ellipsoid.hpp (modified) * src/graph.cpp (modified) * src/graph.hpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/leastsquaremin.cpp (modified) * src/leastsquaremin.hpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/lists.hpp (added) * src/memoryallocator.hpp (modified) * src/memoryusageobserver.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/parser.hpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/tesselationunittest.hpp (modified) * src/vector.hpp (modified) * src/verbose.cpp (modified) * src/verbose.hpp (modified) forward declarations used to untangle interdependet classes. - ... Mon, 05 Oct 2009 22:10:53 GMT Frederik Heber [cee0b57] * src/Makefile.am (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.hpp (modified) * src/graph.hpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (added) * src/molecule_fragmentation.cpp (added) * src/molecule_geometry.cpp (added) * src/molecule_graph.cpp (added) * src/molecule_pointcloud.cpp (added) * src/moleculelist.cpp (modified) * src/verbose.cpp (modified) class molecule implementation split up into six separate parts. - ...