# # ChangeLog for / # # Generated by Trac 1.6 # May 25, 2025, 4:49:42 AM Sat, 28 Aug 2010 03:21:11 GMT Frederik Heber [6c438f] * .gitignore (modified) * AUTHORS (modified) * COPYING (modified) * Makefile.am (modified) * README (modified) * TestRunnerClient.cpp (added) * TestRunnerClient.h (added) * autogen.sh (deleted) * bootstrap (added) * config/ltmain.sh (added) * configure.ac (modified) * doc/molecuilder_logo.png (added) * doc/molecuilder_logo.xcf (added) * libmolecuilder_config.h.in (added) * m4/gwqt4.m4 (modified) * molecuilder.pc.in (added) * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Action_impl_header.hpp (added) * src/Actions/Action_impl_pre.hpp (added) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (added) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (added) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (added) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.def (added) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/Remove.def (added) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.def (added) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (added) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (added) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp (added) * src/Actions/AtomAction/TranslateAction.cpp (added) * src/Actions/AtomAction/TranslateAction.def (added) * src/Actions/AtomAction/TranslateAction.hpp (added) * src/Actions/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (deleted) * src/Actions/CmdAction/BondLengthTableAction.hpp (deleted) * src/Actions/CmdAction/ElementDbAction.cpp (deleted) * src/Actions/CmdAction/ElementDbAction.hpp (deleted) * src/Actions/CmdAction/FastParsingAction.cpp (deleted) * src/Actions/CmdAction/FastParsingAction.hpp (deleted) * src/Actions/CmdAction/HelpAction.cpp (deleted) * src/Actions/CmdAction/HelpAction.hpp (deleted) * src/Actions/CmdAction/VerboseAction.cpp (deleted) * src/Actions/CmdAction/VerboseAction.hpp (deleted) * src/Actions/CmdAction/VersionAction.cpp (deleted) * src/Actions/CmdAction/VersionAction.hpp (deleted) * src/Actions/CommandAction/BondLengthTableAction.cpp (added) * src/Actions/CommandAction/BondLengthTableAction.def (added) * src/Actions/CommandAction/BondLengthTableAction.hpp (added) * src/Actions/CommandAction/ElementDbAction.cpp (added) * src/Actions/CommandAction/ElementDbAction.def (added) * src/Actions/CommandAction/ElementDbAction.hpp (added) * src/Actions/CommandAction/FastParsingAction.cpp (added) * src/Actions/CommandAction/FastParsingAction.def (added) * src/Actions/CommandAction/FastParsingAction.hpp (added) * src/Actions/CommandAction/HelpAction.cpp (added) * src/Actions/CommandAction/HelpAction.def (added) * src/Actions/CommandAction/HelpAction.hpp (added) * src/Actions/CommandAction/VerboseAction.cpp (added) * src/Actions/CommandAction/VerboseAction.def (added) * src/Actions/CommandAction/VerboseAction.hpp (added) * src/Actions/CommandAction/VersionAction.cpp (added) * src/Actions/CommandAction/VersionAction.def (added) * src/Actions/CommandAction/VersionAction.hpp (added) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (added) * src/Actions/FragmentationAction/ConstructBondGraphAction.def (added) * src/Actions/FragmentationAction/ConstructBondGraphAction.hpp (added) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.def (added) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (added) * src/Actions/FragmentationAction/FragmentationAction.hpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.def (added) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.def (added) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.def (added) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (added) * src/Actions/MoleculeAction/CopyAction.def (added) * src/Actions/MoleculeAction/CopyAction.hpp (added) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (added) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (added) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (added) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (added) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.def (added) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.def (added) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (added) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.def (added) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (deleted) * src/Actions/MoleculeAction/TranslateAction.hpp (deleted) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (added) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.def (added) * src/Actions/ParserAction/LoadXyzAction.hpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.def (added) * src/Actions/ParserAction/SaveXyzAction.hpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.def (added) * src/Actions/SelectionAction/AllAtomsAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (added) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (added) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.hpp (added) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (added) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.def (added) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.hpp (added) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.def (added) * src/Actions/SelectionAction/AllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (added) * src/Actions/SelectionAction/AtomByElementAction.def (added) * src/Actions/SelectionAction/AtomByElementAction.hpp (added) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.def (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (added) * src/Actions/SelectionAction/ClearAllAtomsAction.def (added) * src/Actions/SelectionAction/ClearAllAtomsAction.hpp (added) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (added) * src/Actions/SelectionAction/ClearAllMoleculesAction.def (added) * src/Actions/SelectionAction/ClearAllMoleculesAction.hpp (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.def (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.hpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.def (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (added) * src/Actions/SelectionAction/MoleculeOfAtomAction.def (added) * src/Actions/SelectionAction/MoleculeOfAtomAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.def (added) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (added) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (added) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.hpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.def (added) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (added) * src/Actions/SelectionAction/NotAtomByElementAction.def (added) * src/Actions/SelectionAction/NotAtomByElementAction.hpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.def (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (added) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.def (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (added) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.hpp (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.def (added) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/ValueStorage.cpp (added) * src/Actions/ValueStorage.hpp (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.def (added) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.def (added) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (added) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.def (added) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.def (added) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.def (added) * src/Actions/WorldAction/OutputAction.hpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (deleted) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (deleted) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (added) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.def (added) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.def (added) * src/Actions/WorldAction/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.def (added) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.def (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) * src/AtomSet.hpp (added) * src/AtomicInfo.cpp (added) * src/AtomicInfo.hpp (added) * 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/Box.cpp (modified) * src/Box.hpp (modified) * src/CandidateForTesselation.cpp (added) * src/CandidateForTesselation.hpp (added) * src/CommandLineParser.cpp (modified) * src/CommandLineParser.hpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.hpp (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/Descriptors/SelectiveIterator_impl.hpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/Makefile.am (added) * 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/Formula.hpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/Assert.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/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * 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 (deleted) * src/Legacy/oldmenu.hpp (deleted) * src/LinearAlgebra/BoxVector.cpp (added) * src/LinearAlgebra/BoxVector.hpp (added) * src/LinearAlgebra/Line.cpp (moved) * src/LinearAlgebra/Line.hpp (moved) * src/LinearAlgebra/LineSegment.cpp (moved) * src/LinearAlgebra/LineSegment.hpp (moved) * src/LinearAlgebra/LineSegmentSet.cpp (moved) * src/LinearAlgebra/LineSegmentSet.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/VectorInterface.cpp (added) * src/LinearAlgebra/VectorInterface.hpp (added) * 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/LinearAlgebra/vector_ops.cpp (moved) * src/LinearAlgebra/vector_ops.hpp (moved) * src/Makefile.am (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/Makefile.am (added) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Parser/PdbParser.cpp (added) * src/Parser/PdbParser.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/ObservedContainer_impl.hpp (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Registry_impl.hpp (modified) * src/PointCloud.cpp (added) * src/PointCloud.hpp (added) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/Shape_impl.hpp (modified) * src/TesselPoint.cpp (added) * src/TesselPoint.hpp (added) * src/ThermoStatContainer.cpp (modified) * src/ThermoStatContainer.hpp (modified) * src/Thermostats/Berendsen.cpp (added) * src/Thermostats/Berendsen.hpp (added) * src/Thermostats/GaussianThermostat.cpp (added) * src/Thermostats/GaussianThermostat.hpp (added) * src/Thermostats/Langevin.cpp (added) * src/Thermostats/Langevin.hpp (added) * src/Thermostats/NoThermostat.cpp (added) * src/Thermostats/NoThermostat.hpp (added) * src/Thermostats/NoseHoover.cpp (added) * src/Thermostats/NoseHoover.hpp (added) * src/Thermostats/Thermostat.cpp (added) * src/Thermostats/Thermostat.hpp (added) * src/Thermostats/Woodcock.cpp (added) * src/Thermostats/Woodcock.hpp (added) * 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/CommandLineUI/CommandLineWindow.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Makefile.am (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/Menu/TextMenu.hpp (modified) * src/UIElements/QT4/IntQTQuery.ui (added) * src/UIElements/QT4/IntsQTQuery.ui (added) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (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/ValueStorage.cpp (deleted) * src/UIElements/ValueStorage.hpp (deleted) * 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/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_bonds.hpp (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_atominfo.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_bondedparticleinfo.hpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnode.hpp (modified) * src/atom_graphnodeinfo.cpp (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.cpp (modified) * src/atom_trajectoryparticleinfo.hpp (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/config.hpp (modified) * src/datacreator.cpp (modified) * src/defs.cpp (added) * src/defs.hpp (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/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/molecule_template.hpp (deleted) * src/moleculelist.cpp (modified) * src/parser.cpp (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/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/triangleintersectionlist.hpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/AtomDescriptorTest.hpp (modified) * src/unittests/BoxUnittest.cpp (added) * src/unittests/BoxUnittest.hpp (added) * src/unittests/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/DummyUI.hpp (added) * src/unittests/FormulaUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MapofActionsTest.cpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MatrixUnittest.hpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/MoleculeDescriptorTest.hpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/ShapeUnittest.hpp (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/atomsCalculationTest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.hpp (modified) * src/unittests/gslmatrixunittest.cpp (modified) * src/unittests/gslmatrixunittest.hpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/manipulateAtomsTest.hpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/memoryusageobserverunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (modified) * src/unittests/periodentafelTest.hpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.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/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/version.h (modified) * test_all.sh (modified) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/defs.in (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/10/post/test-rotated-xYz20.xyz (added) * tests/regression/Molecules/10/post/test-rotated-z180.xyz (added) * tests/regression/Molecules/10/post/test-rotated-z360.xyz (added) * tests/regression/Molecules/10/post/test-rotated-z90.xyz (added) * tests/regression/Molecules/10/pre/test.xyz (added) * tests/regression/Molecules/11/post/test-copy.xyz (added) * tests/regression/Molecules/11/pre/test.xyz (added) * tests/regression/Molecules/2/post/test.adj (modified) * tests/regression/Molecules/8/post/test-rotated-xYz20.xyz (added) * tests/regression/Molecules/8/post/test-rotated-z180.xyz (added) * tests/regression/Molecules/8/post/test-rotated-z360.xyz (added) * tests/regression/Molecules/8/post/test-rotated-z90.xyz (added) * tests/regression/Molecules/8/pre/test-rotated-xYz20.xyz (added) * tests/regression/Molecules/8/pre/test-rotated-z180.xyz (added) * tests/regression/Molecules/8/pre/test-rotated-z360.xyz (added) * tests/regression/Molecules/8/pre/test-rotated-z90.xyz (added) * tests/regression/Molecules/9/post/test-rotated-xYz20.xyz (added) * tests/regression/Molecules/9/post/test-rotated-z180.xyz (added) * tests/regression/Molecules/9/post/test-rotated-z360.xyz (added) * tests/regression/Molecules/9/post/test-rotated-z90.xyz (added) * tests/regression/Molecules/9/pre/test.xyz (added) * tests/regression/Simple_configuration/2/post/test.pdb (added) * tests/regression/Simple_configuration/3/post/empty.conf (moved) * tests/regression/Simple_configuration/5/pre/test.conf (modified) * tests/regression/Simple_configuration/8/post/test-cuboid.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test-sphere.xyz-sorted (moved) * tests/regression/Simple_configuration/8/post/test-withoutcuboid.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test-withoutsphere.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test.xyz-sorted (modified) * tests/regression/Simple_configuration/8/pre/test.conf (deleted) * tests/regression/Simple_configuration/8/pre/test.xyz (added) * tests/regression/Simple_configuration/9/post/test-shifted.xyz (added) * tests/regression/Simple_configuration/9/post/test.xyz (added) * tests/regression/Simple_configuration/9/pre/test.xyz (added) * tests/regression/atlocal.in (modified) * tests/regression/molecuilder.in (modified) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-graph.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-standard_options.at (modified) * tests/regression/testsuite.at (modified) Merge branch 'StructureRefactoring' into Shapes Conflicts: ... Sat, 28 Aug 2010 01:45:13 GMT Frederik Heber [fd4905] * .gitignore (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/Action_impl_header.hpp (added) * src/Actions/Action_impl_pre.hpp (added) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (added) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (added) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (added) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.def (added) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/Remove.def (added) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.def (added) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (added) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.def (added) * src/Actions/AtomAction/TranslateAction.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (deleted) * src/Actions/CmdAction/BondLengthTableAction.hpp (deleted) * src/Actions/CmdAction/ElementDbAction.hpp (deleted) * src/Actions/CmdAction/FastParsingAction.cpp (deleted) * src/Actions/CmdAction/FastParsingAction.hpp (deleted) * src/Actions/CmdAction/HelpAction.cpp (deleted) * src/Actions/CmdAction/HelpAction.hpp (deleted) * src/Actions/CmdAction/VerboseAction.cpp (deleted) * src/Actions/CmdAction/VerboseAction.hpp (deleted) * src/Actions/CmdAction/VersionAction.cpp (deleted) * src/Actions/CmdAction/VersionAction.hpp (deleted) * src/Actions/CommandAction/BondLengthTableAction.cpp (added) * src/Actions/CommandAction/BondLengthTableAction.def (added) * src/Actions/CommandAction/BondLengthTableAction.hpp (added) * src/Actions/CommandAction/ElementDbAction.cpp (moved) * src/Actions/CommandAction/ElementDbAction.def (added) * src/Actions/CommandAction/ElementDbAction.hpp (added) * src/Actions/CommandAction/FastParsingAction.cpp (added) * src/Actions/CommandAction/FastParsingAction.def (added) * src/Actions/CommandAction/FastParsingAction.hpp (added) * src/Actions/CommandAction/HelpAction.cpp (added) * src/Actions/CommandAction/HelpAction.def (added) * src/Actions/CommandAction/HelpAction.hpp (added) * src/Actions/CommandAction/VerboseAction.cpp (added) * src/Actions/CommandAction/VerboseAction.def (added) * src/Actions/CommandAction/VerboseAction.hpp (added) * src/Actions/CommandAction/VersionAction.cpp (added) * src/Actions/CommandAction/VersionAction.def (added) * src/Actions/CommandAction/VersionAction.hpp (added) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (added) * src/Actions/FragmentationAction/ConstructBondGraphAction.def (added) * src/Actions/FragmentationAction/ConstructBondGraphAction.hpp (added) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.def (added) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (added) * src/Actions/FragmentationAction/FragmentationAction.hpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.def (added) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.def (added) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.def (added) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (added) * src/Actions/MoleculeAction/CopyAction.def (added) * src/Actions/MoleculeAction/CopyAction.hpp (added) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (added) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (added) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (added) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.def (added) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.def (added) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (added) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.def (added) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (added) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.def (added) * src/Actions/ParserAction/LoadXyzAction.hpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.def (added) * src/Actions/ParserAction/SaveXyzAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.def (added) * src/Actions/SelectionAction/AllAtomsAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (added) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.def (added) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.hpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.def (added) * src/Actions/SelectionAction/AllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.def (added) * src/Actions/SelectionAction/AtomByElementAction.hpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.def (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.def (added) * src/Actions/SelectionAction/ClearAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.def (added) * src/Actions/SelectionAction/ClearAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.def (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.hpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.def (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.def (added) * src/Actions/SelectionAction/MoleculeOfAtomAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.def (added) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (added) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (added) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.hpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.def (added) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.def (added) * src/Actions/SelectionAction/NotAtomByElementAction.hpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.def (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (added) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.def (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (added) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.hpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.def (added) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.def (added) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.def (added) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (added) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.def (added) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.def (added) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.def (added) * src/Actions/WorldAction/OutputAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (added) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.def (added) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.def (added) * src/Actions/WorldAction/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.def (added) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.def (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) * src/CommandLineParser.hpp (modified) * src/LinearAlgebra/BoxVector.cpp (added) * src/LinearAlgebra/BoxVector.hpp (added) * src/LinearAlgebra/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/Makefile.am (modified) * src/Parser/PdbParser.cpp (added) * src/Parser/PdbParser.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/Shape_impl.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnode.hpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * tests/regression/Molecules/11/post/test-copy.xyz (added) * tests/regression/Molecules/11/pre/test.xyz (added) * tests/regression/Molecules/2/post/test.adj (modified) * tests/regression/Simple_configuration/2/post/test.pdb (added) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) Merge branch 'stable' into StructureRefactoring Sat, 28 Aug 2010 01:39:35 GMT Frederik Heber [653542] Merge branch 'FixSubgraphDissectionMerge' into stable Conflicts: ... Sat, 28 Aug 2010 01:36:03 GMT Frederik Heber [701ad6] * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) FIX: Merge stuff still left inside. Sat, 28 Aug 2010 00:58:44 GMT Frederik Heber [74a444] * src/Parser/TremoloParser.cpp (modified) TremoloParser can now deal with copied molecules/atoms. - as some ... Sat, 28 Aug 2010 00:58:44 GMT Frederik Heber [dc1d9e] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/unittests/ParserUnitTest.cpp (modified) Several bugfixes for TremoloParser. - overloaded readAtomDataLine ... Sat, 28 Aug 2010 00:58:44 GMT Frederik Heber [1a7fd2] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (added) * src/Actions/MoleculeAction/CopyAction.def (added) * src/Actions/MoleculeAction/CopyAction.hpp (added) * tests/regression/Molecules/11/post/test-copy.xyz (added) * tests/regression/Molecules/11/pre/test.xyz (added) * tests/regression/testsuite-molecules.at (modified) New Action MoleculeAction/CopyAction. Sat, 28 Aug 2010 00:58:44 GMT Frederik Heber [76ff55] * src/molecule.cpp (modified) BUGFIX: molecule::CopyMolecule() was broken. fixes: - for loop ... Sat, 28 Aug 2010 00:57:57 GMT Frederik Heber [7d8342] * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) SubgraphDissectionAction does not delete bonds anymore and bugfixes ... Sat, 28 Aug 2010 00:57:57 GMT Frederik Heber [c449d9] * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (added) * src/Actions/FragmentationAction/ConstructBondGraphAction.def (added) * src/Actions/FragmentationAction/ConstructBondGraphAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) Added new Action ConstructBondGraphAction. Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [af2c424] * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) LinkedCell constructor rewritten. - had to introduce ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [21585f] * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) Added getter/setter for PdbParser::atomIdMap(). Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [bb6193] * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * tests/regression/Simple_configuration/2/post/test.pdb (added) * tests/regression/testsuite-simple_configuration.at (modified) Added PdbParser with save capability. - load does not yet work. - ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [5c6946] * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) FormatParserStorage extended a bit. - new functions add(type) that ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [3ae731] * src/Parser/Makefile.am (modified) * src/Parser/PdbParser.cpp (added) * src/Parser/PdbParser.hpp (added) Added initial PdbParser. Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [fbcd5c] * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) BUGFIX: FragmentationSubgraphDissectionAction::performCall() did not ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [b5cf6c] * src/bondgraph.cpp (modified) * tests/regression/Molecules/2/post/test.adj (modified) BUGFIX: BondGraph::max_distance is used for LinkedCell cell length ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [e8926e] * src/molecule.cpp (modified) BUGFIX: molecule::AddCopyAtom() did not set the copied atom's molecule. Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [f9183b] * src/atom_graphnode.cpp (modified) * src/atom_graphnode.hpp (modified) * src/molecule_graph.cpp (modified) BUGFIX: graph info per bond is now output nicely. - added ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [231b5e] * .gitignore (modified) Added debug* to .gitignore. Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [73a857] * src/molecule.cpp (modified) * src/molecule.hpp (modified) FIX: some getter functions (name, id, formula) in class molecule were ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [c66537] * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule_graph.cpp (modified) FIX: changed minimal bondddistance threshold to 0.1, as otherwise ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [10fa1d] * src/Actions/Action.hpp (modified) DOCU: Updated Action Howto to contain the new macro framework. Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [966e12] * src/Actions/createCpp.sh (deleted) * src/Actions/createHeader.sh (deleted) * src/Actions/createdef.sh (deleted) Removed the conversion script files again. They have been added to ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [1fd675] * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.def (added) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/Remove.def (added) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.def (added) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (added) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.def (added) * src/Actions/AtomAction/TranslateAction.hpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (added) * src/Actions/CommandAction/BondLengthTableAction.hpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.def (added) * src/Actions/CommandAction/ElementDbAction.hpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.def (added) * src/Actions/CommandAction/FastParsingAction.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpAction.def (added) * src/Actions/CommandAction/HelpAction.hpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.def (added) * src/Actions/CommandAction/VerboseAction.hpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/VersionAction.def (added) * src/Actions/CommandAction/VersionAction.hpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.def (added) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (added) * src/Actions/FragmentationAction/FragmentationAction.hpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.def (added) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.def (added) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.def (added) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (added) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (added) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (added) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.def (added) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.def (added) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (added) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.def (added) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (added) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.def (added) * src/Actions/ParserAction/LoadXyzAction.hpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.def (added) * src/Actions/ParserAction/SaveXyzAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.def (added) * src/Actions/SelectionAction/AllAtomsAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (added) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.def (added) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.hpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.def (added) * src/Actions/SelectionAction/AllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.def (added) * src/Actions/SelectionAction/AtomByElementAction.hpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.def (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.def (added) * src/Actions/SelectionAction/ClearAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.def (added) * src/Actions/SelectionAction/ClearAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.def (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.hpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.def (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.def (added) * src/Actions/SelectionAction/MoleculeOfAtomAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.def (added) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (added) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (added) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.hpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.def (added) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.def (added) * src/Actions/SelectionAction/NotAtomByElementAction.hpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.def (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (added) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.def (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (added) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.hpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.def (added) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.def (added) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.def (added) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (added) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.def (added) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.def (added) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.def (added) * src/Actions/WorldAction/OutputAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (added) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.def (added) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.def (added) * src/Actions/WorldAction/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.def (added) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.def (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) * src/Actions/createCpp.sh (added) * src/Actions/createHeader.sh (added) * src/Actions/createdef.sh (added) * tests/regression/testsuite-simple_configuration.at (modified) All Actions are converted to the new macro framework. - included ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [53d01c] * src/Actions/CommandAction/BondLengthTableAction.cpp (moved) * src/Actions/CommandAction/BondLengthTableAction.hpp (moved) * src/Actions/CommandAction/ElementDbAction.cpp (moved) * src/Actions/CommandAction/ElementDbAction.hpp (moved) * src/Actions/CommandAction/FastParsingAction.cpp (moved) * src/Actions/CommandAction/FastParsingAction.hpp (moved) * src/Actions/CommandAction/HelpAction.cpp (moved) * src/Actions/CommandAction/HelpAction.hpp (moved) * src/Actions/CommandAction/VerboseAction.cpp (moved) * src/Actions/CommandAction/VerboseAction.hpp (moved) * src/Actions/CommandAction/VersionAction.cpp (moved) * src/Actions/CommandAction/VersionAction.hpp (moved) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.hpp (modified) Renamed dir Actions/CmdAction -> Actions/CommandAction, renamed class ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [8bb05e] * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (added) * src/Actions/AtomAction/AddAction.hpp (modified) AtomAddAction converted to use macro framework. - State generation ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [72f611] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/UIElements/Dialog.cpp (modified) Added set/queryCurrentValue for BoxVector and Dialog::quer<> ... Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [e3e6e2] * src/LinearAlgebra/BoxVector.cpp (added) * src/LinearAlgebra/BoxVector.hpp (added) * src/LinearAlgebra/Makefile.am (modified) Added BoxVector class. BoxVector is simply a Vector with a ... Sat, 28 Aug 2010 00:57:50 GMT Frederik Heber [b4fa106] * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (modified) Extended action generating macro framework to create specialized ... Sat, 28 Aug 2010 00:52:58 GMT Frederik Heber [9ee38b] * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_post.hpp (deleted) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (added) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (added) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/unittests/Makefile.am (modified) Extended macro framework. Extensions: - all central definitions ... Thu, 26 Aug 2010 21:13:11 GMT Frederik Heber [0b2ce9] * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/Action_impl_header.hpp (added) * src/Actions/Action_impl_post.hpp (added) * src/Actions/Action_impl_pre.hpp (added) * 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/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.hpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.hpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.hpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/HelpAction.hpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.hpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/CmdAction/VersionAction.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.hpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.hpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.hpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.hpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.hpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.hpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.hpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.hpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.hpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.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/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.hpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) Implemented macros for automatically generating repetitive stuff ... Thu, 26 Aug 2010 13:28:45 GMT Frederik Heber [9c1c89] * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/Shape_impl.hpp (modified) FIX: all ...:getHomogeneousPointsOnSurface() now have size_t instead ... Thu, 26 Aug 2010 12:46:06 GMT Tillmann Crueger [8fd934] * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_template.hpp (deleted) Removed template structure from molecule class 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() Thu, 26 Aug 2010 12:20:17 GMT Tillmann Crueger [e8a21f] * src/atom.cpp (modified) * src/atom.hpp (modified) Added an atom::getNr() method to atom class Thu, 26 Aug 2010 11:02:41 GMT Tillmann Crueger [882a8a] * src/atom.cpp (modified) * src/atom.hpp (modified) * src/molecule.cpp (modified) made the atom::OutputTrajectories() method use an enumeration of ... Thu, 26 Aug 2010 10:46:37 GMT Tillmann Crueger [487ebb] * src/atom.cpp (modified) Removed old debug output from atom.cpp Thu, 26 Aug 2010 10:37:47 GMT Tillmann Crueger [aed558] * src/molecule.cpp (modified) Removed old debug message from molecule::Output() Thu, 26 Aug 2010 10:35:39 GMT Tillmann Crueger [e5f64de] * src/atom.cpp (modified) * src/atom.hpp (modified) Added a method that allows comparison of atoms by their atomic number Thu, 26 Aug 2010 09:55:05 GMT Tillmann Crueger [9e7813] * src/config.cpp (modified) Removed ActOnAllAtoms from config.cpp Thu, 26 Aug 2010 09:34:49 GMT Tillmann Crueger [0dc86e2] * src/Parser/MpqcParser.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/config.cpp (modified) Removed unused AtomNo parameter in atom::OutputMPQCLine() Wed, 25 Aug 2010 16:12:17 GMT Tillmann Crueger [5cd333c] * src/molecule_dynamics.cpp (modified) Replaced call to Vector::Scale() with operator notation Wed, 25 Aug 2010 16:10:54 GMT Tillmann Crueger [00ef5c] * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) Removed several calls to molecule::ActOnEachAtom() from ... Wed, 25 Aug 2010 16:10:02 GMT Tillmann Crueger [14b65e] * src/atom.cpp (modified) * src/atom.hpp (modified) Added a method to reset the graphNr of an atom Wed, 25 Aug 2010 15:32:29 GMT Tillmann Crueger [a3948b] * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) Removed unused TrajectoryParticle::CorrectVelocity() method Wed, 25 Aug 2010 14:03:45 GMT Tillmann Crueger [9b355f] * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) Removed unused TrajectoryParticle::SumUpKineticEnergy() method Wed, 25 Aug 2010 14:01:19 GMT Tillmann Crueger [259b2b] * src/molecule_dynamics.cpp (modified) Made the molecule::VerletForceIntegration() use the atomSetMixin to ... Wed, 25 Aug 2010 14:00:33 GMT Tillmann Crueger [5ac690] * src/AtomSet.hpp (modified) Added a method to the AtomSetMixin that allows adding a velocity to ... Wed, 25 Aug 2010 13:41:56 GMT Tillmann Crueger [1f8337] * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) Moved AtomInfo::getMass() method to class atom to avoid problems with ... Wed, 25 Aug 2010 13:37:01 GMT Tillmann Crueger [5e99bc] * src/AtomSet.hpp (modified) Added a method to the AtomSetMixin that allows calculating the total ... Wed, 25 Aug 2010 13:06:42 GMT Tillmann Crueger [e95a59] * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) Added a method that allows querying the momentum of a particle Wed, 25 Aug 2010 13:02:26 GMT Tillmann Crueger [cddda7] * src/AtomSet.hpp (modified) Added a method to the AtomSetMixin that allows calculating the total ... Wed, 25 Aug 2010 12:58:02 GMT Tillmann Crueger [9184bd] * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) Added a method that allows querying the mass of an atom directly - ... Wed, 25 Aug 2010 12:33:00 GMT Tillmann Crueger [2be37b] * src/molecule_dynamics.cpp (modified) Removed some more calls to molecule::ActOnAllAtoms() 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: ... Wed, 25 Aug 2010 12:04:11 GMT Tillmann Crueger [14c57a] * src/Parser/PcpParser.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/ThermoStatContainer.hpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/Berendsen.hpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/GaussianThermostat.hpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/Langevin.hpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoThermostat.hpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/NoseHoover.hpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Thermostat.hpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/Thermostats/Woodcock.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) * src/config.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) Made all parts of the programm use the new thermostat structure Wed, 25 Aug 2010 10:42:21 GMT Tillmann Crueger [8d1dd4] * src/config.cpp (modified) * src/config.hpp (modified) Removed obsolete load methods from config class Wed, 25 Aug 2010 10:16:11 GMT Tillmann Crueger [3e4162] * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/Berendsen.hpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/GaussianThermostat.hpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/Langevin.hpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/NoseHoover.hpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/Thermostats/Woodcock.hpp (modified) Added several default constructors with some default values to ... Wed, 25 Aug 2010 09:24:25 GMT Tillmann Crueger [c0c650] * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/Berendsen.hpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/GaussianThermostat.hpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/Langevin.hpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoThermostat.hpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/NoseHoover.hpp (modified) * src/Thermostats/Thermostat.hpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/Thermostats/Woodcock.hpp (modified) Added structure that allows construction of thermostats from ... Wed, 25 Aug 2010 08:57:44 GMT Tillmann Crueger [0b882a] * src/Thermostats/Berendsen.hpp (modified) * src/Thermostats/GaussianThermostat.hpp (modified) * src/Thermostats/Langevin.hpp (modified) * src/Thermostats/NoThermostat.hpp (modified) * src/Thermostats/NoseHoover.hpp (modified) * src/Thermostats/Woodcock.hpp (modified) Added Inheritance structure to ThermostatTraits Fri, 20 Aug 2010 13:54:23 GMT Tillmann Crueger [579a81] * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/Berendsen.hpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/GaussianThermostat.hpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/Langevin.hpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoThermostat.hpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/NoseHoover.hpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Thermostat.hpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/Thermostats/Woodcock.hpp (modified) Added a basic self-descriptive structure for Thermostats Fri, 20 Aug 2010 11:43:39 GMT Tillmann Crueger [194649] * src/Makefile.am (modified) * src/Thermostats/Berendsen.cpp (added) * src/Thermostats/Berendsen.hpp (added) * src/Thermostats/GaussianThermostat.cpp (added) * src/Thermostats/GaussianThermostat.hpp (added) * src/Thermostats/Langevin.cpp (added) * src/Thermostats/Langevin.hpp (added) * src/Thermostats/NoThermostat.cpp (added) * src/Thermostats/NoThermostat.hpp (added) * src/Thermostats/NoseHoover.cpp (added) * src/Thermostats/NoseHoover.hpp (added) * src/Thermostats/Thermostat.cpp (added) * src/Thermostats/Thermostat.hpp (added) * src/Thermostats/Woodcock.cpp (added) * src/Thermostats/Woodcock.hpp (added) Added class structure to represent thermostats Thu, 19 Aug 2010 16:59:34 GMT Frederik Heber [d17f3d] * src/UIElements/TextUI/TextWindow.cpp (modified) FIX: Using getSuitableShortForm() in TextWindow::TextWindow() for all ... Thu, 19 Aug 2010 16:59:34 GMT Frederik Heber [9c7e0f] * src/UIElements/TextUI/TextWindow.cpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) deleted function MoleculeListClass::flipChosen() and ... Thu, 19 Aug 2010 16:59:10 GMT Frederik Heber [994713] * src/Actions/ActionHistory.cpp (modified) Merge branch 'FixRedoAction_isActive' into stable Thu, 19 Aug 2010 16:58:24 GMT Frederik Heber [8006ee] * src/Actions/ActionHistory.cpp (modified) FIX: "Redo" message was in wrong function. - in ... Thu, 19 Aug 2010 16:27:32 GMT Frederik Heber [4b7650] * src/UIElements/TextUI/TextWindow.cpp (modified) Merge branch 'FixTextUI_undo' into stable Thu, 19 Aug 2010 16:26:53 GMT Frederik Heber [c6081e] * src/UIElements/TextUI/TextWindow.cpp (modified) BUGFIX: TextWindow::TextWindow() has Undo/Redo names still with ... Thu, 19 Aug 2010 15:23:37 GMT Frederik Heber [80cecb5] * src/LinearAlgebra/Matrix.cpp (modified) MEMFIX: Matrix::transformToEigenbasis() did not free evec and eval. Thu, 19 Aug 2010 15:23:37 GMT Frederik Heber [654394] * src/World.cpp (modified) MEMFIX: World::numMoleculeDefragSkips and World::lastMoleculePoolSize ... Thu, 19 Aug 2010 15:23:37 GMT Frederik Heber [146cff2] * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/analysis_correlation.hpp (modified) FIX: include missing in some files. Thu, 19 Aug 2010 15:23:37 GMT Frederik Heber [73c5ca] * src/atom_trajectoryparticle.hpp (modified) FIX: gsl/gsl_inline.h not needed in atom_trajectoryparticle.hpp. Thu, 19 Aug 2010 15:23:37 GMT Frederik Heber [9f99b3] * src/periodentafel.cpp (modified) MEMFIX: periodentafel::LoadElementsDatabase() leaked memory. - if ... Thu, 19 Aug 2010 15:23:37 GMT Frederik Heber [2a7457] * src/LinearAlgebra/Matrix.cpp (modified) MEMFIX: operator*(Matrix,Vector) leaked memory. - a gsl_vector was ... 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 16:11:16 GMT Frederik Heber [1ee380f] * autogen.sh (deleted) * bootstrap (added) Replaced autogen.sh with TREMOLO-derivate bootstrap shell. - ... Wed, 18 Aug 2010 16:10:07 GMT Frederik Heber [2f6f51] * tests/regression/molecuilder.in (modified) Enabled XML file of valgrind errors, can be viewed with memcheckview. Wed, 18 Aug 2010 16:09:47 GMT Tillmann Crueger [ea2c76] * src/ThermoStatContainer.hpp (modified) Removed definition of unused method in ThermostatContainer class Wed, 18 Aug 2010 14:10:33 GMT Tillmann Crueger [bc8a41] * src/LinearAlgebra/VectorContent.hpp (modified) Added a warning to keep people from using VectorContent directly 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 Wed, 18 Aug 2010 13:34:33 GMT Tillmann Crueger [7329c3] * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) Removed obsolete method for summing up temperature Wed, 18 Aug 2010 13:30:26 GMT Tillmann Crueger [900402] * src/molecule.cpp (modified) Made the molecule::OutputTemperatureFromTrajectories() method use the ... Wed, 18 Aug 2010 13:30:16 GMT Tillmann Crueger [ddc85b] * src/AtomSet.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) Added a method that allows calculation of the total temperature of a ... Tue, 17 Aug 2010 17:16:34 GMT Frederik Heber [490038] * configure.ac (modified) * src/builder.cpp (modified) * test_all.sh (modified) * tests/regression/Makefile.am (modified) * tests/regression/atlocal.in (modified) * tests/regression/molecuilder.in (modified) added --with-valgrind switch to configure script. - if given, we ... Tue, 17 Aug 2010 13:34:08 GMT Frederik Heber [293afd] * configure.ac (modified) * tests/regression/testsuite.at (modified) Merge remote branch 'wildenhues/stable' into stable Tue, 17 Aug 2010 13:19:54 GMT Frederik Heber [5f8660a] * configure.ac (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Makefile.am (modified) * src/UIElements/QT4/QTUIFactory.cpp (modified) * src/builder.cpp (modified) * src/version.h (modified) Changed PACKAGENAME and version. - rename ESPACKVersion in ... 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 ... Tue, 17 Aug 2010 12:50:34 GMT Frederik Heber [9cd807] * AUTHORS (modified) FIX: Other authors were missing again in AUTHORS (thx Ralf!). - ... Tue, 17 Aug 2010 12:43:46 GMT Frederik Heber [49a136] * COPYING (modified) * README (modified) Merge branch 'FixMerge_TestSHBranch' into stable Tue, 17 Aug 2010 12:43:04 GMT Frederik Heber [8e463e] * COPYING (modified) * README (modified) FIX: COPYING AND README still had conflict markers (thx Ralf!). Tue, 17 Aug 2010 12:28:29 GMT Ralf Wildenhues [f30490] * configure.ac (modified) * tests/regression/testsuite.at (modified) Enable colored testsuite output if available. * configure.ac: ... Fri, 13 Aug 2010 16:42:47 GMT Frederik Heber [a19d73e] * src/tesselationhelpers.cpp (modified) FIX: GetCenterofCircumcircle() has check for division by zero. Fri, 13 Aug 2010 16:36:03 GMT Frederik Heber [bb4408] * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Parser/XyzParser.cpp (modified) BUGFIX: Removed adding of parsed atoms in LoadXyzAction. - a ... Fri, 13 Aug 2010 16:16:37 GMT Frederik Heber [0adac1] * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.hpp (modified) Added "periodic" as optional argument to TranslateAction. - entails ... Fri, 13 Aug 2010 14:08:39 GMT Frederik Heber [5f1d5b8] * src/Patterns/ObservedContainer_impl.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) BUGFIX: fixed undefined ref to ... Thu, 12 Aug 2010 18:15:33 GMT Frederik Heber [ae959a] * src/element.cpp (modified) * src/element.hpp (modified) element::group, period, block converted from char[] to std::string. ... Thu, 12 Aug 2010 16:34:46 GMT Frederik Heber [faa1c9] * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-graph.at (modified) BUGFIX: SubgraphDissectionAction() does not copy system anymore, has ... Thu, 12 Aug 2010 16:31:02 GMT Frederik Heber [a7a087] * src/World.cpp (modified) * src/World.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) new function World::changeMoleculeId(). - copied from ... Thu, 12 Aug 2010 15:08:47 GMT Frederik Heber [51769f] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (added) * src/Actions/SelectionAction/AtomByElementAction.hpp (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.hpp (added) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (added) * src/Actions/SelectionAction/NotAtomByElementAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.hpp (added) Added (un)select-molecule-by-formula/..-atom-by-element actions..