# # ChangeLog for src/Actions # # Generated by Trac 1.6 # Jun 14, 2025, 7:17:10 PM Wed, 30 Jun 2010 15:16:10 GMT Tillmann Crueger [3dcb1f] * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) Added two functions to Box class to translate Vectors from Box-Space ... Wed, 30 Jun 2010 14:37:40 GMT Tillmann Crueger [ac2724] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) FIX: RepeatBoxAction was using a reference to the Box size instead of ... Wed, 30 Jun 2010 14:03:43 GMT Tillmann Crueger [082215] * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) FIX: ScaleBoxAction did not set the new Box Matrix in the World Wed, 30 Jun 2010 13:55:42 GMT Tillmann Crueger [84c494] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) Made the world store the cell_size within a Box object. Wed, 30 Jun 2010 09:00:19 GMT Tillmann Crueger [5108e1] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/ellipsoid.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Removed MatrixMultiplication() method from Vector class Sat, 26 Jun 2010 11:52:50 GMT Tillmann Crueger [d10eb6] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Matrix.cpp (modified) * src/Matrix.hpp (modified) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) Made the ReturnFullMatrixForSymmetric return a Matrix object ... Fri, 25 Jun 2010 15:54:48 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 15:27:35 GMT Tillmann Crueger [c94eeb] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/ellipsoid.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Replaced several double* that were used as Matrixes with actuall ... 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 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 ... Fri, 25 Jun 2010 08:08:59 GMT Frederik Heber [d0fbec] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) Added const_iterator get[Begin\End]Iter() and ostream& operator << to ... Wed, 23 Jun 2010 15:52:50 GMT Frederik Heber [35b698] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/Makefile.am (modified) * tests/regression/Domain/6/post/test-x.conf.xyz (modified) * tests/regression/Domain/6/post/test-y.conf.xyz (modified) * tests/regression/Domain/6/post/test-z.conf.xyz (modified) * tests/regression/Domain/6/post/test.conf.xyz (modified) * tests/regression/Filling/1/post/test.conf (modified) * tests/regression/Simple_configuration/2/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/3/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/4/post/test.conf (modified) * tests/regression/Simple_configuration/4/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/5/post/test.conf (modified) * tests/regression/Simple_configuration/8/post/test.conf.xyz (modified) * tests/regression/testsuite-fragmentation.at (modified) BIG CHANGE: config::load and config::save in ... Mon, 21 Jun 2010 13:07:58 GMT Frederik Heber [a1e929] * src/Actions/MapOfActions.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/builder.cpp (modified) Case 'p' is now handled by CommandLineUI. - ~XyzParser() did ... 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: ... Sat, 19 Jun 2010 15:58:32 GMT Frederik Heber [da3024] * src/Actions/Process.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/builder.cpp (modified) Fixed various compiler warnings. - Process::Process() - Action and ... 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 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 10:34:14 GMT Frederik Heber [980dd6] * src/Actions/MapOfActions.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/builder.cpp (modified) * tests/Tesselations/defs.in (modified) * tests/regression/testsuite-tesselation.at (modified) Case 'N' is now handled by CommandLineUI. - TESTFIX: Tesselation/1 ... Fri, 11 Jun 2010 19:22:37 GMT Frederik Heber [f6bd32] * src/Actions/MapOfActions.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-tesselation.at (modified) Case 'o' is now handled by CommandLineUI. - As of now, multiple ... Fri, 11 Jun 2010 15:59:53 GMT Frederik Heber [6866aa] * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'I' is now handled by CommandLineUI. Fri, 11 Jun 2010 15:52:44 GMT Frederik Heber [a307af] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Case 'S' is now handled by CommandLineUI. Fri, 11 Jun 2010 15:48:32 GMT Frederik Heber [a02462] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Case 'L' is now handled by CommandLineUI. Fri, 11 Jun 2010 15:27:20 GMT Frederik Heber [aacce8] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Case 'P' is now handled by CommandLineUI. - TESTFIX: ... Fri, 11 Jun 2010 15:21:51 GMT Frederik Heber [77b2d7] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Cases 't' and 'T' are now handled by CommandLineUI. - TESTFIX: both ... Fri, 11 Jun 2010 15:07:11 GMT Frederik Heber [e2b47c] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) Case 'R' is now handled by CommandLineUI. - again, for each atom to ... Fri, 11 Jun 2010 14:38:34 GMT Frederik Heber [f4bd01] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Case 'A' is now handled by CommandLineUI. - TESTFIX: ... Fri, 11 Jun 2010 14:37:51 GMT Frederik Heber [d55743e] * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'r' is now handled by CommandLineUI. Fri, 11 Jun 2010 14:20:11 GMT Frederik Heber [77de81] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Cases 'J' and 'j' are now handled by CommandLineUI. - TESTFIX: ... Fri, 11 Jun 2010 12:20:08 GMT Frederik Heber [54b953] * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) Case 'E' is now handled by CommandLineUI. - TESTFIX: --element is ... Fri, 11 Jun 2010 12:19:50 GMT Frederik Heber [f0a3ec] * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) Case 'a' is now handled by CommandLineUI. - NOTE: atom has still to ... Fri, 11 Jun 2010 12:19:27 GMT Frederik Heber [387b36] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) Case 'X' is now handled by CommandLineUI, World::get/setDefaultName() ... Fri, 11 Jun 2010 12:19:18 GMT Frederik Heber [f821d6] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-standard_options.at (modified) Case 'n' is now handled by CommandLineUI. - TESTFIX: fastparsing ... Fri, 11 Jun 2010 10:45:06 GMT Frederik Heber [bdaacd] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/builder.cpp (modified) Case 'M' is now handled by CommandLineUI. Thu, 10 Jun 2010 16:24:24 GMT Frederik Heber [39af9f] * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'g' is now handled by CommandLineUI. Thu, 10 Jun 2010 16:20:36 GMT Frederik Heber [198494] * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'e' is now handled by CommandLineUI. - BUGFIX: ElementDbAction ... Thu, 10 Jun 2010 16:13:23 GMT Frederik Heber [7e6b00] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/CommandLineParser.cpp (modified) * src/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/builder.cpp (modified) FIX: Sequence of actions called from command line is now corrected. ... Thu, 10 Jun 2010 16:05:53 GMT Frederik Heber [623e89] * 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/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/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) Compilation took ages because of CommandLineParser.hpp being ... Thu, 10 Jun 2010 15:10:19 GMT Tillmann Crueger [6d6b54] * src/Actions/Action.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) Made the memory-tracker output the function from which it was called. Thu, 10 Jun 2010 13:11:28 GMT Tillmann Crueger [112b09] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/CommandLineParser.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Line.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Observer.cpp (modified) * src/Plane.cpp (modified) * src/Space.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/graph.cpp (modified) * src/gslmatrix.cpp (modified) * src/gslvector.cpp (modified) * src/helpers.cpp (modified) * src/info.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/log.cpp (modified) * src/logger.cpp (modified) * src/memoryallocator.cpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/vector.cpp (modified) * src/vector_ops.cpp (modified) * src/verbose.cpp (modified) Added #include "Helpers/MemDebug.hpp" to all .cpp files Wed, 09 Jun 2010 15:10:51 GMT Frederik Heber [2b5574] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-analysis.at (modified) Case 'm' is now handled by CommandLineUI. - TESTCHANGE: Analysis/5 ... Wed, 09 Jun 2010 15:08:46 GMT Frederik Heber [58bbd3] * src/Actions/MapOfActions.cpp (modified) * src/analysis_correlation.cpp (modified) * src/builder.cpp (modified) * src/moleculelist.cpp (modified) * tests/regression/Analysis/3/post/bin_output.csv (modified) * tests/regression/testsuite-analysis.at (modified) Cases 'C' are now handled by CommandLineUI. - TESTFIX: ... Wed, 09 Jun 2010 14:30:10 GMT Tillmann Crueger [cd5047] * src/Actions/Process.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Added Logging capabilities to Observer Framework Wed, 09 Jun 2010 14:09:46 GMT Frederik Heber [1e6913] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * tests/regression/testsuite-fragmentation.at (modified) Order of actions called did not conincide with order on command line. ... Wed, 09 Jun 2010 14:04:54 GMT Frederik Heber [104524] * 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/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Legacy/oldmenu.cpp (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) Changed PairCorrelationAction to incorporate all three cases and ... Tue, 08 Jun 2010 13:57:09 GMT Frederik Heber [8540f0] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'D' is now handled by CommandLineUI. Tue, 08 Jun 2010 13:49:27 GMT Frederik Heber [e4b5de] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/builder.cpp (modified) * tests/regression/Fragmentation/3/pre/BondFragment0.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment0.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment1.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment1.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment2.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment2.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment3.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment3.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment4.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment4.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentAdjacency.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentForces-Factors.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentKeySets.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentOrderAtSite.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentTE-Factors.dat (deleted) * tests/regression/testsuite-fragmentation.at (modified) Case 'f' is now handled by CommandLineUI. - ... Tue, 08 Jun 2010 12:13:11 GMT Frederik Heber [48ab70a] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case 'u' is now handled by CommandLineUI. Mon, 07 Jun 2010 23:55:30 GMT Frederik Heber [9907e7] * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-filling.at (modified) Case '-F' is now handled by CommandLineUI. - FIX: ... Mon, 07 Jun 2010 23:53:44 GMT Frederik Heber [0286bc] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/Values.hpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) BUGFIX: ListOfDoubles changed to Box and Vector. - ListOfDoubles is ... Wed, 02 Jun 2010 16:17:17 GMT Frederik Heber [e30ce8] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (added) * src/Descriptors/MoleculePtrDescriptor.hpp (added) * src/Descriptors/MoleculePtrDescriptor_impl.hpp (added) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/builder.cpp (modified) Case 'd' is now handled by CommandLineUI (RepeatBoxAction). - ... Wed, 02 Jun 2010 14:40:30 GMT Frederik Heber [584a2a] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case '-O' is now handled by CommandLineUI (CenterOnEdgeAction). ... Wed, 02 Jun 2010 14:38:07 GMT Frederik Heber [116f37] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/builder.cpp (modified) Case '-c' is now handled by CommandLineUI. - BUGFIX: ... 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 ... Sun, 30 May 2010 23:40:04 GMT Frederik Heber [158c594] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/builder.cpp (modified) Case '-b' now handled by CommandLineUI and fixes. - ... Sun, 30 May 2010 23:18:48 GMT Frederik Heber [2a92ff] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case '-s' now handled by CommandLineUI. - FIX: Type Vector has to ... Sun, 30 May 2010 23:03:49 GMT Frederik Heber [6ca1f7] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) case '-B' now handled by CommandLineUI. Sun, 30 May 2010 22:49:13 GMT Frederik Heber [26f75a] * src/Actions/MapOfActions.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) FIX: Box was not parsed correctly. - ListOf... types have to be ... Sat, 29 May 2010 13:52:51 GMT Frederik Heber [6670a97] * src/Actions/MapOfActions.cpp (modified) * tests/testsuite.at (modified) Change to testsuite as verbosity is now defined as (-v 3) not as ... 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 ... Mon, 17 May 2010 17:31:00 GMT Frederik Heber [a77976] * src/Actions/MapOfActions.cpp (modified) TESTFIX: testsuite looks for a very specific help message. - ... 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 ... Sun, 09 May 2010 11:59:35 GMT Frederik Heber [86466e] * src/Actions/CmdAction/HelpAction.cpp (modified) * src/UIElements/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUIFactory.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextDialog.cpp (modified) * src/UIElements/TextDialog.hpp (modified) new query class EmptyQuery for showing text messages. - new class ... 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 22:00:16 GMT Frederik Heber [fa56f0] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) ActionRegistry now is iterable due to new functons getBeginIter() and ... Sat, 08 May 2010 22:00:03 GMT Frederik Heber [808fd3] * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) performUndo/Redo were missing for ParserLoadXyzAction and ... Sat, 08 May 2010 20:06:45 GMT Frederik Heber [ecb799] * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Parser/TremoloParser.cpp (modified) shortened NAME of ParserLoadXyz and ParserSaveXyz actions, as it is ... 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 ... 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. Mon, 26 Apr 2010 13:49:59 GMT Tillmann Crueger [13d5a9] * src/Actions/small_actions.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/Assert.hpp (modified) Added macros that allow type safe casting using the Assert mechanism Thu, 15 Apr 2010 13:17:15 GMT Tillmann Crueger [8a34392] * src/Actions/Action.hpp (modified) Improved documentation for the Action pattern Thu, 08 Apr 2010 14:28:21 GMT Tillmann Crueger [a295d1] * src/Actions/Action.hpp (modified) More documentation for Action class added Thu, 08 Apr 2010 14:00:11 GMT Tillmann Crueger [2efa90] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) Added detailed documentation for the Action class Fri, 26 Mar 2010 15:13:31 GMT Tillmann Crueger [f9352d] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (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) Added mechanism that deactivates undo and redo menupoint if not ... 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, 25 Mar 2010 10:06:49 GMT Tillmann Crueger [5b0b98] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.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/UIElements/TextDialog.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) Switched type of pointer used for ActionStates Wed, 24 Mar 2010 16:26:21 GMT Tillmann Crueger [67e2b3] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.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/unittests/ActionSequenceTest.cpp (modified) Added methods that allow bookkeeping of actions for undo/redo methods 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 ... Fri, 12 Mar 2010 13:16:01 GMT Tillmann Crueger [ead4e6] * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.hpp (modified) * src/Descriptors/AtomTypeDescriptor_impl.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/World.hpp (modified) * 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/leastsquaremin.hpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) * src/types.hpp (added) * src/unittests/AtomDescriptorTest.hpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/MoleculeDescriptorTest.hpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/atomsCalculationTest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) Made the periodentafel use STL-containers instead of custom llists Thu, 11 Mar 2010 14:08:44 GMT Tillmann Crueger [e73a8a2] * src/Actions/Action.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/builder.cpp (modified) * src/unittests/SingletonTest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Changed ActionRegistry to use the new Singleton Mechanism Thu, 11 Mar 2010 10:37:32 GMT Tillmann Crueger [d7940e] * src/Actions/small_actions.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Patterns/Singleton.hpp (modified) * src/Patterns/Singleton_impl.hpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/builder.cpp (modified) Made the UIFactory an instance of the Singleton Pattern Wed, 10 Mar 2010 17:51:48 GMT Tillmann Crueger [23b547] * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Patterns/Singleton.hpp (added) * src/Patterns/Singleton_impl.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldIterators.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/defs.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Added generic singleton Pattern that can be inherited to any class ... Wed, 03 Mar 2010 13:57:41 GMT Tillmann Crueger [dbb474] * 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/Patterns/Observer.hpp (modified) * src/UIElements/MainWindow.hpp (modified) * src/UIElements/UIFactory.hpp (modified) Improved Doxygen documentation 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 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 16:56:16 GMT Tillmann Crueger [cf1a07] * src/Actions/ActionRegistry.cpp (modified) * src/Patterns/Observer.cpp (modified) FIX: repaired some access violation of STL-iterators in Observer and ... Fri, 19 Feb 2010 14:31:56 GMT Tillmann Crueger [b54ac8] * src/Actions/AtomsCalculation.hpp (added) * src/Actions/AtomsCalculation_impl.hpp (added) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/World.hpp (modified) * src/World_calculations.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/atomsCalculationTest.cpp (added) * src/unittests/atomsCalculationTest.hpp (added) * src/unittests/manipulateAtomsTest.cpp (modified) Added templates that allow arbitrary calculations on atoms to be ... Fri, 19 Feb 2010 11:49:54 GMT Tillmann Crueger [afb47f] * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/manipulateAtomsTest.hpp (modified) Added a mechanism that allows the world to track changes done by the ... 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 16:46:07 GMT Tillmann Crueger [b2cfdb] * src/Actions/ManipulateAtomsProcess.cpp (added) * src/Actions/ManipulateAtomsProcess.hpp (added) * src/unittests/manipulateAtomsTest.cpp (added) * src/unittests/manipulateAtomsTest.hpp (added) Added a method that allows manipulation of selected atoms 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. Tue, 02 Feb 2010 12:21:13 GMT Tillmann Crueger [520c8b] * src/Actions/small_actions.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) Moved method to rename molecules to a seperate Action Tue, 02 Feb 2010 12:14:54 GMT Tillmann Crueger [bfce50] * src/Actions/Action.hpp (modified) * src/Actions/small_actions.cpp (added) * src/Actions/small_actions.hpp (added) * src/Makefile.am (modified) * src/builder.cpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) Moved method to rename molecules to a seperate Action Sat, 09 Jan 2010 11:30:49 GMT Tillmann Crueger [12b845] * src/Actions/ActionRegistry.cpp (modified) * src/UIElements/MainWindow.hpp (modified) * src/UIElements/TextUIFactory.cpp (modified) * src/UIElements/TextUIFactory.hpp (modified) * src/UIElements/TextWindow.cpp (modified) * src/UIElements/TextWindow.hpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/builder.cpp (modified) * src/menu.cpp (modified) * src/menu.hpp (modified) Seperated building of mainWindow and contained Menus - Moved code ... Thu, 07 Jan 2010 14:46:34 GMT Tillmann Crueger [cc04b7] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionRegistry.cpp (added) * src/Actions/ActionRegistry.hpp (added) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Makefile.am (modified) * src/UIElements/TextUIFactory.cpp (modified) * src/UIElements/TextUIFactory.hpp (modified) * src/UIElements/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/builder.cpp (modified) * src/menu.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) Added a central registry that allows access to actions by name. Tue, 05 Jan 2010 13:48:05 GMT Tillmann Crueger [3e026a] * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/menu.cpp (modified) Transitioned MergeMolecule Menu to new menu structure Tue, 05 Jan 2010 10:11:52 GMT Tillmann Crueger [820a42] * src/Actions/ErrorAction.cpp (added) * src/Actions/ErrorAction.hpp (added) * src/Makefile.am (modified) * src/menu.cpp (modified) * src/menu.hpp (modified) Extracted all methods from MergeMolecules Menu - Added new action ... Thu, 17 Dec 2009 14:38:29 GMT Tillmann Crueger [1fa107] * src/Actions/Action.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/MakroAction.cpp (added) * src/Actions/MakroAction.hpp (added) * src/Makefile.am (modified) * src/menu.cpp (modified) Added an action that allows grouping and grouped execution of several ...