#
# ChangeLog for src/molecule.cpp
#
# Generated by Trac 1.4.4
# Dec 28, 2024, 2:56:51 AM

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


Wed, 02 Jun 2010 12:22:47 GMT Frederik Heber <heber@…> [7fd416]
	* src/analysis_correlation.cpp (modified)
	* src/builder.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/moleculelist.cpp (modified)

	FIX: CorrelationToSurface() was broken.

	- DOCU: ...


Mon, 31 May 2010 18:41:12 GMT Frederik Heber <heber@…> [e08c46]
	* src/Legacy/oldmenu.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)

	Removed molecule::first, molecule::last.

	- molecule does not have a ...


Mon, 31 May 2010 17:32:27 GMT Frederik Heber <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 <heber@…> [920c70]
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Makefile.am (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_graphnodeinfo.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/memoryallocatorunittest.cpp (modified)
	* src/unittests/stackclassunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.cpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)
	* src/unittests/vectorunittest.cpp (modified)

	Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and ...


Thu, 27 May 2010 10:46:54 GMT Tillmann Crueger <crueger@…> [a7b761b]
	* src/Helpers/Assert.cpp (modified)
	* src/Legacy/oldmenu.cpp (modified)
	* src/Makefile.am (modified)
	* src/Patterns/Cacheable.hpp (modified)
	* src/Patterns/ObservedIterator.hpp (added)
	* src/Patterns/Observer.cpp (modified)
	* src/Patterns/Observer.hpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/atom.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/helpers.hpp (modified)
	* src/lists.cpp (deleted)
	* src/lists.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/ObserverTest.cpp (modified)
	* src/unittests/ObserverTest.hpp (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/bondgraphunittest.hpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/listofbondsunittest.hpp (modified)

	Merge branch 'MoleculeStartEndSwitch' into StructureRefactoring
 ...


Wed, 19 May 2010 14:03:42 GMT Tillmann Crueger <crueger@…> [bab12a]
	* src/molecule.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)

	FIX: Fix of bug introduced during Vector Refactoring

	Testsuite now ...


Sat, 08 May 2010 12:47:57 GMT Tillmann Crueger <crueger@…> [68f03d]
	* src/Helpers/MemDebug.cpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_graphnode.cpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/atom_particleinfo.hpp (modified)
	* src/bond.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.cpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)

	FIX: Memory corruption in particleInfo class


Thu, 29 Apr 2010 13:55:21 GMT Tillmann Crueger <crueger@…> [8cbb97]
	* src/Exceptions/CustomException.cpp (added)
	* src/Exceptions/CustomException.hpp (added)
	* src/Exceptions/LinearDependenceException.cpp (added)
	* src/Exceptions/LinearDependenceException.hpp (added)
	* src/Helpers/fast_functions.hpp (added)
	* src/Legacy/oldmenu.cpp (modified)
	* src/Makefile.am (modified)
	* src/Plane.cpp (added)
	* src/Plane.hpp (added)
	* src/UIElements/TextDialog.cpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/gslmatrix.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/leastsquaremin.cpp (modified)
	* src/linearsystemofequations.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/test/ActOnAlltest.hpp (modified)
	* src/triangleintersectionlist.cpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/ActOnAllUnitTest.hpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.cpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vector_ops.cpp (added)
	* src/vector_ops.hpp (added)

	Merge branch 'VectorRefactoring' into StructureRefactoring
 ...


Tue, 27 Apr 2010 14:25:42 GMT Frederik Heber <heber@…> [5f612ee]
	* src/Legacy/oldmenu.cpp (modified)
	* src/Makefile.am (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/analysis_bonds.hpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_graphnode.cpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/bond.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/defs.hpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/errorlogger.cpp (modified)
	* src/graph.cpp (modified)
	* src/gslvector.cpp (modified)
	* src/gslvector.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/info.cpp (modified)
	* src/joiner.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/log.cpp (modified)
	* src/log.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/triangleintersectionlist.cpp (added)
	* src/triangleintersectionlist.hpp (added)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (added)
	* src/unittests/CountBondsUnitTest.hpp (added)
	* src/unittests/LinkedCellUnitTest.cpp (added)
	* src/unittests/LinkedCellUnitTest.hpp (added)
	* src/unittests/Makefile.am (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/bondgraphunittest.hpp (modified)
	* src/unittests/gslvectorunittest.cpp (modified)
	* src/unittests/gslvectorunittest.hpp (modified)
	* src/unittests/logunittest.cpp (modified)
	* src/unittests/memoryallocatorunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.hpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.hpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)
	* src/unittests/tesselationunittest.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)
	* src/verbose.hpp (modified)
	* tests/Tesselations/1_2-dimethylbenzene/tecplot.phy (deleted)
	* tests/Tesselations/defs.in (modified)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified)

	Merge branch 'Analysis_PairCorrelation' into StructureRefactoring
 ...


Thu, 22 Apr 2010 14:00:03 GMT Frederik Heber <heber@…> [a67d19]
	* src/analysis_correlation.cpp (modified)
	* src/analyzer.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_graphnode.cpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/graph.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/info.cpp (modified)
	* src/joiner.cpp (modified)
	* src/linkedcell.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/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/unittests/logunittest.cpp (modified)
	* src/unittests/memoryallocatorunittest.cpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/vector.cpp (modified)

	Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) ...


Thu, 15 Apr 2010 10:54:26 GMT Tillmann Crueger <crueger@…> [1bd79e]
	* src/Makefile.am (modified)
	* src/SingleVector.cpp (modified)
	* src/SingleVector.hpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.cpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vector_ops.cpp (modified)

	Changed implementation of Vector to forward operations to contained ...


Tue, 13 Apr 2010 13:22:42 GMT Tillmann Crueger <crueger@…> [273382]
	* src/Legacy/oldmenu.cpp (modified)
	* src/Plane.cpp (modified)
	* src/SingleVector.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/test/ActOnAlltest.hpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vector_ops.cpp (modified)

	Prepared interface of Vector Class for transition to VectorComposites


Wed, 07 Apr 2010 15:45:38 GMT Tillmann Crueger <crueger@…> [0a4f7f]
	* src/Exceptions/CustomException.cpp (added)
	* src/Exceptions/CustomException.hpp (added)
	* src/Exceptions/LinearDependenceException.cpp (added)
	* src/Exceptions/LinearDependenceException.hpp (added)
	* src/Helpers/fast_functions.hpp (added)
	* src/Legacy/oldmenu.cpp (modified)
	* src/Makefile.am (modified)
	* src/Plane.cpp (added)
	* src/Plane.hpp (added)
	* src/UIElements/TextDialog.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/gslmatrix.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/leastsquaremin.cpp (modified)
	* src/linearsystemofequations.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/ActOnAllUnitTest.hpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vector_ops.cpp (added)
	* src/vector_ops.hpp (added)

	Made data internal data-structure of vector class private

	- ...


Wed, 24 Mar 2010 13:58:30 GMT Tillmann Crueger <crueger@…> [05a97c]
	* src/molecule.cpp (modified)
	* src/molecule_graph.cpp (modified)

	Replaced some error conditions with ASSERTs


Fri, 19 Mar 2010 15:50:01 GMT Tillmann Crueger <crueger@…> [e0b6fd]
	* src/Patterns/Cacheable.hpp (modified)
	* src/molecule.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)

	Rebuilt Cacheables using the state pattern


Fri, 19 Mar 2010 13:29:01 GMT Tillmann Crueger <crueger@…> [ea7176]
	* src/Legacy/oldmenu.cpp (modified)
	* src/Patterns/Cacheable.hpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)

	FIX: Made AtomCount a Cacheable so that the number of atoms in a ...


Thu, 18 Mar 2010 16:45:41 GMT Tillmann Crueger <crueger@…> [8d2772]
	* src/Helpers/Assert.cpp (modified)
	* src/molecule.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)

	Changed conditional criticalExit in constructor of ...


Thu, 18 Mar 2010 11:33:54 GMT Frederik Heber <heber@…> [58ed4a]
	* src/analysis_bonds.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/analyzer.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/bond.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/helpers.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/log.cpp (modified)
	* src/log.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/triangleintersectionlist.cpp (modified)
	* src/unittests/logunittest.cpp (modified)
	* src/vector.cpp (modified)

	Log() and eLog() are prepended by a DoLog()/DoeLog() construct.

	- ...


Fri, 12 Mar 2010 13:16:01 GMT Tillmann Crueger <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


Wed, 10 Mar 2010 17:51:48 GMT Tillmann Crueger <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 ...


Fri, 05 Mar 2010 11:40:30 GMT Tillmann Crueger <crueger@…> [d3347e]
	* src/lists.hpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)

	FIX: repaired compiler problems for latest refactoring


Fri, 05 Mar 2010 10:16:47 GMT Frederik Heber <heber@…> [9879f6]
	* src/Legacy/oldmenu.cpp (modified)
	* src/Makefile.am (modified)
	* src/analysis_bonds.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/atom.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/helpers.hpp (modified)
	* src/lists.cpp (deleted)
	* src/lists.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/bondgraphunittest.hpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/listofbondsunittest.hpp (modified)

	Huge Refactoring due to class molecule now being an STL container.
 ...


Thu, 04 Mar 2010 15:22:56 GMT Tillmann Crueger <crueger@…> [e87acf]
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)

	BROKEN: removed legacy AtomList from molecule class


Thu, 04 Mar 2010 15:20:51 GMT Tillmann Crueger <crueger@…> [bd58fb]
	* src/Patterns/ObservedIterator.hpp (added)
	* src/Patterns/Observer.cpp (modified)
	* src/Patterns/Observer.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/unittests/ObserverTest.cpp (modified)
	* src/unittests/ObserverTest.hpp (modified)

	Added an iterator pattern for observed Data structures


Wed, 03 Mar 2010 14:53:07 GMT Frederik Heber <heber@…> [046783]
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/builder.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)

	Default molecule name can be set via command line, BUGFIX: ...


Wed, 03 Mar 2010 10:13:19 GMT Frederik Heber <heber@…> [b34306]
	* src/Makefile.am (modified)
	* src/World.cpp (added)
	* src/World.hpp (added)
	* src/analysis_correlation.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/vector.cpp (modified)

	singleton class World introduced, contains only cell_size from class ...


Fri, 26 Feb 2010 12:40:52 GMT Tillmann Crueger <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 16:43:02 GMT Tillmann Crueger <crueger@…> [cbc5fb]
	* src/Legacy/oldmenu.cpp (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/defs.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (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/Makefile.am (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)

	Made the world solely responsible for creating and erasing molecules.


Wed, 24 Feb 2010 16:21:12 GMT Tillmann Crueger <crueger@…> [46d958]
	* src/Legacy/oldmenu.cpp (modified)
	* src/Makefile.am (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/atom_particleinfo.hpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/lists.cpp (added)
	* src/lists.hpp (modified)
	* src/molecule.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/DescriptorUnittest.cpp (modified)
	* src/unittests/DescriptorUnittest.hpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* src/unittests/atomsCalculationTest.hpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)

	Made the world solely responsible for creating and destroying atoms.


Wed, 03 Feb 2010 16:42:06 GMT Tillmann Crueger <crueger@…> [2ba827]
	* src/Patterns/Observer.hpp (modified)
	* src/molecule.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/CacheableTest.cpp (modified)

	Changed all observed places to new observer structure


Tue, 02 Feb 2010 16:22:22 GMT Tillmann Crueger <crueger@…> [f721c6]
	* src/Patterns/Observer.hpp (modified)
	* src/molecule.cpp (modified)

	Made more methods of the molecule observable


Tue, 02 Feb 2010 15:53:04 GMT Tillmann Crueger <crueger@…> [ac9b56]
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)

	Added simple way to retrieve formula of a molecule using caching


Tue, 02 Feb 2010 12:21:13 GMT Tillmann Crueger <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


Wed, 27 Jan 2010 14:36:09 GMT Tillmann Crueger <crueger@…> [04b6f9]
	* src/Makefile.am (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/analyzer.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/gslmatrix.cpp (added)
	* src/gslmatrix.hpp (added)
	* src/gslvector.cpp (added)
	* src/gslvector.hpp (added)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/linearsystemofequations.cpp (added)
	* src/linearsystemofequations.hpp (added)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/gslmatrixsymmetricunittest.cpp (added)
	* src/unittests/gslmatrixsymmetricunittest.hpp (added)
	* src/unittests/gslmatrixunittest.cpp (added)
	* src/unittests/gslmatrixunittest.hpp (added)
	* src/unittests/gslvectorunittest.cpp (added)
	* src/unittests/gslvectorunittest.hpp (added)
	* src/unittests/linearsystemofequationsunittest.cpp (added)
	* src/unittests/linearsystemofequationsunittest.hpp (added)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.cpp (added)
	* src/unittests/tesselation_boundarytriangleunittest.hpp (added)
	* src/unittests/tesselation_insideoutsideunittest.cpp (added)
	* src/unittests/tesselation_insideoutsideunittest.hpp (added)
	* src/unittests/tesselationunittest.cpp (modified)
	* src/unittests/tesselationunittest.hpp (modified)
	* src/vector.cpp (modified)
	* src/version.h (added)
	* tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified)
	* tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified)
	* tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified)
	* tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified)
	* tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified)
	* tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified)

	Merge commit 'heber/Analysis_PairCorrelation' into MenuRefactoring
 ...


Sun, 10 Jan 2010 19:05:34 GMT Frederik Heber <heber@…> [49e1ae]
	* src/analyzer.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/joiner.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)

	cstring header was missing in files, supplying definition of strlen, ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [c68025]
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)

	Added method to flip ActiveFlag for single molecules. Signed-off-by: ...


Mon, 23 Nov 2009 18:51:50 GMT Frederik Heber <heber@…> [e359a8]
	* src/analysis_correlation.hpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/helpers.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)

	Fixing ticket #18.

	- each eLog() << Verbose(0) is now followed by ...


Mon, 23 Nov 2009 18:22:33 GMT Frederik Heber <heber@…> [717e0c]
	* src/analyzer.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_graphnode.cpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/bond.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/vector.cpp (modified)

	Verbosity corrected for ERROR and WARNING

	- present ERROR and ...


Thu, 05 Nov 2009 18:14:08 GMT Frederik Heber <heber@…> [1614174]
	* src/analysis_correlation.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_geometry.cpp (modified)

	LEAKFIX: ReturnFullMatrixForSymmetric() and InverseMatrix() have ...


Wed, 04 Nov 2009 19:56:04 GMT Frederik Heber <heber@…> [e138de]
	* src/Makefile.am (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/atom_graphnode.cpp (modified)
	* src/atom_graphnode.hpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/bond.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/element.cpp (modified)
	* src/element.hpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/ellipsoid.hpp (modified)
	* src/errorlogger.cpp (moved)
	* src/errorlogger.hpp (moved)
	* src/graph.cpp (modified)
	* src/graph.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/log.cpp (modified)
	* src/log.hpp (modified)
	* src/logger.cpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/test/ActOnAlltest.hpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/logunittest.cpp (modified)
	* src/unittests/memoryallocatorunittest.cpp (modified)
	* src/unittests/stackclassunittest.cpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)

	Huge change from ofstream * (const) out --> Log().

	- first shift ...


Tue, 03 Nov 2009 12:37:55 GMT Frederik Heber <heber@…> [7218f8]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/helpers.hpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/unittests/memoryallocatorunittest.cpp (modified)

	Several memory bugfixes (thx valgrind).

	- main() - shortened case ...


Mon, 02 Nov 2009 12:50:57 GMT Frederik Heber <heber@…> [fa649a]
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)

	Small changes.

	- VolumeOfConvexEnvelope() - setprecision corrected ...


Tue, 27 Oct 2009 16:11:22 GMT Frederik Heber <heber@…> [776b64]
	* configure.ac (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/leastsquaremin.cpp (modified)
	* src/leastsquaremin.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Huge refactoring to make const what is const (ticket #38), continued. ...


Tue, 27 Oct 2009 08:54:44 GMT Frederik Heber <heber@…> [b453f9]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/atom_particleinfo.hpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/atom_trajectoryparticle.hpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_template.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Begun with ticket #38 (make const what is const).

	- basically all ...


Mon, 19 Oct 2009 13:09:29 GMT Frederik Heber <heber@…> [4455f4]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_template.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Huge Refactoring: class atom split up into several inherited classes. ...


Sun, 18 Oct 2009 14:51:38 GMT Frederik Heber <heber@…> [266237]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/builder.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/lists.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/listofbondsunittest.cpp (added)
	* src/unittests/listofbondsunittest.hpp (added)

	Huge refactoring: molecule::ListOfBondsPerAtom and ...


Mon, 12 Oct 2009 10:30:02 GMT Frederik Heber <heber@…> [4a7776a]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_template.hpp (modified)

	Complete refactoring of molecule_dynamics.cpp

	- new small ...


Fri, 09 Oct 2009 11:57:41 GMT Frederik Heber <heber@…> [49f802c]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_template.hpp (modified)

	Implementing templated iterators done for molecule.cpp

	- new ...


Fri, 09 Oct 2009 10:54:52 GMT Frederik Heber <heber@…> [f66195]
	* src/ActOnAllUnitTest.cpp (modified)
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)
	* src/element.hpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/ellipsoid.hpp (modified)
	* src/graph.cpp (modified)
	* src/graph.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/leastsquaremin.cpp (modified)
	* src/leastsquaremin.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/lists.hpp (added)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/tesselationunittest.hpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)
	* src/verbose.hpp (modified)

	forward declarations used to untangle interdependet classes.

	- ...


Wed, 07 Oct 2009 14:29:57 GMT Frederik Heber <heber@…> [e41951]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/molecule.cpp (modified)

	used forward declaration to untangle atom and bond declarations, ...


Wed, 07 Oct 2009 13:18:59 GMT Frederik Heber <heber@…> [23b830]
	* src/molecule.cpp (modified)

	molecule::CountElements() changed to use ...


Wed, 07 Oct 2009 13:16:13 GMT Frederik Heber <heber@…> [681a8a]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (modified)

	in molecule::OutputTrajectoriesXYZ() ActOnAllAtoms used by new ...


Wed, 07 Oct 2009 13:11:28 GMT Frederik Heber <heber@…> [fcd7b6]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_geometry.cpp (modified)

	In molecule::OutputTrajectories() ActOnAllAtoms() with new function ...


Tue, 06 Oct 2009 17:57:01 GMT Frederik Heber <heber@…> [e9f8f9]
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_template.hpp (added)

	More functions of molecule now use templated iterators.

	- the ...


Mon, 05 Oct 2009 22:10:53 GMT Frederik Heber <heber@…> [cee0b57]
	* src/Makefile.am (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.hpp (modified)
	* src/graph.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (added)
	* src/molecule_fragmentation.cpp (added)
	* src/molecule_geometry.cpp (added)
	* src/molecule_graph.cpp (added)
	* src/molecule_pointcloud.cpp (added)
	* src/moleculelist.cpp (modified)
	* src/verbose.cpp (modified)

	class molecule implementation split up into six separate parts.

	- ...


Mon, 05 Oct 2009 22:08:57 GMT Frederik Heber <heber@…> [e65246]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (moved)
	* src/molecule.hpp (moved)

	New function atom::CorrectFactor() and atom::EqualsFather().

	- are ...