#
# ChangeLog for src/builder.cpp
#
# Generated by Trac 1.6
# May 15, 2025, 8:16:57 AM

Fri, 11 Jun 2010 12:20:08 GMT Frederik Heber <heber@…> [54b953]
	* src/Actions/AtomAction/ChangeElementAction.cpp (modified)
	* src/Actions/MapOfActions.cpp (modified)
	* src/builder.cpp (modified)
	* tests/regression/testsuite-simple_configuration.at (modified)

	Case 'E' is now handled by CommandLineUI.

	- TESTFIX: --element is ...


Fri, 11 Jun 2010 12:19:50 GMT Frederik Heber <heber@…> [f0a3ec]
	* src/Actions/AtomAction/AddAction.cpp (modified)
	* src/Actions/MapOfActions.cpp (modified)
	* src/builder.cpp (modified)
	* tests/regression/testsuite-simple_configuration.at (modified)

	Case 'a' is now handled by CommandLineUI.

	- NOTE: atom has still to ...


Fri, 11 Jun 2010 12:19:42 GMT Frederik Heber <heber@…> [6c7352]
	* src/builder.cpp (modified)

	Removed commented-out LoadPeriodentafel() and (second) ...


Fri, 11 Jun 2010 12:19:27 GMT Frederik Heber <heber@…> [387b36]
	* src/Actions/MapOfActions.cpp (modified)
	* src/Actions/WorldAction/SetDefaultNameAction.cpp (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/builder.cpp (modified)
	* src/molecule.cpp (modified)

	Case 'X' is now handled by CommandLineUI, World::get/setDefaultName() ...


Fri, 11 Jun 2010 12:19:18 GMT Frederik Heber <heber@…> [f821d6]
	* src/Actions/MapOfActions.cpp (modified)
	* src/builder.cpp (modified)
	* tests/regression/testsuite-standard_options.at (modified)

	Case 'n' is now handled by CommandLineUI.

	- TESTFIX: fastparsing ...


Fri, 11 Jun 2010 10:45:06 GMT Frederik Heber <heber@…> [bdaacd]
	* src/Actions/MapOfActions.cpp (modified)
	* src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified)
	* src/builder.cpp (modified)

	Case 'M' is now handled by CommandLineUI.


Thu, 10 Jun 2010 16:24:24 GMT Frederik Heber <heber@…> [39af9f]
	* src/Actions/CmdAction/BondLengthTableAction.cpp (modified)
	* src/Actions/MapOfActions.cpp (modified)
	* src/builder.cpp (modified)

	Case 'g' is now handled by CommandLineUI.


Thu, 10 Jun 2010 16:20:36 GMT Frederik Heber <heber@…> [198494]
	* src/Actions/CmdAction/ElementDbAction.cpp (modified)
	* src/Actions/MapOfActions.cpp (modified)
	* src/builder.cpp (modified)

	Case 'e' is now handled by CommandLineUI.

	- BUGFIX: ElementDbAction ...


Thu, 10 Jun 2010 16:13:23 GMT Frederik Heber <heber@…> [7e6b00]
	* src/Actions/MapOfActions.cpp (modified)
	* src/Actions/MapOfActions.hpp (modified)
	* src/CommandLineParser.cpp (modified)
	* src/CommandLineParser.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified)
	* src/builder.cpp (modified)

	FIX: Sequence of actions called from command line is now corrected.
 ...


Wed, 09 Jun 2010 15:10:51 GMT Frederik Heber <heber@…> [2b5574]
	* src/Actions/MapOfActions.cpp (modified)
	* src/builder.cpp (modified)
	* tests/regression/testsuite-analysis.at (modified)

	Case 'm' is now handled by CommandLineUI.

	- TESTCHANGE: Analysis/5 ...


Wed, 09 Jun 2010 15:08:46 GMT Frederik Heber <heber@…> [58bbd3]
	* src/Actions/MapOfActions.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/builder.cpp (modified)
	* src/moleculelist.cpp (modified)
	* tests/regression/Analysis/3/post/bin_output.csv (modified)
	* tests/regression/testsuite-analysis.at (modified)

	Cases 'C' are now handled by CommandLineUI.

	- TESTFIX: ...


Wed, 09 Jun 2010 11:12:08 GMT Frederik Heber <heber@…> [c78d44]
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/builder.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified)

	Change to PairCorrelation...() functions, accept now vector<element ...


Tue, 08 Jun 2010 13:57:09 GMT Frederik Heber <heber@…> [8540f0]
	* src/Actions/MapOfActions.cpp (modified)
	* src/builder.cpp (modified)

	Case 'D' is now handled by CommandLineUI.


Tue, 08 Jun 2010 13:49:27 GMT Frederik Heber <heber@…> [e4b5de]
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/MapOfActions.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/builder.cpp (modified)
	* tests/regression/Fragmentation/3/pre/BondFragment0.conf (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragment0.conf.xyz (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragment1.conf (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragment1.conf.xyz (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragment2.conf (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragment2.conf.xyz (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragment3.conf (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragment3.conf.xyz (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragment4.conf (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragment4.conf.xyz (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragmentAdjacency.dat (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragmentForces-Factors.dat (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragmentKeySets.dat (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragmentOrderAtSite.dat (deleted)
	* tests/regression/Fragmentation/3/pre/BondFragmentTE-Factors.dat (deleted)
	* tests/regression/testsuite-fragmentation.at (modified)

	Case 'f' is now handled by CommandLineUI.

	- ...


Tue, 08 Jun 2010 12:13:11 GMT Frederik Heber <heber@…> [48ab70a]
	* src/Actions/MapOfActions.cpp (modified)
	* src/builder.cpp (modified)

	Case 'u' is now handled by CommandLineUI.


Mon, 07 Jun 2010 23:55:30 GMT Frederik Heber <heber@…> [9907e7]
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/builder.cpp (modified)
	* tests/regression/testsuite-filling.at (modified)

	Case '-F' is now handled by CommandLineUI.

	- FIX: ...


Wed, 02 Jun 2010 16:17:17 GMT Frederik Heber <heber@…> [e30ce8]
	* src/Actions/MapOfActions.cpp (modified)
	* src/Actions/MapOfActions.hpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Descriptors/MoleculePtrDescriptor.cpp (added)
	* src/Descriptors/MoleculePtrDescriptor.hpp (added)
	* src/Descriptors/MoleculePtrDescriptor_impl.hpp (added)
	* src/Makefile.am (modified)
	* src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified)
	* src/builder.cpp (modified)

	Case 'd' is now handled by CommandLineUI (RepeatBoxAction).

	- ...


Wed, 02 Jun 2010 14:40:30 GMT Frederik Heber <heber@…> [584a2a]
	* src/Actions/MapOfActions.cpp (modified)
	* src/builder.cpp (modified)

	Case '-O' is now handled by CommandLineUI (CenterOnEdgeAction).
 ...


Wed, 02 Jun 2010 14:38:07 GMT Frederik Heber <heber@…> [116f37]
	* src/Actions/MapOfActions.cpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified)
	* src/builder.cpp (modified)

	Case '-c' is now handled by CommandLineUI.

	- BUGFIX: ...


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: ...


Tue, 01 Jun 2010 21:36:36 GMT Frederik Heber <heber@…> [009607e]
	* src/analysis_correlation.cpp (modified)
	* src/builder.cpp (modified)

	Small changes to ...Correlation...().

	- Calling doCountAtoms on all ...


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 14:33:11 GMT Frederik Heber <heber@…> [42af9e]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/periodentafel.cpp (modified)
	* tests/regression/testsuite-simple_configuration.at (modified)

	MEMFIXES: no more default saving/loading of element's db, ...


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 ...


Sun, 30 May 2010 23:40:04 GMT Frederik Heber <heber@…> [158c594]
	* src/Actions/MapOfActions.cpp (modified)
	* src/Actions/WorldAction/CenterInBoxAction.cpp (modified)
	* src/builder.cpp (modified)

	Case '-b' now handled by CommandLineUI and fixes.

	- ...


Sun, 30 May 2010 23:18:48 GMT Frederik Heber <heber@…> [2a92ff]
	* src/Actions/MapOfActions.cpp (modified)
	* src/builder.cpp (modified)

	Case '-s' now handled by CommandLineUI.

	- FIX: Type Vector has to ...


Sun, 30 May 2010 23:03:49 GMT Frederik Heber <heber@…> [6ca1f7]
	* src/Actions/MapOfActions.cpp (modified)
	* src/builder.cpp (modified)

	case '-B' now handled by CommandLineUI.


Sun, 30 May 2010 16:51:45 GMT Frederik Heber <heber@…> [9b7db1]
	* src/builder.cpp (modified)
	* tests/regression/Simple_configuration/8/post/test.conf (added)
	* tests/regression/Simple_configuration/8/pre/test.conf (added)
	* tests/regression/testsuite.at (modified)

	Added case '-R' (removing atoms outside of sphere) to testsuite.

	- ...


Sun, 30 May 2010 15:38:38 GMT Frederik Heber <heber@…> [f8f14d]
	* src/builder.cpp (modified)
	* tests/regression/Molecules/4/post/test.conf (added)
	* tests/regression/Molecules/4/pre/test.conf (added)
	* tests/regression/testsuite.at (modified)

	Added case '-L' (linear interpolation) to testsuite.

	- this just ...


Sun, 30 May 2010 15:18:50 GMT Frederik Heber <heber@…> [c68c90]
	* src/builder.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* tests/regression/Molecules/1/pre/test.conf (added)
	* tests/regression/Molecules/1/pre/test.dbond (added)
	* tests/regression/testsuite.at (modified)

	Added case '-A' (parsing bonds) to testsuite.

	- ...


Sun, 30 May 2010 14:45:50 GMT Frederik Heber <heber@…> [5e11e4]
	* src/builder.cpp (modified)

	In-code created water molecule has been removed in ...


Sun, 30 May 2010 13:42:26 GMT Frederik Heber <heber@…> [08f6ff]
	* src/builder.cpp (modified)
	* tests/regression/Analysis/3/post/bin_output.csv (added)
	* tests/regression/Analysis/3/post/output.csv (added)
	* tests/regression/Analysis/3/pre/test.conf (added)
	* tests/regression/testsuite.at (modified)

	Added case '-C P' (correlation to point) to testsuite.

	- DOCUFIX: ...


Sun, 30 May 2010 13:41:37 GMT Frederik Heber <heber@…> [06f8ee]
	* src/builder.cpp (modified)
	* tests/regression/Analysis/1/post/bin_output.csv (added)
	* tests/regression/Analysis/1/post/output.csv (added)
	* tests/regression/Analysis/1/pre/test.conf (added)
	* tests/regression/Analysis/2/post/bin_output-10.csv (added)
	* tests/regression/Analysis/2/post/bin_output-20.csv (added)
	* tests/regression/Analysis/2/post/bin_output-5.csv (added)
	* tests/regression/Analysis/2/post/output-10.csv (added)
	* tests/regression/Analysis/2/post/output-20.csv (added)
	* tests/regression/Analysis/2/post/output-5.csv (added)
	* tests/regression/Analysis/2/pre/test.conf (added)
	* tests/regression/testsuite.at (modified)

	Added case '-C E' (pair correlation analysis) to testsuite.

	- ...


Sun, 30 May 2010 11:32:05 GMT Frederik Heber <heber@…> [5188f5]
	* src/builder.cpp (modified)
	* tests/regression/testsuite.at (modified)

	Added case '-M' (MPQC basis) to testsuite.

	- ...


Sun, 30 May 2010 11:05:54 GMT Frederik Heber <heber@…> [93d732b]
	* src/World.cpp (modified)
	* src/builder.cpp (modified)
	* tests/regression/testsuite.at (modified)

	Added case '-X' (default mol name) to testsuite and bugfix.

	- ...


Sat, 29 May 2010 14:18:41 GMT Frederik Heber <heber@…> [62680e]
	* src/builder.cpp (modified)

	Merge branch 'FixReintroduceExitFlagtoParseCommandLineCall' into ...


Sat, 29 May 2010 14:15:27 GMT Frederik Heber <heber@…> [99fcaf]
	* src/builder.cpp (modified)

	FIX: Flag returned by ParseCommandLineOptions() needs to be heeded, ...


Sat, 29 May 2010 13:11:22 GMT Frederik Heber <heber@…> [0fb9f6]
	* src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified)
	* src/builder.cpp (modified)
	* src/helpers.cpp (modified)

	Fixes to prevent seg'faults.

	- ...


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 18:46:52 GMT Frederik Heber <heber@…> [8de375]
	* 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)

	Merge branch 'StructureRefactoring' into CommandLineActionMapping
 ...


Wed, 19 May 2010 18:41:05 GMT Frederik Heber <heber@…> [eff648]
	* src/builder.cpp (modified)

	BUGFIX: In ParseCommandLineOptions() -v and -V were mixed.

	- ...


Tue, 18 May 2010 15:20:52 GMT Frederik Heber <heber@…> [4eb4fe]
	* src/analysis_bonds.cpp (modified)
	* src/analysis_bonds.hpp (modified)
	* src/builder.cpp (modified)
	* src/elements.db (modified)
	* src/elements_db.cpp (added)
	* src/elements_db.hpp (added)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.hpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.hpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/ParserUnitTest.cpp (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/analysisbondsunittest.hpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/bondgraphunittest.hpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/listofbondsunittest.hpp (modified)
	* src/unittests/periodentafelTest.cpp (added)
	* src/unittests/periodentafelTest.hpp (added)
	* tests/testsuite.at (modified)

	"-e <db path>" not necessary anymore.

	Removed necessity of ...


Mon, 17 May 2010 17:31:35 GMT Frederik Heber <heber@…> [f65e1f]
	* src/builder.cpp (modified)

	FIX: list of arguments passed to ParseCommandLineOptions() should be ...


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.
 ...


Sun, 09 May 2010 12:00:08 GMT Frederik Heber <heber@…> [50dfda]
	* src/Actions/CmdAction/VersionAction.cpp (added)
	* src/Actions/CmdAction/VersionAction.hpp (added)
	* src/Makefile.am (modified)
	* src/UIElements/CommandLineWindow.cpp (modified)
	* src/UIElements/CommandLineWindow.hpp (modified)
	* src/builder.cpp (modified)

	Added VersionAction.

	- new CmdAction/VersionAction that prints the ...


Sat, 08 May 2010 22:59:14 GMT Frederik Heber <heber@…> [148d8f0]
	* src/builder.cpp (modified)

	FIX: cleanup() still deleted configuration although is part of the ...


Sat, 08 May 2010 21:59:27 GMT Frederik Heber <heber@…> [d893f79]
	* src/UIElements/CommandLineUIFactory.cpp (modified)
	* src/UIElements/CommandLineUIFactory.hpp (modified)
	* src/UIElements/CommandLineWindow.cpp (modified)
	* src/UIElements/CommandLineWindow.hpp (modified)
	* src/UIElements/MainWindow.hpp (modified)
	* src/UIElements/TextUIFactory.cpp (modified)
	* src/UIElements/TextUIFactory.hpp (modified)
	* src/UIElements/TextWindow.cpp (modified)
	* src/UIElements/TextWindow.hpp (modified)
	* src/UIElements/UIFactory.hpp (modified)
	* src/builder.cpp (modified)

	removed menuPopulaters from MainWindow.

	- menuPopulaters is too ...


Sat, 08 May 2010 20:34:05 GMT Frederik Heber <heber@…> [8e1f7af]
	* src/UIElements/TextWindow.cpp (modified)
	* src/UIElements/UIFactory.hpp (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/builder.cpp (modified)

	class config added to World.

	- World now has the global ...


Sat, 08 May 2010 20:14:04 GMT Frederik Heber <heber@…> [4a75d9]
	* src/UIElements/CommandLineUIFactory.cpp (modified)
	* src/UIElements/CommandLineUIFactory.hpp (modified)
	* src/UIElements/CommandLineWindow.cpp (modified)
	* src/UIElements/CommandLineWindow.hpp (modified)
	* src/UIElements/MainWindow.hpp (modified)
	* src/UIElements/TextUIFactory.cpp (modified)
	* src/UIElements/TextUIFactory.hpp (modified)
	* src/UIElements/TextWindow.cpp (modified)
	* src/UIElements/TextWindow.hpp (modified)
	* src/UIElements/UIFactory.hpp (modified)
	* src/builder.cpp (modified)

	...UIFactory::makeMainWindow() now has only a single parameter, ...


Sat, 08 May 2010 19:14:29 GMT Frederik Heber <heber@…> [c6efc1]
	* configure.ac (modified)
	* src/CommandLineParser.cpp (added)
	* src/CommandLineParser.hpp (added)
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)

	Begin of Refactoring of ParseCommandLineOptions().

	- new singleton ...


Sat, 08 May 2010 18:36:22 GMT Frederik Heber <heber@…> [03bb99]
	* src/Actions/MoleculeAction/ChangeNameAction.cpp (moved)
	* src/Actions/MoleculeAction/ChangeNameAction.hpp (moved)
	* src/Actions/ParserAction/LoadXyzAction.cpp (added)
	* src/Actions/ParserAction/LoadXyzAction.hpp (added)
	* src/Actions/ParserAction/SaveXyzAction.cpp (added)
	* src/Actions/ParserAction/SaveXyzAction.hpp (added)
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)

	Introducing small actions.

	- new directory  MoleculeAction to ...


Sat, 08 May 2010 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
 ...


Wed, 28 Apr 2010 13:31:57 GMT Tillmann Crueger <crueger@…> [632bc3]
	* src/Actions/Action.cpp (modified)
	* src/Actions/ActionHistory.cpp (modified)
	* src/Helpers/MemDebug.cpp (added)
	* src/Helpers/MemDebug.hpp (added)
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)

	Added a small memory tracker to the programm.


Tue, 27 Apr 2010 14:25:42 GMT Frederik Heber <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

	- ...


Thu, 01 Apr 2010 13:49:25 GMT Frederik Heber <heber@…> [388049]
	* src/analysis_bonds.cpp (modified)
	* src/analysis_bonds.hpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/builder.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)

	Moved functions CountBondsOfTwo(), CountBondsOfThree() and ...


Thu, 25 Mar 2010 12:01:27 GMT Tillmann Crueger <crueger@…> [d56640]
	* src/Actions/Action.cpp (modified)
	* src/Actions/ActionHistory.cpp (added)
	* src/Actions/ActionHistory.hpp (added)
	* src/Actions/ActionRegistry.cpp (modified)
	* src/Actions/small_actions.cpp (modified)
	* src/Actions/small_actions.hpp (modified)
	* src/Makefile.am (modified)
	* src/Menu/TextMenu.cpp (modified)
	* src/Menu/TextMenu.hpp (modified)
	* src/UIElements/TextDialog.cpp (modified)
	* src/UIElements/TextWindow.cpp (modified)
	* src/UIElements/TextWindow.hpp (modified)
	* src/builder.cpp (modified)

	Added full undo functioniality


Fri, 19 Mar 2010 15:42:58 GMT Frederik Heber <heber@…> [f18185]
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/builder.cpp (modified)

	Implemented counting of bonds over all atoms.

	- new functions in ...


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 15:38:56 GMT Frederik Heber <heber@…> [1cbf47]
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/builder.cpp (modified)

	Introduced CountHydrogenBridgeBonds() function.

	- ...


Thu, 18 Mar 2010 15:06:30 GMT Tillmann Crueger <crueger@…> [75ac0c]
	* src/Helpers/Assert.cpp (added)
	* src/Helpers/Assert.hpp (added)
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)

	Added custom Assert makro that allows ignoring asserts


Thu, 18 Mar 2010 14:48:20 GMT Tillmann Crueger <crueger@…> [229e3c]
	* src/Helpers/Assert.cpp (added)
	* src/Helpers/Assert.hpp (added)
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)
	* src/unittests/AtomDescriptorTest.cpp (modified)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)

	Added custom Assert makro that allows ignoring asserts


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


Thu, 11 Mar 2010 14:08:44 GMT Tillmann Crueger <crueger@…> [e73a8a2]
	* src/Actions/Action.cpp (modified)
	* src/Actions/ActionRegistry.cpp (modified)
	* src/Actions/ActionRegistry.hpp (modified)
	* src/builder.cpp (modified)
	* src/unittests/SingletonTest.cpp (modified)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)

	Changed ActionRegistry to use the new Singleton Mechanism


Thu, 11 Mar 2010 10:37:32 GMT Tillmann Crueger <crueger@…> [d7940e]
	* src/Actions/small_actions.cpp (modified)
	* src/Legacy/oldmenu.cpp (modified)
	* src/Patterns/Singleton.hpp (modified)
	* src/Patterns/Singleton_impl.hpp (modified)
	* src/UIElements/UIFactory.cpp (modified)
	* src/UIElements/UIFactory.hpp (modified)
	* src/builder.cpp (modified)

	Made the UIFactory an instance of the Singleton Pattern


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


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 ...


Tue, 02 Mar 2010 16:12:19 GMT Frederik Heber <heber@…> [cb85c2e]
	* src/builder.cpp (modified)

	ManipulateAtoms() can turn atoms around bonds again, in ...


Mon, 01 Mar 2010 20:41:21 GMT Frederik Heber <heber@…> [b74f7d]
	* src/builder.cpp (modified)

	FIX: ParseCommandLineOptions - case 'C' used wrong LC width, case 'F' ...


Fri, 26 Feb 2010 13:57:01 GMT Tillmann Crueger <crueger@…> [a1510d]
	* configure.ac (modified)
	* src/Actions/small_actions.hpp (modified)
	* src/Makefile.am (modified)
	* src/Patterns/Observer.cpp (modified)
	* src/Patterns/Observer.hpp (modified)
	* src/UIElements/TextStatusIndicator.cpp (added)
	* src/UIElements/TextStatusIndicator.hpp (added)
	* src/UIElements/TextWindow.cpp (modified)
	* src/UIElements/TextWindow.hpp (modified)
	* src/World.cpp (modified)
	* src/builder.cpp (modified)
	* src/element.cpp (modified)
	* src/gslmatrix.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/ActionSequenceTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/CacheableTest.cpp (modified)
	* src/unittests/DescriptorUnittest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/ObserverTest.cpp (modified)
	* src/unittests/TestRunnerMain.cpp (added)
	* src/unittests/UnitTestMain.cpp (added)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/gslmatrixsymmetricunittest.cpp (modified)
	* src/unittests/gslmatrixunittest.cpp (modified)
	* src/unittests/gslvectorunittest.cpp (modified)
	* src/unittests/infounittest.cpp (modified)
	* src/unittests/linearsystemofequationsunittest.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/logunittest.cpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)
	* src/unittests/memoryallocatorunittest.cpp (modified)
	* src/unittests/memoryusageobserverunittest.cpp (modified)
	* src/unittests/stackclassunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.hpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* tests/Tesselations/defs.in (modified)

	Merge branch 'FreddiesRefactoring' into StructureRefactoring
 ...


Fri, 26 Feb 2010 09:54:12 GMT Frederik Heber <heber@…> [aac3ef]
	* src/builder.cpp (modified)

	FIX: Replaced memoryusageobserverunittest.hpp include by correct ...


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.


Sun, 21 Feb 2010 13:34:41 GMT Frederik Heber <heber@…> [775d133]
	* src/analysis_correlation.cpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)

	Filling has a MaxDistance, somes changes to the Correlation Analysis. ...


Thu, 18 Feb 2010 11:38:02 GMT Tillmann Crueger <crueger@…> [0188ea]
	* src/Actions/small_actions.hpp (modified)
	* src/Makefile.am (modified)
	* src/UIElements/TextStatusIndicator.cpp (added)
	* src/UIElements/TextStatusIndicator.hpp (added)
	* src/UIElements/TextWindow.cpp (modified)
	* src/UIElements/TextWindow.hpp (modified)
	* src/builder.cpp (modified)

	Added a progress indicator for the text menu


Thu, 18 Feb 2010 10:59:29 GMT Tillmann Crueger <crueger@…> [7dad10]
	* src/Actions/Process.cpp (added)
	* src/Actions/Process.hpp (added)
	* src/Actions/small_actions.hpp (modified)
	* src/Makefile.am (modified)
	* src/World.cpp (modified)
	* src/builder.cpp (modified)
	* src/helpers.hpp (modified)

	Added a special class of Actions that take some time.


Tue, 16 Feb 2010 17:26:59 GMT Tillmann Crueger <crueger@…> [354859]
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/builder.cpp (modified)

	Moved control of molecules and periode to World.


Mon, 08 Feb 2010 15:29:35 GMT Frederik Heber <heber@…> [164a33]
	* src/builder.cpp (modified)

	changed case 'C' of ParseCommandLineOptions to allow selecting ...


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 12:14:54 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 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 ...


Sat, 30 Jan 2010 17:35:48 GMT Frederik Heber <heber@…> [481601]
	* src/builder.cpp (modified)

	Added output of surfacemap in ParseCommandLineOptions(), case 'C'
	again.


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
 ...


Thu, 14 Jan 2010 17:36:09 GMT Frederik Heber <heber@…> [9473f6]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	FillBoxWithMolecule now allows boundary between filler molecules and ...


Wed, 13 Jan 2010 10:22:29 GMT Tillmann Crueger <crueger@…> [45f5d6]
	* src/UIElements/Dialog.cpp (modified)
	* src/UIElements/Dialog.hpp (modified)
	* src/UIElements/TextDialog.cpp (modified)
	* src/UIElements/TextDialog.hpp (modified)
	* src/builder.cpp (modified)

	Changed dialog structure to  use objects for queries.


Mon, 11 Jan 2010 09:35:52 GMT Frederik Heber <heber@…> [241485]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Removed unnecessary epsilon parameter.

	- epsilon before was used as ...


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, ...


Sat, 09 Jan 2010 11:30:49 GMT Tillmann Crueger <crueger@…> [12b845]
	* src/Actions/ActionRegistry.cpp (modified)
	* src/UIElements/MainWindow.hpp (modified)
	* src/UIElements/TextUIFactory.cpp (modified)
	* src/UIElements/TextUIFactory.hpp (modified)
	* src/UIElements/TextWindow.cpp (modified)
	* src/UIElements/TextWindow.hpp (modified)
	* src/UIElements/UIFactory.hpp (modified)
	* src/builder.cpp (modified)
	* src/menu.cpp (modified)
	* src/menu.hpp (modified)

	Seperated building of mainWindow and contained Menus

	- Moved code ...


Thu, 07 Jan 2010 14:46:34 GMT Tillmann Crueger <crueger@…> [cc04b7]
	* src/Actions/Action.cpp (modified)
	* src/Actions/Action.hpp (modified)
	* src/Actions/ActionRegistry.cpp (added)
	* src/Actions/ActionRegistry.hpp (added)
	* src/Actions/ErrorAction.cpp (modified)
	* src/Actions/ErrorAction.hpp (modified)
	* src/Actions/MakroAction.cpp (modified)
	* src/Actions/MakroAction.hpp (modified)
	* src/Actions/MethodAction.cpp (modified)
	* src/Actions/MethodAction.hpp (modified)
	* src/Makefile.am (modified)
	* src/UIElements/TextUIFactory.cpp (modified)
	* src/UIElements/TextUIFactory.hpp (modified)
	* src/UIElements/TextWindow.cpp (modified)
	* src/UIElements/UIFactory.cpp (modified)
	* src/UIElements/UIFactory.hpp (modified)
	* src/builder.cpp (modified)
	* src/menu.cpp (modified)
	* src/unittests/ActionSequenceTest.cpp (modified)

	Added a central registry that allows access to actions by name.


Tue, 05 Jan 2010 09:23:25 GMT Tillmann Crueger <crueger@…> [235bed]
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/menu.cpp (modified)
	* src/menu.hpp (modified)

	Moved saveConfig method from oldmenu to a method inside config class