#
# ChangeLog for src/Parser
#
# Generated by Trac 1.4.4
# Mar 13, 2025, 5:23:16 AM

Wed, 23 Jun 2010 15:52:50 GMT Frederik Heber <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 ...


Wed, 23 Jun 2010 10:35:25 GMT Frederik Heber <heber@…> [dc0d21]
	* src/Parser/FormatParserStorage.cpp (modified)
	* src/Parser/FormatParserStorage.hpp (modified)

	FIXes to FormatParserStorage.

	- renamed Add..() to add..()
	- new ...


Wed, 23 Jun 2010 08:51:33 GMT Frederik Heber <heber@…> [df481f]
	* src/Parser/XyzParser.cpp (modified)

	BUGFIX: XyzParser::save() - substr needs to be (0, pos), not just ...


Tue, 22 Jun 2010 15:33:06 GMT Frederik Heber <heber@…> [2fd80b5]
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/unittests/ParserUnitTest.cpp (modified)

	FIXES: ParserUnitTest was broken

	- XyzParser: ctime returns ...


Tue, 22 Jun 2010 14:09:14 GMT Frederik Heber <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 ...


Tue, 22 Jun 2010 09:30:03 GMT Frederik Heber <heber@…> [650ca8c]
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/PcpParser.hpp (modified)

	FIX: PcpParser had wrong default values for testsuite cases, number ...


Tue, 22 Jun 2010 09:29:01 GMT Frederik Heber <heber@…> [1434c9]
	* src/Parser/XyzParser.cpp (modified)

	FIX: XyzParser needed comment and correctly formatted numbers to pass ...


Tue, 22 Jun 2010 09:24:54 GMT Frederik Heber <heber@…> [d6b8e1]
	* src/Parser/MpqcParser.cpp (modified)

	FIX: center calculation was missing in order to pass testsuite cases.


Mon, 21 Jun 2010 13:07:58 GMT Frederik Heber <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 12:56:35 GMT Frederik Heber <heber@…> [2f40c0e]
	* src/Parser/ChangeTracker.cpp (modified)
	* src/Parser/ChangeTracker.hpp (modified)
	* src/Parser/FormatParser.cpp (modified)
	* src/unittests/ParserUnitTest.cpp (modified)

	ChangeTracker now uses the Singleton pattern.

	- ChangeTracker is ...


Mon, 21 Jun 2010 07:56:00 GMT Frederik Heber <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, 12 Jun 2010 22:19:48 GMT Frederik Heber <heber@…> [1b2d30]
	* src/ConfigFileBuffer.cpp (modified)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/MpqcParser.hpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/PcpParser.hpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/config.cpp (modified)
	* src/unittests/ParserUnitTest.cpp (modified)
	* src/unittests/ParserUnitTest.hpp (modified)

	Extended PcpParser, completed MpqcParser.

	- BUGFIX: ...


Sat, 12 Jun 2010 15:54:26 GMT Frederik Heber <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 ...


Thu, 10 Jun 2010 13:11:28 GMT Tillmann Crueger <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 14:30:10 GMT Tillmann Crueger <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


Sat, 15 May 2010 17:56:57 GMT Frederik Heber <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.
 ...


Sat, 08 May 2010 20:06:45 GMT Frederik Heber <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 12:17:30 GMT Frederik Heber <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
 ...


Sun, 02 May 2010 16:47:18 GMT Saskia Metzler <metzler@…> [b8d4a3]
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/TremoloParser.hpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/bond.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/unittests/ParserUnitTest.cpp (modified)
	* src/unittests/ParserUnitTest.hpp (modified)
	* src/unittests/SingletonTest.cpp (modified)

	Tremolo format parser


Thu, 01 Apr 2010 12:16:29 GMT Saskia Metzler <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 <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


Fri, 05 Mar 2010 13:45:35 GMT Saskia Metzler <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 13:33:45 GMT Saskia Metzler <metzler@…> [7dc102]
	* src/Parser/TremoloParser.hpp (modified)

	WIP


Fri, 05 Mar 2010 12:53:13 GMT Saskia Metzler <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