# # ChangeLog for src/Makefile.am # # Generated by Trac 1.4.4 # Apr 15, 2025, 12:31:16 PM Thu, 29 Jul 2010 12:23:21 GMT Tillmann Crueger [112f90] * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Fixed ActionSequenceTest and ManipulateAtomsTest Wed, 28 Jul 2010 09:21:14 GMT Tillmann Crueger [677e13] * .gitignore (added) * configure.ac (modified) * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (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 (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (added) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.hpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.hpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.hpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/HelpAction.hpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.hpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/CmdAction/VersionAction.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.hpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.hpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (added) * src/Actions/SelectionAction/AllAtomsAction.hpp (added) * src/Actions/SelectionAction/AllMoleculesAction.cpp (added) * src/Actions/SelectionAction/AllMoleculesAction.hpp (added) * src/Actions/SelectionAction/AtomByIdAction.cpp (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/Values.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.hpp (modified) * src/Actions/WorldAction/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/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/CommandLineParser.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (added) * src/Exceptions/IllegalTypeException.hpp (added) * src/Exceptions/MissingValueException.cpp (added) * src/Exceptions/MissingValueException.hpp (added) * 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/Makefile.am (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.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/ValueStorage.cpp (added) * src/UIElements/ValueStorage.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * test_all.sh (modified) * tests/Tesselations/defs.in (modified) * tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat (modified) * tests/regression/Simple_configuration/3/post/test2.conf (deleted) * tests/regression/Simple_configuration/3/post/test2.in (deleted) * tests/regression/Simple_configuration/3/post/test2.xyz (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-tesselation.at (modified) Merge branch 'stable' into StructureRefactoring Conflicts: ... Fri, 23 Jul 2010 16:28:28 GMT Frederik Heber [4e145c] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Makefile.am (modified) Actions can now be called non-interactively, MissingValueException ... Thu, 22 Jul 2010 17:53:44 GMT Frederik Heber [ab9a27] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Exceptions/IllegalTypeException.cpp (added) * src/Exceptions/IllegalTypeException.hpp (added) * src/Makefile.am (modified) MapOfActions::TypeMap now contains type_info. We are going to use ... Thu, 22 Jul 2010 11:14:08 GMT Tillmann Crueger [6e7147] * src/Descriptors/MoleculeFormulaDescriptor.cpp (added) * src/Descriptors/MoleculeFormulaDescriptor.hpp (added) * src/Descriptors/MoleculeFormulaDescriptor_impl.hpp (added) * src/Makefile.am (modified) Added a Descriptor that allows querying molecules by their Formula Wed, 21 Jul 2010 13:17:18 GMT Tillmann Crueger [574ddc1] * src/Exceptions/ParseError.cpp (added) * src/Exceptions/ParseError.hpp (added) * src/Makefile.am (modified) Added an exception to indicate failures in parsing. Wed, 21 Jul 2010 13:09:11 GMT Tillmann Crueger [6f43ab] * src/Formula.cpp (added) * src/Formula.hpp (added) * src/Makefile.am (modified) Added a class that allow simple handling of molecules formulas Fri, 16 Jul 2010 13:11:45 GMT Tillmann Crueger [cf0ca1] * src/Makefile.am (modified) * src/World.hpp (modified) Added Descriptors that allow description of all Selected molecules Fri, 16 Jul 2010 13:02:31 GMT Tillmann Crueger [48dcbd] * src/Descriptors/AtomSelectionDescriptor.cpp (added) * src/Descriptors/AtomSelectionDescriptor.hpp (added) * src/Descriptors/AtomSelectionDescriptor_impl.hpp (added) * src/Makefile.am (modified) Added descriptors that allow description of all selected atoms 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: ... Tue, 06 Jul 2010 11:48:01 GMT Ralf Wildenhues [f8be39] * src/Makefile.am (modified) Fix .git-version rule. * src/Makefile.am ($(srcdir)/.git-version): ... Fri, 02 Jul 2010 09:51:01 GMT Tillmann Crueger [5ec8e3] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Box.cpp (added) * src/Box.hpp (added) * src/Exceptions/NotInvertibleException.cpp (added) * src/Exceptions/NotInvertibleException.hpp (added) * src/Line.cpp (modified) * src/Line.hpp (modified) * src/Makefile.am (modified) * src/Matrix.cpp (added) * src/Matrix.hpp (added) * src/Parser/PcpParser.cpp (modified) * src/Shapes/BaseShapes.cpp (added) * src/Shapes/BaseShapes.hpp (added) * src/Shapes/BaseShapes_impl.hpp (added) * src/Shapes/Shape.cpp (added) * src/Shapes/Shape.hpp (added) * src/Shapes/ShapeOps.cpp (added) * src/Shapes/ShapeOps.hpp (added) * src/Shapes/ShapeOps_impl.hpp (added) * src/Shapes/Shape_impl.hpp (added) * 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/VectorSet.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (added) * src/unittests/ShapeUnittest.hpp (added) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) * tests/regression/Domain/4/post/test.conf (modified) Merge branch 'VectorRefactoring' into StructureRefactoring ... Thu, 01 Jul 2010 14:57:02 GMT Tillmann Crueger [456341] * src/Makefile.am (modified) Moved all Exceptions and Matrix class from LinAlg module back to main ... Thu, 01 Jul 2010 13:55:08 GMT Tillmann Crueger [8f822c] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (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/MapOfActions.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.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/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (added) * src/Actions/WorldAction/InputAction.hpp (added) * src/Actions/WorldAction/OutputAction.cpp (added) * src/Actions/WorldAction/OutputAction.hpp (added) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Box.cpp (added) * src/Box.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/Exceptions/NotInvertibleException.cpp (added) * src/Exceptions/NotInvertibleException.hpp (added) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Matrix.cpp (added) * src/Matrix.hpp (added) * 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/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/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/VectorSet.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/ellipsoid.cpp (modified) * src/helpers.cpp (modified) * src/helpers.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/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/unittests/LineUnittest.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/PlaneUnittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) * tests/regression/Domain/4/post/test.conf (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 'VectorRefactoring' into Shapes Wed, 30 Jun 2010 09:42:58 GMT Tillmann Crueger [83c09a] * src/Box.cpp (added) * src/Box.hpp (added) * src/Makefile.am (modified) Added a basic Box class to store cell_size as well as inverse of ... 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 15:54:48 GMT Tillmann Crueger [33d774] * 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 'StructureRefactoring' into VectorRefactoring ... Fri, 25 Jun 2010 13:44:07 GMT Tillmann Crueger [325390] * src/Exceptions/NotInvertibleException.cpp (added) * src/Exceptions/NotInvertibleException.hpp (added) * src/Makefile.am (modified) * src/Matrix.cpp (added) * src/Matrix.hpp (added) * src/vector.cpp (modified) * src/vector.hpp (modified) Started work on basic matrix class to be used with Vector class 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 08:11:20 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 ... 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 ... Tue, 22 Jun 2010 14:09:14 GMT Frederik Heber [52baf9] * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (added) * src/Parser/FormatParserStorage.hpp (added) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/TremoloParser.cpp (modified) new class FormatParserStorage takes care of allocation, uniqueness ... Mon, 21 Jun 2010 07:56:00 GMT Frederik Heber [55240c4] * doc/Doxyfile (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/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/MultipleSolutionsException.hpp (added) * src/Exceptions/SkewException.cpp (added) * src/Exceptions/SkewException.hpp (added) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Hbondangle.db (modified) * src/Hbonddistance.db (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/Line.hpp (modified) * src/Makefile.am (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedIterator.hpp (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/Plane.cpp (modified) * src/Plane.hpp (modified) * src/Space.cpp (modified) * src/Space.hpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (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/TextUIFactory.hpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/VectorSet.cpp (added) * src/VectorSet.hpp (added) * src/World.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/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/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/gslvector.hpp (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.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/orbitals.db (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/LineUnittest.cpp (added) * src/unittests/LineUnittest.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/valence.db (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) * src/vector_ops.hpp (modified) * src/verbose.cpp (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 'stable' into PcpAndMpqcParser Conflicts: ... Fri, 18 Jun 2010 10:44:04 GMT Tillmann Crueger [e09b70] * src/Makefile.am (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (added) * src/Shapes/ShapeOps.hpp (added) * src/Shapes/ShapeOps_impl.hpp (added) * src/Shapes/Shape_impl.hpp (modified) Added basic operations on shapes Fri, 18 Jun 2010 10:18:10 GMT Tillmann Crueger [e38447] * src/Makefile.am (modified) * src/Shapes/BaseShapes.cpp (added) * src/Shapes/BaseShapes.hpp (added) * src/Shapes/BaseShapes_impl.hpp (added) Added some basic shapes to the shape framework Fri, 18 Jun 2010 10:03:23 GMT Tillmann Crueger [997784] * src/Makefile.am (modified) * src/Shapes/Shape.cpp (added) * src/Shapes/Shape.hpp (added) * src/Shapes/Shape_impl.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/ShapeUnittest.cpp (added) * src/unittests/ShapeUnittest.hpp (added) Added basic structure for definition of geometric 3D shapes. 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: ... 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 15:54:26 GMT Frederik Heber [43dad6] * src/ConfigFileBuffer.cpp (modified) * src/ConfigFileBuffer.hpp (modified) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (added) * src/Parser/MpqcParser.hpp (added) * src/Parser/PcpParser.cpp (added) * src/Parser/PcpParser.hpp (added) * src/ThermoStatContainer.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule.cpp (modified) Introducing (but not yet incorporated) FormatParser specializations ... Sat, 12 Jun 2010 13:12:51 GMT Frederik Heber [a3fded] * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/ConfigFileBuffer.hpp (modified) * src/Makefile.am (modified) * src/ThermoStatContainer.cpp (added) * src/ThermoStatContainer.hpp (added) * src/atom_trajectoryparticle.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/moleculelist.cpp (modified) New class ThermoStatContainer containing all parameters and changes ... Sat, 12 Jun 2010 11:12:20 GMT Frederik Heber [88104f] * src/ConfigFileBuffer.cpp (added) * src/ConfigFileBuffer.hpp (added) * src/Makefile.am (modified) * src/config.cpp (modified) * src/config.hpp (modified) Placed class ConfigFileBuffer into its own module. - this is a ... Wed, 09 Jun 2010 15:09:55 GMT Frederik Heber [31b09e] * src/Descriptors/MoleculeNameDescriptor.cpp (added) * src/Descriptors/MoleculeNameDescriptor.hpp (added) * src/Descriptors/MoleculeNameDescriptor_impl.hpp (added) * src/Makefile.am (modified) Added new MoleculeDescriptor by name. - molecule Ids are rather ... Tue, 08 Jun 2010 11:18:45 GMT Frederik Heber [f2a1d3] * src/Makefile.am (modified) Merge branch 'FixRemovedElementsDBFromMakefile' into stable - ... Tue, 08 Jun 2010 11:12:24 GMT Frederik Heber [e58856b] * src/Makefile.am (modified) BUGFIX: elements.db has disappeared to early from .._DATA. - we ... Fri, 04 Jun 2010 09:28:46 GMT Tillmann Crueger [76c0d6] * src/Exceptions/MultipleSolutionsException.hpp (added) * src/Exceptions/SkewException.cpp (added) * src/Exceptions/SkewException.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Line.cpp (modified) * src/Line.hpp (modified) * src/Makefile.am (modified) * src/Plane.cpp (modified) * src/Plane.hpp (modified) * src/Space.cpp (modified) * src/Space.hpp (modified) * src/atom.cpp (modified) * src/molecule_geometry.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/LineUnittest.cpp (added) * src/unittests/LineUnittest.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) * src/vector_ops.hpp (modified) Merge branch 'StructureRefactoring' into stable Conflicts: ... Fri, 04 Jun 2010 09:01:15 GMT Tillmann Crueger [e05826] * src/Makefile.am (modified) Small corrections on Makefile 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 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: ... 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 13:09:58 GMT Frederik Heber [920c70] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Makefile.am (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/stackclass.hpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and ... Thu, 27 May 2010 11:28:37 GMT Tillmann Crueger [215df0] * src/Exceptions/SkewException.cpp (added) * src/Exceptions/SkewException.hpp (added) * src/Makefile.am (modified) * src/atom.cpp (modified) * src/tesselation.cpp (modified) * src/vector_ops.cpp (modified) Simplified some methods. 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 ... Tue, 18 May 2010 15:18:24 GMT Frederik Heber [5079a0] * Makefile.am (modified) * configure.ac (modified) * src/Actions/Makefile.am (added) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (moved) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (moved) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (moved) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (moved) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (moved) * src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (moved) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (moved) * src/UIElements/CommandLineUI/CommandLineWindow.hpp (moved) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (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/TextUI/TextDialog.cpp (moved) * src/UIElements/TextUI/TextDialog.hpp (moved) * 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/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) Actions put into libMolecuilderActions, UIElements into ... Sat, 15 May 2010 17:56:57 GMT Frederik Heber [97ebf8] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (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/PairCorrelationToPointAction.cpp (added) * src/Actions/AnalysisAction/PairCorrelationToPointAction.hpp (added) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp (added) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.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 (modified) * src/Actions/CmdAction/VerboseAction.cpp (added) * src/Actions/CmdAction/VerboseAction.hpp (added) * src/Actions/CmdAction/VersionAction.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/MapOfActions.cpp (added) * src/Actions/MapOfActions.hpp (added) * src/Actions/MoleculeAction/BondFileAction.cpp (added) * src/Actions/MoleculeAction/BondFileAction.hpp (added) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * 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 (modified) * src/Actions/ParserAction/SaveXyzAction.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/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/CommandLineParser.cpp (modified) * src/CommandLineParser.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Parser/XyzParser.cpp (modified) * src/UIElements/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineWindow.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextDialog.cpp (modified) * src/UIElements/TextDialog.hpp (modified) * src/UIElements/TextWindow.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/bondgraph.hpp (modified) * src/builder.cpp (modified) * src/molecule.hpp (modified) * src/unittests/MapofActionsTest.cpp (added) * src/unittests/MapofActionsTest.hpp (added) Added all commands defined in ParseCommandLineOptions() as Actions. ... Sun, 09 May 2010 12:00:08 GMT Frederik Heber [50dfda] * src/Actions/CmdAction/VersionAction.cpp (added) * src/Actions/CmdAction/VersionAction.hpp (added) * src/Makefile.am (modified) * src/UIElements/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineWindow.hpp (modified) * src/builder.cpp (modified) Added VersionAction. - new CmdAction/VersionAction that prints the ... Sat, 08 May 2010 22:00:57 GMT Frederik Heber [e3ecc1a] * src/Actions/CmdAction/HelpAction.cpp (added) * src/Actions/CmdAction/HelpAction.hpp (added) * src/CommandLineParser.hpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineWindow.cpp (modified) New HelpAction that will print the help from boost::program_options. ... Sat, 08 May 2010 19:14:29 GMT Frederik Heber [c6efc1] * configure.ac (modified) * src/CommandLineParser.cpp (added) * src/CommandLineParser.hpp (added) * src/Makefile.am (modified) * src/builder.cpp (modified) Begin of Refactoring of ParseCommandLineOptions(). - new singleton ... Sat, 08 May 2010 18:36:22 GMT Frederik Heber [03bb99] * src/Actions/MoleculeAction/ChangeNameAction.cpp (moved) * src/Actions/MoleculeAction/ChangeNameAction.hpp (moved) * 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/Makefile.am (modified) * src/builder.cpp (modified) Introducing small actions. - new directory MoleculeAction to ... Sat, 08 May 2010 18:30:53 GMT Frederik Heber [a2ab15] * src/Makefile.am (modified) * src/UIElements/CommandLineDialog.cpp (added) * src/UIElements/CommandLineDialog.hpp (added) * src/UIElements/CommandLineStatusIndicator.cpp (added) * src/UIElements/CommandLineStatusIndicator.hpp (added) * src/UIElements/CommandLineUIFactory.cpp (added) * src/UIElements/CommandLineUIFactory.hpp (added) * src/UIElements/CommandLineWindow.cpp (added) * src/UIElements/CommandLineWindow.hpp (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextDialog.cpp (modified) * src/UIElements/TextDialog.hpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) Extended UIFactory to a CommandLine derivate. - Dialog now has ... Sat, 08 May 2010 18:27:57 GMT Frederik Heber [efc3cb] * src/Makefile.am (modified) minor change: put entries in molecuilder/src/Makefile.am into ... Sat, 08 May 2010 12:17:30 GMT Frederik Heber [b9b604] * src/Makefile.am (modified) * 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/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_particleinfo.cpp (modified) * src/bond.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ParserUnitTest.cpp (added) * src/unittests/ParserUnitTest.hpp (added) * src/unittests/SingletonTest.cpp (modified) Merge branch 'StateAndFormatParser' into CommandLineActionMapping ... Fri, 30 Apr 2010 14:01:28 GMT Tillmann Crueger [6f646d] * src/Line.cpp (added) * src/Line.hpp (added) * src/Makefile.am (modified) Added a line class that represents one dimensional subspaces Fri, 30 Apr 2010 10:07:23 GMT Tillmann Crueger [1513a74] * src/Makefile.am (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Declared the Vector class as single point spaces Fri, 30 Apr 2010 09:23:37 GMT Tillmann Crueger [3cdd16] * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/LinearDependenceException.hpp (modified) * src/Exceptions/MathException.cpp (added) * src/Exceptions/MathException.hpp (added) * src/Exceptions/ZeroVectorException.cpp (added) * src/Exceptions/ZeroVectorException.hpp (added) * src/Makefile.am (modified) * src/Plane.cpp (modified) Added more Exceptions to the project to signal differen Math erorrs Fri, 30 Apr 2010 09:03:57 GMT Tillmann Crueger [2247a9] * src/Makefile.am (modified) * src/Plane.cpp (modified) * src/Plane.hpp (modified) * src/Space.cpp (added) * src/Space.hpp (added) Added a class Space to represent general subspaces of R^3 (planes and ... Thu, 29 Apr 2010 13:55:21 GMT Tillmann Crueger [8cbb97] * src/Exceptions/CustomException.cpp (added) * src/Exceptions/CustomException.hpp (added) * src/Exceptions/LinearDependenceException.cpp (added) * src/Exceptions/LinearDependenceException.hpp (added) * src/Helpers/fast_functions.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Plane.cpp (added) * src/Plane.hpp (added) * src/UIElements/TextDialog.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/gslmatrix.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActOnAllUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (added) * src/vector_ops.hpp (added) Merge branch 'VectorRefactoring' into StructureRefactoring ... Wed, 28 Apr 2010 14:52:56 GMT Tillmann Crueger [753f02] * src/Helpers/fast_functions.hpp (modified) * src/Makefile.am (modified) * src/SingleVector.cpp (deleted) * src/SingleVector.hpp (deleted) * src/vector.cpp (modified) * src/vector.hpp (modified) Removed Algebraic Hierachy from vector. Wed, 28 Apr 2010 13:31:57 GMT Tillmann Crueger [632bc3] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Helpers/MemDebug.cpp (added) * src/Helpers/MemDebug.hpp (added) * src/Makefile.am (modified) * src/builder.cpp (modified) Added a small memory tracker to the programm. Tue, 27 Apr 2010 14:25:42 GMT Frederik Heber [5f612ee] * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_bonds.hpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.hpp (modified) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/graph.cpp (modified) * src/gslvector.cpp (modified) * src/gslvector.hpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/info.cpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/log.cpp (modified) * src/log.hpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (added) * src/triangleintersectionlist.hpp (added) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/CountBondsUnitTest.cpp (added) * src/unittests/CountBondsUnitTest.hpp (added) * src/unittests/LinkedCellUnitTest.cpp (added) * src/unittests/LinkedCellUnitTest.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.hpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/tesselationunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/verbose.cpp (modified) * src/verbose.hpp (modified) * tests/Tesselations/1_2-dimethylbenzene/tecplot.phy (deleted) * tests/Tesselations/defs.in (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) Merge branch 'Analysis_PairCorrelation' into StructureRefactoring ... Thu, 15 Apr 2010 10:54:26 GMT Tillmann Crueger [1bd79e] * src/Makefile.am (modified) * src/SingleVector.cpp (modified) * src/SingleVector.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/ellipsoid.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) Changed implementation of Vector to forward operations to contained ... Fri, 09 Apr 2010 14:45:49 GMT Tillmann Crueger [72e7fa] * src/Makefile.am (modified) * src/Plane.cpp (modified) * src/Plane.hpp (modified) * src/SingleVector.cpp (added) * src/SingleVector.hpp (added) * src/vector.cpp (modified) * src/vector.hpp (modified) Started work on the VectorComposites Fri, 09 Apr 2010 12:40:27 GMT Tillmann Crueger [82b71a] * src/Makefile.am (modified) * src/UIElements/QT4/QTUIFactory.cpp (modified) * src/UIElements/QT4/QTUIFactory.hpp (modified) * src/UIElements/TextUIFactory.cpp (modified) * src/UIElements/TextUIFactory.hpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/builder.cpp (modified) Merge branch 'MenuRefactoring' into QT4Refactoring Conflicts: ... Wed, 07 Apr 2010 15:45:38 GMT Tillmann Crueger [0a4f7f] * src/Exceptions/CustomException.cpp (added) * src/Exceptions/CustomException.hpp (added) * src/Exceptions/LinearDependenceException.cpp (added) * src/Exceptions/LinearDependenceException.hpp (added) * src/Helpers/fast_functions.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Plane.cpp (added) * src/Plane.hpp (added) * src/UIElements/TextDialog.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/gslmatrix.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActOnAllUnitTest.hpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (added) * src/vector_ops.hpp (added) Made data internal data-structure of vector class private - ... Thu, 01 Apr 2010 12:16:29 GMT Saskia Metzler [4415da] * doc/Doxyfile (modified) * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (added) * src/Actions/ActionHistory.hpp (added) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/small_actions.cpp (modified) * src/Actions/small_actions.hpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.hpp (modified) * src/Descriptors/AtomTypeDescriptor_impl.hpp (modified) * src/Descriptors/DescriptorBase.hpp (added) * src/Descriptors/DescriptorBase_impl.hpp (added) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.hpp (modified) * src/Descriptors/SelectiveIterator.hpp (added) * src/Descriptors/SelectiveIterator_impl.hpp (added) * src/Helpers/Assert.cpp (added) * src/Helpers/Assert.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Menu/ActionMenuItem.cpp (modified) * src/Menu/ActionMenuItem.hpp (modified) * src/Menu/MenuItem.cpp (modified) * src/Menu/MenuItem.hpp (modified) * src/Menu/TextMenu.cpp (modified) * src/Menu/TextMenu.hpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/Patterns/Singleton.hpp (added) * src/Patterns/Singleton_impl.hpp (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextDialog.cpp (modified) * src/UIElements/TextDialog.hpp (modified) * src/UIElements/TextWindow.cpp (modified) * src/UIElements/TextWindow.hpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (deleted) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/defs.hpp (modified) * src/element.cpp (modified) * src/element.hpp (modified) * src/errorlogger.cpp (modified) * src/errorlogger.hpp (modified) * src/helpers.hpp (modified) * src/leastsquaremin.hpp (modified) * src/log.cpp (modified) * src/logger.cpp (modified) * src/logger.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) * src/types.hpp (added) * 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/AtomDescriptorTest.hpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/MoleculeDescriptorTest.hpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/SingletonTest.cpp (added) * src/unittests/SingletonTest.hpp (added) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/atomsCalculationTest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Merge Till's structure refactoring Merge commit ... Tue, 30 Mar 2010 13:22:20 GMT Saskia Metzler [9131f3] * src/Makefile.am (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/ParserUnitTest.hpp (modified) WIP tremolo parser Thu, 25 Mar 2010 13:36:36 GMT Tillmann Crueger [68d781] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (added) * src/Actions/ActionHistory.hpp (added) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/small_actions.cpp (modified) * src/Actions/small_actions.hpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.hpp (modified) * src/Descriptors/AtomTypeDescriptor_impl.hpp (modified) * src/Descriptors/DescriptorBase.hpp (added) * src/Descriptors/DescriptorBase_impl.hpp (added) * src/Descriptors/MoleculeDescriptor.hpp (modified) * src/Descriptors/SelectiveIterator.hpp (added) * src/Descriptors/SelectiveIterator_impl.hpp (added) * src/Helpers/Assert.cpp (added) * src/Helpers/Assert.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Menu/TextMenu.cpp (modified) * src/Menu/TextMenu.hpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/Patterns/Singleton.hpp (modified) * src/Patterns/Singleton_impl.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/TextDialog.cpp (modified) * src/UIElements/TextDialog.hpp (modified) * src/UIElements/TextWindow.cpp (modified) * src/UIElements/TextWindow.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (deleted) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/defs.hpp (modified) * src/element.cpp (modified) * src/element.hpp (modified) * src/helpers.hpp (modified) * src/leastsquaremin.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) * src/types.hpp (added) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/AtomDescriptorTest.hpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MoleculeDescriptorTest.hpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/SingletonTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/atomsCalculationTest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Merge branch 'MenuRefactoring' into QT4Refactoring Conflicts: ... Thu, 25 Mar 2010 12:01:27 GMT Tillmann Crueger [d56640] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (added) * src/Actions/ActionHistory.hpp (added) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/small_actions.cpp (modified) * src/Actions/small_actions.hpp (modified) * src/Makefile.am (modified) * src/Menu/TextMenu.cpp (modified) * src/Menu/TextMenu.hpp (modified) * src/UIElements/TextDialog.cpp (modified) * src/UIElements/TextWindow.cpp (modified) * src/UIElements/TextWindow.hpp (modified) * src/builder.cpp (modified) Added full undo functioniality Thu, 18 Mar 2010 15:06:30 GMT Tillmann Crueger [75ac0c] * src/Helpers/Assert.cpp (added) * src/Helpers/Assert.hpp (added) * src/Makefile.am (modified) * src/builder.cpp (modified) Added custom Assert makro that allows ignoring asserts Thu, 18 Mar 2010 14:48:20 GMT Tillmann Crueger [229e3c] * src/Helpers/Assert.cpp (added) * src/Helpers/Assert.hpp (added) * src/Makefile.am (modified) * src/builder.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Added custom Assert makro that allows ignoring asserts Wed, 17 Mar 2010 15:19:56 GMT Tillmann Crueger [6e97e5] * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/DescriptorBase.hpp (added) * src/Descriptors/DescriptorBase_impl.hpp (added) * src/Descriptors/MoleculeDescriptor.hpp (modified) * src/Descriptors/SelectiveIterator.hpp (added) * src/Descriptors/SelectiveIterator_impl.hpp (added) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (deleted) * src/helpers.hpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Added a generic Iterator that can be used to iterate only over ... Thu, 11 Mar 2010 14:46:41 GMT Tillmann Crueger [cd032d] * src/Actions/Action.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/small_actions.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Patterns/Singleton.hpp (added) * src/Patterns/Singleton_impl.hpp (added) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextDialog.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/Views/QT4/QTStatusBar.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/errorlogger.cpp (modified) * src/errorlogger.hpp (modified) * src/log.cpp (modified) * src/logger.cpp (modified) * src/logger.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/SingletonTest.cpp (added) * src/unittests/SingletonTest.hpp (added) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Merge branch 'StructureRefactoring' into QT4Refactoring Conflicts: ... Thu, 11 Mar 2010 14:19:53 GMT Tillmann Crueger [aee1a3] * src/Makefile.am (modified) * src/log.cpp (modified) * src/logger.cpp (modified) * src/logger.hpp (modified) * src/unittests/logunittest.cpp (modified) Made logger class use the new Singleton framework Fri, 05 Mar 2010 15:17:43 GMT Tillmann Crueger [a77c96] * src/Makefile.am (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/QT4/QTMainWindow.hpp (modified) * src/Views/QT4/QTMoleculeView.cpp (added) * src/Views/QT4/QTMoleculeView.hpp (added) * src/Views/QT4/QTWorldView.cpp (modified) * src/Views/QT4/QTWorldView.hpp (modified) * src/World.cpp (modified) Started work on a tab view for Molecule Content Fri, 05 Mar 2010 13:45:35 GMT Saskia Metzler [cb2146] * src/Descriptors/MoleculeIdDescriptor.cpp (added) * src/Descriptors/MoleculeIdDescriptor.hpp (added) * src/Descriptors/MoleculeIdDescriptor_impl.hpp (added) * src/Makefile.am (modified) * src/Parser/TremoloParser.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/unittests/AtomDescriptorTest.cpp (moved) * src/unittests/AtomDescriptorTest.hpp (moved) * src/unittests/Makefile.am (modified) * src/unittests/MoleculeDescriptorTest.cpp (added) * src/unittests/MoleculeDescriptorTest.hpp (added) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) solve merge conflict Merge commit 'till/StructureRefactoring' into ... Fri, 05 Mar 2010 12:53:13 GMT Saskia Metzler [ab4b55] * src/FormatParser.cpp (deleted) * src/Makefile.am (modified) * src/Matrix.cpp (deleted) * src/Matrix.hpp (deleted) * src/Parser/ChangeTracker.cpp (moved) * src/Parser/ChangeTracker.hpp (moved) * src/Parser/FormatParser.cpp (added) * src/Parser/FormatParser.hpp (moved) * src/Parser/TremoloParser.cpp (moved) * src/Parser/TremoloParser.hpp (moved) * src/Parser/XyzParser.cpp (added) * src/Parser/XyzParser.hpp (added) * src/XyzParser.cpp (deleted) * src/XyzParser.hpp (deleted) * src/unittests/Makefile.am (modified) * src/unittests/MatrixUnitTest.cpp (deleted) * src/unittests/MatrixUnitTest.hpp (deleted) * src/unittests/ParserUnitTest.cpp (added) * src/unittests/ParserUnitTest.hpp (added) the XYZ parser Fri, 05 Mar 2010 10:16:47 GMT Frederik Heber [9879f6] * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.hpp (modified) * src/lists.cpp (deleted) * src/lists.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/listofbondsunittest.hpp (modified) Huge Refactoring due to class molecule now being an STL container. ... Thu, 04 Mar 2010 10:56:58 GMT Tillmann Crueger [63b56a7] * src/Makefile.am (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/QT4/QTMainWindow.hpp (modified) * src/Views/QT4/QTWorldView.cpp (moved) * src/Views/QT4/QTWorldView.hpp (moved) Changed Name of the QTMoleculesView Thu, 04 Mar 2010 10:40:52 GMT Tillmann Crueger [e6a9c1] * src/Actions/Calculation.hpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (added) * src/Descriptors/MoleculeDescriptor.hpp (added) * src/Descriptors/MoleculeDescriptor_impl.hpp (added) * src/Descriptors/MoleculeIdDescriptor.cpp (added) * src/Descriptors/MoleculeIdDescriptor.hpp (added) * src/Descriptors/MoleculeIdDescriptor_impl.hpp (added) * src/Makefile.am (modified) * src/Patterns/Observer.hpp (modified) * src/UIElements/MainWindow.hpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/molecule_template.hpp (modified) * src/unittests/AtomDescriptorTest.cpp (moved) * src/unittests/AtomDescriptorTest.hpp (moved) * src/unittests/Makefile.am (modified) * src/unittests/MoleculeDescriptorTest.cpp (added) * src/unittests/MoleculeDescriptorTest.hpp (added) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Merge branch 'MenuRefactoring' into QT4Refactoring Conflicts: ... Thu, 04 Mar 2010 10:33:44 GMT Tillmann Crueger [57adc7] * src/Descriptors/MoleculeIdDescriptor.cpp (added) * src/Descriptors/MoleculeIdDescriptor.hpp (added) * src/Descriptors/MoleculeIdDescriptor_impl.hpp (added) * src/Makefile.am (modified) * src/World.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/unittests/AtomDescriptorTest.cpp (moved) * src/unittests/AtomDescriptorTest.hpp (moved) * src/unittests/Makefile.am (modified) * src/unittests/MoleculeDescriptorTest.cpp (added) * src/unittests/MoleculeDescriptorTest.hpp (added) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Added methods to query Molecules by ID Thu, 04 Mar 2010 09:49:45 GMT Saskia Metzler [57f5cf] * doc/Doxyfile (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/AtomsCalculation.hpp (added) * src/Actions/AtomsCalculation_impl.hpp (added) * src/Actions/Calculation.hpp (added) * src/Actions/Calculation_impl.hpp (added) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (added) * src/Actions/ManipulateAtomsProcess.hpp (added) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.hpp (modified) * src/Descriptors/AtomIdDescriptor_impl.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (added) * src/Descriptors/AtomTypeDescriptor.hpp (added) * src/Descriptors/AtomTypeDescriptor_impl.hpp (added) * src/Descriptors/MoleculeDescriptor.cpp (added) * src/Descriptors/MoleculeDescriptor.hpp (added) * src/Descriptors/MoleculeDescriptor_impl.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Menu/DisplayMenuItem.cpp (modified) * src/Menu/TextMenu.cpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.hpp (modified) * src/UIElements/TextDialog.cpp (modified) * src/UIElements/TextStatusIndicator.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/Views/MethodStringView.cpp (modified) * src/Views/MethodStringView.hpp (modified) * src/Views/StreamStringView.cpp (modified) * src/Views/StreamStringView.hpp (modified) * src/Views/StringView.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (added) * src/World_calculations.hpp (added) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.hpp (modified) * src/lists.cpp (added) * src/lists.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/DescriptorUnittest.cpp (modified) * src/unittests/DescriptorUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (added) * src/unittests/atomsCalculationTest.hpp (added) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (added) * src/unittests/manipulateAtomsTest.hpp (added) Merge commit 'till/StructureRefactoring' into StateAndFormatParser ... Thu, 04 Mar 2010 09:21:38 GMT Saskia Metzler [706f9b] * src/Makefile.am (modified) * src/unittests/Makefile.am (modified) Work-in-progress commit of parser and changeTracker Wed, 03 Mar 2010 15:46:03 GMT Tillmann Crueger [1c51c8] * src/Descriptors/MoleculeDescriptor.cpp (added) * src/Descriptors/MoleculeDescriptor.hpp (added) * src/Descriptors/MoleculeDescriptor_impl.hpp (added) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (modified) * src/molecule_template.hpp (modified) Added methods for querying molecules using descriptors Wed, 03 Mar 2010 10:13:19 GMT Frederik Heber [b34306] * src/Makefile.am (modified) * src/World.cpp (added) * src/World.hpp (added) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/vector.cpp (modified) singleton class World introduced, contains only cell_size from class ... Mon, 01 Mar 2010 22:10:13 GMT Frederik Heber [8db598] * src/Makefile.am (modified) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/triangleintersectionlist.cpp (added) * src/triangleintersectionlist.hpp (added) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) New class TriangleIntersection List and (hopefully) final fix of ... Fri, 26 Feb 2010 14:11:14 GMT Tillmann Crueger [2561df] * configure.ac (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/Process.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.hpp (modified) * src/Descriptors/AtomIdDescriptor_impl.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor_impl.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Menu/DisplayMenuItem.cpp (modified) * src/Menu/TextMenu.cpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/TextStatusIndicator.cpp (modified) * src/Views/MethodStringView.cpp (modified) * src/Views/MethodStringView.hpp (modified) * src/Views/StreamStringView.cpp (modified) * src/Views/StreamStringView.hpp (modified) * src/Views/StringView.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.hpp (modified) * src/element.cpp (modified) * src/gslmatrix.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.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/CacheableTest.cpp (modified) * src/unittests/DescriptorUnittest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (added) * src/unittests/UnitTestMain.cpp (added) * 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/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * tests/Tesselations/defs.in (modified) Merge branch 'MenuRefactoring' into QT4Refactoring Conflicts: ... Fri, 26 Feb 2010 13:57:01 GMT Tillmann Crueger [a1510d] * configure.ac (modified) * src/Actions/small_actions.hpp (modified) * src/Makefile.am (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/UIElements/TextStatusIndicator.cpp (added) * src/UIElements/TextStatusIndicator.hpp (added) * src/UIElements/TextWindow.cpp (modified) * src/UIElements/TextWindow.hpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * src/element.cpp (modified) * src/gslmatrix.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/tesselation.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/CacheableTest.cpp (modified) * src/unittests/DescriptorUnittest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (added) * src/unittests/UnitTestMain.cpp (added) * 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/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * tests/Tesselations/defs.in (modified) Merge branch 'FreddiesRefactoring' into StructureRefactoring ... Fri, 26 Feb 2010 13:04:59 GMT Tillmann Crueger [1f2217] * src/Makefile.am (modified) * src/datacreator.cpp (modified) Small fixes Fri, 26 Feb 2010 12:40:52 GMT Tillmann Crueger [24a5e0] * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/Process.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor_impl.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor_impl.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Menu/DisplayMenuItem.cpp (modified) * src/Menu/TextMenu.cpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/TextDialog.cpp (modified) * src/Views/MethodStringView.cpp (modified) * src/Views/MethodStringView.hpp (modified) * src/Views/StreamStringView.cpp (modified) * src/Views/StreamStringView.hpp (modified) * src/Views/StringView.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/boundary.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselationhelpers.cpp (modified) Added -Wall flag and fixed several small hickups Thu, 25 Feb 2010 14:23:33 GMT Tillmann Crueger [cbf01e] * doc/Doxyfile (modified) * src/Actions/AtomsCalculation.hpp (added) * src/Actions/AtomsCalculation_impl.hpp (added) * src/Actions/Calculation.hpp (added) * src/Actions/Calculation_impl.hpp (added) * src/Actions/ManipulateAtomsProcess.cpp (added) * src/Actions/ManipulateAtomsProcess.hpp (added) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor_impl.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (added) * src/Descriptors/AtomTypeDescriptor.hpp (added) * src/Descriptors/AtomTypeDescriptor_impl.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (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/TextDialog.cpp (modified) * src/UIElements/TextDialog.hpp (modified) * src/UIElements/TextStatusIndicator.cpp (added) * src/UIElements/TextStatusIndicator.hpp (added) * src/UIElements/TextWindow.cpp (modified) * src/UIElements/TextWindow.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (added) * src/World_calculations.hpp (added) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/lists.cpp (added) * src/lists.hpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/DescriptorUnittest.cpp (modified) * src/unittests/DescriptorUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (added) * src/unittests/atomsCalculationTest.hpp (added) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (added) * src/unittests/manipulateAtomsTest.hpp (added) Merge branch 'MenuRefactoring' into QT4Refactoring Conflicts: ... Thu, 25 Feb 2010 11:15:22 GMT Tillmann Crueger [957c42] * doc/Doxyfile (modified) * src/Actions/AtomsCalculation.hpp (added) * src/Actions/AtomsCalculation_impl.hpp (added) * src/Actions/Calculation.hpp (added) * src/Actions/Calculation_impl.hpp (added) * src/Actions/ManipulateAtomsProcess.cpp (added) * src/Actions/ManipulateAtomsProcess.hpp (added) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor_impl.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (added) * src/Descriptors/AtomTypeDescriptor.hpp (added) * src/Descriptors/AtomTypeDescriptor_impl.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (added) * src/World_calculations.hpp (added) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/lists.cpp (added) * src/lists.hpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/DescriptorUnittest.cpp (modified) * src/unittests/DescriptorUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (added) * src/unittests/atomsCalculationTest.hpp (added) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (added) * src/unittests/manipulateAtomsTest.hpp (added) Merge branch 'StructureRefactoring' into MenuRefactoring Thu, 25 Feb 2010 10:50:54 GMT Tillmann Crueger [d2dbac0] * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (added) moved Iterators for the World to a seperate file Thu, 25 Feb 2010 10:18:50 GMT Tillmann Crueger [f16a4b] * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor_impl.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (added) * src/Descriptors/AtomTypeDescriptor.hpp (added) * src/Descriptors/AtomTypeDescriptor_impl.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) Added Descriptor that allows querying of atoms by their type Wed, 24 Feb 2010 16:21:12 GMT Tillmann Crueger [46d958] * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/lists.cpp (added) * src/lists.hpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/DescriptorUnittest.cpp (modified) * src/unittests/DescriptorUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/atomsCalculationTest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Made the world solely responsible for creating and destroying atoms. Fri, 19 Feb 2010 11:49:42 GMT Tillmann Crueger [7c4e29] * src/Actions/Calculation.hpp (added) * src/Actions/Calculation_impl.hpp (added) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/unittests/Makefile.am (modified) Added a class that allows constructing Processes that have a result Thu, 18 Feb 2010 11:38:02 GMT Tillmann Crueger [0188ea] * src/Actions/small_actions.hpp (modified) * src/Makefile.am (modified) * src/UIElements/TextStatusIndicator.cpp (added) * src/UIElements/TextStatusIndicator.hpp (added) * src/UIElements/TextWindow.cpp (modified) * src/UIElements/TextWindow.hpp (modified) * src/builder.cpp (modified) Added a progress indicator for the text menu Thu, 18 Feb 2010 10:59:29 GMT Tillmann Crueger [7dad10] * src/Actions/Process.cpp (added) * src/Actions/Process.hpp (added) * src/Actions/small_actions.hpp (modified) * src/Makefile.am (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * src/helpers.hpp (modified) Added a special class of Actions that take some time. Wed, 17 Feb 2010 17:07:35 GMT Tillmann Crueger [326a43b] * src/Actions/Process.cpp (added) * src/Actions/Process.hpp (added) * src/Actions/small_actions.hpp (modified) * src/Makefile.am (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/QT4/QTMainWindow.hpp (modified) * src/Views/QT4/QTStatusBar.cpp (added) * src/Views/QT4/QTStatusBar.hpp (added) * src/World.cpp (modified) * src/builder.cpp (modified) * src/helpers.hpp (modified) Added a special class of Actions that take some time. Added a ... Wed, 17 Feb 2010 11:15:27 GMT Tillmann Crueger [b1d8092] * configure.ac (modified) * doc/class structure todo.uxf (added) * m4/m4_ax_boost_thread.m4 (added) * src/Descriptors/AtomDescriptor.cpp (added) * src/Descriptors/AtomDescriptor.hpp (added) * src/Descriptors/AtomDescriptor_impl.hpp (added) * src/Descriptors/AtomIdDescriptor.cpp (added) * src/Descriptors/AtomIdDescriptor.hpp (added) * src/Descriptors/AtomIdDescriptor_impl.hpp (added) * src/Legacy/oldmenu.cpp (moved) * src/Legacy/oldmenu.hpp (moved) * src/Makefile.am (modified) * src/Patterns/Cacheable.hpp (added) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/UIElements/TextWindow.cpp (modified) * src/World.cpp (added) * src/World.hpp (added) * src/atom.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) * src/unittests/CacheableTest.cpp (added) * src/unittests/CacheableTest.hpp (added) * src/unittests/DescriptorUnittest.cpp (added) * src/unittests/DescriptorUnittest.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) Merge branch 'StructureRefactoring' into QT4Refactoring Conflicts: ... Fri, 05 Feb 2010 16:26:18 GMT Tillmann Crueger [fc1b24] * src/Descriptors/AtomDescriptor.cpp (added) * src/Descriptors/AtomDescriptor.hpp (added) * src/Descriptors/AtomIdDescriptor.cpp (added) * src/Descriptors/AtomIdDescriptor.hpp (added) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) Added descriptors that allow multiple kinds of access to atoms