#
# ChangeLog for src/atom.hpp
#
# Generated by Trac 1.4.4
# Dec 28, 2024, 10:04:16 AM

Thu, 20 Oct 2011 22:42:16 GMT Frederik Heber <heber@…> [360c8b]
	* configure.ac (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/LoadAction.cpp (modified)
	* src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified)
	* src/Actions/ParserAction/SetMpqcParametersAction.cpp (modified)
	* src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified)
	* src/Parser/FormatParser.hpp (modified)
	* src/Parser/FormatParserInterface.hpp (added)
	* src/Parser/FormatParserStorage.cpp (modified)
	* src/Parser/FormatParserStorage.hpp (modified)
	* src/Parser/FormatParserTrait.hpp (added)
	* src/Parser/FormatParserTrait_specializations_header.hpp (added)
	* src/Parser/FormatParser_Parameters.cpp (added)
	* src/Parser/FormatParser_Parameters.hpp (modified)
	* src/Parser/FormatParser_common.cpp (moved)
	* src/Parser/FormatParser_common.hpp (added)
	* src/Parser/FormatParser_specializations_header.hpp (added)
	* src/Parser/Makefile.am (modified)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/MpqcParser.hpp (modified)
	* src/Parser/MpqcParser_Parameters.cpp (modified)
	* src/Parser/MpqcParser_Parameters.hpp (modified)
	* src/Parser/Parameters/ContinuousParameter.hpp (added)
	* src/Parser/Parameters/ContinuousParameter_impl.hpp (added)
	* src/Parser/Parameters/ContinuousValue.hpp (added)
	* src/Parser/Parameters/ContinuousValue_impl.hpp (added)
	* src/Parser/Parameters/DiscreteParameter.hpp (added)
	* src/Parser/Parameters/DiscreteParameter_impl.hpp (added)
	* src/Parser/Parameters/DiscreteValue.hpp (added)
	* src/Parser/Parameters/DiscreteValue_impl.hpp (added)
	* src/Parser/Parameters/Parameter.hpp (added)
	* src/Parser/Parameters/ParameterStorage.cpp (added)
	* src/Parser/Parameters/ParameterStorage.hpp (added)
	* src/Parser/Parameters/StringParameter.cpp (added)
	* src/Parser/Parameters/StringParameter.hpp (added)
	* src/Parser/Parameters/ValueInterface.hpp (added)
	* src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (added)
	* src/Parser/Parameters/unittests/ContinuousParameterUnitTest.hpp (added)
	* src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (added)
	* src/Parser/Parameters/unittests/ContinuousValueUnitTest.hpp (added)
	* src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (added)
	* src/Parser/Parameters/unittests/DiscreteParameterUnitTest.hpp (added)
	* src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (added)
	* src/Parser/Parameters/unittests/DiscreteValueUnitTest.hpp (added)
	* src/Parser/Parameters/unittests/Makefile.am (added)
	* src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (added)
	* src/Parser/Parameters/unittests/ParameterStorageUnitTest.hpp (added)
	* src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (added)
	* src/Parser/Parameters/unittests/StringParameterUnitTest.hpp (added)
	* src/Parser/ParserTypes.cpp (added)
	* src/Parser/ParserTypes.def (added)
	* src/Parser/ParserTypes.hpp (added)
	* src/Parser/ParserTypes.undef (added)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/PcpParser.hpp (modified)
	* src/Parser/PdbAtomInfoContainer.hpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/PdbParser.hpp (modified)
	* src/Parser/Psi3Parser.cpp (added)
	* src/Parser/Psi3Parser.hpp (added)
	* src/Parser/Psi3Parser_Parameters.cpp (added)
	* src/Parser/Psi3Parser_Parameters.hpp (added)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/TremoloParser.hpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/Parser/XyzParser.hpp (modified)
	* src/Parser/unittests/Makefile.am (modified)
	* src/Parser/unittests/ParserMpqcUnitTest.cpp (modified)
	* src/Parser/unittests/ParserMpqcUnitTest.hpp (modified)
	* src/Parser/unittests/ParserPcpUnitTest.cpp (modified)
	* src/Parser/unittests/ParserPcpUnitTest.hpp (modified)
	* src/Parser/unittests/ParserPdbUnitTest.cpp (modified)
	* src/Parser/unittests/ParserPdbUnitTest.hpp (modified)
	* src/Parser/unittests/ParserPsi3UnitTest.cpp (added)
	* src/Parser/unittests/ParserPsi3UnitTest.hpp (added)
	* src/Parser/unittests/ParserTremoloUnitTest.cpp (modified)
	* src/Parser/unittests/ParserTremoloUnitTest.hpp (modified)
	* src/Parser/unittests/ParserXyzUnitTest.cpp (modified)
	* src/Parser/unittests/ParserXyzUnitTest.hpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/BoxUnitTest.cpp (modified)
	* src/unittests/FormulaUnitTest.cpp (modified)
	* tests/regression/Makefile.am (modified)
	* tests/regression/Parser/Psi3/post/empty.psi (added)
	* tests/regression/Parser/Psi3/post/test.psi (added)
	* tests/regression/Parser/Psi3/pre/empty.psi (added)
	* tests/regression/Parser/Psi3/pre/test.xyz (added)
	* tests/regression/Parser/Psi3/pre/testrhf.psi (added)
	* tests/regression/Parser/Psi3/pre/testrohf.psi (added)
	* tests/regression/Parser/Psi3/pre/testtwocon.psi (added)
	* tests/regression/Parser/Psi3/pre/testuhf.psi (added)
	* tests/regression/Parser/Psi3/testsuite-parser-psi3-empty.at (added)
	* tests/regression/Parser/Psi3/testsuite-parser-psi3-load.at (added)
	* tests/regression/Parser/Psi3/testsuite-parser-psi3-save.at (added)
	* tests/regression/Parser/testsuite-parser.at (modified)

	Merge branch 'Adding_Psi3Parser' into stable

	Conflicts:
	        ...


Tue, 18 Oct 2011 08:23:11 GMT Frederik Heber <heber@…> [9011c1]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	Added atom::OutputPsi3Line() to output a Psi3 conforming geometry
	line.


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.

	- ...


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, 02 Mar 2011 21:53:08 GMT Frederik Heber <heber@…> [0d9546]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	new function atom::unsetMolecule().

	- is meant along with ...


Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber <heber@…> [1363de]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	DOCUFIX: atom - Moved all doxygen documentation to header file.


Thu, 24 Feb 2011 18:36:33 GMT Frederik Heber <heber@…> [e2373df]
	* src/TesselPoint.cpp (modified)
	* src/TesselPoint.hpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)

	TesselPoint, Atom and AtomInfo have virtual UpdateSteps() to allow ...


Thu, 24 Feb 2011 17:46:46 GMT Frederik Heber <heber@…> [6625c3]
	* src/AtomSet.hpp (modified)
	* src/Makefile.am (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Thermostats/Berendsen.cpp (modified)
	* src/Thermostats/GaussianThermostat.cpp (modified)
	* src/Thermostats/Langevin.cpp (modified)
	* src/Thermostats/Langevin.hpp (modified)
	* src/Thermostats/NoseHoover.cpp (modified)
	* src/Thermostats/Woodcock.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/atom_trajectoryparticle.cpp (deleted)
	* src/atom_trajectoryparticle.hpp (deleted)
	* src/atom_trajectoryparticleinfo.cpp (deleted)
	* src/atom_trajectoryparticleinfo.hpp (deleted)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_geometry.cpp (modified)

	Removed atom_trajectoryparticle*, replaced by AtomInfo class now ...


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, 26 Aug 2010 12:20:17 GMT Tillmann Crueger <crueger@…> [e8a21f]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	Added an atom::getNr() method to atom class


Thu, 26 Aug 2010 11:02:41 GMT Tillmann Crueger <crueger@…> [882a8a]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (modified)

	made the atom::OutputTrajectories() method use an enumeration of ...


Thu, 26 Aug 2010 10:35:39 GMT Tillmann Crueger <crueger@…> [e5f64de]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	Added a method that allows comparison of atoms by their atomic number


Thu, 26 Aug 2010 09:34:49 GMT Tillmann Crueger <crueger@…> [0dc86e2]
	* src/Parser/MpqcParser.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/config.cpp (modified)

	Removed unused AtomNo parameter in atom::OutputMPQCLine()


Wed, 25 Aug 2010 16:10:02 GMT Tillmann Crueger <crueger@…> [14b65e]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	Added a method to reset the graphNr of an atom


Wed, 25 Aug 2010 13:41:56 GMT Tillmann Crueger <crueger@…> [1f8337]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)

	Moved AtomInfo::getMass() method to class atom to avoid problems with ...


Tue, 10 Aug 2010 11:31:36 GMT Frederik Heber <heber@…> [e41c48]
	* src/Actions/AtomAction/RemoveAction.cpp (modified)
	* src/AtomicInfo.cpp (added)
	* src/AtomicInfo.hpp (added)
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* tests/regression/Simple_configuration/5/pre/test.conf (modified)
	* tests/regression/testsuite-simple_configuration.at (modified)

	RemoveAction has Undo/Redo capability.

	- FIX: atom::getMolecule() ...


Sat, 07 Aug 2010 12:07:04 GMT Frederik Heber <heber@…> [8f4df1]
	* 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/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified)
	* src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.cpp (modified)
	* src/AtomSet.hpp (modified)
	* src/BoundaryLineSet.cpp (added)
	* src/BoundaryLineSet.hpp (added)
	* src/BoundaryMaps.hpp (added)
	* src/BoundaryPointSet.cpp (added)
	* src/BoundaryPointSet.hpp (added)
	* src/BoundaryPolygonSet.cpp (added)
	* src/BoundaryPolygonSet.hpp (added)
	* src/BoundaryTriangleSet.cpp (added)
	* src/BoundaryTriangleSet.hpp (added)
	* src/CandidateForTesselation.cpp (added)
	* src/CandidateForTesselation.hpp (added)
	* src/Legacy/oldmenu.cpp (modified)
	* src/LinearAlgebra/Makefile.am (modified)
	* src/LinearAlgebra/Vector.cpp (modified)
	* src/LinearAlgebra/Vector.hpp (modified)
	* src/LinearAlgebra/VectorInterface.cpp (added)
	* src/LinearAlgebra/VectorInterface.hpp (added)
	* src/LinearAlgebra/vector_ops.cpp (moved)
	* src/LinearAlgebra/vector_ops.hpp (moved)
	* src/Makefile.am (modified)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/PointCloud.cpp (added)
	* src/PointCloud.hpp (added)
	* src/TesselPoint.cpp (added)
	* src/TesselPoint.hpp (added)
	* src/UIElements/QT4/QTDialog.cpp (modified)
	* src/UIElements/TextUI/TextDialog.cpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/atom_bondedparticleinfo.hpp (modified)
	* src/atom_graphnodeinfo.hpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/atom_particleinfo.hpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/atom_trajectoryparticle.hpp (modified)
	* src/atom_trajectoryparticleinfo.hpp (modified)
	* src/bond.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.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_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/triangleintersectionlist.cpp (modified)
	* src/triangleintersectionlist.hpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/ParserUnitTest.cpp (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.hpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/unittests/vectorunittest.hpp (modified)

	Merge branch 'AtomicPositionEncapsulation' into stable

	Conflicts:
	 ...


Thu, 05 Aug 2010 15:46:01 GMT Tillmann Crueger <crueger@…> [0ba410]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)

	made the molecule::Output() method use STL algorithms


Thu, 05 Aug 2010 14:45:59 GMT Tillmann Crueger <crueger@…> [00abfc]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	Added a method to class atom that determines if the father of this ...


Sat, 31 Jul 2010 15:23:10 GMT Frederik Heber <heber@…> [d74077]
	* 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/AtomAction/AddAction.cpp (modified)
	* src/Actions/AtomAction/ChangeElementAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified)
	* src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.cpp (modified)
	* src/BoundaryLineSet.cpp (added)
	* src/BoundaryLineSet.hpp (added)
	* src/BoundaryMaps.hpp (added)
	* src/BoundaryPointSet.cpp (added)
	* src/BoundaryPointSet.hpp (added)
	* src/BoundaryPolygonSet.cpp (added)
	* src/BoundaryPolygonSet.hpp (added)
	* src/BoundaryTriangleSet.cpp (added)
	* src/BoundaryTriangleSet.hpp (added)
	* src/CandidateForTesselation.cpp (added)
	* src/CandidateForTesselation.hpp (added)
	* src/Legacy/oldmenu.cpp (modified)
	* src/Makefile.am (modified)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/PointCloud.cpp (added)
	* src/PointCloud.hpp (added)
	* src/TesselPoint.cpp (added)
	* src/TesselPoint.hpp (added)
	* src/UIElements/QT4/QTDialog.cpp (modified)
	* src/UIElements/TextUI/TextDialog.cpp (modified)
	* src/VectorInterface.cpp (added)
	* src/VectorInterface.hpp (added)
	* src/analysis_bonds.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/atom_bondedparticleinfo.hpp (modified)
	* src/atom_graphnodeinfo.hpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/atom_particleinfo.hpp (modified)
	* src/atom_trajectoryparticle.cpp (modified)
	* src/atom_trajectoryparticle.hpp (modified)
	* src/atom_trajectoryparticleinfo.hpp (modified)
	* src/bond.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.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_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/triangleintersectionlist.cpp (modified)
	* src/triangleintersectionlist.hpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/ParserUnitTest.cpp (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.hpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/unittests/vectorunittest.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Member variable Vector and element of class atom are now private.

	- ...


Thu, 15 Jul 2010 15:21:06 GMT Tillmann Crueger <crueger@…> [c084cc]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	Added a method to query the molecule an atom belongs to.


Fri, 02 Jul 2010 13:19:32 GMT Tillmann Crueger <crueger@…> [986ed3]
	* src/Actions/ActionRegistry.hpp (modified)
	* src/Actions/AtomsCalculation_impl.hpp (modified)
	* src/Actions/MapOfActions.cpp (modified)
	* src/ConfigFileBuffer.hpp (modified)
	* src/Exceptions/CustomException.hpp (modified)
	* src/Helpers/Assert.hpp (modified)
	* src/Matrix.hpp (modified)
	* src/Parser/MpqcParser.hpp (modified)
	* src/Parser/PcpParser.hpp (modified)
	* src/Patterns/Cacheable.hpp (modified)
	* src/Plane.hpp (modified)
	* src/UIElements/Views/StreamStringView.hpp (modified)
	* src/atom.hpp (modified)
	* src/atom_particleinfo.hpp (modified)
	* src/bondgraph.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/datacreator.hpp (modified)
	* src/element.hpp (modified)
	* src/errorlogger.cpp (modified)
	* src/errorlogger.hpp (modified)
	* src/gslvector.hpp (modified)
	* src/helpers.cpp (modified)
	* src/logger.cpp (modified)
	* src/logger.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.hpp (modified)

	COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with ...


Thu, 01 Jul 2010 14:37:53 GMT Tillmann Crueger <crueger@…> [c550dd]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/unittests/vectorunittest.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Removed the VectorIsInParallelepiped in favor of more general methods ...


Wed, 30 Jun 2010 12:20:34 GMT Tillmann Crueger <crueger@…> [9df5c6]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Made the Vector::IsInParallelepiped() method take a matrix instead of ...


Mon, 21 Jun 2010 07:56:00 GMT Frederik Heber <heber@…> [55240c4]
	* doc/Doxyfile (modified)
	* src/Actions/Action.cpp (modified)
	* src/Actions/ActionHistory.cpp (modified)
	* src/Actions/ActionRegistry.cpp (modified)
	* src/Actions/ActionSequence.cpp (modified)
	* src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified)
	* src/Actions/AtomAction/AddAction.cpp (modified)
	* src/Actions/AtomAction/ChangeElementAction.cpp (modified)
	* src/Actions/AtomAction/RemoveAction.cpp (modified)
	* src/Actions/CmdAction/BondLengthTableAction.cpp (modified)
	* src/Actions/CmdAction/ElementDbAction.cpp (modified)
	* src/Actions/CmdAction/FastParsingAction.cpp (modified)
	* src/Actions/CmdAction/HelpAction.cpp (modified)
	* src/Actions/CmdAction/VerboseAction.cpp (modified)
	* src/Actions/CmdAction/VersionAction.cpp (modified)
	* src/Actions/ErrorAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MakroAction.cpp (modified)
	* src/Actions/ManipulateAtomsProcess.cpp (modified)
	* src/Actions/MapOfActions.cpp (modified)
	* src/Actions/MethodAction.cpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.cpp (modified)
	* src/Actions/MoleculeAction/ChangeNameAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified)
	* src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified)
	* src/Actions/MoleculeAction/TranslateAction.cpp (modified)
	* src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified)
	* src/Actions/ParserAction/LoadXyzAction.cpp (modified)
	* src/Actions/ParserAction/SaveXyzAction.cpp (modified)
	* src/Actions/Process.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified)
	* src/Actions/WorldAction/BoundInBoxAction.cpp (modified)
	* src/Actions/WorldAction/CenterInBoxAction.cpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified)
	* src/Actions/WorldAction/ChangeBoxAction.cpp (modified)
	* src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.cpp (modified)
	* src/Actions/WorldAction/SetDefaultNameAction.cpp (modified)
	* src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified)
	* src/CommandLineParser.cpp (modified)
	* src/Descriptors/AtomDescriptor.cpp (modified)
	* src/Descriptors/AtomIdDescriptor.cpp (modified)
	* src/Descriptors/AtomTypeDescriptor.cpp (modified)
	* src/Descriptors/MoleculeDescriptor.cpp (modified)
	* src/Descriptors/MoleculeIdDescriptor.cpp (modified)
	* src/Descriptors/MoleculePtrDescriptor.cpp (modified)
	* src/Exceptions/CustomException.cpp (modified)
	* src/Exceptions/LinearDependenceException.cpp (modified)
	* src/Exceptions/MathException.cpp (modified)
	* src/Exceptions/MultipleSolutionsException.hpp (added)
	* src/Exceptions/SkewException.cpp (added)
	* src/Exceptions/SkewException.hpp (added)
	* src/Exceptions/ZeroVectorException.cpp (modified)
	* src/Hbondangle.db (modified)
	* src/Hbonddistance.db (modified)
	* src/Helpers/Assert.cpp (modified)
	* src/Helpers/MemDebug.cpp (modified)
	* src/Helpers/MemDebug.hpp (modified)
	* src/Legacy/oldmenu.cpp (modified)
	* src/Line.cpp (modified)
	* src/Line.hpp (modified)
	* src/Makefile.am (modified)
	* src/Parser/ChangeTracker.cpp (modified)
	* src/Parser/FormatParser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/Patterns/Cacheable.hpp (modified)
	* src/Patterns/ObservedIterator.hpp (modified)
	* src/Patterns/Observer.cpp (modified)
	* src/Patterns/Observer.hpp (modified)
	* src/Plane.cpp (modified)
	* src/Plane.hpp (modified)
	* src/Space.cpp (modified)
	* src/Space.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified)
	* src/UIElements/Dialog.cpp (modified)
	* src/UIElements/MainWindow.cpp (modified)
	* src/UIElements/Menu/ActionMenuItem.cpp (modified)
	* src/UIElements/Menu/DisplayMenuItem.cpp (modified)
	* src/UIElements/Menu/Menu.cpp (modified)
	* src/UIElements/Menu/MenuItem.cpp (modified)
	* src/UIElements/Menu/SeperatorItem.cpp (modified)
	* src/UIElements/Menu/SubMenuItem.cpp (modified)
	* src/UIElements/Menu/TextMenu.cpp (modified)
	* src/UIElements/TextUI/TextDialog.cpp (modified)
	* src/UIElements/TextUI/TextStatusIndicator.cpp (modified)
	* src/UIElements/TextUI/TextUIFactory.cpp (modified)
	* src/UIElements/TextUI/TextUIFactory.hpp (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/StreamStringView.cpp (modified)
	* src/UIElements/Views/StringView.cpp (modified)
	* src/UIElements/Views/View.cpp (modified)
	* src/VectorSet.cpp (added)
	* src/VectorSet.hpp (added)
	* src/World.cpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/analysis_correlation.cpp (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/atom_trajectoryparticleinfo.hpp (modified)
	* src/bond.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/datacreator.cpp (modified)
	* src/element.cpp (modified)
	* src/elements_db.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/errorlogger.cpp (modified)
	* src/graph.cpp (modified)
	* src/gslmatrix.cpp (modified)
	* src/gslvector.cpp (modified)
	* src/gslvector.hpp (modified)
	* src/helpers.cpp (modified)
	* src/info.cpp (modified)
	* src/joiner.cpp (modified)
	* src/leastsquaremin.cpp (modified)
	* src/linearsystemofequations.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/log.cpp (modified)
	* src/logger.cpp (modified)
	* src/memoryallocator.cpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.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/orbitals.db (modified)
	* src/parser.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/triangleintersectionlist.cpp (modified)
	* src/unittests/CacheableTest.cpp (modified)
	* src/unittests/LineUnittest.cpp (added)
	* src/unittests/LineUnittest.hpp (added)
	* src/unittests/Makefile.am (modified)
	* src/unittests/ObserverTest.cpp (modified)
	* src/unittests/PlaneUnittest.cpp (modified)
	* src/unittests/PlaneUnittest.hpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/unittests/vectorunittest.hpp (modified)
	* src/valence.db (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vector_ops.cpp (modified)
	* src/vector_ops.hpp (modified)
	* src/verbose.cpp (modified)
	* tests/regression/Domain/2/post/test.conf (modified)
	* tests/regression/Domain/3/post/test.conf (modified)
	* tests/regression/Domain/4/post/test.conf (modified)
	* tests/regression/Domain/5/post/test.conf (modified)
	* tests/regression/Filling/1/post/test.conf (modified)
	* tests/regression/Filling/1/pre/test.conf (modified)
	* tests/regression/Molecules/6/post/test.conf (modified)
	* tests/regression/Molecules/6/pre/test.conf (modified)
	* tests/regression/Molecules/7/post/test.conf (modified)
	* tests/regression/Molecules/7/pre/test.conf (modified)
	* tests/regression/Simple_configuration/2/post/test.conf (modified)
	* tests/regression/Simple_configuration/3/post/test.conf (modified)
	* tests/regression/Simple_configuration/4/post/test.conf (modified)
	* tests/regression/Simple_configuration/5/post/test.conf (modified)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified)
	* tests/regression/testsuite-tesselation.at (modified)

	Merge branch 'stable' into PcpAndMpqcParser

	Conflicts:
	        ...


Sat, 19 Jun 2010 12:13:45 GMT Frederik Heber <heber@…> [ad2b411]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	atom::getId() should be a const function as it changes nothing in the ...


Sat, 12 Jun 2010 22:19:48 GMT Frederik Heber <heber@…> [1b2d30]
	* src/ConfigFileBuffer.cpp (modified)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/MpqcParser.hpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/PcpParser.hpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/config.cpp (modified)
	* src/unittests/ParserUnitTest.cpp (modified)
	* src/unittests/ParserUnitTest.hpp (modified)

	Extended PcpParser, completed MpqcParser.

	- BUGFIX: ...


Sat, 12 Jun 2010 15:54:26 GMT Frederik Heber <heber@…> [43dad6]
	* src/ConfigFileBuffer.cpp (modified)
	* src/ConfigFileBuffer.hpp (modified)
	* src/Makefile.am (modified)
	* src/Parser/MpqcParser.cpp (added)
	* src/Parser/MpqcParser.hpp (added)
	* src/Parser/PcpParser.cpp (added)
	* src/Parser/PcpParser.hpp (added)
	* src/ThermoStatContainer.cpp (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/molecule.cpp (modified)

	Introducing (but not yet incorporated) FormatParser specializations ...


Fri, 11 Jun 2010 15:41:41 GMT Tillmann Crueger <crueger@…> [6cfa36]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)

	Made atoms remove themselves from molecules upon destruction


Fri, 12 Mar 2010 13:16:01 GMT Tillmann Crueger <crueger@…> [ead4e6]
	* src/Actions/AtomsCalculation_impl.hpp (modified)
	* src/Actions/Calculation_impl.hpp (modified)
	* src/Descriptors/AtomTypeDescriptor.cpp (modified)
	* src/Descriptors/AtomTypeDescriptor.hpp (modified)
	* src/Descriptors/AtomTypeDescriptor_impl.hpp (modified)
	* src/Legacy/oldmenu.cpp (modified)
	* src/World.hpp (modified)
	* src/atom.hpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/defs.hpp (modified)
	* src/element.cpp (modified)
	* src/element.hpp (modified)
	* src/leastsquaremin.hpp (modified)
	* src/molecule.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/types.hpp (added)
	* src/unittests/AtomDescriptorTest.hpp (modified)
	* src/unittests/CacheableTest.cpp (modified)
	* src/unittests/MoleculeDescriptorTest.hpp (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* src/unittests/atomsCalculationTest.hpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)

	Made the periodentafel use STL-containers instead of custom llists


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

	Added methods to query Molecules by ID


Wed, 03 Mar 2010 17:47:40 GMT Tillmann Crueger <crueger@…> [88d586]
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	Added mechanisms that allow reuse of IDs and changing Ids of Atoms


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

	Made the world solely responsible for creating and destroying atoms.


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

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

	- first shift ...


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

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

	- basically all ...


Tue, 20 Oct 2009 08:55:17 GMT Frederik Heber <heber@…> [6b919f8]
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_atominfo.cpp (added)
	* src/atom_atominfo.hpp (added)
	* src/atom_bondedparticle.cpp (added)
	* src/atom_bondedparticle.hpp (added)
	* src/atom_bondedparticleinfo.cpp (added)
	* src/atom_bondedparticleinfo.hpp (added)
	* src/atom_graphnode.cpp (added)
	* src/atom_graphnode.hpp (added)
	* src/atom_graphnodeinfo.cpp (added)
	* src/atom_graphnodeinfo.hpp (added)
	* src/atom_particleinfo.cpp (added)
	* src/atom_particleinfo.hpp (added)
	* src/atom_trajectoryparticle.cpp (added)
	* src/atom_trajectoryparticle.hpp (added)
	* src/atom_trajectoryparticleinfo.cpp (added)
	* src/atom_trajectoryparticleinfo.hpp (added)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Refactored atom.cpp into multiple files.

	After the class atom was ...


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

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


Sun, 18 Oct 2009 16:09:26 GMT Frederik Heber <heber@…> [2cc75c3]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Shifted molecuke::InitComponentNumbers() to atom::InitComponentNr.
 ...


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

	Huge refactoring: molecule::ListOfBondsPerAtom and ...


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

	First half of molecule_fragmentation.cpp refactoring.

	- new ...


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

	Complete refactoring of molecule_dynamics.cpp

	- new small ...


Fri, 09 Oct 2009 14:35:14 GMT Frederik Heber <heber@…> [ccd9f5]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)

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


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

	Implementing templated iterators done for molecule.cpp

	- new ...


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

	forward declarations used to untangle interdependet classes.

	- ...


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

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


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

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


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

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


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

	More functions of molecule now use templated iterators.

	- the ...


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

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

	- are ...


Sat, 08 Aug 2009 19:17:51 GMT Frederik Heber <heber@…> [055861]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	new stream operator with just one parameter and virtual destructor


Mon, 03 Aug 2009 20:21:05 GMT Frederik Heber <heber@…> [ab1932]
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (added)
	* src/bond.cpp (modified)
	* src/bond.hpp (added)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (added)
	* src/element.cpp (modified)
	* src/element.hpp (added)
	* src/ellipsoid.cpp (modified)
	* src/ellipsoid.hpp (modified)
	* src/helpers.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (added)
	* src/tesselation.hpp (added)
	* src/tesselationhelpers.cpp (added)
	* src/tesselationhelpers.hpp (added)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.hpp (added)

	Merge branch 'TesselationRefactoring' into ConcaveHull

	Conflicts:
 ...


Mon, 03 Aug 2009 15:09:12 GMT Frederik Heber <heber@…> [cd4ccc]
	* src/Makefile.am (modified)
	* src/atom.hpp (modified)
	* src/bond.hpp (modified)
	* src/config.hpp (modified)
	* src/element.cpp (modified)
	* src/element.hpp (added)
	* src/helpers.hpp (modified)
	* src/molecules.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/verbose.hpp (added)

	definitions for class element and verbose moved to their own header ...


Mon, 03 Aug 2009 14:48:42 GMT Frederik Heber <heber@…> [357fba]
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (added)
	* src/bond.cpp (modified)
	* src/bond.hpp (added)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/ellipsoid.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/tesselation.cpp (added)
	* src/tesselation.hpp (added)
	* src/tesselationhelpers.cpp (added)
	* src/tesselationhelpers.hpp (added)
	* src/vector.hpp (modified)

	Huge refactoring of Tesselation routines, but not finished yet.

	- ...