#
# ChangeLog for src
#
# Generated by Trac 1.6
# May 24, 2025, 9:12:46 PM

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
 ...


Mon, 26 Apr 2010 16:38:47 GMT Frederik Heber <heber@…> [d6c485]
	* src/World.cpp (modified)

	Merge branch 'FixWorld_wrongauthor' into Analysis_PairCorrelation


Mon, 26 Apr 2010 16:38:14 GMT Frederik Heber <heber@…> [70378e]
	* src/World.cpp (modified)

	FIX: Author of World.cpp has been wrongly set (by eclipse) to heber ...


Mon, 26 Apr 2010 16:35:42 GMT Frederik Heber <heber@…> [b8c9d8]
	* src/World.cpp (modified)

	Merge branch 'FixWorld_differentdefaultcell_size' into ...


Mon, 26 Apr 2010 16:34:22 GMT Frederik Heber <heber@…> [fd179f]
	* src/World.cpp (modified)

	FIX: cell_size in World has not been set to a default size, i.e. has ...


Mon, 26 Apr 2010 16:22:17 GMT Frederik Heber <heber@…> [6cd16b]
	* src/unittests/analysisbondsunittest.cpp (modified)

	Merge branch 'FixAnalysisBonds_carbonwrongZ' into ...


Mon, 26 Apr 2010 16:19:32 GMT Frederik Heber <heber@…> [6056f1]
	* src/unittests/analysisbondsunittest.cpp (modified)

	FIX: AnalysisBondsUnitTests has been broken due to Z of carbon same ...


Mon, 26 Apr 2010 16:13:02 GMT Frederik Heber <heber@…> [fe6c3e]
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)

	Merge branch 'FixAnalysisCorrelation_zeroinitallbins' into ...


Mon, 26 Apr 2010 16:11:23 GMT Frederik Heber <heber@…> [3d9df5]
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)

	FIX: AnalysisCorrelationToPointUnitTest has been broken due to init ...


Mon, 26 Apr 2010 16:04:41 GMT Frederik Heber <heber@…> [3b9e34]
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)

	Merge branch 'FixAnalysisCorrelation_zeroinitallbins' into ...


Mon, 26 Apr 2010 16:00:24 GMT Frederik Heber <heber@…> [c6394d]
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)

	FIX: AnalysisCorrelationToSurfaceUnitTest has been broken since ...


Mon, 26 Apr 2010 15:47:54 GMT Frederik Heber <heber@…> [ee7e25]
	* src/molecule_graph.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/bondgraphunittest.hpp (modified)

	Merge branch 'FixBondGraphUnitTest_hydrogencarbon' into ...


Mon, 26 Apr 2010 15:42:45 GMT Frederik Heber <heber@…> [e5ad5c]
	* src/molecule_graph.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/bondgraphunittest.hpp (modified)

	BUGFIX: BondGraphUnitTest was not working.

	Changes:
	 - atoms are ...


Mon, 26 Apr 2010 13:49:59 GMT Tillmann Crueger <crueger@…> [13d5a9]
	* src/Actions/small_actions.cpp (modified)
	* src/Helpers/Assert.cpp (modified)
	* src/Helpers/Assert.hpp (modified)

	Added macros that allow type safe casting using the Assert mechanism


Sun, 25 Apr 2010 13:36:17 GMT Tillmann Crueger <crueger@…> [8bb2fd]
	* src/Helpers/Assert.hpp (modified)

	FIX: Repaired some of the NDEBUG macros for ASSERT


Sun, 25 Apr 2010 13:16:09 GMT Tillmann Crueger <crueger@…> [8de8f7]
	* src/UIElements/TextDialog.cpp (modified)

	Made the input methods more robust to invalid inputs.


Sun, 25 Apr 2010 12:48:24 GMT Tillmann Crueger <crueger@…> [033a05]
	* src/Helpers/Assert.hpp (modified)
	* src/Patterns/Observer.cpp (modified)
	* src/Patterns/Observer.hpp (modified)
	* src/unittests/ObserverTest.cpp (modified)

	Small improvements to Observer code


Sat, 24 Apr 2010 15:27:00 GMT Tillmann Crueger <crueger@…> [ccacba]
	* src/Helpers/Assert.hpp (modified)
	* src/Patterns/Observer.cpp (modified)
	* src/Patterns/Observer.hpp (modified)
	* src/unittests/ObserverTest.cpp (modified)
	* src/unittests/ObserverTest.hpp (modified)

	Added methods for specialized Notifications from the Observer
	Framework


Fri, 23 Apr 2010 08:09:40 GMT Frederik Heber <heber@…> [b5c2d7]
	* src/boundary.cpp (modified)

	Don't exit when no starting triangle has been found.

	- The issue is ...


Thu, 22 Apr 2010 20:09:48 GMT Frederik Heber <heber@…> [b1a6d8]
	* src/tesselation.cpp (modified)

	BUGFIX in Tesselation::FindThirdPointForTesselation() - ThirdPoint of ...


Thu, 22 Apr 2010 15:47:22 GMT Frederik Heber <heber@…> [ce70970]
	* src/boundary.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	FIX: Tesselation::FindStartingTriangle() returns false when no ...


Thu, 22 Apr 2010 15:03:42 GMT Frederik Heber <heber@…> [cfe56d]
	* src/tesselation.cpp (modified)

	BUGFIX of Tesselation::FindStartingTriangle() - second Point ...


Thu, 22 Apr 2010 14:13:32 GMT Frederik Heber <heber@…> [b0a5f1]
	* src/tesselation.cpp (modified)

	BUGFIX of Tesselation::AddTesselationLine() - comparing Vector ...


Thu, 22 Apr 2010 14:10:08 GMT Frederik Heber <heber@…> [620a3f]
	* src/tesselation.cpp (modified)

	BUGFIX in Tesselation::FindThirdPointForTesselation() - regarding ...


Thu, 22 Apr 2010 14:07:14 GMT Frederik Heber <heber@…> [f04f11]
	* src/tesselation.cpp (modified)

	small changes to tesselation.

	- ...


Thu, 22 Apr 2010 14:05:32 GMT Frederik Heber <heber@…> [b40a93]
	* src/boundary.cpp (modified)

	FindNonConvexBorder(): Instead of listing all open lines, just list ...


Thu, 22 Apr 2010 14:02:09 GMT Frederik Heber <heber@…> [299554]
	* src/tesselationhelpers.cpp (modified)

	Changed verbosity of "sum of angle"-warning in ...


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(.) ...


Wed, 21 Apr 2010 12:07:01 GMT Frederik Heber <heber@…> [6613ec]
	* src/boundary.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Rewrite of tesselation: treatment of degenerated triangles and ...


Wed, 21 Apr 2010 11:46:40 GMT Frederik Heber <heber@…> [bc84ffc]
	* src/moleculelist.cpp (modified)
	* src/triangleintersectionlist.cpp (modified)
	* src/vector.cpp (modified)

	Made some remaining cout's "info Log() << Verbose(.)"'s ...

	- ...


Wed, 21 Apr 2010 11:42:54 GMT Frederik Heber <heber@…> [90f680]
	* src/errorlogger.cpp (modified)
	* src/log.cpp (modified)
	* src/verbose.cpp (modified)
	* src/verbose.hpp (modified)

	FIX: errorLogger now has absolute verbosity (i.e. CRITIAL is whatever ...


Tue, 20 Apr 2010 12:20:10 GMT Frederik Heber <heber@…> [711ac2]
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Memory leak fixes and code cleanup after tesselation rewrite.

	- ...


Tue, 20 Apr 2010 12:19:24 GMT Frederik Heber <heber@…> [a26ca5]
	* src/bondgraph.cpp (modified)

	Fixed a warning in BondGraph::LoadBondLengthTable() due to missing ...


Tue, 20 Apr 2010 10:35:15 GMT Frederik Heber <heber@…> [b60a29]
	* src/tesselationhelpers.cpp (modified)

	WriteTecplotFile() checked whether Tesselation::LastTriangle is not
	NULL.


Tue, 20 Apr 2010 10:34:43 GMT Frederik Heber <heber@…> [f07f86d]
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Rewrite of tesselation procedure: treatment of degenerated triangles. ...


Tue, 20 Apr 2010 09:21:51 GMT Frederik Heber <heber@…> [061b06]
	* src/linkedcell.cpp (modified)

	BUGFIXES: LinkedCell::SetIndexToNode() had wrong boundaries in zero ...


Fri, 16 Apr 2010 13:52:20 GMT Frederik Heber <heber@…> [d5fea7]
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	FIX: If multiple open lines can be chosen in AddTesselationLine(), ...


Fri, 16 Apr 2010 12:26:16 GMT Frederik Heber <heber@…> [474961]
	* src/boundary.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)

	New approach to degenerated triangles: Recognize on creation and add ...


Thu, 15 Apr 2010 15:22:51 GMT Frederik Heber <heber@…> [ebb50e]
	* src/boundary.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)

	Renamed AddCandidateTriangle() -> AddCandidatePolygon()

	- ...


Thu, 15 Apr 2010 15:01:27 GMT Frederik Heber <heber@…> [bc3f2a]
	* src/World.cpp (modified)

	FIX: string instead of string.h was included for strcpy()


Thu, 15 Apr 2010 13:17:15 GMT Tillmann Crueger <crueger@…> [8a34392]
	* src/Actions/Action.hpp (modified)

	Improved documentation for the Action pattern


Mon, 12 Apr 2010 16:45:07 GMT Frederik Heber <heber@…> [f8bd7d]
	* src/boundary.cpp (modified)

	FIX: changed the order in which triangles are picked next during ...


Mon, 12 Apr 2010 16:44:29 GMT Frederik Heber <heber@…> [09898c]
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Changes to BoundaryTriangleSet and CandidateForTesselation.

	- ...


Mon, 12 Apr 2010 16:25:50 GMT Frederik Heber <heber@…> [ffe885]
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)

	BUGFIX: LinkedCell::GetPointsInsideSphere() did not work if center of ...


Fri, 09 Apr 2010 13:41:52 GMT Frederik Heber <heber@…> [4f9e47]
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.hpp (modified)

	Full-working LinkedCellUnitTest.

	- new unit test for class ...


Fri, 09 Apr 2010 13:41:26 GMT Frederik Heber <heber@…> [a3696f]
	* src/atom_particleinfo.cpp (modified)

	ofstream operators now check for Name being NULL and print NULL in ...


Fri, 09 Apr 2010 13:39:03 GMT Frederik Heber <heber@…> [893bea]
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)

	changes to LinkedCell::GetNeighbourBounds(), ...


Fri, 09 Apr 2010 10:14:20 GMT heber <heber@…> [dcea0f]
	* src/unittests/LinkedCellUnitTest.cpp (added)
	* src/unittests/LinkedCellUnitTest.hpp (added)
	* src/unittests/Makefile.am (modified)

	New Unit test for class LinkedCell.

	- this is just the skeleton, so ...


Fri, 09 Apr 2010 09:55:39 GMT heber <heber@…> [734816]
	* src/boundary.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.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)

	LinkedNodes is now declared inside LinkedCell and some new functions. ...


Thu, 08 Apr 2010 14:28:21 GMT Tillmann Crueger <crueger@…> [a295d1]
	* src/Actions/Action.hpp (modified)

	More documentation for Action class added


Thu, 08 Apr 2010 14:00:11 GMT Tillmann Crueger <crueger@…> [2efa90]
	* src/Actions/Action.cpp (modified)
	* src/Actions/Action.hpp (modified)
	* src/Actions/ActionHistory.cpp (modified)
	* src/Actions/ActionSequence.cpp (modified)
	* src/Actions/ActionSequence.hpp (modified)
	* src/Actions/MakroAction.cpp (modified)
	* src/Actions/Process.cpp (modified)
	* src/Actions/Process.hpp (modified)
	* src/unittests/ActionSequenceTest.cpp (modified)

	Added detailed documentation for the Action class


Thu, 01 Apr 2010 18:52:09 GMT Frederik Heber <heber@…> [fe238c]
	* src/analysis_bonds.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)

	Enhanced CountHydrogenBridgeBonds() a bit.

	- new functions ...


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, 01 Apr 2010 09:35:42 GMT Frederik Heber <heber@…> [62c9c0]
	* src/unittests/CountBondsUnitTest.cpp (modified)

	Added output of test cases for visualization. Is commented out ...


Tue, 30 Mar 2010 18:52:14 GMT Frederik Heber <heber@…> [dfe8ef]
	* src/bondgraph.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (added)
	* src/unittests/CountBondsUnitTest.hpp (added)
	* src/unittests/Makefile.am (modified)

	BUGFIX: CountHydrogenBridgeBonds() was half-broken, ...


Fri, 26 Mar 2010 15:13:31 GMT Tillmann Crueger <crueger@…> [f9352d]
	* src/Actions/Action.cpp (modified)
	* src/Actions/Action.hpp (modified)
	* src/Actions/ActionHistory.cpp (modified)
	* src/Actions/ActionHistory.hpp (modified)
	* src/Menu/ActionMenuItem.cpp (modified)
	* src/Menu/ActionMenuItem.hpp (modified)
	* src/Menu/MenuItem.cpp (modified)
	* src/Menu/MenuItem.hpp (modified)
	* src/Menu/TextMenu.cpp (modified)

	Added mechanism that deactivates undo and redo menupoint if not ...


Thu, 25 Mar 2010 13:08:39 GMT Tillmann Crueger <crueger@…> [f6bbc6]
	* src/UIElements/TextWindow.cpp (modified)

	Added undo and redo menupoints

	TODO: make it possible to disable ...


Thu, 25 Mar 2010 13:01:35 GMT Tillmann Crueger <crueger@…> [5605032]
	* src/UIElements/Dialog.cpp (modified)
	* src/UIElements/Dialog.hpp (modified)
	* src/UIElements/TextDialog.cpp (modified)
	* src/UIElements/TextDialog.hpp (modified)

	Repaired code that was broken by merge


Thu, 25 Mar 2010 13:00:29 GMT Tillmann Crueger <crueger@…> [9848ba]
	* src/unittests/manipulateAtomsTest.cpp (modified)

	Merge branch 'StructureRefactoring' into MenuRefactoring


Thu, 25 Mar 2010 12:59:20 GMT Tillmann Crueger <crueger@…> [975a11]
	* src/unittests/manipulateAtomsTest.cpp (modified)

	Repaired broken unittest


Thu, 25 Mar 2010 12:01:58 GMT Tillmann Crueger <crueger@…> [b31bc4]
	* src/Actions/Action.cpp (modified)
	* src/Actions/Action.hpp (modified)
	* src/Actions/ActionHistory.cpp (added)
	* src/Actions/ActionHistory.hpp (added)
	* src/Actions/ActionRegistry.cpp (modified)
	* src/Actions/ActionRegistry.hpp (modified)
	* src/Actions/ActionSequence.cpp (modified)
	* src/Actions/ActionSequence.hpp (modified)
	* src/Actions/AtomsCalculation_impl.hpp (modified)
	* src/Actions/Calculation.hpp (modified)
	* src/Actions/Calculation_impl.hpp (modified)
	* src/Actions/ErrorAction.cpp (modified)
	* src/Actions/ErrorAction.hpp (modified)
	* src/Actions/MakroAction.cpp (modified)
	* src/Actions/MakroAction.hpp (modified)
	* src/Actions/ManipulateAtomsProcess.cpp (modified)
	* src/Actions/ManipulateAtomsProcess.hpp (modified)
	* src/Actions/MethodAction.cpp (modified)
	* src/Actions/MethodAction.hpp (modified)
	* src/Actions/small_actions.cpp (modified)
	* src/Actions/small_actions.hpp (modified)
	* src/Descriptors/AtomDescriptor.cpp (modified)
	* src/Descriptors/AtomDescriptor.hpp (modified)
	* src/Descriptors/AtomTypeDescriptor.cpp (modified)
	* src/Descriptors/AtomTypeDescriptor.hpp (modified)
	* src/Descriptors/AtomTypeDescriptor_impl.hpp (modified)
	* src/Descriptors/DescriptorBase.hpp (added)
	* src/Descriptors/DescriptorBase_impl.hpp (added)
	* src/Descriptors/MoleculeDescriptor.cpp (modified)
	* src/Descriptors/MoleculeDescriptor.hpp (modified)
	* src/Descriptors/SelectiveIterator.hpp (added)
	* src/Descriptors/SelectiveIterator_impl.hpp (added)
	* src/Helpers/Assert.cpp (added)
	* src/Helpers/Assert.hpp (added)
	* src/Legacy/oldmenu.cpp (modified)
	* src/Makefile.am (modified)
	* src/Menu/TextMenu.cpp (modified)
	* src/Menu/TextMenu.hpp (modified)
	* src/Patterns/Cacheable.hpp (modified)
	* src/Patterns/Observer.cpp (modified)
	* src/Patterns/Observer.hpp (modified)
	* src/Patterns/Singleton.hpp (added)
	* src/Patterns/Singleton_impl.hpp (added)
	* src/UIElements/TextWindow.cpp (modified)
	* src/UIElements/TextWindow.hpp (modified)
	* src/UIElements/UIFactory.cpp (modified)
	* src/UIElements/UIFactory.hpp (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/WorldIterators.cpp (deleted)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/defs.hpp (modified)
	* src/element.cpp (modified)
	* src/element.hpp (modified)
	* src/errorlogger.cpp (modified)
	* src/errorlogger.hpp (modified)
	* src/helpers.hpp (modified)
	* src/leastsquaremin.hpp (modified)
	* src/log.cpp (modified)
	* src/logger.cpp (modified)
	* src/logger.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/types.hpp (added)
	* src/unittests/ActionSequenceTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/AtomDescriptorTest.cpp (modified)
	* src/unittests/AtomDescriptorTest.hpp (modified)
	* src/unittests/CacheableTest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/MoleculeDescriptorTest.cpp (modified)
	* src/unittests/MoleculeDescriptorTest.hpp (modified)
	* src/unittests/ObserverTest.cpp (modified)
	* src/unittests/ObserverTest.hpp (modified)
	* src/unittests/SingletonTest.cpp (added)
	* src/unittests/SingletonTest.hpp (added)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* src/unittests/atomsCalculationTest.hpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/logunittest.cpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)

	Merge branch 'StructureRefactoring' into MenuRefactoring


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


Thu, 25 Mar 2010 10:06:49 GMT Tillmann Crueger <crueger@…> [5b0b98]
	* src/Actions/Action.cpp (modified)
	* src/Actions/Action.hpp (modified)
	* src/Actions/ActionSequence.cpp (modified)
	* src/Actions/ActionSequence.hpp (modified)
	* src/Actions/Calculation.hpp (modified)
	* src/Actions/Calculation_impl.hpp (modified)
	* src/Actions/ErrorAction.cpp (modified)
	* src/Actions/ErrorAction.hpp (modified)
	* src/Actions/MakroAction.cpp (modified)
	* src/Actions/MakroAction.hpp (modified)
	* src/Actions/ManipulateAtomsProcess.cpp (modified)
	* src/Actions/ManipulateAtomsProcess.hpp (modified)
	* src/Actions/MethodAction.cpp (modified)
	* src/Actions/MethodAction.hpp (modified)
	* src/Actions/small_actions.cpp (modified)
	* src/Actions/small_actions.hpp (modified)
	* src/UIElements/TextDialog.cpp (modified)
	* src/unittests/ActionSequenceTest.cpp (modified)

	Switched type of pointer used for ActionStates


Wed, 24 Mar 2010 16:26:21 GMT Tillmann Crueger <crueger@…> [67e2b3]
	* src/Actions/Action.cpp (modified)
	* src/Actions/Action.hpp (modified)
	* src/Actions/ActionSequence.cpp (modified)
	* src/Actions/ActionSequence.hpp (modified)
	* src/Actions/Calculation.hpp (modified)
	* src/Actions/Calculation_impl.hpp (modified)
	* src/Actions/ErrorAction.cpp (modified)
	* src/Actions/ErrorAction.hpp (modified)
	* src/Actions/MakroAction.cpp (modified)
	* src/Actions/MakroAction.hpp (modified)
	* src/Actions/ManipulateAtomsProcess.cpp (modified)
	* src/Actions/ManipulateAtomsProcess.hpp (modified)
	* src/Actions/MethodAction.cpp (modified)
	* src/Actions/MethodAction.hpp (modified)
	* src/Actions/small_actions.cpp (modified)
	* src/Actions/small_actions.hpp (modified)
	* src/unittests/ActionSequenceTest.cpp (modified)

	Added methods that allow bookkeeping of actions for undo/redo methods


Wed, 24 Mar 2010 10:27:37 GMT Tillmann Crueger <crueger@…> [ce1d8c]
	* src/Helpers/Assert.hpp (modified)

	Added detailed instruction on how to use ASSERT()


Fri, 19 Mar 2010 16:55:28 GMT Tillmann Crueger <crueger@…> [adc42b]
	* src/Patterns/Cacheable.hpp (modified)

	Made the cacheable always recalculate when the owner is in the ...


Fri, 19 Mar 2010 16:44:08 GMT Tillmann Crueger <crueger@…> [4fb5a3]
	* src/Patterns/Observer.cpp (modified)
	* src/Patterns/Observer.hpp (modified)
	* src/unittests/ObserverTest.cpp (modified)
	* src/unittests/ObserverTest.hpp (modified)

	Improved Observer Framework to include methods to report the state
 ...


Fri, 19 Mar 2010 16:40:04 GMT Tillmann Crueger <crueger@…> [052b8d0]
	* src/Patterns/Cacheable.hpp (modified)

	Rebuilt Cacheables using the state pattern


Fri, 19 Mar 2010 16:30:57 GMT Tillmann Crueger <crueger@…> [5be0eb]
	* src/Helpers/Assert.cpp (modified)
	* src/Helpers/Assert.hpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)

	Added more functionality to custom asserts.

	- Asserts allow now ...


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 ...


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 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 11:39:57 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 11:39:21 GMT Frederik Heber <heber@…> [b48ba6]
	* src/bondgraph.hpp (modified)
	* src/defs.hpp (modified)

	Shifted BONDTHRESHOLD from defs.hpp over to bondgraph.hpp and lowered ...


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 ...


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.

	- ...


Thu, 18 Mar 2010 10:21:13 GMT Frederik Heber <heber@…> [7ee87f]
	* src/World.cpp (modified)

	BUGFIX: DefaultName of molecule was too small an array.

	- We saw ...


Wed, 17 Mar 2010 15:19:56 GMT Tillmann Crueger <crueger@…> [6e97e5]
	* src/Actions/AtomsCalculation_impl.hpp (modified)
	* src/Actions/ManipulateAtomsProcess.cpp (modified)
	* src/Actions/ManipulateAtomsProcess.hpp (modified)
	* src/Descriptors/AtomDescriptor.hpp (modified)
	* src/Descriptors/DescriptorBase.hpp (added)
	* src/Descriptors/DescriptorBase_impl.hpp (added)
	* src/Descriptors/MoleculeDescriptor.hpp (modified)
	* src/Descriptors/SelectiveIterator.hpp (added)
	* src/Descriptors/SelectiveIterator_impl.hpp (added)
	* src/Makefile.am (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/WorldIterators.cpp (deleted)
	* src/helpers.hpp (modified)
	* src/unittests/AtomDescriptorTest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)

	Added a generic Iterator that can be used to iterate only over ...


Fri, 12 Mar 2010 14:20:15 GMT Tillmann Crueger <crueger@…> [745a85]
	* src/periodentafel.cpp (modified)

	Fixed memory leak in periodentafel


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 16:53:08 GMT Tillmann Crueger <crueger@…> [c3dbe0]
	* src/Patterns/Singleton.hpp (modified)

	Improved documentation for Singleton


Thu, 11 Mar 2010 15:17:29 GMT Tillmann Crueger <crueger@…> [0f6f3a]
	* src/Patterns/Singleton.hpp (modified)
	* src/Patterns/Singleton_impl.hpp (modified)
	* src/unittests/SingletonTest.cpp (modified)

	Small improvements to singleton pattern


Thu, 11 Mar 2010 14:29:04 GMT Tillmann Crueger <crueger@…> [ed58ad]
	* src/errorlogger.cpp (modified)
	* src/errorlogger.hpp (modified)
	* src/log.cpp (modified)

	Made the errorLogger use the new Singleton framework


Thu, 11 Mar 2010 14:19:53 GMT Tillmann Crueger <crueger@…> [aee1a3]
	* src/Makefile.am (modified)
	* src/log.cpp (modified)
	* src/logger.cpp (modified)
	* src/logger.hpp (modified)
	* src/unittests/logunittest.cpp (modified)

	Made logger class use the new Singleton framework


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 11:32:17 GMT Tillmann Crueger <crueger@…> [7ca806]
	* src/Patterns/Singleton.hpp (modified)
	* src/Patterns/Singleton_impl.hpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)

	Changed the mutex type used in the Singleton pattern to allow ...


Thu, 11 Mar 2010 11:21:55 GMT Tillmann Crueger <crueger@…> [d25863]
	* src/unittests/SingletonTest.cpp (added)
	* src/unittests/SingletonTest.hpp (added)

	Added Unittest for Singleton pattern


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 ...


Thu, 04 Mar 2010 16:03:57 GMT Tillmann Crueger <crueger@…> [31af19]
	* src/World.hpp (modified)

	Made the World Iterators conform to STL-Structure


Thu, 04 Mar 2010 14:57:48 GMT Frederik Heber <heber@…> [6e6e10]
	* src/config.cpp (modified)

	BUGFIX: config::SaveTREMOLO() - TREMOLO does not like particle Id 0
 ...


Thu, 04 Mar 2010 10:34:52 GMT Tillmann Crueger <crueger@…> [66e95e]
	* src/Actions/Calculation.hpp (modified)
	* src/Actions/Process.cpp (modified)
	* src/Actions/Process.hpp (modified)
	* src/Descriptors/AtomDescriptor.hpp (modified)
	* src/Descriptors/AtomDescriptor_impl.hpp (modified)
	* src/Descriptors/MoleculeDescriptor.cpp (added)
	* src/Descriptors/MoleculeDescriptor.hpp (added)
	* src/Descriptors/MoleculeDescriptor_impl.hpp (added)
	* src/Descriptors/MoleculeIdDescriptor.cpp (added)
	* src/Descriptors/MoleculeIdDescriptor.hpp (added)
	* src/Descriptors/MoleculeIdDescriptor_impl.hpp (added)
	* src/Makefile.am (modified)
	* src/Patterns/Observer.hpp (modified)
	* src/UIElements/MainWindow.hpp (modified)
	* src/UIElements/UIFactory.hpp (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/WorldIterators.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule_template.hpp (modified)
	* src/unittests/AtomDescriptorTest.cpp (moved)
	* src/unittests/AtomDescriptorTest.hpp (moved)
	* src/unittests/Makefile.am (modified)
	* src/unittests/MoleculeDescriptorTest.cpp (added)
	* src/unittests/MoleculeDescriptorTest.hpp (added)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)

	Merge branch 'StructureRefactoring' into MenuRefactoring


Thu, 04 Mar 2010 10:33:44 GMT Tillmann Crueger <crueger@…> [57adc7]
	* src/Descriptors/MoleculeIdDescriptor.cpp (added)
	* src/Descriptors/MoleculeIdDescriptor.hpp (added)
	* src/Descriptors/MoleculeIdDescriptor_impl.hpp (added)
	* src/Makefile.am (modified)
	* src/World.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/unittests/AtomDescriptorTest.cpp (moved)
	* src/unittests/AtomDescriptorTest.hpp (moved)
	* src/unittests/Makefile.am (modified)
	* src/unittests/MoleculeDescriptorTest.cpp (added)
	* src/unittests/MoleculeDescriptorTest.hpp (added)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)

	Added methods to query Molecules by ID


Wed, 03 Mar 2010 19:17:58 GMT Frederik Heber <heber@…> [70429af]
	* src/moleculelist.cpp (modified)

	Merge branch 'FixDissectIntoSubgraphs_ConstructBondGraphcheck' into ...


Wed, 03 Mar 2010 19:17:49 GMT Frederik Heber <heber@…> [f42e95]
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)

	Merge branch 'FixBinDataStartEnd' into Analysis_PairCorrelation


Wed, 03 Mar 2010 19:17:19 GMT Frederik Heber <heber@…> [6e8dc2]
	* src/linkedcell.cpp (modified)

	Merge branch 'FixLinkedCellConstructor_Setempytcheck' into ...


Wed, 03 Mar 2010 19:14:31 GMT Frederik Heber <heber@…> [85da4e]
	* src/analysis_correlation.hpp (modified)

	BUGFIX: in BinData() binmap should be initialized from start to end ...


Wed, 03 Mar 2010 19:13:43 GMT Frederik Heber <heber@…> [271e17]
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)

	Merge branch 'FixGetBin_tointeger' into FixBinDataStartEnd


Wed, 03 Mar 2010 19:10:36 GMT Frederik Heber <heber@…> [bd61b41]
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)

	BUGFIX: rounding imprecision let values appear twice in BinMap.

	- ...