#
# ChangeLog for src/molecule.hpp
#
# Generated by Trac 1.4.4
# Apr 19, 2025, 10:40:53 AM

Tue, 01 Jun 2010 07:28:15 GMT Frederik Heber <heber@…> [bd6bfa]
	* src/bondgraph.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* tests/regression/Molecules/6/post/test.conf (modified)
	* tests/regression/Molecules/7/post/test.conf (modified)

	Fixes after first,last removal.

	- BUGFIX: ...


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 ...


Sun, 30 May 2010 17:29:38 GMT Frederik Heber <heber@…> [eddea2]
	* src/molecule.hpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/vector.cpp (modified)
	* tests/regression/Molecules/7/post/test.conf (added)
	* tests/regression/Molecules/7/pre/test.conf (added)
	* tests/regression/testsuite.at (modified)

	Added case '-T' (periodic translation) to testsuite.

	- BUGFIX: ...


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
 ...


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.
 ...


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
 ...


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, 24 Mar 2010 12:54:47 GMT Tillmann Crueger <crueger@…> [c72112]
	* src/Patterns/Cacheable.hpp (modified)
	* src/boundary.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)

	Repaired GetMAxId() method of molecule


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 11:39:57 GMT Frederik Heber <heber@…> [c7b1e7]
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)

	Merge branch 'FixGeneralizeStoreAdjacencyToFile' into ...


Thu, 18 Mar 2010 11:37:26 GMT Frederik Heber <heber@…> [8ab0407]
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)

	molecule::StoreAdjacencyToFile() and molecule::StoreBondsToFile() now ...


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 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.


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 12:22:06 GMT Tillmann Crueger <crueger@…> [a25aae]
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Merge commit 'heber/Analysis_PairCorrelation' into MenuRefactoring


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


Tue, 02 Feb 2010 12:14:54 GMT Tillmann Crueger <crueger@…> [bfce50]
	* src/Actions/Action.hpp (modified)
	* src/Actions/small_actions.cpp (added)
	* src/Actions/small_actions.hpp (added)
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)
	* src/molecule.hpp (modified)
	* src/moleculelist.cpp (modified)

	Moved method to rename molecules to a seperate Action


Tue, 02 Feb 2010 12:00:19 GMT Tillmann Crueger <crueger@…> [d5f216]
	* src/Makefile.am (modified)
	* src/Patterns/Observer.hpp (modified)
	* src/molecule.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/ObserverTest.cpp (modified)
	* src/unittests/ObserverTest.hpp (modified)

	Added a view that displays all molecules using a QTableWidget


Tue, 02 Feb 2010 09:43:52 GMT Frederik Heber <heber@…> [1f1b23]
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/builder.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Possibility to store all bonds to file added.

	So far we only could ...


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
 ...


Tue, 26 Jan 2010 12:52:31 GMT Frederik Heber <heber@…> [244a84]
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/bondgraph.cpp (modified)
	* src/builder.cpp (modified)
	* src/molecule.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	GetDistanceToSurface() separated, filling now with water instead of ...


Tue, 26 Jan 2010 12:45:41 GMT Tillmann Crueger <crueger@…> [1ca488]
	* src/Makefile.am (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/info.cpp (added)
	* src/info.hpp (added)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/infounittest.cpp (added)
	* src/unittests/infounittest.hpp (added)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)
	* tests/Tesselations/1_2-dimethoxyethane/NonConvexEnvelope-1_2-dimethoxyethane.dat (modified)
	* tests/Tesselations/1_2-dimethylbenzene/NonConvexEnvelope-1_2-dimethylbenzene.dat (modified)
	* tests/Tesselations/2-methylcyclohexanone/NonConvexEnvelope-2-methylcyclohexanone.dat (modified)
	* tests/Tesselations/C16_0-Torus/NonConvexEnvelope-C16_0-Torus.dat (modified)
	* tests/Tesselations/Makefile.am (modified)
	* tests/Tesselations/N_N-dimethylacetamide/NonConvexEnvelope-N_N-dimethylacetamide.dat (modified)
	* tests/Tesselations/benzene.test (added)
	* tests/Tesselations/benzene/NonConvexEnvelope-benzene.dat (added)
	* tests/Tesselations/benzene/benzene.xyz (added)
	* tests/Tesselations/cholesterol/NonConvexEnvelope-cholesterol.dat (modified)
	* tests/Tesselations/cluster/NonConvexEnvelope-cluster.dat (modified)
	* tests/Tesselations/cycloheptane/NonConvexEnvelope-cycloheptane.dat (modified)
	* tests/Tesselations/defs.in (modified)
	* tests/Tesselations/dimethyl_bromomalonate/NonConvexEnvelope-dimethyl_bromomalonate.dat (modified)
	* tests/Tesselations/glucose/NonConvexEnvelope-glucose.dat (modified)
	* tests/Tesselations/heptan/NonConvexEnvelope-heptan.dat (modified)
	* tests/Tesselations/isoleucine/NonConvexEnvelope-isoleucine.dat (modified)
	* tests/Tesselations/neohexane/NonConvexEnvelope-neohexane.dat (modified)
	* tests/Tesselations/proline/NonConvexEnvelope-proline.dat (modified)
	* tests/Tesselations/putrescine/NonConvexEnvelope-putrescine.dat (modified)
	* tests/Tesselations/round_cluster/NonConvexEnvelope-round_cluster.dat (modified)
	* tests/Tesselations/tartaric_acid/NonConvexEnvelope-tartaric_acid.dat (modified)
	* 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)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified)
	* tests/testsuite.at (modified)

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


Sat, 02 Jan 2010 15:49:40 GMT Tillmann Crueger <crueger@…> [477bb2]
	* src/menu.cpp (modified)
	* src/molecule.hpp (modified)
	* src/moleculelist.cpp (modified)

	Moved several Methods from Menu to MoleculeListClass


Tue, 29 Dec 2009 11:57:09 GMT Tillmann Crueger <crueger@…> [77675f]
	* src/menu.cpp (modified)
	* src/menu.hpp (modified)
	* src/molecule.hpp (modified)
	* src/moleculelist.cpp (modified)

	Moved flipChosen method from oldmenu to MoleculeListClass


Sat, 19 Dec 2009 19:32:24 GMT Frederik Heber <heber@…> [71b20e]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)

	Attempt to fix the embedding.

	Basically it would be working, but ...


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: ...


Tue, 24 Nov 2009 15:34:49 GMT Frederik Heber <heber@…> [6a7f78c]
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* tests/Tesselations/1_2-dimethoxyethane/NonConvexEnvelope-1_2-dimethoxyethane.dat (modified)
	* tests/Tesselations/1_2-dimethylbenzene/NonConvexEnvelope-1_2-dimethylbenzene.dat (modified)
	* tests/Tesselations/2-methylcyclohexanone/NonConvexEnvelope-2-methylcyclohexanone.dat (modified)
	* tests/Tesselations/C16_0-Torus/NonConvexEnvelope-C16_0-Torus.dat (modified)
	* tests/Tesselations/Makefile.am (modified)
	* tests/Tesselations/N_N-dimethylacetamide/NonConvexEnvelope-N_N-dimethylacetamide.dat (modified)
	* tests/Tesselations/benzene.test (added)
	* tests/Tesselations/benzene/NonConvexEnvelope-benzene.dat (added)
	* tests/Tesselations/benzene/benzene.xyz (added)
	* tests/Tesselations/cholesterol/NonConvexEnvelope-cholesterol.dat (modified)
	* tests/Tesselations/cluster/NonConvexEnvelope-cluster.dat (modified)
	* tests/Tesselations/cycloheptane/NonConvexEnvelope-cycloheptane.dat (modified)
	* tests/Tesselations/dimethyl_bromomalonate/NonConvexEnvelope-dimethyl_bromomalonate.dat (modified)
	* tests/Tesselations/glucose/NonConvexEnvelope-glucose.dat (modified)
	* tests/Tesselations/heptan/NonConvexEnvelope-heptan.dat (modified)
	* tests/Tesselations/isoleucine/NonConvexEnvelope-isoleucine.dat (modified)
	* tests/Tesselations/neohexane/NonConvexEnvelope-neohexane.dat (modified)
	* tests/Tesselations/proline/NonConvexEnvelope-proline.dat (modified)
	* tests/Tesselations/putrescine/NonConvexEnvelope-putrescine.dat (modified)
	* tests/Tesselations/round_cluster/NonConvexEnvelope-round_cluster.dat (modified)
	* tests/Tesselations/tartaric_acid/NonConvexEnvelope-tartaric_acid.dat (modified)

	Fixes and naming of final Tecplot output file is now molecule name.
 ...


Sat, 07 Nov 2009 12:16:57 GMT Frederik Heber <heber@…> [568be7]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/molecule.hpp (modified)
	* src/moleculelist.cpp (modified)

	Added config::SavePDB() and config::SaveMPQC().

	- note: for CODICE ...


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 ...


Wed, 04 Nov 2009 15:08:11 GMT Frederik Heber <heber@…> [c9bce3e]
	* src/config.cpp (modified)
	* src/molecule.hpp (modified)
	* src/moleculelist.cpp (modified)

	config::Load() refactored: Dissection into connected subgraphs -> ...


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 ...


Fri, 30 Oct 2009 09:05:30 GMT Frederik Heber <heber@…> [b70721]
	* src/Makefile.am (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/bondgraph.cpp (added)
	* src/bondgraph.hpp (added)
	* src/builder.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/bondgraphunittest.cpp (added)
	* src/unittests/bondgraphunittest.hpp (added)

	New class BondGraph.

	- BondGraph parses a file containing bond ...


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 11:51:52 GMT Frederik Heber <heber@…> [ad37ab]
	* src/analyzer.cpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/molecule.hpp (modified)

	analyzer.cpp and boundary.cpp refactored.

	- ticket #39 is done with ...


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 16:35:25 GMT Frederik Heber <heber@…> [df8b19]
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_template.hpp (modified)

	Removed ResetAllAtomNumbers(), replaced by templated ...


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 ...


Sat, 17 Oct 2009 19:47:58 GMT Frederik Heber <heber@…> [b8b75d]
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Refactored CreateAdjacencyList().

	- new auxiliary functions: ...


Sat, 17 Oct 2009 17:06:42 GMT Frederik Heber <heber@…> [44a59b]
	* src/builder.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Renamed and rewritten CreateAdjacencyList2().

	- rename ...


Mon, 12 Oct 2009 12:10:43 GMT Frederik Heber <heber@…> [5034e1]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_template.hpp (modified)

	First half of molecule_fragmentation.cpp refactoring.

	- new ...


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 14:35:14 GMT Frederik Heber <heber@…> [ccd9f5]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)

	First half of molecule_dynamics.cpp is refactored into smaller parts. ...


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 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 ...