#
# ChangeLog for src/unittests
#
# Generated by Trac 1.4.4
# Jan 19, 2025, 2:02:20 AM

Mon, 17 Oct 2011 16:18:55 GMT Frederik Heber <heber@…> [9d4ff35]
	* src/RandomNumbers/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Reduced library dependencies of RandomNumbers and BoxUnitTest.


Mon, 17 Oct 2011 16:18:55 GMT Frederik Heber <heber@…> [592be9]
	* src/Element/unittests/ElementUnitTest.cpp (moved)
	* src/Element/unittests/ElementUnitTest.hpp (moved)
	* src/Element/unittests/Makefile.am (added)
	* src/Element/unittests/PeriodentafelUnitTest.cpp (moved)
	* src/Element/unittests/PeriodentafelUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved unitests on Element... into subfolder src/Element/unittests.
 ...


Mon, 17 Oct 2011 16:18:54 GMT Frederik Heber <heber@…> [3bdb6d]
	* src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/Actions/AtomAction/AddAction.cpp (modified)
	* src/Actions/AtomAction/ChangeElementAction.cpp (modified)
	* src/Actions/CommandAction/ElementDbAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified)
	* src/Actions/ValueStorage.cpp (modified)
	* src/Analysis/analysis_bonds.cpp (modified)
	* src/Analysis/analysis_correlation.cpp (modified)
	* src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified)
	* src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/Analysis/unittests/CountBondsUnitTest.cpp (modified)
	* src/AtomicInfo.cpp (modified)
	* src/Bond/bond.cpp (modified)
	* src/Descriptors/AtomTypeDescriptor.cpp (modified)
	* src/Dynamics/MinimiseConstrainedPotential.cpp (modified)
	* src/Element/Hbondangle.db (moved)
	* src/Element/Hbonddistance.db (moved)
	* src/Element/Makefile.am (added)
	* src/Element/element.cpp (moved)
	* src/Element/element.hpp (moved)
	* src/Element/elements.db (moved)
	* src/Element/elements_db.cpp (moved)
	* src/Element/elements_db.hpp (moved)
	* src/Element/orbitals.db (moved)
	* src/Element/periodentafel.cpp (moved)
	* src/Element/periodentafel.hpp (moved)
	* src/Element/valence.db (moved)
	* src/Formula.cpp (modified)
	* src/Fragmentation/analyzer.cpp (modified)
	* src/Fragmentation/joiner.cpp (modified)
	* src/Graph/BondGraph.cpp (modified)
	* src/Graph/BondGraph.hpp (modified)
	* src/Graph/CyclicStructureAnalysis.cpp (modified)
	* src/Graph/unittests/BondGraphUnitTest.cpp (modified)
	* src/Makefile.am (modified)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/Parser/unittests/ParserMpqcUnitTest.cpp (modified)
	* src/Parser/unittests/ParserPcpUnitTest.cpp (modified)
	* src/Parser/unittests/ParserPdbUnitTest.cpp (modified)
	* src/Parser/unittests/ParserTremoloUnitTest.cpp (modified)
	* src/Parser/unittests/ParserXyzUnitTest.cpp (modified)
	* src/Tesselation/boundary.cpp (modified)
	* src/Thermostats/Berendsen.cpp (modified)
	* src/Thermostats/GaussianThermostat.cpp (modified)
	* src/Thermostats/Langevin.cpp (modified)
	* src/Thermostats/NoseHoover.cpp (modified)
	* src/Thermostats/Woodcock.cpp (modified)
	* src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified)
	* src/UIElements/Makefile.am (modified)
	* src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified)
	* src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified)
	* src/UIElements/TextUI/TextWindow.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified)
	* src/World.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/builder_init.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/unittests/ElementUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/PeriodentafelUnitTest.cpp (modified)

	Moved all stuff related to elements into own subfolder and has its ...


Mon, 17 Oct 2011 16:18:42 GMT Frederik Heber <heber@…> [9b5a2c]
	* src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/Analysis/Makefile.am (added)
	* src/Analysis/analysis_bonds.cpp (moved)
	* src/Analysis/analysis_bonds.hpp (moved)
	* src/Analysis/analysis_correlation.cpp (moved)
	* src/Analysis/analysis_correlation.hpp (moved)
	* src/Analysis/unittests/AnalysisBondsUnitTest.cpp (moved)
	* src/Analysis/unittests/AnalysisBondsUnitTest.hpp (moved)
	* src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (moved)
	* src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp (moved)
	* src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (moved)
	* src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (moved)
	* src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (moved)
	* src/Analysis/unittests/AnalysisPairCorrelationUnitTest.hpp (moved)
	* src/Analysis/unittests/CountBondsUnitTest.cpp (moved)
	* src/Analysis/unittests/CountBondsUnitTest.hpp (moved)
	* src/Analysis/unittests/Makefile.am (added)
	* src/Makefile.am (modified)
	* src/UIElements/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Moved analysis modules into subfolder Analysis along with its unit ...


Fri, 14 Oct 2011 14:08:41 GMT Frederik Heber <heber@…> [629e43]
	* src/Graph/unittests/BondGraphUnitTest.cpp (moved)
	* src/Graph/unittests/BondGraphUnitTest.hpp (moved)
	* src/Graph/unittests/Makefile.am (added)
	* src/unittests/Makefile.am (modified)

	Moved unitests on BondGraph into subfolder src/Graph/unittests.

	- ...


Thu, 13 Oct 2011 19:00:47 GMT Frederik Heber <heber@…> [0b004b]
	* src/Tesselation/unittests/Makefile.am (added)
	* src/Tesselation/unittests/TesselationUnitTest.cpp (moved)
	* src/Tesselation/unittests/TesselationUnitTest.hpp (moved)
	* src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (moved)
	* src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (moved)
	* src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (moved)
	* src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved all unittests on Tesselation into subfolder ...


Thu, 13 Oct 2011 19:00:47 GMT Frederik Heber <heber@…> [d127c8]
	* src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified)
	* src/Makefile.am (modified)
	* src/PointCloudAdaptor.hpp (modified)
	* src/Tesselation/BoundaryLineSet.cpp (moved)
	* src/Tesselation/BoundaryLineSet.hpp (moved)
	* src/Tesselation/BoundaryMaps.hpp (moved)
	* src/Tesselation/BoundaryPointSet.cpp (moved)
	* src/Tesselation/BoundaryPointSet.hpp (moved)
	* src/Tesselation/BoundaryPolygonSet.cpp (moved)
	* src/Tesselation/BoundaryPolygonSet.hpp (moved)
	* src/Tesselation/BoundaryTriangleSet.cpp (moved)
	* src/Tesselation/BoundaryTriangleSet.hpp (moved)
	* src/Tesselation/CandidateForTesselation.cpp (moved)
	* src/Tesselation/CandidateForTesselation.hpp (moved)
	* src/Tesselation/TesselPoint.cpp (moved)
	* src/Tesselation/TesselPoint.hpp (moved)
	* src/Tesselation/boundary.cpp (moved)
	* src/Tesselation/boundary.hpp (moved)
	* src/Tesselation/ellipsoid.cpp (moved)
	* src/Tesselation/ellipsoid.hpp (moved)
	* src/Tesselation/tesselation.cpp (moved)
	* src/Tesselation/tesselation.hpp (moved)
	* src/Tesselation/tesselationhelpers.cpp (moved)
	* src/Tesselation/tesselationhelpers.hpp (moved)
	* src/Tesselation/triangleintersectionlist.cpp (moved)
	* src/Tesselation/triangleintersectionlist.hpp (moved)
	* src/analysis_correlation.cpp (modified)
	* src/atom.hpp (modified)
	* src/builder_init.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/molecule.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/TesselationUnitTest.cpp (modified)
	* src/unittests/TesselationUnitTest.hpp (modified)
	* src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified)
	* src/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified)

	Moved modules related to Tesselation into own source subfolder.

	- ...


Thu, 13 Oct 2011 19:00:47 GMT Frederik Heber <heber@…> [feb7df]
	* src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (added)
	* src/Fragmentation/unittests/KeySetsContainerUnitTest.hpp (added)
	* src/Fragmentation/unittests/Makefile.am (added)
	* src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (added)
	* src/Fragmentation/unittests/MatrixContainerUnitTest.hpp (added)
	* src/unittests/Makefile.am (modified)

	Added unittests to Fragmentation subfolder.

	- added empty tests for ...


Wed, 12 Oct 2011 14:10:51 GMT Frederik Heber <heber@…> [220cf64]
	* src/Actions/CommandAction/ElementDbAction.cpp (modified)
	* src/Actions/CommandAction/ElementDbAction.def (modified)
	* src/Actions/CommandAction/ElementDbAction.hpp (modified)
	* src/unittests/PeriodentafelUnitTest.hpp (modified)
	* tests/regression/Options/ElementsDb/pre/test.conf (added)
	* tests/regression/Options/ElementsDb/testsuite-options-elements-db.at (modified)

	Added Undo/Redo capability to ElementDbAction.

	- thanks to ...


Mon, 10 Oct 2011 16:58:25 GMT Frederik Heber <heber@…> [b60804]
	* src/analyzer.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/unittests/PeriodentafelUnitTest.cpp (modified)
	* src/unittests/PeriodentafelUnitTest.hpp (modified)

	Added serialization to class periodentafel.

	- added unit test on ...


Mon, 10 Oct 2011 16:58:25 GMT Frederik Heber <heber@…> [d7d022]
	* configure.ac (modified)
	* src/UIElements/Makefile.am (modified)
	* src/element.cpp (modified)
	* src/element.hpp (modified)
	* src/unittests/ElementUnitTest.cpp (added)
	* src/unittests/ElementUnitTest.hpp (added)
	* src/unittests/Makefile.am (modified)

	Added serialization functionality to class element.

	- also added ...


Mon, 10 Oct 2011 16:58:24 GMT Frederik Heber <heber@…> [f08ae7]
	* LinearAlgebra/configure.ac (modified)
	* LinearAlgebra/src/LinearAlgebra/Makefile.am (modified)
	* LinearAlgebra/src/unittests/Makefile.am (modified)
	* configure.ac (modified)
	* m4/ax_codepatterns.m4 (modified)
	* m4/boost.m4 (modified)
	* src/Actions/unittests/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/RandomNumbers/Makefile.am (modified)
	* src/RandomNumbers/unittests/Makefile.am (modified)
	* src/UIElements/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Extension of usage of Tsuna's boost.m4 macro.

	- boost.m4 from ...


Thu, 06 Oct 2011 16:06:10 GMT Frederik Heber <heber@…> [5e2f80]
	* src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/CopyAction.cpp (modified)
	* src/Graph/BondGraph.hpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/atom_bondedparticleinfo.cpp (modified)
	* src/atom_bondedparticleinfo.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)

	BondedParticle no more hands out non-const ListOfBonds.

	- the few ...


Thu, 06 Oct 2011 09:16:19 GMT Frederik Heber <heber@…> [064178]
	* src/Helpers/defs.cpp (modified)
	* src/Helpers/defs.hpp (modified)
	* src/element.cpp (modified)
	* src/element.hpp (modified)
	* src/elements_db.cpp (modified)
	* src/elements_db.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/unittests/PeriodentafelUnitTest.cpp (modified)

	Added color database to periodentafel.

	- ...


Fri, 30 Sep 2011 08:19:37 GMT Frederik Heber <heber@…> [79de12]
	* LinearAlgebra/configure.ac (modified)
	* LinearAlgebra/src/unittests/Makefile.am (modified)
	* configure.ac (modified)
	* m4/ax_boost_base.m4 (deleted)
	* m4/ax_boost_filesystem.m4 (deleted)
	* m4/ax_boost_program_options.m4 (deleted)
	* m4/ax_boost_system.m4 (deleted)
	* m4/ax_codepatterns.m4 (modified)
	* m4/boost.m4 (added)
	* m4/m4_ax_boost_thread.m4 (deleted)
	* src/Descriptors/unittests/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/Parser/unittests/Makefile.am (modified)
	* src/RandomNumbers/unittests/Makefile.am (modified)
	* src/Shapes/unittests/Makefile.am (modified)
	* src/UIElements/CommandLineUI/unittests/Makefile.am (modified)
	* src/UIElements/Makefile.am (modified)
	* src/UIElements/Menu/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Replaced *_boost_*.m4 by boost.m4 from tsuna.

	- ...


Thu, 21 Apr 2011 16:39:45 GMT Frederik Heber <heber@…> [fdcd1b]
	* src/Actions/unittests/ActionSequenceUnitTest.cpp (modified)
	* src/Actions/unittests/Makefile.am (modified)
	* src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified)
	* src/Actions/unittests/stubs/DummyUI.hpp (moved)

	Moved DummyUI.hpp from unittests to Actions/unittests/stubs.

	- note ...


Thu, 21 Apr 2011 16:34:18 GMT Frederik Heber <heber@…> [1e882a]
	* src/unittests/Makefile.am (modified)

	DISTFIX: Removed unnecessary header file analysis_correlation.hpp in ...


Mon, 18 Apr 2011 12:45:06 GMT Frederik Heber <heber@…> [455573]
	* configure.ac (modified)
	* src/Actions/Makefile.am (modified)
	* src/Actions/unittests/ActionRegistryUnitTest.cpp (modified)
	* src/Actions/unittests/Makefile.am (modified)
	* src/Descriptors/unittests/Makefile.am (modified)
	* src/Graph/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/Parser/Makefile.am (modified)
	* src/Parser/unittests/Makefile.am (modified)
	* src/RandomNumbers/Makefile.am (modified)
	* src/RandomNumbers/unittests/Makefile.am (modified)
	* src/Shapes/Makefile.am (modified)
	* src/Shapes/unittests/Makefile.am (modified)
	* src/UIElements/CommandLineUI/unittests/Makefile.am (modified)
	* src/UIElements/Makefile.am (modified)
	* src/UIElements/Menu/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Large Commit: SUBDIRS in src/Makefile.am replaced by include.

	- ...


Fri, 08 Apr 2011 15:48:50 GMT Frederik Heber <heber@…> [bf4b9f]
	* LinearAlgebra/.gitignore (added)
	* LinearAlgebra/AUTHORS (added)
	* LinearAlgebra/COPYING (added)
	* LinearAlgebra/ChangeLog (added)
	* LinearAlgebra/INSTALL (added)
	* LinearAlgebra/LinearAlgebra-debug.pc.in (added)
	* LinearAlgebra/LinearAlgebra.pc.in (moved)
	* LinearAlgebra/Makefile.am (added)
	* LinearAlgebra/NEWS (added)
	* LinearAlgebra/README (added)
	* LinearAlgebra/bootstrap (added)
	* LinearAlgebra/build-aux/README (added)
	* LinearAlgebra/configure.ac (added)
	* LinearAlgebra/doc/Doxyfile (added)
	* LinearAlgebra/doc/Makefile.am (added)
	* LinearAlgebra/libLinearAlgebra_config.h.in (added)
	* LinearAlgebra/m4 (added)
	* LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/Exceptions.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/Line.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/Line.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/LineSegment.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/LineSegmentSet.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/Makefile.am (moved)
	* LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/Plane.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/Plane.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/Space.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/Space.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/Vector.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/Vector.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/VectorContent.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/VectorInterface.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/defs.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/fast_functions.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/leastsquaremin.hpp (moved)
	* LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (moved)
	* LinearAlgebra/src/LinearAlgebra/vector_ops.hpp (moved)
	* LinearAlgebra/src/unittests/LineUnitTest.cpp (moved)
	* LinearAlgebra/src/unittests/LineUnitTest.hpp (moved)
	* LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (moved)
	* LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.hpp (moved)
	* LinearAlgebra/src/unittests/Makefile.am (moved)
	* LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (moved)
	* LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.hpp (moved)
	* LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (moved)
	* LinearAlgebra/src/unittests/MatrixContentUnitTest.hpp (moved)
	* LinearAlgebra/src/unittests/MatrixUnitTest.cpp (moved)
	* LinearAlgebra/src/unittests/MatrixUnitTest.hpp (moved)
	* LinearAlgebra/src/unittests/PlaneUnitTest.cpp (moved)
	* LinearAlgebra/src/unittests/PlaneUnitTest.hpp (moved)
	* LinearAlgebra/src/unittests/TestRunnerMain.cpp (added)
	* LinearAlgebra/src/unittests/UnitTestMain.cpp (added)
	* LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (moved)
	* LinearAlgebra/src/unittests/VectorContentUnitTest.hpp (moved)
	* LinearAlgebra/src/unittests/VectorUnitTest.cpp (moved)
	* LinearAlgebra/src/unittests/VectorUnitTest.hpp (moved)
	* LinearAlgebra/tests/CodeChecks/Makefile.am (added)
	* LinearAlgebra/tests/CodeChecks/atlocal.in (added)
	* LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (added)
	* LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (added)
	* LinearAlgebra/tests/CodeChecks/testsuite.at (added)
	* Makefile.am (modified)
	* bootstrap (modified)
	* build-aux/README (added)
	* config/depcomp (deleted)
	* config/install-sh (deleted)
	* config/ltmain.sh (deleted)
	* config/missing (deleted)
	* configure.ac (modified)
	* src/Actions/Makefile.am (modified)
	* src/Actions/unittests/Makefile.am (modified)
	* src/Descriptors/unittests/Makefile.am (modified)
	* src/Graph/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/Parser/Makefile.am (modified)
	* src/Parser/unittests/Makefile.am (modified)
	* src/Shapes/Makefile.am (modified)
	* src/Shapes/unittests/Makefile.am (modified)
	* src/UIElements/CommandLineUI/unittests/Makefile.am (modified)
	* src/UIElements/Makefile.am (modified)
	* src/UIElements/Menu/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Moved LinearAlgebra from folder src/ into distinct sub-package.

	- ...


Wed, 06 Apr 2011 13:50:42 GMT Frederik Heber <heber@…> [3e2225f]
	* configure.ac (modified)
	* src/Actions/unittests/Makefile.am (modified)
	* src/Descriptors/unittests/Makefile.am (modified)
	* src/Exceptions/CustomException.cpp (deleted)
	* src/Exceptions/CustomException.hpp (deleted)
	* src/Exceptions/Makefile.am (deleted)
	* src/Makefile.am (modified)
	* src/Parser/unittests/Makefile.am (modified)
	* src/Shapes/Makefile.am (modified)
	* src/Shapes/unittests/Makefile.am (modified)
	* src/UIElements/CommandLineUI/unittests/Makefile.am (modified)
	* src/UIElements/Menu/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Removed subdir Exceptions and libMolecuilderExceptions.

	- changes ...


Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber <heber@…> [255829]
	* configure.ac (modified)
	* src/BoundaryPolygonSet.cpp (modified)
	* src/ConfigFileBuffer.cpp (modified)
	* src/Dynamics/MinimiseConstrainedPotential.cpp (modified)
	* src/Dynamics/OutputTemperature.hpp (modified)
	* src/Dynamics/VerletForceIntegration.hpp (modified)
	* src/Formula.hpp (modified)
	* src/Graph/CheckAgainstAdjacencyFile.cpp (modified)
	* src/Helpers/Makefile.am (deleted)
	* src/Helpers/defs.hpp (modified)
	* src/Helpers/helpers.cpp (deleted)
	* src/Helpers/helpers.hpp (modified)
	* src/Makefile.am (modified)
	* src/Parser/unittests/ParserPcpUnitTest.cpp (modified)
	* src/Parser/unittests/ParserPdbUnitTest.cpp (modified)
	* src/Parser/unittests/ParserXyzUnitTest.cpp (modified)
	* src/Shapes/unittests/Makefile.am (modified)
	* src/Thermostats/Berendsen.cpp (modified)
	* src/Thermostats/GaussianThermostat.cpp (modified)
	* src/Thermostats/Langevin.cpp (modified)
	* src/Thermostats/NoseHoover.cpp (modified)
	* src/Thermostats/Woodcock.cpp (modified)
	* src/UIElements/Views/Qt4/QtStatusBar.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/analyzer.cpp (modified)
	* src/atom.hpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/joiner.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/parser.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/triangleintersectionlist.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/TesselationUnitTest.cpp (modified)
	* src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified)

	Removed Helpers.hpp, deleted Helpers.cpp and libMoleCuilderHelpers.la ...


Wed, 06 Apr 2011 13:50:40 GMT Frederik Heber <heber@…> [a9c556]
	* src/LinearAlgebra/Eigenspace.cpp (deleted)
	* src/LinearAlgebra/Eigenspace.hpp (deleted)
	* src/LinearAlgebra/Makefile.am (modified)
	* src/LinearAlgebra/Subspace.cpp (deleted)
	* src/LinearAlgebra/Subspace.hpp (deleted)
	* src/Makefile.am (modified)
	* src/SubspaceFactorizer.cpp (deleted)
	* src/unittests/Makefile.am (modified)
	* src/unittests/SubspaceFactorizerUnitTest.cpp (deleted)
	* src/unittests/SubspaceFactorizerUnitTest.hpp (deleted)

	Removed Subspace stuff from this project.

	- has been relayed along ...


Mon, 07 Mar 2011 11:40:27 GMT Frederik Heber <heber@…> [dda246]
	* configure.ac (modified)
	* src/Helpers/Makefile.am (added)
	* src/LinearAlgebra/Makefile.am (modified)
	* src/LinearAlgebra/unittests/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/Shapes/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Made Helpers into commodity library to prevent double inclusion.

	- ...


Mon, 07 Mar 2011 11:40:27 GMT Frederik Heber <heber@…> [19290f]
	* configure.ac (modified)
	* src/UIElements/CommandLineUI/CommandLineParser.hpp (modified)
	* src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistenyUnitTest.cpp (added)
	* src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistenyUnitTest.hpp (added)
	* src/UIElements/CommandLineUI/unittests/Makefile.am (added)
	* src/unittests/Makefile.am (modified)

	Added CommandLineParser_ActionRegistry_ConsistenyUnitTest to check ...


Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber <heber@…> [129204]
	* src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/CopyAction.cpp (modified)
	* src/Bond/GraphEdge.cpp (added)
	* src/Bond/GraphEdge.hpp (added)
	* src/Bond/bond.cpp (moved)
	* src/Bond/bond.hpp (moved)
	* src/Graph/BondGraph.cpp (modified)
	* src/Graph/BondGraph.hpp (modified)
	* src/Graph/BreadthFirstSearchAdd.cpp (modified)
	* src/Graph/BreadthFirstSearchAdd.hpp (modified)
	* src/Makefile.am (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/graph.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/unittests/AnalysisBondsUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)

	Moved bond.* to Bond/, new class GraphEdge which contains graph parts ...


Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber <heber@…> [632508]
	* src/Actions/CommandAction/BondLengthTableAction.cpp (modified)
	* src/Actions/CommandAction/BondLengthTableAction.def (modified)
	* src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/Graph/BondGraph.cpp (moved)
	* src/Graph/BondGraph.hpp (moved)
	* src/Makefile.am (modified)
	* src/World.cpp (modified)
	* src/builder_init.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/unittests/AnalysisBondsUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)

	Moved files bondgraph.?pp -> Graph/BondGraph.?pp.


Tue, 01 Mar 2011 12:49:28 GMT Frederik Heber <heber@…> [3738f0]
	* src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/AtomSet.hpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/unittests/AnalysisBondsUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* tests/Fragmentations/defs.in (modified)
	* tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified)
	* tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified)
	* tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified)
	* tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at (modified)

	Moved molecule::CreateAdjacencyList over to class BondGraph.

	to ...


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [4b5cf8]
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)

	BondedParticle::OutputBondOfAtom() now takes stream to print to.


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [458c31]
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)

	molecule::BondCount is now Cachable and private.

	- renamed ...


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [715b67]
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/unittests/AnalysisBondsUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)

	Renamed BondGraph::ConstructBondGraph -> CreateAdjacencyForMolecule.
 ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [a479fa]
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/BoundaryPointSet.cpp (modified)
	* src/BoundaryPointSet.hpp (modified)
	* src/Helpers/helpers.hpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/atom_particleinfo.hpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.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/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/unittests/TesselationUnitTest.cpp (modified)
	* src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified)

	Renamed ParticleInfo::nr to ParticleInfo::ParticleInfo_nr for easier ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [caa06ef]
	* src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified)
	* src/IPointCloud.hpp (modified)
	* src/PointCloudAdaptor.hpp (modified)
	* src/boundary.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/TesselationUnitTest.cpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified)
	* tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified)
	* tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified)
	* tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified)

	Added name to PointCloudAdaptor, set by constructor.

	- name is used ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [34c43a]
	* configure.ac (modified)
	* src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified)
	* src/IPointCloud.hpp (added)
	* src/Makefile.am (modified)
	* src/PointCloud.cpp (deleted)
	* src/PointCloud.hpp (deleted)
	* src/PointCloudAdaptor.hpp (added)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/TesselationUnitTest.cpp (modified)
	* src/unittests/TesselationUnitTest.hpp (modified)
	* src/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified)
	* tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified)
	* tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified)
	* tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified)
	* tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified)

	Bigger change: Replaced PointCloud by PointCloudAdaptor.

	- ...


Thu, 24 Feb 2011 19:43:03 GMT Frederik Heber <heber@…> [03c77c]
	* src/ConfigFileBuffer.cpp (modified)
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/config.cpp (modified)
	* src/graph.hpp (modified)
	* src/lists.hpp (deleted)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)

	bonds::previous and ::next removed, lists.hpp deleted.

	- the last ...


Thu, 24 Feb 2011 19:39:42 GMT Frederik Heber <heber@…> [8aba3c]
	* src/unittests/ListOfBondsUnitTest.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.hpp (modified)

	TEST: Extended ListOfBondsUnitTest for multiple time steps ...


Thu, 24 Feb 2011 19:26:14 GMT Frederik Heber <heber@…> [073a9e4]
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/unittests/ParserTremoloUnitTest.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/molecule.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)

	BondedParticle::(Un)RegisterBond,AddBond,IsBondedTo with step.

	- ...


Thu, 24 Feb 2011 18:51:32 GMT Frederik Heber <heber@…> [9d83b6]
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/CopyAction.cpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/WorldTime.hpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticleinfo.cpp (modified)
	* src/atom_bondedparticleinfo.hpp (modified)
	* src/boundary.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/unittests/ListOfBondsUnitTest.cpp (modified)

	BondedParticleInfo now has vector<BondList>

	- vector<BondList> ...


Thu, 24 Feb 2011 16:05:50 GMT Frederik Heber <heber@…> [6bb605]
	* src/Actions/WorldAction/SetWorldTimeAction.cpp (modified)
	* src/Makefile.am (modified)
	* src/WorldTime.cpp (modified)
	* src/WorldTime.hpp (modified)
	* src/unittests/WorldTimeUnitTest.cpp (modified)

	Worldtime now has static CurrentTime and static (inline) ...


Thu, 24 Feb 2011 15:54:52 GMT Frederik Heber <heber@…> [f649de]
	* src/Makefile.am (modified)
	* src/WorldTime.cpp (added)
	* src/WorldTime.hpp (added)
	* src/unittests/Makefile.am (modified)
	* src/unittests/WorldTimeUnitTest.cpp (added)
	* src/unittests/WorldTimeUnitTest.hpp (added)

	Implemented class WorldTime.

	- WorldTime contains the current, ...


Mon, 07 Feb 2011 10:25:52 GMT Frederik Heber <heber@…> [9e4fd1]
	* src/Parser/unittests/Makefile.am (modified)
	* src/Parser/unittests/ParserCommonUnitTest.hpp (deleted)
	* src/Parser/unittests/ParserMpqcUnitTest.cpp (added)
	* src/Parser/unittests/ParserMpqcUnitTest.hpp (added)
	* src/Parser/unittests/ParserPcpUnitTest.cpp (moved)
	* src/Parser/unittests/ParserPcpUnitTest.hpp (added)
	* src/Parser/unittests/ParserPdbUnitTest.cpp (added)
	* src/Parser/unittests/ParserPdbUnitTest.hpp (added)
	* src/Parser/unittests/ParserXyzUnitTest.cpp (added)
	* src/Parser/unittests/ParserXyzUnitTest.hpp (added)
	* src/unittests/Makefile.am (modified)

	Split up ParserCommonUnitTest into a UnitTest for each Parser.


Fri, 04 Feb 2011 18:56:38 GMT Frederik Heber <heber@…> [266875]
	* src/Descriptors/MoleculeFormulaDescriptor.cpp (modified)
	* src/Descriptors/MoleculeFormulaDescriptor.hpp (modified)
	* src/Exceptions/FormulaStringParseException.cpp (moved)
	* src/Exceptions/FormulaStringParseException.hpp (moved)
	* src/Exceptions/Makefile.am (modified)
	* src/Formula.cpp (modified)
	* src/Formula.hpp (modified)
	* src/unittests/FormulaUnitTest.cpp (modified)

	FIX: ParserError did not adhere to naming convention.

	- excepetions ...


Fri, 04 Feb 2011 18:56:38 GMT Frederik Heber <heber@…> [4e855e]
	* src/Actions/CommandAction/BondLengthTableAction.cpp (modified)
	* src/Actions/CommandAction/BondLengthTableAction.def (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/builder_init.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)
	* src/unittests/AnalysisBondsUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.hpp (modified)
	* tests/regression/Graph/1/pre/test2.conf (added)
	* tests/regression/testsuite-graph.at (modified)

	BondGraph::LoadBondLengthTable() now accepts istream instead of const ...


Thu, 03 Feb 2011 09:59:58 GMT Frederik Heber <heber@…> [a5028f]
	* src/LinearAlgebra/RealSpaceMatrix.cpp (modified)
	* src/SubspaceFactorizer.cpp (modified)
	* src/Thermostats/Langevin.cpp (modified)
	* src/boundary.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/unittests/SubspaceFactorizerUnitTest.cpp (modified)

	RandomNumberGeneratorFactory is now used instead of rand() throughout ...


Thu, 03 Feb 2011 09:59:57 GMT Frederik Heber <heber@…> [0275ad]
	* configure.ac (modified)
	* src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified)
	* src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.def (modified)
	* src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified)
	* src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.def (modified)
	* src/Actions/ValueStorage.cpp (modified)
	* src/Actions/ValueStorage.hpp (modified)
	* src/RandomNumbers/Makefile.am (modified)
	* src/RandomNumbers/RandomNumberDistribution.hpp (modified)
	* src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified)
	* src/RandomNumbers/RandomNumberDistributionFactory.def (modified)
	* src/RandomNumbers/RandomNumberDistributionFactory.hpp (modified)
	* src/RandomNumbers/RandomNumberDistributionFactory.undef (modified)
	* src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified)
	* src/RandomNumbers/RandomNumberDistribution_Encapsulation.hpp (modified)
	* src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (added)
	* src/RandomNumbers/RandomNumberDistribution_Parameters.hpp (added)
	* src/RandomNumbers/RandomNumberEngine.hpp (modified)
	* src/RandomNumbers/RandomNumberEngineFactory.cpp (modified)
	* src/RandomNumbers/RandomNumberEngineFactory.def (modified)
	* src/RandomNumbers/RandomNumberEngineFactory.hpp (modified)
	* src/RandomNumbers/RandomNumberEngineFactory.undef (modified)
	* src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (modified)
	* src/RandomNumbers/RandomNumberEngine_Parameters.cpp (added)
	* src/RandomNumbers/RandomNumberEngine_Parameters.hpp (added)
	* src/RandomNumbers/RandomNumberGeneratorFactory.def (modified)
	* src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified)
	* src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.hpp (modified)
	* src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified)
	* src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser.cpp (modified)
	* src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified)
	* src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (added)
	* src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified)
	* src/UIElements/CommandLineUI/TypeEnumContainer.hpp (modified)
	* src/UIElements/Dialog.cpp (modified)
	* src/UIElements/Dialog.hpp (modified)
	* src/UIElements/Makefile.am (modified)
	* src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp (added)
	* src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.hpp (added)
	* src/UIElements/Qt4/QtDialog.cpp (modified)
	* src/UIElements/Qt4/QtDialog.hpp (modified)
	* src/UIElements/Qt4/Query/QtQuery.hpp (modified)
	* src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (added)
	* src/UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp (added)
	* src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (added)
	* src/UIElements/TextUI/Query/TextQuery.hpp (modified)
	* src/UIElements/TextUI/TextDialog.cpp (modified)
	* src/UIElements/TextUI/TextDialog.hpp (modified)
	* src/unittests/DummyUI.hpp (modified)
	* tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified)
	* tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified)

	Final step in Random numbers is done ...

	- requires CodePatterns ...


Thu, 03 Feb 2011 09:59:28 GMT Frederik Heber <heber@…> [1ee3b8d]
	* configure.ac (modified)
	* src/Actions/unittests/Makefile.am (modified)
	* src/Descriptors/unittests/Makefile.am (modified)
	* src/LinearAlgebra/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/Parser/unittests/Makefile.am (modified)
	* src/RandomNumbers/Makefile.am (added)
	* src/RandomNumbers/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Made RandomNumbers sources into its own library ...


Thu, 03 Feb 2011 09:51:19 GMT Frederik Heber <heber@…> [3f9eba]
	* configure.ac (modified)
	* src/Actions/Makefile.am (modified)
	* src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (added)
	* src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.def (added)
	* src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.hpp (added)
	* src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (added)
	* src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.def (added)
	* src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.hpp (added)
	* src/Makefile.am (modified)
	* src/RandomNumbers/RandomNumberDistribution.hpp (added)
	* src/RandomNumbers/RandomNumberDistribution_Encapsulation.hpp (added)
	* src/RandomNumbers/RandomNumberEngine.hpp (added)
	* src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (added)
	* src/RandomNumbers/RandomNumberGenerator.cpp (added)
	* src/RandomNumbers/RandomNumberGenerator.hpp (added)
	* src/RandomNumbers/RandomNumberGeneratorFactory.cpp (added)
	* src/RandomNumbers/RandomNumberGeneratorFactory.def (added)
	* src/RandomNumbers/RandomNumberGeneratorFactory.hpp (added)
	* src/RandomNumbers/RandomNumberGeneratorFactory.undef (added)
	* src/RandomNumbers/RandomNumberGenerator_Encapsulation.hpp (added)
	* src/RandomNumbers/TemplatePowerSetGenerator.hpp (added)
	* src/RandomNumbers/unittests/Makefile.am (added)
	* src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (added)
	* src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.hpp (added)
	* src/builder_init.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* tests/regression/Makefile.am (modified)
	* tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (added)
	* tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (added)
	* tests/regression/RandomNumbers/testsuite-randomnumbers.at (added)
	* tests/regression/testsuite.at (modified)

	New classes for random number generation.

	- we use boost::random as ...


Thu, 03 Feb 2011 09:51:19 GMT Frederik Heber <heber@…> [92e5cb]
	* src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* tests/regression/Analysis/1/post/bin_output.csv (modified)
	* tests/regression/Analysis/1/post/output.csv (modified)
	* tests/regression/Analysis/2/post/bin_output-10.csv (modified)
	* tests/regression/Analysis/2/post/bin_output-20.csv (modified)
	* tests/regression/Analysis/2/post/bin_output-5.csv (modified)
	* tests/regression/Analysis/3/post/bin_output.csv (modified)
	* tests/regression/Analysis/4/post/bin_output.csv (modified)
	* tests/regression/Analysis/6/post/emptybox_histogram.dat (modified)
	* tests/regression/Analysis/6/post/hydrogenbox_histogram.dat (modified)

	Refactored Output..Correlation...() code into a single templated one. ...


Thu, 03 Feb 2011 09:51:18 GMT Frederik Heber <heber@…> [67c92b]
	* src/Helpers/defs.cpp (modified)
	* src/Helpers/defs.hpp (modified)
	* src/element.cpp (modified)
	* src/element.hpp (modified)
	* src/elements_db.cpp (modified)
	* src/elements_db.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/unittests/PeriodentafelUnitTest.cpp (modified)

	Added Electronegativity database and member value to class element.
 ...


Thu, 23 Dec 2010 17:41:54 GMT Frederik Heber <heber@…> [6d2207]
	* configure.ac (modified)
	* src/Actions/unittests/Makefile.am (modified)
	* src/Descriptors/unittests/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/Parser/unittests/Makefile.am (modified)
	* src/Shapes/Makefile.am (added)
	* src/Shapes/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	FIX: Forgot Shapes/unittests and made Shapes into own library.

	- ...


Thu, 23 Dec 2010 17:41:54 GMT Frederik Heber <heber@…> [acbe1b]
	* MoleCuilder.pc.in (added)
	* configure.ac (modified)
	* molecuilder.pc.in (deleted)
	* src/Actions/Makefile.am (modified)
	* src/Actions/unittests/Makefile.am (modified)
	* src/Descriptors/unittests/Makefile.am (modified)
	* src/Exceptions/Makefile.am (modified)
	* src/LinearAlgebra/Makefile.am (modified)
	* src/LinearAlgebra/unittests/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/Parser/Makefile.am (modified)
	* src/Parser/unittests/Makefile.am (modified)
	* src/UIElements/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	All libraries don't have version in name anymore.

	- we used gained ...


Thu, 23 Dec 2010 17:40:13 GMT Frederik Heber <heber@…> [56f73b]
	* src/Actions/Action.hpp (modified)
	* src/Actions/ActionHistory.hpp (modified)
	* src/Actions/ActionRegistry.hpp (modified)
	* src/Actions/ActionSequence.hpp (modified)
	* src/Actions/Action_impl_header.hpp (modified)
	* src/Actions/Action_impl_pre.hpp (modified)
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified)
	* src/Actions/AtomAction/AddAction.hpp (modified)
	* src/Actions/AtomAction/ChangeElementAction.hpp (modified)
	* src/Actions/AtomAction/RemoveAction.hpp (modified)
	* src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp (modified)
	* src/Actions/AtomAction/TranslateAction.hpp (modified)
	* src/Actions/AtomsCalculation.hpp (modified)
	* src/Actions/AtomsCalculation_impl.hpp (modified)
	* src/Actions/Calculation.hpp (modified)
	* src/Actions/Calculation_impl.hpp (modified)
	* src/Actions/CommandAction/BondLengthTableAction.hpp (modified)
	* src/Actions/CommandAction/ElementDbAction.hpp (modified)
	* src/Actions/CommandAction/FastParsingAction.hpp (modified)
	* src/Actions/CommandAction/HelpAction.hpp (modified)
	* src/Actions/CommandAction/VerboseAction.hpp (modified)
	* src/Actions/CommandAction/VersionAction.hpp (modified)
	* src/Actions/CommandAction/WarrantyAction.hpp (modified)
	* src/Actions/ErrorAction.hpp (modified)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.hpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.hpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified)
	* src/Actions/MakroAction.hpp (modified)
	* src/Actions/ManipulateAtomsProcess.hpp (modified)
	* src/Actions/MethodAction.hpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.hpp (modified)
	* src/Actions/MoleculeAction/ChangeNameAction.hpp (modified)
	* src/Actions/MoleculeAction/CopyAction.hpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.hpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified)
	* src/Actions/MoleculeAction/LoadAction.hpp (modified)
	* src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified)
	* src/Actions/MoleculeAction/SaveAction.hpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.hpp (modified)
	* src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified)
	* src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified)
	* src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified)
	* src/Actions/OptionRegistry.hpp (modified)
	* src/Actions/OptionTrait.hpp (modified)
	* src/Actions/Process.hpp (modified)
	* src/Actions/SelectionAction/Atoms/AllAtomsAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/AtomByElementAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/AtomByIdAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAllAtomsAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAtomByElementAction.hpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAtomByIdAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/AllMoleculesAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/MoleculeByIdAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/MoleculeByNameAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.hpp (modified)
	* src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.hpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified)
	* src/Actions/ValueStorage.hpp (modified)
	* src/Actions/Values.hpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified)
	* src/Actions/WorldAction/BoundInBoxAction.hpp (modified)
	* src/Actions/WorldAction/CenterInBoxAction.hpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified)
	* src/Actions/WorldAction/ChangeBoxAction.hpp (modified)
	* src/Actions/WorldAction/InputAction.hpp (modified)
	* src/Actions/WorldAction/OutputAction.hpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.hpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.hpp (modified)
	* src/Actions/WorldAction/SetDefaultNameAction.hpp (modified)
	* src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified)
	* src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified)
	* src/Actions/unittests/ActionRegistryUnitTest.hpp (modified)
	* src/Actions/unittests/ActionSequenceUnitTest.hpp (modified)
	* src/Actions/unittests/AtomsCalculationUnitTest.hpp (modified)
	* src/Actions/unittests/ManipulateAtomsUnitTest.hpp (modified)
	* src/AtomSet.hpp (modified)
	* src/AtomicInfo.hpp (modified)
	* src/BoundaryLineSet.hpp (modified)
	* src/BoundaryMaps.hpp (modified)
	* src/BoundaryPointSet.hpp (modified)
	* src/BoundaryPolygonSet.hpp (modified)
	* src/BoundaryTriangleSet.hpp (modified)
	* src/Box.hpp (modified)
	* src/CandidateForTesselation.hpp (modified)
	* src/Descriptors/AtomDescriptor.hpp (modified)
	* src/Descriptors/AtomDescriptor_impl.hpp (modified)
	* src/Descriptors/AtomIdDescriptor.hpp (modified)
	* src/Descriptors/AtomIdDescriptor_impl.hpp (modified)
	* src/Descriptors/AtomOfMoleculeSelectionDescriptor.hpp (modified)
	* src/Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp (modified)
	* src/Descriptors/AtomSelectionDescriptor.hpp (modified)
	* src/Descriptors/AtomSelectionDescriptor_impl.hpp (modified)
	* src/Descriptors/AtomShapeDescriptor.hpp (modified)
	* src/Descriptors/AtomShapeDescriptor_impl.hpp (modified)
	* src/Descriptors/AtomTypeDescriptor.hpp (modified)
	* src/Descriptors/AtomTypeDescriptor_impl.hpp (modified)
	* src/Descriptors/DescriptorBase.hpp (modified)
	* src/Descriptors/DescriptorBase_impl.hpp (modified)
	* src/Descriptors/MoleculeDescriptor.hpp (modified)
	* src/Descriptors/MoleculeDescriptor_impl.hpp (modified)
	* src/Descriptors/MoleculeFormulaDescriptor.hpp (modified)
	* src/Descriptors/MoleculeFormulaDescriptor_impl.hpp (modified)
	* src/Descriptors/MoleculeIdDescriptor.hpp (modified)
	* src/Descriptors/MoleculeIdDescriptor_impl.hpp (modified)
	* src/Descriptors/MoleculeNameDescriptor.hpp (modified)
	* src/Descriptors/MoleculeNameDescriptor_impl.hpp (modified)
	* src/Descriptors/MoleculeOfAtomSelectionDescriptor.hpp (modified)
	* src/Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp (modified)
	* src/Descriptors/MoleculeOrderDescriptor.hpp (modified)
	* src/Descriptors/MoleculeOrderDescriptor_impl.hpp (modified)
	* src/Descriptors/MoleculePtrDescriptor.hpp (modified)
	* src/Descriptors/MoleculePtrDescriptor_impl.hpp (modified)
	* src/Descriptors/MoleculeSelectionDescriptor.hpp (modified)
	* src/Descriptors/MoleculeSelectionDescriptor_impl.hpp (modified)
	* src/Descriptors/SelectiveIterator.hpp (modified)
	* src/Descriptors/SelectiveIterator_impl.hpp (modified)
	* src/Descriptors/unittests/AtomDescriptorUnitTest.hpp (modified)
	* src/Descriptors/unittests/MoleculeDescriptorUnitTest.hpp (modified)
	* src/Exceptions/CustomException.hpp (modified)
	* src/Exceptions/IllegalTypeException.hpp (modified)
	* src/Exceptions/LinearDependenceException.hpp (modified)
	* src/Exceptions/MathException.hpp (modified)
	* src/Exceptions/MissingValueException.hpp (modified)
	* src/Exceptions/MultipleSolutionsException.hpp (modified)
	* src/Exceptions/NotInvertibleException.hpp (modified)
	* src/Exceptions/NotOnSurfaceException.hpp (modified)
	* src/Exceptions/ParseError.hpp (modified)
	* src/Exceptions/ShapeException.hpp (modified)
	* src/Exceptions/SkewException.hpp (modified)
	* src/Exceptions/ZeroVectorException.hpp (modified)
	* src/Formula.hpp (modified)
	* src/Helpers/defs.hpp (modified)
	* src/Helpers/fast_functions.hpp (modified)
	* src/LinearAlgebra/BoxVector.hpp (modified)
	* src/LinearAlgebra/Eigenspace.hpp (modified)
	* src/LinearAlgebra/Line.hpp (modified)
	* src/LinearAlgebra/LineSegment.hpp (modified)
	* src/LinearAlgebra/LineSegmentSet.hpp (modified)
	* src/LinearAlgebra/MatrixContent.hpp (modified)
	* src/LinearAlgebra/MatrixVector_ops.hpp (modified)
	* src/LinearAlgebra/Plane.hpp (modified)
	* src/LinearAlgebra/RealSpaceMatrix.hpp (modified)
	* src/LinearAlgebra/Space.hpp (modified)
	* src/LinearAlgebra/Subspace.hpp (modified)
	* src/LinearAlgebra/VectorContent.hpp (modified)
	* src/LinearAlgebra/VectorInterface.hpp (modified)
	* src/LinearAlgebra/VectorSet.hpp (modified)
	* src/LinearAlgebra/unittests/LineUnitTest.hpp (modified)
	* src/LinearAlgebra/unittests/LinearSystemOfEquationsUnitTest.hpp (modified)
	* src/LinearAlgebra/unittests/MatrixContentSymmetricUnitTest.hpp (modified)
	* src/LinearAlgebra/unittests/MatrixContentUnitTest.hpp (modified)
	* src/LinearAlgebra/unittests/MatrixUnitTest.hpp (modified)
	* src/LinearAlgebra/unittests/PlaneUnitTest.hpp (modified)
	* src/LinearAlgebra/unittests/VectorContentUnitTest.hpp (modified)
	* src/LinearAlgebra/unittests/VectorUnitTest.hpp (modified)
	* src/LinearAlgebra/vector_ops.hpp (modified)
	* src/Parser/ChangeTracker.hpp (modified)
	* src/Parser/FormatParser.hpp (modified)
	* src/Parser/MpqcParser.hpp (modified)
	* src/Parser/PcpParser.hpp (modified)
	* src/Parser/PdbAtomInfoContainer.hpp (modified)
	* src/Parser/PdbKey.hpp (modified)
	* src/Parser/PdbParser.hpp (modified)
	* src/Parser/TremoloAtomInfoContainer.hpp (modified)
	* src/Parser/TremoloKey.hpp (modified)
	* src/Parser/TremoloParser.hpp (modified)
	* src/Parser/XyzParser.hpp (modified)
	* src/Parser/unittests/ParserCommonUnitTest.hpp (modified)
	* src/Parser/unittests/ParserTremoloUnitTest.hpp (modified)
	* src/PointCloud.hpp (modified)
	* src/Shapes/BaseShapes.hpp (modified)
	* src/Shapes/BaseShapes_impl.hpp (modified)
	* src/Shapes/Shape.hpp (modified)
	* src/Shapes/ShapeOps.hpp (modified)
	* src/Shapes/ShapeOps_impl.hpp (modified)
	* src/Shapes/Shape_impl.hpp (modified)
	* src/Shapes/unittests/ShapeUnitTest.hpp (modified)
	* src/SubspaceFactorizer.cpp (modified)
	* src/TesselPoint.hpp (modified)
	* src/Thermostats/Berendsen.hpp (modified)
	* src/Thermostats/GaussianThermostat.hpp (modified)
	* src/Thermostats/Langevin.hpp (modified)
	* src/Thermostats/NoThermostat.hpp (modified)
	* src/Thermostats/NoseHoover.hpp (modified)
	* src/Thermostats/Thermostat.hpp (modified)
	* src/Thermostats/Woodcock.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser_validate.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineWindow.hpp (modified)
	* src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified)
	* src/UIElements/CommandLineUI/TypeEnumContainer.hpp (modified)
	* src/UIElements/Dialog.hpp (modified)
	* src/UIElements/MainWindow.hpp (modified)
	* src/UIElements/Menu/Menu.hpp (modified)
	* src/UIElements/Menu/MenuDescription.hpp (modified)
	* src/UIElements/Menu/MenuInterface.hpp (modified)
	* src/UIElements/Menu/Qt4/QtMenu.hpp (modified)
	* src/UIElements/Menu/Qt4/QtMenuPipe.hpp (modified)
	* src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (modified)
	* src/UIElements/Menu/TextMenu/DisplayMenuItem.hpp (modified)
	* src/UIElements/Menu/TextMenu/MenuItem.hpp (modified)
	* src/UIElements/Menu/TextMenu/SeparatorMenuItem.hpp (modified)
	* src/UIElements/Menu/TextMenu/SubMenuItem.hpp (modified)
	* src/UIElements/Menu/TextMenu/TextMenu.hpp (modified)
	* src/UIElements/Menu/TextMenu/TxMenu.hpp (modified)
	* src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified)
	* src/UIElements/Menu/unittests/MenuDescriptionUnitTest.hpp (modified)
	* src/UIElements/Qt4/Pipe/AtomQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/ElementQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/FileQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/IntQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/QtQueryListPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/QtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/StringQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/VectorQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/QtDialog.hpp (modified)
	* src/UIElements/Qt4/QtMainWindow.hpp (modified)
	* src/UIElements/Qt4/QtUIFactory.hpp (modified)
	* src/UIElements/Qt4/Query/QtQuery.hpp (modified)
	* src/UIElements/TextUI/Query/TextQuery.hpp (modified)
	* src/UIElements/TextUI/TextDialog.hpp (modified)
	* src/UIElements/TextUI/TextStatusIndicator.hpp (modified)
	* src/UIElements/TextUI/TextUIFactory.hpp (modified)
	* src/UIElements/TextUI/TextWindow.hpp (modified)
	* src/UIElements/UIFactory.hpp (modified)
	* src/UIElements/Views/MethodStringView.hpp (modified)
	* src/UIElements/Views/Qt4/GLMoleculeView.hpp (modified)
	* src/UIElements/Views/Qt4/QtMoleculeView.hpp (modified)
	* src/UIElements/Views/Qt4/QtStatusBar.hpp (modified)
	* src/UIElements/Views/Qt4/QtWorldView.hpp (modified)
	* src/UIElements/Views/StreamStringView.hpp (modified)
	* src/UIElements/Views/StringView.hpp (modified)
	* src/UIElements/Views/View.hpp (modified)
	* src/World_calculations.hpp (modified)
	* src/builder_init.hpp (modified)
	* src/datacreator.hpp (modified)
	* src/elements_db.hpp (modified)
	* src/lists.hpp (modified)
	* src/types.hpp (modified)
	* src/unittests/AnalysisBondsUnitTest.hpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified)
	* src/unittests/BondGraphUnitTest.hpp (modified)
	* src/unittests/BoxUnitTest.hpp (modified)
	* src/unittests/CountBondsUnitTest.hpp (modified)
	* src/unittests/DummyUI.hpp (modified)
	* src/unittests/FormulaUnitTest.hpp (modified)
	* src/unittests/LinkedCellUnitTest.hpp (modified)
	* src/unittests/ListOfBondsUnitTest.hpp (modified)
	* src/unittests/PeriodentafelUnitTest.hpp (modified)
	* src/unittests/SubspaceFactorizerUnitTest.hpp (modified)
	* src/unittests/TesselationUnitTest.hpp (modified)
	* src/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified)
	* tests/CodeChecks/Makefile.am (modified)
	* tests/CodeChecks/testsuite-config_h.at (added)
	* tests/CodeChecks/testsuite-memdebug.at (added)
	* tests/CodeChecks/testsuite.at (modified)

	Added config.h also to all header files, code check test ascertain ...


Thu, 23 Dec 2010 17:40:13 GMT Frederik Heber <heber@…> [ad011c]
	* m4/ax_codepatterns.m4 (modified)
	* src/Actions/Action.cpp (modified)
	* src/Actions/ActionHistory.cpp (modified)
	* src/Actions/ActionHistory.hpp (modified)
	* src/Actions/ActionRegistry.cpp (modified)
	* src/Actions/ActionRegistry.hpp (modified)
	* src/Actions/ActionSequence.cpp (modified)
	* src/Actions/ActionTraits.cpp (modified)
	* src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/Actions/AtomAction/AddAction.cpp (modified)
	* src/Actions/AtomAction/ChangeElementAction.cpp (modified)
	* src/Actions/AtomAction/RemoveAction.cpp (modified)
	* src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified)
	* src/Actions/AtomAction/TranslateAction.cpp (modified)
	* src/Actions/CommandAction/BondLengthTableAction.cpp (modified)
	* src/Actions/CommandAction/ElementDbAction.cpp (modified)
	* src/Actions/CommandAction/FastParsingAction.cpp (modified)
	* src/Actions/CommandAction/HelpAction.cpp (modified)
	* src/Actions/CommandAction/VerboseAction.cpp (modified)
	* src/Actions/CommandAction/VersionAction.cpp (modified)
	* src/Actions/CommandAction/WarrantyAction.cpp (modified)
	* src/Actions/ErrorAction.cpp (modified)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MakroAction.cpp (modified)
	* src/Actions/ManipulateAtomsProcess.cpp (modified)
	* src/Actions/MethodAction.cpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.cpp (modified)
	* src/Actions/MoleculeAction/ChangeNameAction.cpp (modified)
	* src/Actions/MoleculeAction/CopyAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified)
	* src/Actions/MoleculeAction/LoadAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified)
	* src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified)
	* src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified)
	* src/Actions/OptionRegistry.cpp (modified)
	* src/Actions/OptionRegistry.hpp (modified)
	* src/Actions/OptionTrait.cpp (modified)
	* src/Actions/Process.cpp (modified)
	* src/Actions/Process.hpp (modified)
	* src/Actions/RedoAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified)
	* src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified)
	* src/Actions/UndoAction.cpp (modified)
	* src/Actions/ValueStorage.cpp (modified)
	* src/Actions/ValueStorage.hpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified)
	* src/Actions/WorldAction/BoundInBoxAction.cpp (modified)
	* src/Actions/WorldAction/CenterInBoxAction.cpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified)
	* src/Actions/WorldAction/ChangeBoxAction.cpp (modified)
	* src/Actions/WorldAction/InputAction.cpp (modified)
	* src/Actions/WorldAction/OutputAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.cpp (modified)
	* src/Actions/WorldAction/SetDefaultNameAction.cpp (modified)
	* src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified)
	* src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified)
	* src/AtomicInfo.cpp (modified)
	* src/BoundaryLineSet.cpp (modified)
	* src/BoundaryPointSet.cpp (modified)
	* src/BoundaryPolygonSet.cpp (modified)
	* src/BoundaryTriangleSet.cpp (modified)
	* src/Box.cpp (modified)
	* src/CandidateForTesselation.cpp (modified)
	* src/ConfigFileBuffer.cpp (modified)
	* src/Descriptors/AtomDescriptor.cpp (modified)
	* src/Descriptors/AtomIdDescriptor.cpp (modified)
	* src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified)
	* src/Descriptors/AtomSelectionDescriptor.cpp (modified)
	* src/Descriptors/AtomShapeDescriptor.cpp (modified)
	* src/Descriptors/AtomTypeDescriptor.cpp (modified)
	* src/Descriptors/MoleculeDescriptor.cpp (modified)
	* src/Descriptors/MoleculeFormulaDescriptor.cpp (modified)
	* src/Descriptors/MoleculeIdDescriptor.cpp (modified)
	* src/Descriptors/MoleculeNameDescriptor.cpp (modified)
	* src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified)
	* src/Descriptors/MoleculeOrderDescriptor.cpp (modified)
	* src/Descriptors/MoleculePtrDescriptor.cpp (modified)
	* src/Descriptors/MoleculeSelectionDescriptor.cpp (modified)
	* src/Exceptions/CustomException.cpp (modified)
	* src/Exceptions/IllegalTypeException.cpp (modified)
	* src/Exceptions/LinearDependenceException.cpp (modified)
	* src/Exceptions/MathException.cpp (modified)
	* src/Exceptions/MissingValueException.cpp (modified)
	* src/Exceptions/NotInvertibleException.cpp (modified)
	* src/Exceptions/NotOnSurfaceException.cpp (modified)
	* src/Exceptions/ParseError.cpp (modified)
	* src/Exceptions/ShapeException.cpp (modified)
	* src/Exceptions/SkewException.cpp (modified)
	* src/Exceptions/ZeroVectorException.cpp (modified)
	* src/Formula.cpp (modified)
	* src/Formula.hpp (modified)
	* src/Helpers/defs.cpp (modified)
	* src/Helpers/helpers.cpp (modified)
	* src/Helpers/helpers.hpp (modified)
	* src/LinearAlgebra/BoxVector.cpp (modified)
	* src/LinearAlgebra/Eigenspace.cpp (modified)
	* src/LinearAlgebra/Line.cpp (modified)
	* src/LinearAlgebra/LineSegment.cpp (modified)
	* src/LinearAlgebra/LineSegmentSet.cpp (modified)
	* src/LinearAlgebra/LinearSystemOfEquations.cpp (modified)
	* src/LinearAlgebra/MatrixContent.cpp (modified)
	* src/LinearAlgebra/MatrixVector_ops.cpp (modified)
	* src/LinearAlgebra/Plane.cpp (modified)
	* src/LinearAlgebra/RealSpaceMatrix.cpp (modified)
	* src/LinearAlgebra/Space.cpp (modified)
	* src/LinearAlgebra/Subspace.cpp (modified)
	* src/LinearAlgebra/Vector.cpp (modified)
	* src/LinearAlgebra/VectorContent.cpp (modified)
	* src/LinearAlgebra/VectorInterface.cpp (modified)
	* src/LinearAlgebra/leastsquaremin.cpp (modified)
	* src/LinearAlgebra/unittests/VectorUnitTest.cpp (modified)
	* src/LinearAlgebra/vector_ops.cpp (modified)
	* src/Parser/ChangeTracker.cpp (modified)
	* src/Parser/ChangeTracker.hpp (modified)
	* src/Parser/FormatParser.cpp (modified)
	* src/Parser/FormatParser.hpp (modified)
	* src/Parser/FormatParserStorage.cpp (modified)
	* src/Parser/FormatParserStorage.hpp (modified)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/PdbAtomInfoContainer.cpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/TremoloAtomInfoContainer.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/PointCloud.cpp (modified)
	* src/Shapes/BaseShapes.cpp (modified)
	* src/Shapes/Shape.cpp (modified)
	* src/Shapes/ShapeOps.cpp (modified)
	* src/SubspaceFactorizer.cpp (modified)
	* src/TesselPoint.cpp (modified)
	* src/ThermoStatContainer.cpp (modified)
	* src/Thermostats/Berendsen.cpp (modified)
	* src/Thermostats/GaussianThermostat.cpp (modified)
	* src/Thermostats/Langevin.cpp (modified)
	* src/Thermostats/NoThermostat.cpp (modified)
	* src/Thermostats/NoseHoover.cpp (modified)
	* src/Thermostats/Thermostat.cpp (modified)
	* src/Thermostats/Woodcock.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified)
	* src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified)
	* src/UIElements/Dialog.cpp (modified)
	* src/UIElements/MainWindow.cpp (modified)
	* src/UIElements/Menu/Menu.cpp (modified)
	* src/UIElements/Menu/MenuDescription.cpp (modified)
	* src/UIElements/Menu/MenuDescription.hpp (modified)
	* src/UIElements/Menu/MenuInterface.cpp (modified)
	* src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified)
	* src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified)
	* src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified)
	* src/UIElements/Menu/TextMenu/MenuItem.cpp (modified)
	* src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified)
	* src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified)
	* src/UIElements/Menu/TextMenu/TextMenu.hpp (modified)
	* src/UIElements/Menu/TextMenu/TxMenu.cpp (modified)
	* src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified)
	* src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/QtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/QtDialog.cpp (modified)
	* src/UIElements/Qt4/QtMainWindow.cpp (modified)
	* src/UIElements/Qt4/QtUIFactory.cpp (modified)
	* src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/FileQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/IntQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/StringQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified)
	* src/UIElements/Query/AtomQuery.cpp (modified)
	* src/UIElements/Query/AtomsQuery.cpp (modified)
	* src/UIElements/Query/BooleanQuery.cpp (modified)
	* src/UIElements/Query/BoxQuery.cpp (modified)
	* src/UIElements/Query/DoubleQuery.cpp (modified)
	* src/UIElements/Query/DoublesQuery.cpp (modified)
	* src/UIElements/Query/ElementQuery.cpp (modified)
	* src/UIElements/Query/ElementsQuery.cpp (modified)
	* src/UIElements/Query/EmptyQuery.cpp (modified)
	* src/UIElements/Query/FileQuery.cpp (modified)
	* src/UIElements/Query/IntQuery.cpp (modified)
	* src/UIElements/Query/IntsQuery.cpp (modified)
	* src/UIElements/Query/MoleculeQuery.cpp (modified)
	* src/UIElements/Query/MoleculesQuery.cpp (modified)
	* src/UIElements/Query/Query.cpp (modified)
	* src/UIElements/Query/StringQuery.cpp (modified)
	* src/UIElements/Query/StringsQuery.cpp (modified)
	* src/UIElements/Query/VectorQuery.cpp (modified)
	* src/UIElements/Query/VectorsQuery.cpp (modified)
	* src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/FileTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/IntTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/StringTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified)
	* src/UIElements/TextUI/TextDialog.cpp (modified)
	* src/UIElements/TextUI/TextStatusIndicator.cpp (modified)
	* src/UIElements/TextUI/TextStatusIndicator.hpp (modified)
	* src/UIElements/TextUI/TextUIFactory.cpp (modified)
	* src/UIElements/TextUI/TextWindow.cpp (modified)
	* src/UIElements/UIFactory.cpp (modified)
	* src/UIElements/UIFactory.hpp (modified)
	* src/UIElements/Views/MethodStringView.cpp (modified)
	* src/UIElements/Views/Qt4/GLMoleculeView.cpp (modified)
	* src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified)
	* src/UIElements/Views/Qt4/QtMoleculeView.hpp (modified)
	* src/UIElements/Views/Qt4/QtStatusBar.cpp (modified)
	* src/UIElements/Views/Qt4/QtStatusBar.hpp (modified)
	* src/UIElements/Views/Qt4/QtWorldView.cpp (modified)
	* src/UIElements/Views/Qt4/QtWorldView.hpp (modified)
	* src/UIElements/Views/StreamStringView.cpp (modified)
	* src/UIElements/Views/StringView.cpp (modified)
	* src/UIElements/Views/View.cpp (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticleinfo.cpp (modified)
	* src/atom_graphnode.cpp (modified)
	* src/atom_graphnodeinfo.cpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/atom_trajectoryparticleinfo.cpp (modified)
	* src/bond.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder_init.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/element.cpp (modified)
	* src/elements_db.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/graph.cpp (modified)
	* src/joiner.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.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/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/triangleintersectionlist.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)
	* src/unittests/BoxUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* src/unittests/PeriodentafelUnitTest.cpp (modified)
	* src/unittests/SubspaceFactorizerUnitTest.cpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified)

	CodePatterns places all includes now in subfolder CodePatterns/.

	- ...


Thu, 23 Dec 2010 17:40:04 GMT Frederik Heber <heber@…> [a0064e]
	* configure.ac (modified)
	* m4/ax_codepatterns.m4 (added)
	* src/Actions/Makefile.am (modified)
	* src/Actions/unittests/Makefile.am (modified)
	* src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified)
	* src/Descriptors/unittests/Makefile.am (modified)
	* src/Exceptions/Makefile.am (modified)
	* src/Formula.hpp (modified)
	* src/Helpers/Assert.cpp (deleted)
	* src/Helpers/Assert.hpp (deleted)
	* src/Helpers/Info.cpp (deleted)
	* src/Helpers/Info.hpp (deleted)
	* src/Helpers/Log.cpp (deleted)
	* src/Helpers/Log.hpp (deleted)
	* src/Helpers/Makefile.am (deleted)
	* src/Helpers/MemDebug.cpp (deleted)
	* src/Helpers/MemDebug.hpp (deleted)
	* src/Helpers/Range.hpp (deleted)
	* src/Helpers/Verbose.cpp (deleted)
	* src/Helpers/Verbose.hpp (deleted)
	* src/Helpers/errorlogger.cpp (deleted)
	* src/Helpers/errorlogger.hpp (deleted)
	* src/Helpers/fast_functions.hpp (modified)
	* src/Helpers/helpers.cpp (modified)
	* src/Helpers/helpers.hpp (modified)
	* src/Helpers/logger.cpp (deleted)
	* src/Helpers/logger.hpp (deleted)
	* src/Helpers/toString.hpp (deleted)
	* src/Helpers/unittests/InfoUnitTest.cpp (deleted)
	* src/Helpers/unittests/InfoUnitTest.hpp (deleted)
	* src/Helpers/unittests/LogUnitTest.cpp (deleted)
	* src/Helpers/unittests/LogUnitTest.hpp (deleted)
	* src/Helpers/unittests/Makefile.am (deleted)
	* src/LinearAlgebra/Makefile.am (modified)
	* src/LinearAlgebra/unittests/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/Parser/Makefile.am (modified)
	* src/Parser/unittests/Makefile.am (modified)
	* src/Patterns/Cacheable.hpp (deleted)
	* src/Patterns/ObservedContainer.hpp (deleted)
	* src/Patterns/ObservedContainer_impl.hpp (deleted)
	* src/Patterns/ObservedIterator.hpp (deleted)
	* src/Patterns/Observer.cpp (deleted)
	* src/Patterns/Observer.hpp (deleted)
	* src/Patterns/Registry.hpp (deleted)
	* src/Patterns/Registry_impl.hpp (deleted)
	* src/Patterns/Singleton.hpp (deleted)
	* src/Patterns/Singleton_impl.hpp (deleted)
	* src/Patterns/unittests/CacheableUnitTest.cpp (deleted)
	* src/Patterns/unittests/CacheableUnitTest.hpp (deleted)
	* src/Patterns/unittests/Makefile.am (deleted)
	* src/Patterns/unittests/ObserverUnitTest.cpp (deleted)
	* src/Patterns/unittests/ObserverUnitTest.hpp (deleted)
	* src/Patterns/unittests/RegistryUnitTest.cpp (deleted)
	* src/Patterns/unittests/RegistryUnitTest.hpp (deleted)
	* src/Patterns/unittests/SingletonUnitTest.cpp (deleted)
	* src/Patterns/unittests/SingletonUnitTest.hpp (deleted)
	* src/Shapes/unittests/Makefile.am (modified)
	* src/SubspaceFactorizer.cpp (modified)
	* src/UIElements/Makefile.am (modified)
	* src/UIElements/Menu/unittests/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom.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/tesselation.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/SubspaceFactorizerUnitTest.cpp (modified)

	Moved stuff in src/Helpers and src/Patterns out to stand-alone ...


Thu, 16 Dec 2010 23:47:45 GMT Frederik Heber <heber@…> [f844ef]
	* src/LinearAlgebra/Subspace.hpp (modified)
	* src/periodentafel.hpp (modified)
	* src/unittests/AnalysisBondsUnitTest.cpp (moved)
	* src/unittests/AnalysisBondsUnitTest.hpp (moved)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (moved)
	* src/unittests/BondGraphUnitTest.hpp (moved)
	* src/unittests/BoxUnitTest.cpp (moved)
	* src/unittests/BoxUnitTest.hpp (moved)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* src/unittests/FormulaUnitTest.cpp (moved)
	* src/unittests/FormulaUnitTest.hpp (moved)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (moved)
	* src/unittests/ListOfBondsUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)
	* src/unittests/MapofActionsTest.cpp (deleted)
	* src/unittests/MapofActionsTest.hpp (deleted)
	* src/unittests/PeriodentafelUnitTest.cpp (moved)
	* src/unittests/PeriodentafelUnitTest.hpp (moved)
	* src/unittests/SubspaceFactorizerUnitTest.cpp (moved)
	* src/unittests/SubspaceFactorizerUnitTest.hpp (moved)
	* src/unittests/TesselationUnitTest.cpp (moved)
	* src/unittests/TesselationUnitTest.hpp (moved)
	* src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (moved)
	* src/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (moved)
	* src/unittests/Tesselation_InsideOutsideUnitTest.cpp (moved)
	* src/unittests/Tesselation_InsideOutsideUnitTest.hpp (moved)
	* src/unittests/memoryallocatorunittest.cpp (deleted)
	* src/unittests/memoryallocatorunittest.hpp (deleted)
	* src/unittests/memoryusageobserverunittest.cpp (deleted)
	* src/unittests/memoryusageobserverunittest.hpp (deleted)

	Renamed all remaining unit tests in src/unittests to Capitalized ...


Thu, 16 Dec 2010 23:47:45 GMT Frederik Heber <heber@…> [dfafe7]
	* src/LinearAlgebra/unittests/Makefile.am (modified)
	* src/LinearAlgebra/unittests/VectorContentUnitTest.cpp (moved)
	* src/LinearAlgebra/unittests/VectorContentUnitTest.hpp (moved)
	* src/LinearAlgebra/unittests/VectorUnitTest.cpp (moved)
	* src/LinearAlgebra/unittests/VectorUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved VectorContentUnittest and vectorunittest to ...


Thu, 16 Dec 2010 23:47:45 GMT Frederik Heber <heber@…> [0b3cbdf]
	* src/Shapes/unittests/Makefile.am (added)
	* src/Shapes/unittests/ShapeUnitTest.cpp (moved)
	* src/Shapes/unittests/ShapeUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved ShapeUnittest to Shapes/unittests/ShapeUnitTest.


Thu, 16 Dec 2010 23:47:45 GMT Frederik Heber <heber@…> [57d976]
	* src/Patterns/unittests/Makefile.am (modified)
	* src/Patterns/unittests/RegistryUnitTest.cpp (moved)
	* src/Patterns/unittests/RegistryUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved RegistryUnitTest to Patterns/unittests/RegistryUnitTest.

	- ...


Thu, 16 Dec 2010 23:47:45 GMT Frederik Heber <heber@…> [5bc8229]
	* src/LinearAlgebra/unittests/Makefile.am (modified)
	* src/LinearAlgebra/unittests/PlaneUnitTest.cpp (moved)
	* src/LinearAlgebra/unittests/PlaneUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved PlaneUnittest to LinearAlgebra/unittests/PlaneUnitTest.


Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber <heber@…> [f89024]
	* src/LinearAlgebra/unittests/LineUnitTest.cpp (moved)
	* src/LinearAlgebra/unittests/LineUnitTest.hpp (moved)
	* src/LinearAlgebra/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Moved LineUnittest to LinearAlgebra/unittests/LineUnitTest.


Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber <heber@…> [41396a]
	* configure.ac (modified)
	* src/Parser/unittests/Makefile.am (added)
	* src/Parser/unittests/ParserCommonUnitTest.cpp (moved)
	* src/Parser/unittests/ParserCommonUnitTest.hpp (moved)
	* src/Parser/unittests/ParserTremoloUnitTest.cpp (moved)
	* src/Parser/unittests/ParserTremoloUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved Parser...UnitTest to  Parser/unittests/Parser...UnitTest.


Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber <heber@…> [a2c4f3]
	* src/Patterns/unittests/Makefile.am (modified)
	* src/Patterns/unittests/ObserverUnitTest.cpp (moved)
	* src/Patterns/unittests/ObserverUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved ObserverTest to Patterns/unittests/ObserverUnitTest.


Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber <heber@…> [6c9adc]
	* src/Descriptors/unittests/Makefile.am (modified)
	* src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (moved)
	* src/Descriptors/unittests/MoleculeDescriptorUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved MoleculeDescriptorTest to ...


Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber <heber@…> [0e2031]
	* configure.ac (modified)
	* src/UIElements/Menu/unittests/Makefile.am (added)
	* src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (moved)
	* src/UIElements/Menu/unittests/MenuDescriptionUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved MenuDescriptionUnitTest to UIElements/Menu/unittests.


Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber <heber@…> [efd61b]
	* src/Actions/unittests/Makefile.am (modified)
	* src/Actions/unittests/ManipulateAtomsUnitTest.cpp (moved)
	* src/Actions/unittests/ManipulateAtomsUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved manipulateAtomsTest to
	Actions/unittests/ManipulateAtomsUnitTest.


Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber <heber@…> [4076fcc]
	* src/Helpers/unittests/LogUnitTest.cpp (moved)
	* src/Helpers/unittests/LogUnitTest.hpp (moved)
	* src/Helpers/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Moved logunittest to Helpers/unittests/LogUnitTest.


Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber <heber@…> [78b593]
	* src/LinearAlgebra/LinearSystemOfEquations.cpp (moved)
	* src/LinearAlgebra/LinearSystemOfEquations.hpp (moved)
	* src/LinearAlgebra/Makefile.am (modified)
	* src/LinearAlgebra/unittests/LinearSystemOfEquationsUnitTest.cpp (moved)
	* src/LinearAlgebra/unittests/LinearSystemOfEquationsUnitTest.hpp (moved)
	* src/LinearAlgebra/unittests/Makefile.am (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/unittests/Makefile.am (modified)

	Moved linearsystemofequations to ...


Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber <heber@…> [fff54f]
	* configure.ac (modified)
	* src/Actions/unittests/Makefile.am (modified)
	* src/Helpers/unittests/InfoUnitTest.cpp (moved)
	* src/Helpers/unittests/InfoUnitTest.hpp (moved)
	* src/Helpers/unittests/Makefile.am (added)
	* src/LinearAlgebra/unittests/Makefile.am (added)
	* src/LinearAlgebra/unittests/MatrixContentSymmetricUnitTest.cpp (moved)
	* src/LinearAlgebra/unittests/MatrixContentSymmetricUnitTest.hpp (moved)
	* src/LinearAlgebra/unittests/MatrixContentUnitTest.cpp (moved)
	* src/LinearAlgebra/unittests/MatrixContentUnitTest.hpp (moved)
	* src/LinearAlgebra/unittests/MatrixUnitTest.cpp (moved)
	* src/LinearAlgebra/unittests/MatrixUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved all Matrix...Unittest to
	LinearAlgebra/unittests/Matrix...UnitTest.


Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber <heber@…> [3c8e8b]
	* src/Actions/unittests/AtomsCalculationUnitTest.cpp (moved)
	* src/Actions/unittests/AtomsCalculationUnitTest.hpp (moved)
	* src/Actions/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Moved atomsCalculationTest to
	Actions/unittests/AtomsCalculationUnitTest.


Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber <heber@…> [e7da1f]
	* src/Patterns/unittests/CacheableUnitTest.cpp (moved)
	* src/Patterns/unittests/CacheableUnitTest.hpp (moved)
	* src/Patterns/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Moved CacheableTest to Patterns/unittests/CacheableUnitTest.


Thu, 16 Dec 2010 23:47:43 GMT Frederik Heber <heber@…> [d766b5]
	* configure.ac (modified)
	* src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (moved)
	* src/Descriptors/unittests/AtomDescriptorUnitTest.hpp (moved)
	* src/Descriptors/unittests/Makefile.am (added)
	* src/unittests/Makefile.am (modified)

	Moved AtomDescriptorTest to
	Descriptors/unittests/AtomDescriptorUnitTest.


Thu, 16 Dec 2010 23:45:30 GMT Frederik Heber <heber@…> [456e78]
	* src/molecule_dynamics.cpp (modified)
	* src/test/ActOnAlltest.hpp (deleted)
	* src/unittests/ActOnAllUnitTest.cpp (deleted)
	* src/unittests/ActOnAllUnitTest.hpp (deleted)
	* src/unittests/Makefile.am (modified)

	Removed ActOnAllUnitTest.

	- Till had replaced all ActOnAll by ...


Thu, 16 Dec 2010 23:45:30 GMT Frederik Heber <heber@…> [f7c0c4]
	* src/Actions/unittests/ActionSequenceUnitTest.cpp (moved)
	* src/Actions/unittests/ActionSequenceUnitTest.hpp (moved)
	* src/Actions/unittests/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Moved ActionSequenceTest to Actions/unittests, renamed to ...


Thu, 16 Dec 2010 23:45:27 GMT Frederik Heber <heber@…> [deddf6]
	* configure.ac (modified)
	* src/Actions/unittests/ActionRegistryUnitTest.cpp (added)
	* src/Actions/unittests/ActionRegistryUnitTest.hpp (added)
	* src/Actions/unittests/Makefile.am (added)
	* src/unittests/Makefile.am (modified)

	New unit test for ActionRegistry.

	- checks whether a short form has ...


Thu, 16 Dec 2010 23:32:21 GMT Frederik Heber <heber@…> [c0bccb]
	* configure.ac (modified)
	* src/Patterns/Singleton_impl.hpp (modified)
	* src/Patterns/unittests/Makefile.am (added)
	* src/Patterns/unittests/SingletonUnitTest.cpp (moved)
	* src/Patterns/unittests/SingletonUnitTest.hpp (moved)
	* src/unittests/Makefile.am (modified)

	Moved SingletonTest to Patterns/unittests/SingletonUnitTest.


Thu, 16 Dec 2010 17:32:22 GMT Frederik Heber <heber@…> [73916f]
	* src/Actions/MoleculeAction/LoadAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAction.def (modified)
	* src/Actions/WorldAction/InputAction.cpp (modified)
	* src/Parser/FormatParser.cpp (modified)
	* src/Parser/FormatParser.hpp (modified)
	* src/Parser/FormatParserStorage.cpp (modified)
	* src/Parser/FormatParserStorage.hpp (modified)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/MpqcParser.hpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/PcpParser.hpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/PdbParser.hpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/TremoloParser.hpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/Parser/XyzParser.hpp (modified)
	* src/unittests/ParserCommonUnitTest.cpp (modified)
	* src/unittests/ParserTremoloUnitTest.cpp (modified)

	Extended FormatParser::save() to use vector<atom *> to save.

	- This ...


Mon, 06 Dec 2010 19:37:05 GMT Frederik Heber <heber@…> [a564be]
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Makefile.am (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/stackclass.hpp (deleted)
	* src/unittests/Makefile.am (modified)
	* src/unittests/stackclassunittest.cpp (deleted)
	* src/unittests/stackclassunittest.hpp (deleted)

	Removed ancient StackClass, replaced by std::deque.

	- all PopLast ...


Sun, 05 Dec 2010 00:20:07 GMT Frederik Heber <heber@…> [cabb46]
	* src/Actions/Makefile.am (modified)
	* src/Actions/MoleculeAction/LoadAction.cpp (added)
	* src/Actions/MoleculeAction/LoadAction.def (moved)
	* src/Actions/MoleculeAction/LoadAction.hpp (moved)
	* src/Actions/MoleculeAction/SaveAction.cpp (moved)
	* src/Actions/MoleculeAction/SaveAction.def (moved)
	* src/Actions/MoleculeAction/SaveAction.hpp (moved)
	* src/Actions/ParserAction/LoadXyzAction.cpp (deleted)
	* src/Actions/WorldAction/InputAction.cpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.def (modified)
	* src/Parser/FormatParserStorage.cpp (modified)
	* src/Parser/FormatParserStorage.hpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/unittests/ParserCommonUnitTest.cpp (modified)
	* tests/regression/Simple_configuration/2/post/test.conf (modified)
	* tests/regression/Simple_configuration/2/post/test.pdb (modified)
	* tests/regression/Simple_configuration/2/pre/test.conf (added)
	* tests/regression/Simple_configuration/2/pre/test.pdb (added)
	* tests/regression/Simple_configuration/2/pre/test.xyz (modified)
	* tests/regression/testsuite-domain.at (modified)
	* tests/regression/testsuite-molecules.at (modified)
	* tests/regression/testsuite-simple_configuration.at (modified)

	Extended LoadXyz and SaveXyz to any format.

	- renamed ...


Sun, 05 Dec 2010 00:01:43 GMT Frederik Heber <heber@…> [4fbca9c]
	* src/Parser/Makefile.am (modified)
	* src/Parser/PdbAtomInfoContainer.cpp (added)
	* src/Parser/PdbAtomInfoContainer.hpp (added)
	* src/Parser/PdbKey.hpp (added)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/PdbParser.hpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/ParserCommonUnitTest.cpp (moved)
	* src/unittests/ParserCommonUnitTest.hpp (added)
	* src/unittests/ParserTremoloUnitTest.cpp (added)
	* src/unittests/ParserTremoloUnitTest.hpp (moved)

	PdbParser::save() fully working.

	- added UnitTest for PdbParser.
	- ...


Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber <heber@…> [e828c0]
	* src/LinearAlgebra/Eigenspace.cpp (modified)
	* src/LinearAlgebra/MatrixContent.cpp (modified)
	* src/LinearAlgebra/MatrixContent.hpp (modified)
	* src/LinearAlgebra/Subspace.cpp (modified)
	* src/LinearAlgebra/Subspace.hpp (modified)
	* src/LinearAlgebra/VectorContent.cpp (modified)
	* src/Makefile.am (modified)
	* src/SubspaceFactorizer.cpp (added)
	* src/unittests/SubspaceFactorizerUnittest.cpp (modified)
	* src/unittests/SubspaceFactorizerUnittest.hpp (modified)

	SubspaceFactorizer is now hierarchical.

	- higher order subspace ...


Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber <heber@…> [286af5f]
	* src/LinearAlgebra/Eigenspace.cpp (modified)
	* src/LinearAlgebra/Eigenspace.hpp (modified)
	* src/LinearAlgebra/Subspace.cpp (modified)
	* src/LinearAlgebra/Subspace.hpp (modified)
	* src/unittests/SubspaceFactorizerUnittest.cpp (modified)
	* src/unittests/SubspaceFactorizerUnittest.hpp (modified)

	SubspaceFactorizerUnittest::SubspaceTest() - fully working compared ...


Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber <heber@…> [a06042]
	* src/LinearAlgebra/Eigenspace.cpp (modified)
	* src/LinearAlgebra/Eigenspace.hpp (modified)
	* src/LinearAlgebra/Subspace.cpp (modified)
	* src/LinearAlgebra/Subspace.hpp (modified)
	* src/unittests/SubspaceFactorizerUnittest.cpp (modified)

	SubspaceFactorizerUnittest::SubspaceTest() enhanced.

	- Now ...


Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber <heber@…> [9c5296]
	* src/LinearAlgebra/Eigenspace.cpp (added)
	* src/LinearAlgebra/Eigenspace.hpp (added)
	* src/LinearAlgebra/Makefile.am (modified)
	* src/LinearAlgebra/Subspace.cpp (added)
	* src/LinearAlgebra/Subspace.hpp (added)
	* src/unittests/SubspaceFactorizerUnittest.cpp (modified)
	* src/unittests/SubspaceFactorizerUnittest.hpp (modified)

	New classes Eigenspace and Subspace that contain eigen(sub)spaces.
 ...


Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber <heber@…> [f5bca2]
	* src/unittests/SubspaceFactorizerUnittest.cpp (modified)
	* src/unittests/SubspaceFactorizerUnittest.hpp (modified)

	SubspaceFactorizer now has the matrix dimension as an enum.


Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber <heber@…> [742371]
	* src/LinearAlgebra/MatrixContent.cpp (modified)
	* src/unittests/SubspaceFactorizerUnittest.cpp (modified)
	* src/unittests/SubspaceFactorizerUnittest.hpp (modified)

	Subspace Factorizer is almost working.

	- for the testing (4x4) ...


Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber <heber@…> [40be55]
	* src/unittests/SubspaceFactorizerUnittest.cpp (modified)
	* src/unittests/SubspaceFactorizerUnittest.hpp (modified)

	Current stable version of SubspaceFactorizer.

	can:
	- functions ...


Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber <heber@…> [5eec98]
	* src/unittests/Makefile.am (modified)

	Subspacefactorizer can now be linked with just GSLLIBS.

	- i.e. we ...


Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber <heber@…> [e4fe8d]
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified)
	* src/Descriptors/AtomIdDescriptor.hpp (modified)
	* src/Descriptors/AtomShapeDescriptor.hpp (modified)
	* src/Descriptors/MoleculeIdDescriptor.hpp (modified)
	* src/Descriptors/MoleculeNameDescriptor.hpp (modified)
	* src/Descriptors/MoleculePtrDescriptor.hpp (modified)
	* src/Helpers/Makefile.am (modified)
	* src/Helpers/defs.cpp (moved)
	* src/Helpers/defs.hpp (moved)
	* src/Helpers/fast_functions.hpp (modified)
	* src/Helpers/helpers.hpp (modified)
	* src/LinearAlgebra/MatrixContent.cpp (modified)
	* src/LinearAlgebra/Plane.cpp (modified)
	* src/LinearAlgebra/RealSpaceMatrix.cpp (modified)
	* src/LinearAlgebra/RealSpaceMatrix.hpp (modified)
	* src/LinearAlgebra/Space.cpp (modified)
	* src/LinearAlgebra/Vector.cpp (modified)
	* src/LinearAlgebra/Vector.hpp (modified)
	* src/LinearAlgebra/VectorContent.cpp (modified)
	* src/LinearAlgebra/linearsystemofequations.cpp (modified)
	* src/Makefile.am (modified)
	* src/Patterns/Singleton.hpp (modified)
	* src/Shapes/BaseShapes.cpp (modified)
	* src/UIElements/Menu/TextMenu/DisplayMenuItem.hpp (modified)
	* src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified)
	* src/UIElements/Menu/TextMenu/TxMenu.hpp (modified)
	* src/UIElements/Qt4/QtUIFactory.cpp (modified)
	* src/UIElements/TextUI/TextWindow.cpp (modified)
	* src/World.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/boundary.hpp (modified)
	* src/element.hpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/unittests/logunittest.cpp (modified)
	* src/unittests/memoryallocatorunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.cpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)
	* src/unittests/vectorunittest.cpp (modified)

	Moved defs.?pp to subdir (and library) Helpers.

	- hence, include ...


Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber <heber@…> [b4cf2b]
	* src/LinearAlgebra/MatrixContent.cpp (modified)
	* src/LinearAlgebra/MatrixContent.hpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/SubspaceFactorizerUnittest.cpp (added)
	* src/unittests/SubspaceFactorizerUnittest.hpp (added)

	First commit of SubspaceFactorizerUnitTest.


Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber <heber@…> [bbf1bd]
	* src/LinearAlgebra/Makefile.am (modified)
	* src/LinearAlgebra/MatrixContent.cpp (modified)
	* src/LinearAlgebra/MatrixContent.hpp (modified)
	* src/LinearAlgebra/RealSpaceMatrix.cpp (modified)
	* src/LinearAlgebra/Vector.cpp (modified)
	* src/LinearAlgebra/Vector.hpp (modified)
	* src/LinearAlgebra/VectorContent.cpp (added)
	* src/LinearAlgebra/VectorContent.hpp (modified)
	* src/LinearAlgebra/linearsystemofequations.cpp (modified)
	* src/LinearAlgebra/linearsystemofequations.hpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/MatrixContentSymmetricUnittest.cpp (modified)
	* src/unittests/MatrixContentUnittest.cpp (modified)
	* src/unittests/VectorContentUnittest.cpp (moved)
	* src/unittests/VectorContentUnittest.hpp (moved)

	Extended VectorContent class.

	- VectorContent formerly has been ...


Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber <heber@…> [0d4424]
	* src/LinearAlgebra/Line.cpp (modified)
	* src/LinearAlgebra/MatrixContent.cpp (modified)
	* src/LinearAlgebra/MatrixContent.hpp (modified)
	* src/LinearAlgebra/linearsystemofequations.cpp (modified)
	* src/LinearAlgebra/linearsystemofequations.hpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/MatrixContentSymmetricUnittest.cpp (moved)
	* src/unittests/MatrixContentSymmetricUnittest.hpp (moved)
	* src/unittests/MatrixContentUnittest.cpp (moved)
	* src/unittests/MatrixContentUnittest.hpp (moved)

	Made gslmatrix obsolete.

	- Transfered property and swap...() ...


Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber <heber@…> [cca9ef]
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified)
	* src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified)
	* src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified)
	* src/Actions/ValueStorage.cpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified)
	* src/Actions/WorldAction/ChangeBoxAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.cpp (modified)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/LinearAlgebra/Makefile.am (modified)
	* src/LinearAlgebra/MatrixContent.cpp (modified)
	* src/LinearAlgebra/MatrixContent.hpp (modified)
	* src/LinearAlgebra/RealSpaceMatrix.cpp (moved)
	* src/LinearAlgebra/RealSpaceMatrix.hpp (moved)
	* src/LinearAlgebra/Vector.hpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Shapes/ShapeOps.cpp (modified)
	* src/Shapes/ShapeOps.hpp (modified)
	* src/Shapes/ShapeOps_impl.hpp (modified)
	* src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified)
	* src/UIElements/Dialog.cpp (modified)
	* src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp (modified)
	* src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified)
	* src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.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/tesselationhelpers.cpp (modified)
	* src/unittests/BoxUnittest.cpp (modified)
	* src/unittests/BoxUnittest.hpp (modified)
	* src/unittests/MatrixUnittest.cpp (modified)
	* src/unittests/MatrixUnittest.hpp (modified)
	* src/unittests/vectorunittest.cpp (modified)

	Renamed Matrix to RealSpaceMatrix.

	- class Matrix only represents ...


Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber <heber@…> [3bc926]
	* src/LinearAlgebra/Makefile.am (modified)
	* src/LinearAlgebra/Matrix.cpp (modified)
	* src/LinearAlgebra/Matrix.hpp (modified)
	* src/LinearAlgebra/MatrixContent.cpp (added)
	* src/LinearAlgebra/MatrixContent.hpp (modified)
	* src/LinearAlgebra/Vector.hpp (modified)
	* src/LinearAlgebra/gslmatrix.cpp (modified)
	* src/LinearAlgebra/gslmatrix.hpp (modified)
	* src/unittests/MatrixUnittest.cpp (modified)

	Extended MatrixContent class.

	- MatrixContent formerly has been ...


Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber <heber@…> [9eb7580]
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified)
	* src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified)
	* src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified)
	* src/Box.cpp (modified)
	* src/LinearAlgebra/Matrix.cpp (modified)
	* src/LinearAlgebra/Matrix.hpp (modified)
	* src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified)
	* src/unittests/BoxUnittest.cpp (modified)
	* src/unittests/MatrixUnittest.cpp (modified)

	Renamed Matrix setter functions to unify naming.

	- Matrix::one -> ...


Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber <heber@…> [c82d0c]
	* src/UIElements/Menu/Menu.cpp (modified)
	* src/UIElements/Menu/Menu.hpp (modified)
	* src/UIElements/Menu/MenuDescription.cpp (modified)
	* src/UIElements/Menu/MenuDescription.hpp (modified)
	* src/builder.cpp (modified)
	* src/unittests/MenuDescriptionUnitTest.cpp (modified)

	MenuDescription is now a singleton.

	- also all Maps are static ...


Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber <heber@…> [d5240d]
	* configure.ac (modified)
	* src/Actions/Makefile.am (modified)
	* src/Exceptions/Makefile.am (modified)
	* src/Helpers/Makefile.am (modified)
	* src/LinearAlgebra/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/Parser/Makefile.am (modified)
	* src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified)
	* src/UIElements/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	FIX: Linking to non-system boost is working now.

	- FIX: ...


Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber <heber@…> [694d84]
	* src/UIElements/UIFactory.cpp (modified)
	* src/unittests/ActionSequenceTest.cpp (modified)
	* src/unittests/ActionSequenceTest.hpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)
	* src/unittests/manipulateAtomsTest.hpp (modified)

	MEMFIX: static factories map of UIFactory was not clear()'ed in ...


Tue, 09 Nov 2010 15:38:03 GMT Frederik Heber <heber@…> [ffb9ad]
	* src/UIElements/Menu/MenuDescription.cpp (modified)
	* src/UIElements/Menu/MenuDescription.hpp (modified)
	* src/UIElements/Qt4/QtMainWindow.cpp (modified)
	* src/UIElements/Qt4/QtMainWindow.hpp (modified)
	* src/UIElements/TextUI/TextWindow.cpp (modified)
	* src/unittests/MenuDescriptionUnitTest.cpp (modified)

	FIX: Menu entries are again correctly added to QtGui part.

	- also ...


Sat, 30 Oct 2010 20:42:44 GMT Frederik Heber <heber@…> [e4afb4]
	* src/Actions/Action.cpp (modified)
	* src/Actions/Action.hpp (modified)
	* src/Actions/ActionHistory.cpp (modified)
	* src/Actions/ActionHistory.hpp (modified)
	* src/Actions/ActionRegistry.cpp (modified)
	* src/Actions/ActionRegistry.hpp (modified)
	* src/Actions/ActionTraits.cpp (modified)
	* src/Actions/ActionTraits.hpp (modified)
	* src/Actions/Action_impl_header.hpp (modified)
	* src/Actions/Action_impl_pre.hpp (modified)
	* src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified)
	* src/Actions/AnalysisAction/MolecularVolumeAction.def (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.def (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.def (modified)
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified)
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.def (modified)
	* src/Actions/AtomAction/AddAction.cpp (modified)
	* src/Actions/AtomAction/AddAction.def (modified)
	* src/Actions/AtomAction/ChangeElementAction.cpp (modified)
	* src/Actions/AtomAction/ChangeElementAction.def (modified)
	* src/Actions/AtomAction/RemoveAction.cpp (modified)
	* src/Actions/AtomAction/RemoveAction.def (modified)
	* src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified)
	* src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (modified)
	* src/Actions/AtomAction/TranslateAction.cpp (modified)
	* src/Actions/AtomAction/TranslateAction.def (modified)
	* src/Actions/AtomsCalculation.hpp (modified)
	* src/Actions/AtomsCalculation_impl.hpp (modified)
	* src/Actions/Calculation.hpp (modified)
	* src/Actions/Calculation_impl.hpp (modified)
	* src/Actions/CommandAction/BondLengthTableAction.cpp (modified)
	* src/Actions/CommandAction/BondLengthTableAction.def (modified)
	* src/Actions/CommandAction/ElementDbAction.cpp (modified)
	* src/Actions/CommandAction/ElementDbAction.def (modified)
	* src/Actions/CommandAction/FastParsingAction.cpp (modified)
	* src/Actions/CommandAction/FastParsingAction.def (modified)
	* src/Actions/CommandAction/HelpAction.cpp (modified)
	* src/Actions/CommandAction/HelpAction.def (modified)
	* src/Actions/CommandAction/VerboseAction.cpp (modified)
	* src/Actions/CommandAction/VerboseAction.def (modified)
	* src/Actions/CommandAction/VersionAction.cpp (modified)
	* src/Actions/CommandAction/VersionAction.def (modified)
	* src/Actions/CommandAction/WarrantyAction.cpp (modified)
	* src/Actions/CommandAction/WarrantyAction.def (modified)
	* src/Actions/ErrorAction.cpp (modified)
	* src/Actions/ErrorAction.hpp (modified)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.def (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.def (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.def (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.def (modified)
	* src/Actions/Makefile.am (modified)
	* src/Actions/MakroAction.cpp (modified)
	* src/Actions/MakroAction.hpp (modified)
	* src/Actions/ManipulateAtomsProcess.cpp (modified)
	* src/Actions/ManipulateAtomsProcess.hpp (modified)
	* src/Actions/MapOfActions.cpp (deleted)
	* src/Actions/MapOfActions.hpp (deleted)
	* src/Actions/MethodAction.cpp (modified)
	* src/Actions/MethodAction.hpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.cpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.def (modified)
	* src/Actions/MoleculeAction/ChangeNameAction.cpp (modified)
	* src/Actions/MoleculeAction/ChangeNameAction.def (modified)
	* src/Actions/MoleculeAction/CopyAction.cpp (modified)
	* src/Actions/MoleculeAction/CopyAction.def (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.def (modified)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified)
	* src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.def (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.def (modified)
	* src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveTemperatureAction.def (modified)
	* src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified)
	* src/Actions/MoleculeAction/SuspendInWaterAction.def (modified)
	* src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified)
	* src/Actions/MoleculeAction/VerletIntegrationAction.def (modified)
	* src/Actions/OptionRegistry.cpp (added)
	* src/Actions/OptionRegistry.hpp (added)
	* src/Actions/OptionTrait.cpp (added)
	* src/Actions/OptionTrait.hpp (added)
	* src/Actions/ParserAction/LoadXyzAction.cpp (modified)
	* src/Actions/ParserAction/LoadXyzAction.def (modified)
	* src/Actions/ParserAction/SaveXyzAction.cpp (modified)
	* src/Actions/ParserAction/SaveXyzAction.def (modified)
	* src/Actions/Process.cpp (modified)
	* src/Actions/Process.hpp (modified)
	* src/Actions/RedoAction.cpp (added)
	* src/Actions/RedoAction.def (added)
	* src/Actions/RedoAction.hpp (added)
	* src/Actions/SelectionAction/AllAtomsAction.cpp (modified)
	* src/Actions/SelectionAction/AllAtomsAction.def (modified)
	* src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified)
	* src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (modified)
	* src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified)
	* src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (modified)
	* src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified)
	* src/Actions/SelectionAction/AllAtomsOfMoleculeAction.def (modified)
	* src/Actions/SelectionAction/AllMoleculesAction.cpp (modified)
	* src/Actions/SelectionAction/AllMoleculesAction.def (modified)
	* src/Actions/SelectionAction/AtomByElementAction.cpp (modified)
	* src/Actions/SelectionAction/AtomByElementAction.def (modified)
	* src/Actions/SelectionAction/AtomByIdAction.cpp (modified)
	* src/Actions/SelectionAction/AtomByIdAction.def (modified)
	* src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified)
	* src/Actions/SelectionAction/ClearAllAtomsAction.def (modified)
	* src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified)
	* src/Actions/SelectionAction/ClearAllMoleculesAction.def (modified)
	* src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified)
	* src/Actions/SelectionAction/MoleculeByFormulaAction.def (modified)
	* src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified)
	* src/Actions/SelectionAction/MoleculeByIdAction.def (modified)
	* src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified)
	* src/Actions/SelectionAction/MoleculeOfAtomAction.def (modified)
	* src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified)
	* src/Actions/SelectionAction/NotAllAtomsAction.def (modified)
	* src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified)
	* src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (modified)
	* src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified)
	* src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (modified)
	* src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified)
	* src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (modified)
	* src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified)
	* src/Actions/SelectionAction/NotAllMoleculesAction.def (modified)
	* src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified)
	* src/Actions/SelectionAction/NotAtomByElementAction.def (modified)
	* src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified)
	* src/Actions/SelectionAction/NotAtomByIdAction.def (modified)
	* src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified)
	* src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (modified)
	* src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified)
	* src/Actions/SelectionAction/NotMoleculeByIdAction.def (modified)
	* src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified)
	* src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.def (modified)
	* src/Actions/UndoAction.cpp (added)
	* src/Actions/UndoAction.def (moved)
	* src/Actions/UndoAction.hpp (added)
	* src/Actions/ValueStorage.cpp (modified)
	* src/Actions/ValueStorage.hpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.def (modified)
	* src/Actions/WorldAction/BoundInBoxAction.cpp (modified)
	* src/Actions/WorldAction/BoundInBoxAction.def (modified)
	* src/Actions/WorldAction/CenterInBoxAction.cpp (modified)
	* src/Actions/WorldAction/CenterInBoxAction.def (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.def (modified)
	* src/Actions/WorldAction/ChangeBoxAction.cpp (modified)
	* src/Actions/WorldAction/ChangeBoxAction.def (modified)
	* src/Actions/WorldAction/InputAction.cpp (modified)
	* src/Actions/WorldAction/InputAction.def (modified)
	* src/Actions/WorldAction/OutputAction.cpp (modified)
	* src/Actions/WorldAction/OutputAction.def (modified)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.def (modified)
	* src/Actions/WorldAction/ScaleBoxAction.cpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.def (modified)
	* src/Actions/WorldAction/SetDefaultNameAction.cpp (modified)
	* src/Actions/WorldAction/SetDefaultNameAction.def (modified)
	* src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified)
	* src/Actions/WorldAction/SetGaussianBasisAction.def (modified)
	* src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified)
	* src/Actions/WorldAction/SetOutputFormatsAction.def (modified)
	* src/Actions/convert5.sh (added)
	* src/CommandLineParser.cpp (deleted)
	* src/Makefile.am (modified)
	* src/Patterns/Registry.hpp (modified)
	* src/Patterns/Registry_impl.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser.cpp (added)
	* src/UIElements/CommandLineUI/CommandLineParser.hpp (moved)
	* src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified)
	* src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/TypeEnumContainer.cpp (added)
	* src/UIElements/CommandLineUI/TypeEnumContainer.hpp (added)
	* src/UIElements/Dialog.cpp (modified)
	* src/UIElements/Dialog.hpp (modified)
	* src/UIElements/Makefile.am (modified)
	* src/UIElements/Menu/MenuDescription.cpp (modified)
	* src/UIElements/Menu/MenuDescription.hpp (modified)
	* src/UIElements/Menu/TextMenu.cpp (modified)
	* src/UIElements/Menu/TextMenu.hpp (modified)
	* src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified)
	* src/UIElements/Qt4/QtDialog.hpp (modified)
	* src/UIElements/Qt4/QtMainWindow.cpp (modified)
	* src/UIElements/TextUI/TextWindow.cpp (modified)
	* src/UIElements/TextUI/TextWindow.hpp (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/World_calculations.hpp (modified)
	* src/builder.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/unittests/ActionSequenceTest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/MenuDescriptionUnitTest.cpp (modified)
	* src/unittests/MenuDescriptionUnitTest.hpp (modified)
	* src/unittests/RegistryUnitTest.cpp (added)
	* src/unittests/RegistryUnitTest.hpp (added)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* tests/regression/testsuite-simple_configuration.at (modified)

	Huge refactoring: Introduction of Traits to Actions.

	This change is ...


Sat, 30 Oct 2010 19:25:29 GMT Frederik Heber <heber@…> [8bcf3f]
	* src/UIElements/Makefile.am (modified)
	* src/UIElements/Menu/MenuDescription.cpp (added)
	* src/UIElements/Menu/MenuDescription.hpp (added)
	* src/unittests/Makefile.am (modified)
	* src/unittests/MenuDescriptionUnitTest.cpp (added)
	* src/unittests/MenuDescriptionUnitTest.hpp (added)

	New class MenuDescription containing information on menu items.

	- ...


Fri, 22 Oct 2010 16:13:36 GMT Frederik Heber <heber@…> [6f5dfe]
	* src/Actions/MapOfActions.cpp (modified)
	* src/Actions/MapOfActions.hpp (modified)
	* src/Actions/WorldAction/InputAction.cpp (modified)
	* src/Actions/WorldAction/InputAction.def (modified)
	* src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified)
	* src/UIElements/Dialog.cpp (modified)
	* src/UIElements/Dialog.hpp (modified)
	* src/UIElements/QT4/QTDialog.cpp (modified)
	* src/UIElements/QT4/QTDialog.hpp (modified)
	* src/UIElements/TextUI/TextDialog.cpp (modified)
	* src/UIElements/TextUI/TextDialog.hpp (modified)
	* src/unittests/DummyUI.hpp (modified)

	Added boost::filesystem usage for input files.

	- parameters for ...