# # ChangeLog for src/builder.cpp # # Generated by Trac 1.4.4 # Jan 8, 2025, 3:35:54 PM Wed, 26 Sep 2012 17:24:47 GMT Frederik Heber [94d5ac6] * LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Line.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LinePoint.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Plane.cpp (modified) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Space.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Vector.cpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (modified) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (modified) * LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (modified) * LinearAlgebra/src/unittests/LineUnitTest.cpp (modified) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (modified) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (modified) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (modified) * LinearAlgebra/src/unittests/PlaneUnitTest.cpp (modified) * LinearAlgebra/src/unittests/RealSpaceMatrixUnitTest.cpp (modified) * LinearAlgebra/src/unittests/TestRunnerMain.cpp (modified) * LinearAlgebra/src/unittests/UnitTestMain.cpp (modified) * LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (modified) * LinearAlgebra/src/unittests/VectorSetUnitTest.cpp (modified) * LinearAlgebra/src/unittests/VectorUnitTest.cpp (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpRedistributeAction.cpp (added) * src/Actions/CommandAction/HelpRedistributeAction.def (added) * src/Actions/CommandAction/HelpRedistributeAction.hpp (added) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSphericalSurfaceAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_SaturateDanglingBonds.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_graphnode.cpp (modified) * src/Atom/atom_graphnodeinfo.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_particleinfo.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (modified) * src/AtomIdSet.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/Box_BoundaryConditions.cpp (modified) * src/ControllerOptions_MPQCCommandJob.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomOrderDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Filling/Cluster.cpp (modified) * src/Filling/Filler.cpp (modified) * src/Filling/Generators/NodeGenerator.cpp (modified) * src/Filling/Inserter/Inserter.cpp (modified) * src/Filling/Inserter/RandomInserter.cpp (modified) * src/Filling/Inserter/SimpleInserter.cpp (modified) * src/Filling/Inserter/SurfaceInserter.cpp (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Filling/Mesh/Mesh.cpp (modified) * src/Filling/Predicates/AnyFillPredicate.cpp (modified) * src/Filling/Predicates/FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideSurface_FillPredicate.cpp (modified) * src/Filling/Predicates/IsValidInDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsVoidNode_FillPredicate.cpp (modified) * src/Filling/Predicates/Ops_FillPredicate.cpp (modified) * src/Filling/unittests/ClusterUnitTest.cpp (modified) * src/Filling/unittests/FillerUnitTest.cpp (modified) * src/Filling/unittests/IsInsideDomain_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsInsideSurface_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsValidInDomain_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsVoidNode_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/Ops_FillPredicateUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCCommandJob_MPQCData.cpp (modified) * src/Jobs/unittests/MPQCCommandJobUnitTest.cpp (modified) * src/Jobs/unittests/MPQCDataUnitTest.cpp (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp (modified) * src/LinkedCell/LinkedCell_Model_Update.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/tripleIndex.cpp (modified) * src/LinkedCell/unittests/LinkedCellUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomDataValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomIdValidator.cpp (modified) * src/Parameters/Validators/Specific/BoundaryConditionValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxLengthValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxVectorValidator.cpp (modified) * src/Parameters/Validators/Specific/FileSuffixValidator.cpp (modified) * src/Parameters/Validators/Specific/FormulaValidator.cpp (modified) * src/Parameters/Validators/Specific/KeyValueValidator.cpp (modified) * src/Parameters/Validators/Specific/MoleculeIdValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserFileValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/RandomNumberValidators.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixInvertibleValidator.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixSymmetricValidator.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorNotZeroValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorPositiveComponentsValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorZeroOneComponentsValidator.cpp (modified) * src/Parameters/unittests/ContinuousParameterTest.cpp (modified) * src/Parameters/unittests/ContinuousValueTest.cpp (modified) * src/Parameters/unittests/DiscreteParameterTest.cpp (modified) * src/Parameters/unittests/DiscreteValueTest.cpp (modified) * src/Parameters/unittests/Ops_ValidatorTest.cpp (modified) * src/Parameters/unittests/stubs/ActionNameValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxLengthValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxVectorValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/TimeStepPresentValidatorStub.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser_ElementKeys.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.cpp (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Server.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/BaseShapesUnitTest.cpp (modified) * src/Shapes/unittests/ShapeOpsUnitTest.cpp (modified) * src/Shapes/unittests/Shape_HomogeneousPointsUnitTest.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp (modified) * src/Tesselation/ApproximateShapeArea.cpp (modified) * src/Tesselation/ApproximateShapeVolume.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FilesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RealSpaceMatrixCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FilesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQueryList.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RealSpaceMatrixQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FilesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RealSpaceMatrixTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/controller.cpp (modified) * src/controller_AddOn_MPQCCommandJob.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/poolworker.cpp (modified) * src/unittests/AtomIdSetUnitTest.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/Box_BoundaryConditionsUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/MoleculeUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * src/unittests/stubs/AtomStub.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) * tests/JobMarket/mpqc.cpp (modified) FIX: As we use GSL internally, we are as of now required to use GPL ... Wed, 08 Aug 2012 13:35:12 GMT Michael Ankele [05a05e] * src/builder.cpp (modified) only saveAll() on exit when using CommandLineUI Wed, 04 Jan 2012 14:28:40 GMT Frederik Heber [0aa122] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_graphnode.cpp (modified) * src/Atom/atom_graphnodeinfo.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_particleinfo.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp (modified) * src/LinkedCell/LinkedCell_Model_Update.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/tripleIndex.cpp (modified) * src/LinkedCell/unittests/LinkedCellUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/AtomStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldStub.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/StringParameter.cpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/ShapeUnitTest.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/AtomQuery.cpp (modified) * src/UIElements/Query/AtomsQuery.cpp (modified) * src/UIElements/Query/BooleanQuery.cpp (modified) * src/UIElements/Query/BoxQuery.cpp (modified) * src/UIElements/Query/DoubleQuery.cpp (modified) * src/UIElements/Query/DoublesQuery.cpp (modified) * src/UIElements/Query/ElementQuery.cpp (modified) * src/UIElements/Query/ElementsQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/FileQuery.cpp (modified) * src/UIElements/Query/IntQuery.cpp (modified) * src/UIElements/Query/IntsQuery.cpp (modified) * src/UIElements/Query/MoleculeQuery.cpp (modified) * src/UIElements/Query/MoleculesQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp (modified) * src/UIElements/Query/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.cpp (modified) * src/UIElements/Query/UnsignedIntQuery.cpp (modified) * src/UIElements/Query/UnsignedIntsQuery.cpp (modified) * src/UIElements/Query/VectorQuery.cpp (modified) * src/UIElements/Query/VectorsQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) Updated all source files's copyright note to current year 2012. Wed, 28 Dec 2011 15:24:58 GMT Frederik Heber [d103d3] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/AtomicInfo.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/StringParameter.cpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/ShapeUnitTest.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/TesselPoint.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/AtomQuery.cpp (modified) * src/UIElements/Query/AtomsQuery.cpp (modified) * src/UIElements/Query/BooleanQuery.cpp (modified) * src/UIElements/Query/BoxQuery.cpp (modified) * src/UIElements/Query/DoubleQuery.cpp (modified) * src/UIElements/Query/DoublesQuery.cpp (modified) * src/UIElements/Query/ElementQuery.cpp (modified) * src/UIElements/Query/ElementsQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/FileQuery.cpp (modified) * src/UIElements/Query/IntQuery.cpp (modified) * src/UIElements/Query/IntsQuery.cpp (modified) * src/UIElements/Query/MoleculeQuery.cpp (modified) * src/UIElements/Query/MoleculesQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp (modified) * src/UIElements/Query/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.cpp (modified) * src/UIElements/Query/UnsignedIntQuery.cpp (modified) * src/UIElements/Query/UnsignedIntsQuery.cpp (modified) * src/UIElements/Query/VectorQuery.cpp (modified) * src/UIElements/Query/VectorsQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_observable.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) Added additional check in CodeCheck's project disclaimer for current ... Mon, 07 Nov 2011 16:13:01 GMT Frederik Heber [b5d38d] * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/builder_init.hpp (modified) * src/cleanUp.cpp (modified) * src/cleanUp.hpp (modified) Moved dumpMemory() and saveAll() from module builder_init to cleanUp. Mon, 31 Oct 2011 17:13:52 GMT Frederik Heber [750cff] * src/Actions/Action.hpp (modified) * src/builder.cpp (modified) * src/documentation/code.dox (modified) * src/documentation/constructs/actions.dox (modified) * src/documentation/constructs/atoms.dox (added) * src/documentation/constructs/bondgraph.dox (modified) * src/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/descriptors.dox (modified) * src/documentation/constructs/fragmentation.dox (modified) * src/documentation/constructs/linearalgebra.dox (added) * src/documentation/constructs/logger.dox (added) * src/documentation/constructs/molecules.dox (added) * src/documentation/constructs/observers_observables.dox (modified) * src/documentation/constructs/parsers.dox (modified) * src/documentation/constructs/randomnumbers.dox (modified) * src/documentation/constructs/serialization.dox (modified) * src/documentation/constructs/shapes.dox (modified) * src/documentation/constructs/tesselation.dox (modified) * src/documentation/constructs/world.dox (added) * src/documentation/copyright.dox (added) * src/documentation/faq.dox (modified) * src/documentation/fileformats.dox (added) * src/documentation/howtos/action.dox (added) * src/documentation/howtos/howtos.dox (added) * src/documentation/install.dox (modified) * src/documentation/launch.dox (modified) * src/documentation/mainpage.dox (modified) * src/documentation/tests/code-tests.dox (modified) * src/documentation/tests/regression-tests.dox (modified) * src/documentation/tests/tests.dox (modified) * src/documentation/tests/unit-tests.dox (modified) * src/documentation/userinterfaces/commandline.dox (added) * src/documentation/userinterfaces/graphical.dox (added) * src/documentation/userinterfaces/textmenu.dox (added) * src/documentation/userinterfaces/userinterfaces.dox (added) HUGE: Update on documenation. - a general skeleton of the ... Thu, 16 Dec 2010 17:32:23 GMT Frederik Heber [f4d063] * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Makefile.am (modified) * src/builder.cpp (modified) * src/builder_init.cpp (added) * src/builder_init.hpp (added) MEMFIX: MemDebug ignores all unknown sources. Removed all ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [c82d0c] * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/Menu.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuDescription.hpp (modified) * src/builder.cpp (modified) * src/unittests/MenuDescriptionUnitTest.cpp (modified) MenuDescription is now a singleton. - also all Maps are static ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [ae21cbd] * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/Vector.hpp (modified) * src/Patterns/Registry_impl.hpp (modified) * src/builder.cpp (modified) MEMFIX: new function AddStaticEntitiestoIgnoreList() for putting ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [41449c] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/builder.cpp (modified) MEMFIX: Action::success and Action::failure are not recognized by ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [052afe] * src/Helpers/errorlogger.cpp (modified) * src/Helpers/logger.cpp (modified) * src/builder.cpp (modified) MEMFIX: ofstreams in ...logger.hpp as static objects were not ... Sat, 04 Dec 2010 23:33:47 GMT Frederik Heber [b59da6] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionTraits.cpp (modified) * src/Actions/ActionTraits.hpp (modified) * src/Makefile.am (modified) * src/Patterns/Registry_impl.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/Menu.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuDescription.hpp (modified) * src/UIElements/Menu/MenuInterface.cpp (added) * src/UIElements/Menu/MenuInterface.hpp (added) * src/UIElements/Menu/Qt4/QtMenu.cpp (deleted) * src/UIElements/Menu/Qt4/QtMenu.hpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (added) * src/UIElements/Menu/Qt4/QtMenuPipe.hpp (added) * src/UIElements/Menu/SubMenuItem.hpp (deleted) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (moved) * src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (moved) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (moved) * src/UIElements/Menu/TextMenu/DisplayMenuItem.hpp (moved) * src/UIElements/Menu/TextMenu/MenuItem.cpp (moved) * src/UIElements/Menu/TextMenu/MenuItem.hpp (moved) * src/UIElements/Menu/TextMenu/SeperatorItem.cpp (moved) * src/UIElements/Menu/TextMenu/SeperatorItem.hpp (moved) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (moved) * src/UIElements/Menu/TextMenu/SubMenuItem.hpp (added) * src/UIElements/Menu/TextMenu/TextMenu.hpp (added) * src/UIElements/Menu/TextMenu/TxMenu.cpp (moved) * src/UIElements/Menu/TextMenu/TxMenu.hpp (moved) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/builder.cpp (modified) Refactoring of Menu structure for Qt and Text UI done. - Menu is ... Tue, 09 Nov 2010 15:35:53 GMT Frederik Heber [76cec6] * src/builder.cpp (modified) MEMFIX: OptionRegistry has not been purged in cleanUp(). Sat, 30 Oct 2010 20:42:44 GMT Frederik Heber [e4afb4] * 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/ActionRegistry.hpp (modified) * src/Actions/ActionTraits.cpp (modified) * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.def (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.def (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.def (modified) * src/Actions/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.def (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.def (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpAction.def (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.def (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/VersionAction.def (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.def (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.def (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.def (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.def (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 (deleted) * src/Actions/MapOfActions.hpp (deleted) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.def (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.def (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.def (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.def (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.def (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.def (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/OptionRegistry.cpp (added) * src/Actions/OptionRegistry.hpp (added) * src/Actions/OptionTrait.cpp (added) * src/Actions/OptionTrait.hpp (added) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.def (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.def (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/RedoAction.cpp (added) * src/Actions/RedoAction.def (added) * src/Actions/RedoAction.hpp (added) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.def (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.def (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.def (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.def (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.def (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.def (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.def (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.def (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.def (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.def (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.def (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.def (modified) * src/Actions/UndoAction.cpp (added) * src/Actions/UndoAction.def (moved) * src/Actions/UndoAction.hpp (added) * src/Actions/ValueStorage.cpp (modified) * src/Actions/ValueStorage.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.def (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.def (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.def (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.def (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.def (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.def (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.def (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.def (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.def (modified) * src/Actions/convert5.sh (added) * src/CommandLineParser.cpp (deleted) * src/Makefile.am (modified) * src/Patterns/Registry.hpp (modified) * src/Patterns/Registry_impl.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (added) * src/UIElements/CommandLineUI/CommandLineParser.hpp (moved) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (added) * src/UIElements/CommandLineUI/TypeEnumContainer.hpp (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuDescription.hpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.hpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/World_calculations.hpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MenuDescriptionUnitTest.cpp (modified) * src/unittests/MenuDescriptionUnitTest.hpp (modified) * src/unittests/RegistryUnitTest.cpp (added) * src/unittests/RegistryUnitTest.hpp (added) * src/unittests/atomsCalculationTest.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) Huge refactoring: Introduction of Traits to Actions. This change is ... Mon, 25 Oct 2010 12:08:39 GMT Frederik Heber [4cf323d] * src/Makefile.am (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Menu/Qt4/QtMenu.cpp (moved) * src/UIElements/Menu/Qt4/QtMenu.hpp (moved) * src/UIElements/Qt4/IntQtQuery.ui (moved) * src/UIElements/Qt4/IntsQtQuery.ui (moved) * src/UIElements/Qt4/QtDialog.cpp (moved) * src/UIElements/Qt4/QtDialog.hpp (moved) * src/UIElements/Qt4/QtMainWindow.cpp (moved) * src/UIElements/Qt4/QtMainWindow.hpp (moved) * src/UIElements/Qt4/QtUIFactory.cpp (moved) * src/UIElements/Qt4/QtUIFactory.hpp (moved) * src/UIElements/Views/Qt4/GLMoleculeView.cpp (moved) * src/UIElements/Views/Qt4/GLMoleculeView.hpp (moved) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (moved) * src/UIElements/Views/Qt4/QtMoleculeView.hpp (moved) * src/UIElements/Views/Qt4/QtStatusBar.cpp (moved) * src/UIElements/Views/Qt4/QtStatusBar.hpp (moved) * src/UIElements/Views/Qt4/QtWorldView.cpp (moved) * src/UIElements/Views/Qt4/QtWorldView.hpp (moved) * src/builder.cpp (modified) Renamed QT -> Qt in files, dirs, and class names. Thu, 14 Oct 2010 10:00:28 GMT Frederik Heber [7230be] * src/Actions/CommandAction/WarrantyAction.cpp (added) * src/Actions/CommandAction/WarrantyAction.def (added) * src/Actions/CommandAction/WarrantyAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-standard_options.at (modified) Added WarrantyAction. This closed ticket #117. 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 13:19:54 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 ... Wed, 11 Aug 2010 09:27:47 GMT Frederik Heber [bf3817] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/BoundaryLineSet.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPolygonSet.cpp (modified) * src/BoundaryTriangleSet.cpp (modified) * src/Box.cpp (modified) * src/CandidateForTesselation.cpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MissingValueException.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (modified) * src/Exceptions/ParseError.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Formula.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/Info.cpp (modified) * src/Helpers/Log.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/Verbose.cpp (modified) * src/Helpers/errorlogger.cpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/logger.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Matrix.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorInterface.cpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/gslvector.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Observer.cpp (modified) * src/PointCloud.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/TesselPoint.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/QT4/QTMenu.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/QT4/GLMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/UIElements/Views/QT4/QTWorldView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/FormulaUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/MapofActionsTest.cpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/SingletonTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (modified) * src/unittests/gslmatrixunittest.cpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/memoryusageobserverunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Added ifdef HAVE_CONFIG and config.h include to each and every cpp ... Fri, 06 Aug 2010 09:34:59 GMT Frederik Heber [d223d5] * Makefile.am (modified) * TestRunnerClient.cpp (added) * TestRunnerClient.h (added) * config/ltmain.sh (added) * configure.ac (modified) * libmolecuilder_config.h.in (added) * m4/gwqt4.m4 (modified) * molecuilder.pc.in (added) * src/Actions/Action.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/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/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (moved) * src/Actions/ValueStorage.hpp (moved) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/SelectiveIterator_impl.hpp (modified) * src/Exceptions/Makefile.am (added) * src/Formula.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.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 (modified) * src/LinearAlgebra/Line.cpp (moved) * src/LinearAlgebra/Line.hpp (moved) * src/LinearAlgebra/Makefile.am (added) * src/LinearAlgebra/Matrix.cpp (moved) * src/LinearAlgebra/Matrix.hpp (moved) * src/LinearAlgebra/MatrixContent.hpp (moved) * src/LinearAlgebra/Plane.cpp (moved) * src/LinearAlgebra/Plane.hpp (moved) * src/LinearAlgebra/Space.cpp (moved) * src/LinearAlgebra/Space.hpp (moved) * src/LinearAlgebra/Vector.cpp (moved) * src/LinearAlgebra/Vector.hpp (moved) * src/LinearAlgebra/VectorContent.hpp (moved) * src/LinearAlgebra/VectorSet.hpp (moved) * src/LinearAlgebra/gslmatrix.cpp (moved) * src/LinearAlgebra/gslmatrix.hpp (moved) * src/LinearAlgebra/gslvector.cpp (moved) * src/LinearAlgebra/gslvector.hpp (moved) * src/LinearAlgebra/linearsystemofequations.cpp (moved) * src/LinearAlgebra/linearsystemofequations.hpp (moved) * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/Makefile.am (added) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/QT4/IntQTQuery.ui (added) * src/UIElements/QT4/IntsQTQuery.ui (added) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/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.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/ShapeUnittest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.hpp (modified) * src/unittests/gslmatrixunittest.hpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.hpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector_ops.cpp (modified) Merge branch 'SharedLibraries' into stable - BUGFIX: MemDebug.cpp ... Thu, 05 Aug 2010 19:41:21 GMT Frederik Heber [952f38] * configure.ac (modified) * src/Actions/Action.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/SelectiveIterator_impl.hpp (modified) * src/Helpers/Info.cpp (moved) * src/Helpers/Info.hpp (moved) * src/Helpers/Log.cpp (moved) * src/Helpers/Log.hpp (moved) * src/Helpers/Makefile.am (added) * src/Helpers/Verbose.cpp (moved) * src/Helpers/Verbose.hpp (moved) * src/Helpers/errorlogger.cpp (moved) * src/Helpers/errorlogger.hpp (moved) * src/Helpers/helpers.cpp (moved) * src/Helpers/helpers.hpp (moved) * src/Helpers/logger.cpp (moved) * src/Helpers/logger.hpp (moved) * src/Legacy/oldmenu.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector_ops.cpp (modified) created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> ... Thu, 05 Aug 2010 14:31:09 GMT Tillmann Crueger [097902] * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/builder.cpp (modified) Made the Programm dump some memory statistics to a file when an ... Thu, 05 Aug 2010 12:12:25 GMT Tillmann Crueger [007839] * src/builder.cpp (modified) Made the Programm abbort when an assertion fails in non-interactive mode Wed, 07 Jul 2010 16:08:32 GMT Tillmann Crueger [4e10f5] * COPYING (added) * INSTALL (added) * README (modified) * config/config.guess (added) * config/config.sub (added) * config/depcomp (added) * config/install-sh (added) * config/missing (added) * configure.ac (modified) * m4/ax_lang_compiler_ms.m4 (added) * m4/cppunit.m4 (added) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (added) * src/CommandLineParser.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * tests/Tesselations/defs.in (modified) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-filling.at (modified) * tests/regression/testsuite-fragmentation.at (modified) * tests/regression/testsuite-graph.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-specifics.at (modified) * tests/regression/testsuite-standard_options.at (modified) * tests/regression/testsuite-tesselation.at (modified) Merge branch 'stable' into StructureRefactoring Conflicts: ... Fri, 02 Jul 2010 13:44:23 GMT Frederik Heber [b9c847] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-tesselation.at (modified) New SetOutputFormatsAction introduced. Fixes: - World::setDomain() ... Fri, 02 Jul 2010 13:09:37 GMT Tillmann Crueger [36166d] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/graph.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/memoryallocator.cpp (deleted) * src/memoryallocator.hpp (deleted) * src/memoryusageobserver.cpp (deleted) * src/memoryusageobserver.hpp (deleted) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Removed left over parts from old memory-tracker Mon, 28 Jun 2010 15:38:05 GMT Frederik Heber [bdb143] * src/Legacy/oldmenu.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_bonds.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat (modified) * tests/Tesselations/heptan/2.5/NonConvexEnvelope-heptan.dat (modified) * tests/Tesselations/heptan/2/NonConvexEnvelope-heptan.dat (modified) * tests/Tesselations/heptan/25/NonConvexEnvelope-heptan.dat (modified) * tests/Tesselations/heptan/3.5/NonConvexEnvelope-heptan.dat (modified) * tests/Tesselations/heptan/3/NonConvexEnvelope-heptan.dat (modified) * tests/Tesselations/heptan/4/NonConvexEnvelope-heptan.dat (modified) * tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified) * tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) Merge branch 'StructureRefactoring' into stable Conflicts: ... Sat, 26 Jun 2010 22:14:22 GMT Frederik Heber [b0acc3] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/builder.cpp (modified) Merge branch 'stable' into QT4Refactoring Conflicts: ... Fri, 25 Jun 2010 13:04:13 GMT Frederik Heber [326bbe] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/builder.cpp (modified) Legacy/oldmenu is no more. - TextWindow::TextWindow() now properly ... Fri, 25 Jun 2010 09:57:15 GMT Tillmann Crueger [04488a] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (added) * src/Actions/WorldAction/InputAction.hpp (added) * src/Actions/WorldAction/OutputAction.cpp (added) * src/Actions/WorldAction/OutputAction.hpp (added) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (added) * src/ConfigFileBuffer.hpp (added) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ChangeTracker.hpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (added) * src/Parser/FormatParserStorage.hpp (added) * src/Parser/MpqcParser.cpp (added) * src/Parser/MpqcParser.hpp (added) * src/Parser/PcpParser.cpp (added) * src/Parser/PcpParser.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * src/Patterns/Singleton.hpp (modified) * src/Patterns/Singleton_impl.hpp (modified) * src/ThermoStatContainer.cpp (added) * src/ThermoStatContainer.hpp (added) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/ParserUnitTest.hpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * tests/regression/Domain/6/post/test-x.conf.xyz (modified) * tests/regression/Domain/6/post/test-y.conf.xyz (modified) * tests/regression/Domain/6/post/test-z.conf.xyz (modified) * tests/regression/Domain/6/post/test.conf.xyz (modified) * tests/regression/Filling/1/post/test.conf (modified) * tests/regression/Simple_configuration/2/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/3/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/4/post/test.conf (modified) * tests/regression/Simple_configuration/4/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/5/post/test.conf (modified) * tests/regression/Simple_configuration/8/post/test.conf.xyz (modified) * tests/regression/testsuite-fragmentation.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-standard_options.at (modified) Merge branch 'StructureRefactoring' into QT4Refactoring Conflicts: ... Fri, 25 Jun 2010 08:31:18 GMT Frederik Heber [a356f2] * src/builder.cpp (modified) Cleaned up builder.cpp - ParseComandLineOptions() along with the ... Fri, 25 Jun 2010 08:11:20 GMT Frederik Heber [4f7f34e] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (added) * src/Actions/WorldAction/InputAction.hpp (added) * src/Actions/WorldAction/OutputAction.cpp (added) * src/Actions/WorldAction/OutputAction.hpp (added) * src/CommandLineParser.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-standard_options.at (modified) ParseCommandLineOptions() is not used anymore. - new Actions ... Thu, 24 Jun 2010 10:33:22 GMT Tillmann Crueger [ce4487] * doc/Doxyfile (modified) * src/Actions/Process.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Hbondangle.db (modified) * src/Hbonddistance.db (modified) * src/Patterns/ObservedIterator.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/orbitals.db (modified) * src/periodentafel.cpp (modified) * src/valence.db (modified) * tests/regression/Domain/2/post/test.conf (modified) * tests/regression/Domain/3/post/test.conf (modified) * tests/regression/Domain/4/post/test.conf (modified) * tests/regression/Domain/5/post/test.conf (modified) * tests/regression/Filling/1/post/test.conf (modified) * tests/regression/Filling/1/pre/test.conf (modified) * tests/regression/Molecules/6/post/test.conf (modified) * tests/regression/Molecules/6/pre/test.conf (modified) * tests/regression/Molecules/7/post/test.conf (modified) * tests/regression/Molecules/7/pre/test.conf (modified) * tests/regression/Simple_configuration/2/post/test.conf (modified) * tests/regression/Simple_configuration/3/post/test.conf (modified) * tests/regression/Simple_configuration/4/post/test.conf (modified) * tests/regression/Simple_configuration/5/post/test.conf (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) * tests/regression/testsuite-tesselation.at (modified) Merge branch 'MenuRefactoring' into QT4Refactoring Wed, 23 Jun 2010 15:52:50 GMT Frederik Heber [35b698] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/Makefile.am (modified) * tests/regression/Domain/6/post/test-x.conf.xyz (modified) * tests/regression/Domain/6/post/test-y.conf.xyz (modified) * tests/regression/Domain/6/post/test-z.conf.xyz (modified) * tests/regression/Domain/6/post/test.conf.xyz (modified) * tests/regression/Filling/1/post/test.conf (modified) * tests/regression/Simple_configuration/2/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/3/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/4/post/test.conf (modified) * tests/regression/Simple_configuration/4/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/5/post/test.conf (modified) * tests/regression/Simple_configuration/8/post/test.conf.xyz (modified) * tests/regression/testsuite-fragmentation.at (modified) BIG CHANGE: config::load and config::save in ... Mon, 21 Jun 2010 13:07:58 GMT Frederik Heber [a1e929] * src/Actions/MapOfActions.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/builder.cpp (modified) Case 'p' is now handled by CommandLineUI. - ~XyzParser() did ... Sat, 19 Jun 2010 15:58:32 GMT Frederik Heber [da3024] * src/Actions/Process.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/builder.cpp (modified) Fixed various compiler warnings. - Process::Process() - Action and ... Thu, 17 Jun 2010 14:55:56 GMT Tillmann Crueger [257c77] * Makefile.am (modified) * configure.ac (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (added) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (added) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (added) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (added) * src/Actions/AtomAction/AddAction.cpp (added) * src/Actions/AtomAction/AddAction.hpp (added) * src/Actions/AtomAction/ChangeElementAction.cpp (added) * src/Actions/AtomAction/ChangeElementAction.hpp (added) * src/Actions/AtomAction/RemoveAction.cpp (added) * src/Actions/AtomAction/RemoveAction.hpp (added) * src/Actions/CmdAction/BondLengthTableAction.cpp (added) * src/Actions/CmdAction/BondLengthTableAction.hpp (added) * src/Actions/CmdAction/ElementDbAction.cpp (added) * src/Actions/CmdAction/ElementDbAction.hpp (added) * src/Actions/CmdAction/FastParsingAction.cpp (added) * src/Actions/CmdAction/FastParsingAction.hpp (added) * src/Actions/CmdAction/HelpAction.cpp (added) * src/Actions/CmdAction/HelpAction.hpp (added) * src/Actions/CmdAction/VerboseAction.cpp (added) * src/Actions/CmdAction/VerboseAction.hpp (added) * src/Actions/CmdAction/VersionAction.cpp (added) * src/Actions/CmdAction/VersionAction.hpp (added) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (added) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (added) * src/Actions/FragmentationAction/FragmentationAction.cpp (added) * src/Actions/FragmentationAction/FragmentationAction.hpp (added) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (added) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (added) * src/Actions/Makefile.am (added) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (added) * src/Actions/MapOfActions.hpp (added) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (added) * src/Actions/MoleculeAction/BondFileAction.hpp (added) * src/Actions/MoleculeAction/ChangeNameAction.cpp (added) * src/Actions/MoleculeAction/ChangeNameAction.hpp (moved) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (added) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (added) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (added) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (added) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (added) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (added) * src/Actions/MoleculeAction/SaveBondsAction.cpp (added) * src/Actions/MoleculeAction/SaveBondsAction.hpp (added) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (added) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (added) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (added) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (added) * src/Actions/MoleculeAction/TranslateAction.cpp (added) * src/Actions/MoleculeAction/TranslateAction.hpp (added) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (added) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (added) * src/Actions/ParserAction/LoadXyzAction.cpp (added) * src/Actions/ParserAction/LoadXyzAction.hpp (added) * src/Actions/ParserAction/SaveXyzAction.cpp (added) * src/Actions/ParserAction/SaveXyzAction.hpp (added) * src/Actions/Process.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (added) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (added) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (added) * src/Actions/Values.hpp (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (added) * src/Actions/WorldAction/BoundInBoxAction.cpp (added) * src/Actions/WorldAction/BoundInBoxAction.hpp (added) * src/Actions/WorldAction/CenterInBoxAction.cpp (added) * src/Actions/WorldAction/CenterInBoxAction.hpp (added) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (added) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (added) * src/Actions/WorldAction/ChangeBoxAction.cpp (added) * src/Actions/WorldAction/ChangeBoxAction.hpp (added) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (added) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (added) * src/Actions/WorldAction/RepeatBoxAction.cpp (added) * src/Actions/WorldAction/RepeatBoxAction.hpp (added) * src/Actions/WorldAction/ScaleBoxAction.cpp (added) * src/Actions/WorldAction/ScaleBoxAction.hpp (added) * src/Actions/WorldAction/SetDefaultNameAction.cpp (added) * src/Actions/WorldAction/SetDefaultNameAction.hpp (added) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (added) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (added) * src/Actions/small_actions.cpp (deleted) * src/CommandLineParser.cpp (added) * src/CommandLineParser.hpp (added) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (added) * src/Descriptors/MoleculeNameDescriptor.hpp (added) * src/Descriptors/MoleculeNameDescriptor_impl.hpp (added) * src/Descriptors/MoleculePtrDescriptor.cpp (added) * src/Descriptors/MoleculePtrDescriptor.hpp (added) * src/Descriptors/MoleculePtrDescriptor_impl.hpp (added) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Line.cpp (modified) * src/Makefile.am (modified) * src/Menu/QT4/QTMenu.cpp (deleted) * src/Menu/QT4/QTMenu.hpp (deleted) * src/Parser/ChangeTracker.cpp (added) * src/Parser/ChangeTracker.hpp (added) * src/Parser/FormatParser.cpp (added) * src/Parser/FormatParser.hpp (added) * src/Parser/TremoloParser.cpp (added) * src/Parser/TremoloParser.hpp (added) * src/Parser/XyzParser.cpp (added) * src/Parser/XyzParser.hpp (added) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedIterator.hpp (added) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/Plane.cpp (modified) * src/Space.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (added) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (added) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (added) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (added) * src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (added) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (added) * src/UIElements/CommandLineUI/CommandLineWindow.hpp (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/MainWindow.hpp (modified) * src/UIElements/Makefile.am (added) * src/UIElements/Menu/ActionMenuItem.cpp (moved) * src/UIElements/Menu/ActionMenuItem.hpp (moved) * src/UIElements/Menu/DisplayMenuItem.cpp (moved) * src/UIElements/Menu/DisplayMenuItem.hpp (moved) * src/UIElements/Menu/Menu.cpp (moved) * src/UIElements/Menu/Menu.hpp (moved) * src/UIElements/Menu/MenuItem.cpp (moved) * src/UIElements/Menu/MenuItem.hpp (moved) * src/UIElements/Menu/SeperatorItem.cpp (moved) * src/UIElements/Menu/SeperatorItem.hpp (moved) * src/UIElements/Menu/SubMenuItem.cpp (moved) * src/UIElements/Menu/SubMenuItem.hpp (moved) * src/UIElements/Menu/TextMenu.cpp (moved) * src/UIElements/Menu/TextMenu.hpp (moved) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/QT4/QTMainWindow.hpp (modified) * src/UIElements/QT4/QTUIFactory.cpp (modified) * src/UIElements/QT4/QTUIFactory.hpp (modified) * src/UIElements/TextDialog.cpp (deleted) * src/UIElements/TextDialog.hpp (deleted) * src/UIElements/TextUI/TextDialog.cpp (added) * src/UIElements/TextUI/TextDialog.hpp (added) * src/UIElements/TextUI/TextStatusIndicator.cpp (moved) * src/UIElements/TextUI/TextStatusIndicator.hpp (moved) * src/UIElements/TextUI/TextUIFactory.cpp (moved) * src/UIElements/TextUI/TextUIFactory.hpp (moved) * src/UIElements/TextUI/TextWindow.cpp (moved) * src/UIElements/TextUI/TextWindow.hpp (moved) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/UIElements/Views/MethodStringView.cpp (moved) * src/UIElements/Views/MethodStringView.hpp (moved) * src/UIElements/Views/StreamStringView.cpp (moved) * src/UIElements/Views/StreamStringView.hpp (moved) * src/UIElements/Views/StringView.cpp (moved) * src/UIElements/Views/StringView.hpp (moved) * src/UIElements/Views/View.cpp (moved) * src/UIElements/Views/View.hpp (moved) * src/Views/QT4/GLMoleculeView.cpp (deleted) * src/Views/QT4/GLMoleculeView.hpp (deleted) * src/Views/QT4/QTMoleculeView.cpp (deleted) * src/Views/QT4/QTMoleculeView.hpp (deleted) * src/Views/QT4/QTStatusBar.cpp (deleted) * src/Views/QT4/QTStatusBar.hpp (deleted) * src/Views/QT4/QTWorldView.cpp (deleted) * src/Views/QT4/QTWorldView.hpp (deleted) * 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_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (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/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/element.cpp (modified) * src/elements.db (modified) * src/elements_db.cpp (added) * src/elements_db.hpp (added) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/graph.cpp (modified) * src/gslmatrix.cpp (modified) * src/gslvector.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/info.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/lists.cpp (deleted) * src/lists.hpp (modified) * src/log.cpp (modified) * src/logger.cpp (modified) * src/memoryallocator.cpp (added) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.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/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.hpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MapofActionsTest.cpp (added) * src/unittests/MapofActionsTest.hpp (added) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/ParserUnitTest.cpp (added) * src/unittests/ParserUnitTest.hpp (added) * src/unittests/SingletonTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/analysisbondsunittest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/listofbondsunittest.hpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (added) * src/unittests/periodentafelTest.hpp (added) * 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/vector.cpp (modified) * src/vector_ops.cpp (modified) * src/verbose.cpp (modified) * tests/Makefile.am (modified) * tests/Tesselations/defs.in (modified) * tests/regression/Analysis/1/post/bin_output.csv (added) * tests/regression/Analysis/1/post/output.csv (added) * tests/regression/Analysis/1/pre/test.conf (added) * tests/regression/Analysis/2/post/bin_output-10.csv (added) * tests/regression/Analysis/2/post/bin_output-20.csv (added) * tests/regression/Analysis/2/post/bin_output-5.csv (added) * tests/regression/Analysis/2/post/output-10.csv (added) * tests/regression/Analysis/2/post/output-20.csv (added) * tests/regression/Analysis/2/post/output-5.csv (added) * tests/regression/Analysis/2/pre/test.conf (added) * tests/regression/Analysis/3/post/bin_output.csv (added) * tests/regression/Analysis/3/post/output.csv (added) * tests/regression/Analysis/3/pre/test.conf (added) * tests/regression/Analysis/4/post/bin_output.csv (added) * tests/regression/Analysis/4/post/output.csv (added) * tests/regression/Analysis/4/pre/test.conf (added) * tests/regression/Analysis/5/pre/test.conf (added) * tests/regression/Domain/1/post/test.conf (added) * tests/regression/Domain/2/post/test.conf (moved) * tests/regression/Domain/2/pre/test.conf (added) * tests/regression/Domain/3/post/test.conf (moved) * tests/regression/Domain/3/pre/test.conf (added) * tests/regression/Domain/4/post/test.conf (moved) * tests/regression/Domain/4/pre/test.conf (added) * tests/regression/Domain/5/post/test.conf (moved) * tests/regression/Domain/5/pre/test.conf (added) * tests/regression/Domain/6/post/test-x.conf.xyz (added) * tests/regression/Domain/6/post/test-y.conf.xyz (added) * tests/regression/Domain/6/post/test-z.conf.xyz (added) * tests/regression/Domain/6/post/test.conf.xyz (moved) * tests/regression/Domain/6/pre/test.conf (added) * tests/regression/Filling/1/post/test.conf (added) * tests/regression/Filling/1/pre/test.conf (added) * tests/regression/Filling/2/pre/test.conf (added) * tests/regression/Fragmentation/3/pre/BondFragment0.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment1.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment2.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment3.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentAdjacency.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentForces-Factors.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentKeySets.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentOrderAtSite.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentTE-Factors.dat (deleted) * tests/regression/Graph/2/pre/test.conf (added) * tests/regression/Makefile.am (added) * tests/regression/Molecules/1/pre/test.conf (added) * tests/regression/Molecules/1/pre/test.dbond (added) * tests/regression/Molecules/2/post/test.adj (added) * tests/regression/Molecules/2/post/test.dbond (added) * tests/regression/Molecules/2/pre/test.conf (moved) * tests/regression/Molecules/3/post/test.ekin (added) * tests/regression/Molecules/3/pre/test.conf (added) * tests/regression/Molecules/4/post/test.conf (added) * tests/regression/Molecules/4/pre/test.conf (added) * tests/regression/Molecules/5/pre/test.conf (added) * tests/regression/Molecules/5/pre/test.forces (added) * tests/regression/Molecules/6/post/test.conf (added) * tests/regression/Molecules/6/pre/test.conf (added) * tests/regression/Molecules/7/post/test.conf (added) * tests/regression/Molecules/7/pre/test.conf (added) * tests/regression/Molecules/8/pre/test.conf (added) * tests/regression/Simple_configuration/2/post/test.conf.in (added) * tests/regression/Simple_configuration/3/post/test.conf.in (added) * tests/regression/Simple_configuration/5/post/test.conf.in (added) * tests/regression/Simple_configuration/8/post/test.conf.xyz (added) * tests/regression/Simple_configuration/8/pre/test.conf (added) * tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) * tests/regression/atlocal.in (moved) * tests/regression/molecuilder.in (moved) * tests/regression/testsuite-analysis.at (added) * tests/regression/testsuite-domain.at (added) * tests/regression/testsuite-filling.at (added) * tests/regression/testsuite-fragmentation.at (added) * tests/regression/testsuite-graph.at (added) * tests/regression/testsuite-molecules.at (added) * tests/regression/testsuite-simple_configuration.at (added) * tests/regression/testsuite-specifics.at (added) * tests/regression/testsuite-standard_options.at (added) * tests/regression/testsuite-tesselation.at (added) * tests/regression/testsuite.at (added) * tests/testsuite.at (deleted) Merge branch 'stable' into QT4Refactoring Conflicts: ... Thu, 17 Jun 2010 12:56:48 GMT Tillmann Crueger [5f5a7b] * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextUIFactory.hpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/builder.cpp (modified) Merge branch 'MenuRefactoring' into stable Conflicts: ... Wed, 16 Jun 2010 12:24:21 GMT Tillmann Crueger [e6317b] * configure.ac (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp (deleted) * src/Actions/AnalysisAction/PairCorrelationToPointAction.hpp (deleted) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp (deleted) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp (deleted) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/Values.hpp (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/CommandLineParser.cpp (modified) * src/CommandLineParser.hpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (added) * src/Descriptors/MoleculeNameDescriptor.hpp (added) * src/Descriptors/MoleculeNameDescriptor_impl.hpp (added) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (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) * tests/Tesselations/defs.in (modified) * tests/regression/Analysis/3/post/bin_output.csv (modified) * tests/regression/Fragmentation/3/pre/BondFragment0.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment0.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment1.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment1.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment2.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment2.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment3.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment3.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment4.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment4.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentAdjacency.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentForces-Factors.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentKeySets.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentOrderAtSite.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentTE-Factors.dat (deleted) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-filling.at (modified) * tests/regression/testsuite-fragmentation.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-tesselation.at (modified) Broken: Merge commit 'Gitosis/stable' into stable Conflicts: ... Sat, 12 Jun 2010 10:34:14 GMT Frederik Heber [980dd6] * src/Actions/MapOfActions.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/builder.cpp (modified) * tests/Tesselations/defs.in (modified) * tests/regression/testsuite-tesselation.at (modified) Case 'N' is now handled by CommandLineUI. - TESTFIX: Tesselation/1 ... Fri, 11 Jun 2010 19:22:37 GMT Frederik Heber [f6bd32] * src/Actions/MapOfActions.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-tesselation.at (modified) Case 'o' is now handled by CommandLineUI. - As of now, multiple ... Fri, 11 Jun 2010 15:59:53 GMT Frederik Heber [6866aa] * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'I' is now handled by CommandLineUI. Fri, 11 Jun 2010 15:52:44 GMT Frederik Heber [a307af] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Case 'S' is now handled by CommandLineUI. Fri, 11 Jun 2010 15:48:32 GMT Frederik Heber [a02462] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Case 'L' is now handled by CommandLineUI. Fri, 11 Jun 2010 15:27:20 GMT Frederik Heber [aacce8] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Case 'P' is now handled by CommandLineUI. - TESTFIX: ... Fri, 11 Jun 2010 15:21:51 GMT Frederik Heber [77b2d7] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Cases 't' and 'T' are now handled by CommandLineUI. - TESTFIX: both ... Fri, 11 Jun 2010 15:07:11 GMT Frederik Heber [e2b47c] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) Case 'R' is now handled by CommandLineUI. - again, for each atom to ... Fri, 11 Jun 2010 14:49:15 GMT Frederik Heber [9d2a92] * src/builder.cpp (modified) ParseCommandLineOptions() - re-added removed argument count checking ... Fri, 11 Jun 2010 14:38:34 GMT Frederik Heber [f4bd01] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Case 'A' is now handled by CommandLineUI. - TESTFIX: ... Fri, 11 Jun 2010 14:37:51 GMT Frederik Heber [d55743e] * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'r' is now handled by CommandLineUI. Fri, 11 Jun 2010 14:20:11 GMT Frederik Heber [77de81] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Cases 'J' and 'j' are now handled by CommandLineUI. - TESTFIX: ... Fri, 11 Jun 2010 12:20:08 GMT Frederik Heber [54b953] * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) Case 'E' is now handled by CommandLineUI. - TESTFIX: --element is ... Fri, 11 Jun 2010 12:19:50 GMT Frederik Heber [f0a3ec] * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) Case 'a' is now handled by CommandLineUI. - NOTE: atom has still to ... Fri, 11 Jun 2010 12:19:42 GMT Frederik Heber [6c7352] * src/builder.cpp (modified) Removed commented-out LoadPeriodentafel() and (second) ... Fri, 11 Jun 2010 12:19:27 GMT Frederik Heber [387b36] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) Case 'X' is now handled by CommandLineUI, World::get/setDefaultName() ... Fri, 11 Jun 2010 12:19:18 GMT Frederik Heber [f821d6] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-standard_options.at (modified) Case 'n' is now handled by CommandLineUI. - TESTFIX: fastparsing ... Fri, 11 Jun 2010 10:45:06 GMT Frederik Heber [bdaacd] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/builder.cpp (modified) Case 'M' is now handled by CommandLineUI. Thu, 10 Jun 2010 16:24:24 GMT Frederik Heber [39af9f] * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'g' is now handled by CommandLineUI. Thu, 10 Jun 2010 16:20:36 GMT Frederik Heber [198494] * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'e' is now handled by CommandLineUI. - BUGFIX: ElementDbAction ... Thu, 10 Jun 2010 16:13:23 GMT Frederik Heber [7e6b00] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/CommandLineParser.cpp (modified) * src/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/builder.cpp (modified) FIX: Sequence of actions called from command line is now corrected. ... Thu, 10 Jun 2010 13:11:28 GMT Tillmann Crueger [112b09] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/CommandLineParser.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Line.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Observer.cpp (modified) * src/Plane.cpp (modified) * src/Space.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/graph.cpp (modified) * src/gslmatrix.cpp (modified) * src/gslvector.cpp (modified) * src/helpers.cpp (modified) * src/info.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/log.cpp (modified) * src/logger.cpp (modified) * src/memoryallocator.cpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/vector.cpp (modified) * src/vector_ops.cpp (modified) * src/verbose.cpp (modified) Added #include "Helpers/MemDebug.hpp" to all .cpp files Wed, 09 Jun 2010 15:10:51 GMT Frederik Heber [2b5574] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-analysis.at (modified) Case 'm' is now handled by CommandLineUI. - TESTCHANGE: Analysis/5 ... Wed, 09 Jun 2010 15:08:46 GMT Frederik Heber [58bbd3] * src/Actions/MapOfActions.cpp (modified) * src/analysis_correlation.cpp (modified) * src/builder.cpp (modified) * src/moleculelist.cpp (modified) * tests/regression/Analysis/3/post/bin_output.csv (modified) * tests/regression/testsuite-analysis.at (modified) Cases 'C' are now handled by CommandLineUI. - TESTFIX: ... Wed, 09 Jun 2010 14:30:10 GMT Tillmann Crueger [cd5047] * src/Actions/Process.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Added Logging capabilities to Observer Framework Wed, 09 Jun 2010 11:12:08 GMT Frederik Heber [c78d44] * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/builder.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) Change to PairCorrelation...() functions, accept now vector [8540f0] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'D' is now handled by CommandLineUI. Tue, 08 Jun 2010 13:49:27 GMT Frederik Heber [e4b5de] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/builder.cpp (modified) * tests/regression/Fragmentation/3/pre/BondFragment0.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment0.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment1.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment1.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment2.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment2.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment3.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment3.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment4.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment4.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentAdjacency.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentForces-Factors.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentKeySets.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentOrderAtSite.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentTE-Factors.dat (deleted) * tests/regression/testsuite-fragmentation.at (modified) Case 'f' is now handled by CommandLineUI. - ... Tue, 08 Jun 2010 12:13:11 GMT Frederik Heber [48ab70a] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'u' is now handled by CommandLineUI. Mon, 07 Jun 2010 23:55:30 GMT Frederik Heber [9907e7] * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-filling.at (modified) Case '-F' is now handled by CommandLineUI. - FIX: ... Wed, 02 Jun 2010 16:17:17 GMT Frederik Heber [e30ce8] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (added) * src/Descriptors/MoleculePtrDescriptor.hpp (added) * src/Descriptors/MoleculePtrDescriptor_impl.hpp (added) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/builder.cpp (modified) Case 'd' is now handled by CommandLineUI (RepeatBoxAction). - ... Wed, 02 Jun 2010 14:40:30 GMT Frederik Heber [584a2a] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case '-O' is now handled by CommandLineUI (CenterOnEdgeAction). ... Wed, 02 Jun 2010 14:38:07 GMT Frederik Heber [116f37] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/builder.cpp (modified) Case '-c' is now handled by CommandLineUI. - BUGFIX: ... Wed, 02 Jun 2010 12:22:47 GMT Frederik Heber [7fd416] * src/analysis_correlation.cpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/moleculelist.cpp (modified) FIX: CorrelationToSurface() was broken. - DOCU: ... Wed, 02 Jun 2010 11:44:00 GMT Tillmann Crueger [67c75b] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/small_actions.cpp (modified) * src/Exceptions/CustomException.cpp (added) * src/Exceptions/CustomException.hpp (added) * src/Exceptions/LinearDependenceException.cpp (added) * src/Exceptions/LinearDependenceException.hpp (added) * src/Exceptions/MathException.cpp (added) * src/Exceptions/MathException.hpp (added) * src/Exceptions/MultipleSolutionsException.hpp (added) * src/Exceptions/SkewException.cpp (added) * src/Exceptions/SkewException.hpp (added) * src/Exceptions/ZeroVectorException.cpp (added) * src/Exceptions/ZeroVectorException.hpp (added) * src/Helpers/Assert.cpp (modified) * src/Helpers/Assert.hpp (modified) * src/Helpers/MemDebug.cpp (added) * src/Helpers/MemDebug.hpp (added) * src/Helpers/fast_functions.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Line.cpp (added) * src/Line.hpp (added) * src/Makefile.am (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/Plane.cpp (added) * src/Plane.hpp (added) * src/Space.cpp (added) * src/Space.hpp (added) * src/UIElements/TextDialog.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_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.hpp (modified) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/graph.cpp (modified) * src/gslmatrix.cpp (modified) * src/gslvector.cpp (modified) * src/gslvector.hpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/info.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/log.cpp (modified) * src/log.hpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (added) * src/triangleintersectionlist.hpp (added) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActOnAllUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (added) * src/unittests/CountBondsUnitTest.hpp (added) * src/unittests/LineUnittest.cpp (added) * src/unittests/LineUnittest.hpp (added) * src/unittests/LinkedCellUnitTest.cpp (added) * src/unittests/LinkedCellUnitTest.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/PlaneUnittest.cpp (added) * src/unittests/PlaneUnittest.hpp (added) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.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/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (added) * src/vector_ops.hpp (added) * src/verbose.cpp (modified) * src/verbose.hpp (modified) * tests/Tesselations/1_2-dimethoxyethane.test (modified) * tests/Tesselations/1_2-dimethoxyethane/1.5/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/2.5/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/2/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/25/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/3.5/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/3/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/4/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/NonConvexEnvelope-1_2-dimethoxyethane.dat (deleted) * tests/Tesselations/1_2-dimethylbenzene.test (modified) * tests/Tesselations/1_2-dimethylbenzene/1.5/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/2.5/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/2/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/25/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/3.5/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/3/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/4/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/NonConvexEnvelope-1_2-dimethylbenzene.dat (deleted) * tests/Tesselations/1_2-dimethylbenzene/tecplot.phy (deleted) * tests/Tesselations/2-methylcyclohexanone.test (modified) * tests/Tesselations/2-methylcyclohexanone/1.5/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/2.5/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/2/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/25/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/3.5/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/3/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/4/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/NonConvexEnvelope-2-methylcyclohexanone.dat (deleted) * tests/Tesselations/C16_0-Torus.test (deleted) * tests/Tesselations/C16_0-Torus/C16_0-Torus.xyz (deleted) * tests/Tesselations/C16_0-Torus/NonConvexEnvelope-C16_0-Torus.dat (deleted) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/N_N-dimethylacetamide.test (modified) * tests/Tesselations/N_N-dimethylacetamide/1.5/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/2.5/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/2/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/25/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/3.5/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/3/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/4/NonConvexEnvelope-N_N-dimethylacetamide.dat (moved) * tests/Tesselations/benzene.test (modified) * tests/Tesselations/benzene/1.5/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/2.5/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/2/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/25/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/3.5/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/3/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/4/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/NonConvexEnvelope-benzene.dat (deleted) * tests/Tesselations/cholesterol.test (modified) * tests/Tesselations/cholesterol/1.5/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/2.5/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/2/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/25/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/3.5/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/3/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/4/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/NonConvexEnvelope-cholesterol.dat (deleted) * tests/Tesselations/cluster.test (deleted) * tests/Tesselations/cluster/NonConvexEnvelope-cluster.dat (deleted) * tests/Tesselations/cluster/cluster.dbond (deleted) * tests/Tesselations/cluster/cluster.xyz (deleted) * tests/Tesselations/cycloheptane.test (modified) * tests/Tesselations/cycloheptane/1.5/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/2.5/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/2/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/25/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/3.5/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/3/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/4/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/NonConvexEnvelope-cycloheptane.dat (deleted) * tests/Tesselations/defs.in (modified) * tests/Tesselations/dimethyl_bromomalonate.test (modified) * tests/Tesselations/dimethyl_bromomalonate/1.5/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/2.5/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/2/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/25/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/3.5/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/3/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/4/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/NonConvexEnvelope-dimethyl_bromomalonate.dat (deleted) * tests/Tesselations/glucose.test (modified) * tests/Tesselations/glucose/1.5/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/2.5/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/2/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/25/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/3.5/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/3/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/4/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/NonConvexEnvelope-glucose.dat (deleted) * tests/Tesselations/heptan.test (modified) * tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/2.5/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/2/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/25/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/3.5/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/3/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/4/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/NonConvexEnvelope-heptan.dat (deleted) * tests/Tesselations/isoleucine.test (modified) * tests/Tesselations/isoleucine/1.5/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/2.5/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/2/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/25/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/3.5/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/3/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/4/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/NonConvexEnvelope-isoleucine.dat (deleted) * tests/Tesselations/neohexane.test (modified) * tests/Tesselations/neohexane/1.5/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/2.5/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/2/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/25/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/3.5/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/3/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/4/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/NonConvexEnvelope-neohexane.dat (deleted) * tests/Tesselations/proline.test (modified) * tests/Tesselations/proline/1.5/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/2.5/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/2/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/25/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/3.5/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/3/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/4/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/NonConvexEnvelope-proline.dat (deleted) * tests/Tesselations/putrescine.test (modified) * tests/Tesselations/putrescine/1.5/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/2.5/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/2/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/25/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/3.5/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/3/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/4/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/NonConvexEnvelope-putrescine.dat (deleted) * tests/Tesselations/round_cluster.test (deleted) * tests/Tesselations/round_cluster/NonConvexEnvelope-round_cluster.dat (deleted) * tests/Tesselations/round_cluster/round_cluster.dbond (deleted) * tests/Tesselations/round_cluster/round_cluster.xyz (deleted) * tests/Tesselations/tartaric_acid.test (modified) * tests/Tesselations/tartaric_acid/1.5/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/2.5/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/2/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/25/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/3.5/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/3/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/4/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/NonConvexEnvelope-tartaric_acid.dat (deleted) * tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) Merge branch 'MenuRefactoring' into QT4Refactoring Conflicts: ... Wed, 02 Jun 2010 11:19:27 GMT Tillmann Crueger [190326] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/small_actions.cpp (modified) * src/Exceptions/CustomException.cpp (added) * src/Exceptions/CustomException.hpp (added) * src/Exceptions/LinearDependenceException.cpp (added) * src/Exceptions/LinearDependenceException.hpp (added) * src/Exceptions/MathException.cpp (added) * src/Exceptions/MathException.hpp (added) * src/Exceptions/MultipleSolutionsException.hpp (added) * src/Exceptions/SkewException.cpp (added) * src/Exceptions/SkewException.hpp (added) * src/Exceptions/ZeroVectorException.cpp (added) * src/Exceptions/ZeroVectorException.hpp (added) * src/Helpers/Assert.cpp (modified) * src/Helpers/Assert.hpp (modified) * src/Helpers/MemDebug.cpp (added) * src/Helpers/MemDebug.hpp (added) * src/Helpers/fast_functions.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Line.cpp (added) * src/Line.hpp (added) * src/Makefile.am (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/Plane.cpp (added) * src/Plane.hpp (added) * src/Space.cpp (added) * src/Space.hpp (added) * src/UIElements/TextDialog.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_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.hpp (modified) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/graph.cpp (modified) * src/gslmatrix.cpp (modified) * src/gslvector.cpp (modified) * src/gslvector.hpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/info.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/log.cpp (modified) * src/log.hpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (added) * src/triangleintersectionlist.hpp (added) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActOnAllUnitTest.hpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (added) * src/unittests/CountBondsUnitTest.hpp (added) * src/unittests/LineUnittest.cpp (added) * src/unittests/LineUnittest.hpp (added) * src/unittests/LinkedCellUnitTest.cpp (added) * src/unittests/LinkedCellUnitTest.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/PlaneUnittest.cpp (added) * src/unittests/PlaneUnittest.hpp (added) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.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/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (added) * src/vector_ops.hpp (added) * src/verbose.cpp (modified) * src/verbose.hpp (modified) * tests/Tesselations/1_2-dimethoxyethane.test (modified) * tests/Tesselations/1_2-dimethoxyethane/1.5/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/2.5/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/2/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/25/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/3.5/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/3/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/4/NonConvexEnvelope-1_2-dimethoxyethane.dat (added) * tests/Tesselations/1_2-dimethoxyethane/NonConvexEnvelope-1_2-dimethoxyethane.dat (deleted) * tests/Tesselations/1_2-dimethylbenzene.test (modified) * tests/Tesselations/1_2-dimethylbenzene/1.5/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/2.5/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/2/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/25/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/3.5/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/3/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/4/NonConvexEnvelope-1_2-dimethylbenzene.dat (added) * tests/Tesselations/1_2-dimethylbenzene/NonConvexEnvelope-1_2-dimethylbenzene.dat (deleted) * tests/Tesselations/1_2-dimethylbenzene/tecplot.phy (deleted) * tests/Tesselations/2-methylcyclohexanone.test (modified) * tests/Tesselations/2-methylcyclohexanone/1.5/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/2.5/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/2/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/25/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/3.5/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/3/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/4/NonConvexEnvelope-2-methylcyclohexanone.dat (added) * tests/Tesselations/2-methylcyclohexanone/NonConvexEnvelope-2-methylcyclohexanone.dat (deleted) * tests/Tesselations/C16_0-Torus.test (deleted) * tests/Tesselations/C16_0-Torus/C16_0-Torus.xyz (deleted) * tests/Tesselations/C16_0-Torus/NonConvexEnvelope-C16_0-Torus.dat (deleted) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/N_N-dimethylacetamide.test (modified) * tests/Tesselations/N_N-dimethylacetamide/1.5/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/2.5/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/2/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/25/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/3.5/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/3/NonConvexEnvelope-N_N-dimethylacetamide.dat (added) * tests/Tesselations/N_N-dimethylacetamide/4/NonConvexEnvelope-N_N-dimethylacetamide.dat (moved) * tests/Tesselations/benzene.test (modified) * tests/Tesselations/benzene/1.5/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/2.5/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/2/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/25/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/3.5/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/3/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/4/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/NonConvexEnvelope-benzene.dat (deleted) * tests/Tesselations/cholesterol.test (modified) * tests/Tesselations/cholesterol/1.5/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/2.5/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/2/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/25/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/3.5/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/3/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/4/NonConvexEnvelope-cholesterol.dat (added) * tests/Tesselations/cholesterol/NonConvexEnvelope-cholesterol.dat (deleted) * tests/Tesselations/cluster.test (deleted) * tests/Tesselations/cluster/NonConvexEnvelope-cluster.dat (deleted) * tests/Tesselations/cluster/cluster.dbond (deleted) * tests/Tesselations/cluster/cluster.xyz (deleted) * tests/Tesselations/cycloheptane.test (modified) * tests/Tesselations/cycloheptane/1.5/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/2.5/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/2/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/25/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/3.5/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/3/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/4/NonConvexEnvelope-cycloheptane.dat (added) * tests/Tesselations/cycloheptane/NonConvexEnvelope-cycloheptane.dat (deleted) * tests/Tesselations/defs.in (modified) * tests/Tesselations/dimethyl_bromomalonate.test (modified) * tests/Tesselations/dimethyl_bromomalonate/1.5/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/2.5/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/2/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/25/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/3.5/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/3/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/4/NonConvexEnvelope-dimethyl_bromomalonate.dat (added) * tests/Tesselations/dimethyl_bromomalonate/NonConvexEnvelope-dimethyl_bromomalonate.dat (deleted) * tests/Tesselations/glucose.test (modified) * tests/Tesselations/glucose/1.5/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/2.5/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/2/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/25/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/3.5/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/3/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/4/NonConvexEnvelope-glucose.dat (added) * tests/Tesselations/glucose/NonConvexEnvelope-glucose.dat (deleted) * tests/Tesselations/heptan.test (modified) * tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/2.5/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/2/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/25/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/3.5/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/3/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/4/NonConvexEnvelope-heptan.dat (added) * tests/Tesselations/heptan/NonConvexEnvelope-heptan.dat (deleted) * tests/Tesselations/isoleucine.test (modified) * tests/Tesselations/isoleucine/1.5/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/2.5/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/2/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/25/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/3.5/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/3/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/4/NonConvexEnvelope-isoleucine.dat (added) * tests/Tesselations/isoleucine/NonConvexEnvelope-isoleucine.dat (deleted) * tests/Tesselations/neohexane.test (modified) * tests/Tesselations/neohexane/1.5/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/2.5/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/2/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/25/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/3.5/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/3/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/4/NonConvexEnvelope-neohexane.dat (added) * tests/Tesselations/neohexane/NonConvexEnvelope-neohexane.dat (deleted) * tests/Tesselations/proline.test (modified) * tests/Tesselations/proline/1.5/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/2.5/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/2/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/25/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/3.5/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/3/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/4/NonConvexEnvelope-proline.dat (added) * tests/Tesselations/proline/NonConvexEnvelope-proline.dat (deleted) * tests/Tesselations/putrescine.test (modified) * tests/Tesselations/putrescine/1.5/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/2.5/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/2/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/25/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/3.5/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/3/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/4/NonConvexEnvelope-putrescine.dat (added) * tests/Tesselations/putrescine/NonConvexEnvelope-putrescine.dat (deleted) * tests/Tesselations/round_cluster.test (deleted) * tests/Tesselations/round_cluster/NonConvexEnvelope-round_cluster.dat (deleted) * tests/Tesselations/round_cluster/round_cluster.dbond (deleted) * tests/Tesselations/round_cluster/round_cluster.xyz (deleted) * tests/Tesselations/tartaric_acid.test (modified) * tests/Tesselations/tartaric_acid/1.5/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/2.5/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/2/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/25/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/3.5/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/3/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/4/NonConvexEnvelope-tartaric_acid.dat (added) * tests/Tesselations/tartaric_acid/NonConvexEnvelope-tartaric_acid.dat (deleted) * tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) Merge branch 'StructureRefactoring' into MenuRefactoring Tue, 01 Jun 2010 21:36:36 GMT Frederik Heber [009607e] * src/analysis_correlation.cpp (modified) * src/builder.cpp (modified) Small changes to ...Correlation...(). - Calling doCountAtoms on all ... Mon, 31 May 2010 18:41:12 GMT Frederik Heber [e08c46] * src/Legacy/oldmenu.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) Removed molecule::first, molecule::last. - molecule does not have a ... Mon, 31 May 2010 17:32:27 GMT Frederik Heber [1024cb] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedIterator.hpp (added) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/Plane.cpp (modified) * src/Plane.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/lists.cpp (deleted) * src/lists.hpp (modified) * src/memoryallocator.cpp (added) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/listofbondsunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * tests/regression/Domain/5/post/test.conf (modified) * tests/regression/Domain/5/pre/test.conf (modified) * tests/regression/Domain/6/post/test-x.conf (deleted) * tests/regression/Domain/6/post/test-x.conf.xyz (added) * tests/regression/Domain/6/post/test-y.conf (deleted) * tests/regression/Domain/6/post/test-y.conf.xyz (added) * tests/regression/Domain/6/post/test-z.conf (deleted) * tests/regression/Domain/6/post/test-z.conf.xyz (added) * tests/regression/Domain/6/post/test.conf (deleted) * tests/regression/Domain/6/pre/test.conf (modified) * tests/regression/Simple_configuration/8/post/test.conf (deleted) * tests/regression/Simple_configuration/8/post/test.conf.xyz (added) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) Merge commit 'jupiter/MoleculeStartEndSwitch' into ... Mon, 31 May 2010 14:33:11 GMT Frederik Heber [42af9e] * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/periodentafel.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) MEMFIXES: no more default saving/loading of element's db, ... Mon, 31 May 2010 13:09:58 GMT Frederik Heber [920c70] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Makefile.am (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/stackclass.hpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and ... Sun, 30 May 2010 23:40:04 GMT Frederik Heber [158c594] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/builder.cpp (modified) Case '-b' now handled by CommandLineUI and fixes. - ... Sun, 30 May 2010 23:18:48 GMT Frederik Heber [2a92ff] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case '-s' now handled by CommandLineUI. - FIX: Type Vector has to ... Sun, 30 May 2010 23:03:49 GMT Frederik Heber [6ca1f7] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) case '-B' now handled by CommandLineUI. Sun, 30 May 2010 16:51:45 GMT Frederik Heber [9b7db1] * src/builder.cpp (modified) * tests/regression/Simple_configuration/8/post/test.conf (added) * tests/regression/Simple_configuration/8/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-R' (removing atoms outside of sphere) to testsuite. - ... Sun, 30 May 2010 15:38:38 GMT Frederik Heber [f8f14d] * src/builder.cpp (modified) * tests/regression/Molecules/4/post/test.conf (added) * tests/regression/Molecules/4/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-L' (linear interpolation) to testsuite. - this just ... Sun, 30 May 2010 15:18:50 GMT Frederik Heber [c68c90] * src/builder.cpp (modified) * src/molecule_graph.cpp (modified) * tests/regression/Molecules/1/pre/test.conf (added) * tests/regression/Molecules/1/pre/test.dbond (added) * tests/regression/testsuite.at (modified) Added case '-A' (parsing bonds) to testsuite. - ... Sun, 30 May 2010 14:45:50 GMT Frederik Heber [5e11e4] * src/builder.cpp (modified) In-code created water molecule has been removed in ... Sun, 30 May 2010 13:42:26 GMT Frederik Heber [08f6ff] * src/builder.cpp (modified) * tests/regression/Analysis/3/post/bin_output.csv (added) * tests/regression/Analysis/3/post/output.csv (added) * tests/regression/Analysis/3/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-C P' (correlation to point) to testsuite. - DOCUFIX: ... Sun, 30 May 2010 13:41:37 GMT Frederik Heber [06f8ee] * src/builder.cpp (modified) * tests/regression/Analysis/1/post/bin_output.csv (added) * tests/regression/Analysis/1/post/output.csv (added) * tests/regression/Analysis/1/pre/test.conf (added) * tests/regression/Analysis/2/post/bin_output-10.csv (added) * tests/regression/Analysis/2/post/bin_output-20.csv (added) * tests/regression/Analysis/2/post/bin_output-5.csv (added) * tests/regression/Analysis/2/post/output-10.csv (added) * tests/regression/Analysis/2/post/output-20.csv (added) * tests/regression/Analysis/2/post/output-5.csv (added) * tests/regression/Analysis/2/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-C E' (pair correlation analysis) to testsuite. - ... Sun, 30 May 2010 11:32:05 GMT Frederik Heber [5188f5] * src/builder.cpp (modified) * tests/regression/testsuite.at (modified) Added case '-M' (MPQC basis) to testsuite. - ... Sun, 30 May 2010 11:05:54 GMT Frederik Heber [93d732b] * src/World.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite.at (modified) Added case '-X' (default mol name) to testsuite and bugfix. - ... Sat, 29 May 2010 14:18:41 GMT Frederik Heber [62680e] * src/builder.cpp (modified) Merge branch 'FixReintroduceExitFlagtoParseCommandLineCall' into ... Sat, 29 May 2010 14:15:27 GMT Frederik Heber [99fcaf] * src/builder.cpp (modified) FIX: Flag returned by ParseCommandLineOptions() needs to be heeded, ... Sat, 29 May 2010 13:11:22 GMT Frederik Heber [0fb9f6] * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/builder.cpp (modified) * src/helpers.cpp (modified) Fixes to prevent seg'faults. - ... Sat, 29 May 2010 12:59:31 GMT Frederik Heber [b32dbb] * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) Fixes and changes to tesselation and concavity measurements. Here, ... Thu, 27 May 2010 10:46:54 GMT Tillmann Crueger [a7b761b] * src/Helpers/Assert.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedIterator.hpp (added) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.hpp (modified) * src/lists.cpp (deleted) * src/lists.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/listofbondsunittest.hpp (modified) Merge branch 'MoleculeStartEndSwitch' into StructureRefactoring ... Thu, 27 May 2010 09:17:11 GMT Frederik Heber [bfd839] * src/Legacy/oldmenu.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_bonds.hpp (modified) * src/builder.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) Changed and added counting of hydrogen bonds to menu. - ... Wed, 19 May 2010 18:46:52 GMT Frederik Heber [8de375] * src/Helpers/MemDebug.cpp (modified) * src/analysis_bonds.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/bond.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) Merge branch 'StructureRefactoring' into CommandLineActionMapping ... Wed, 19 May 2010 18:41:05 GMT Frederik Heber [eff648] * src/builder.cpp (modified) BUGFIX: In ParseCommandLineOptions() -v and -V were mixed. - ...