#
# ChangeLog for src/Box.hpp
#
# Generated by Trac 1.4.4
# Jan 4, 2025, 1:55:32 PM

Wed, 22 Feb 2012 11:29:22 GMT Frederik Heber <heber@…> [2a0271]
	* src/Actions/Values.cpp (modified)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/LinkedCell/LinkedCell_Model.cpp (modified)
	* src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified)
	* src/Tesselation/boundary.cpp (modified)
	* src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified)
	* src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified)
	* tests/regression/Atoms/Add/testsuite-atoms-add.at (modified)

	New function Box::isValid() to be discerned from ::isInside().

	- ...


Wed, 22 Feb 2012 11:28:42 GMT Frederik Heber <heber@…> [712886]
	* src/Actions/AtomAction/TranslateAction.cpp (modified)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/unittests/BoxUnitTest.cpp (modified)

	Renamed Box::WrapPeriodically -> ::enforceBoundaryConditions.


Wed, 22 Feb 2012 11:28:42 GMT Frederik Heber <heber@…> [7b9fe0]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	New function Box::periodicDistanceVector(), using ...


Wed, 22 Feb 2012 11:28:42 GMT Frederik Heber <heber@…> [c52e08]
	* src/Actions/GlobalListOfActions.hpp (modified)
	* src/Actions/Makefile.am (modified)
	* src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (added)
	* src/Actions/WorldAction/SetBoundaryConditionsAction.def (added)
	* src/Actions/WorldAction/SetBoundaryConditionsAction.hpp (added)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/Box_BoundaryConditions.cpp (modified)
	* src/Box_BoundaryConditions.hpp (modified)
	* src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified)
	* tests/Python/AllActions/options.dat (modified)
	* tests/regression/Domain/SetBoundaryConditions/testsuite-domain-set-boundary-conditions.at (added)
	* tests/regression/Domain/testsuite-domain.at (modified)
	* tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/water-bounced.xyz (added)
	* tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/water-wrapped.xyz (added)
	* tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/water.xyz (added)
	* tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at (added)
	* tests/regression/Graph/testsuite-graph.at (modified)
	* tests/regression/Makefile.am (modified)

	Added new action SetBoundaryConditionsAction.

	- Added new ...


Wed, 22 Feb 2012 11:28:41 GMT Frederik Heber <heber@…> [d66cb7]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/LinkedCell/LinkedCell_Model.cpp (modified)
	* src/LinkedCell/unittests/Makefile.am (modified)
	* src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified)
	* src/unittests/BoxUnitTest.cpp (modified)

	Replaced Conditions_t by BoundaryConditions::BCContainer in class
	Box.


Mon, 02 Jan 2012 13:34:58 GMT Frederik Heber <heber@…> [99f4ee]
	* src/Atom/unittests/Makefile.am (modified)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/unittests/BoxUnitTest.cpp (modified)
	* src/unittests/BoxUnitTest.hpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/stubs/ObserverStub.cpp (moved)
	* src/unittests/stubs/ObserverStub.hpp (moved)

	Class Box is now also an Observable.

	- it has two channels to ...


Wed, 28 Dec 2011 15:24:23 GMT Frederik Heber <heber@…> [de29ad6]
	* LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (modified)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/Graph/BondGraph.cpp (modified)
	* src/unittests/BoxUnitTest.cpp (modified)

	Some optimization to speed up Subgraph dissections.

	- Replaced ...


Thu, 20 Oct 2011 12:39:01 GMT Frederik Heber <heber@…> [025048]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	Enhanced Box::periodicDistanceSquared() by an internal_explode().

	- ...


Thu, 10 Feb 2011 19:09:30 GMT Frederik Heber <heber@…> [528b3e]
	* src/Actions/Makefile.am (modified)
	* src/Actions/Values.cpp (added)
	* src/Actions/Values.hpp (modified)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified)
	* src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified)

	Added conversion functions to VectorValue and BoxValue and changed ...


Thu, 03 Feb 2011 09:51:18 GMT Frederik Heber <heber@…> [66fd49]
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (modified)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/LinearAlgebra/RealSpaceMatrix.cpp (modified)
	* src/LinearAlgebra/RealSpaceMatrix.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* tests/regression/Filling/3/post/empty.xyz (added)
	* tests/regression/Filling/3/post/tensid.data (modified)
	* tests/regression/Filling/3/post/test.xyz (modified)
	* tests/regression/testsuite-filling.at (modified)

	Rewrite of FillVoidWithMoleculeAction.

	FillVoidWithMoleculeAction: ...


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 ...


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, 28 Aug 2010 03:21:11 GMT Frederik Heber <heber@…> [6c438f]
	* .gitignore (modified)
	* AUTHORS (modified)
	* COPYING (modified)
	* Makefile.am (modified)
	* README (modified)
	* TestRunnerClient.cpp (added)
	* TestRunnerClient.h (added)
	* autogen.sh (deleted)
	* bootstrap (added)
	* config/ltmain.sh (added)
	* configure.ac (modified)
	* doc/molecuilder_logo.png (added)
	* doc/molecuilder_logo.xcf (added)
	* libmolecuilder_config.h.in (added)
	* m4/gwqt4.m4 (modified)
	* molecuilder.pc.in (added)
	* 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/ActionSequence.cpp (modified)
	* src/Actions/ActionSequence.hpp (modified)
	* src/Actions/Action_impl_header.hpp (added)
	* src/Actions/Action_impl_pre.hpp (added)
	* src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified)
	* src/Actions/AnalysisAction/MolecularVolumeAction.def (added)
	* src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.def (added)
	* src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.def (added)
	* src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified)
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified)
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (added)
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.def (added)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified)
	* src/Actions/AtomAction/AddAction.cpp (modified)
	* src/Actions/AtomAction/AddAction.def (added)
	* src/Actions/AtomAction/AddAction.hpp (modified)
	* src/Actions/AtomAction/ChangeElementAction.cpp (modified)
	* src/Actions/AtomAction/ChangeElementAction.def (added)
	* src/Actions/AtomAction/ChangeElementAction.hpp (modified)
	* src/Actions/AtomAction/Remove.def (added)
	* src/Actions/AtomAction/RemoveAction.cpp (modified)
	* src/Actions/AtomAction/RemoveAction.def (added)
	* src/Actions/AtomAction/RemoveAction.hpp (modified)
	* src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (added)
	* src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (added)
	* src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp (added)
	* src/Actions/AtomAction/TranslateAction.cpp (added)
	* src/Actions/AtomAction/TranslateAction.def (added)
	* src/Actions/AtomAction/TranslateAction.hpp (added)
	* src/Actions/AtomsCalculation.hpp (modified)
	* src/Actions/AtomsCalculation_impl.hpp (modified)
	* src/Actions/Calculation.hpp (modified)
	* src/Actions/Calculation_impl.hpp (modified)
	* src/Actions/CmdAction/BondLengthTableAction.cpp (deleted)
	* src/Actions/CmdAction/BondLengthTableAction.hpp (deleted)
	* src/Actions/CmdAction/ElementDbAction.cpp (deleted)
	* src/Actions/CmdAction/ElementDbAction.hpp (deleted)
	* src/Actions/CmdAction/FastParsingAction.cpp (deleted)
	* src/Actions/CmdAction/FastParsingAction.hpp (deleted)
	* src/Actions/CmdAction/HelpAction.cpp (deleted)
	* src/Actions/CmdAction/HelpAction.hpp (deleted)
	* src/Actions/CmdAction/VerboseAction.cpp (deleted)
	* src/Actions/CmdAction/VerboseAction.hpp (deleted)
	* src/Actions/CmdAction/VersionAction.cpp (deleted)
	* src/Actions/CmdAction/VersionAction.hpp (deleted)
	* src/Actions/CommandAction/BondLengthTableAction.cpp (added)
	* src/Actions/CommandAction/BondLengthTableAction.def (added)
	* src/Actions/CommandAction/BondLengthTableAction.hpp (added)
	* src/Actions/CommandAction/ElementDbAction.cpp (added)
	* src/Actions/CommandAction/ElementDbAction.def (added)
	* src/Actions/CommandAction/ElementDbAction.hpp (added)
	* src/Actions/CommandAction/FastParsingAction.cpp (added)
	* src/Actions/CommandAction/FastParsingAction.def (added)
	* src/Actions/CommandAction/FastParsingAction.hpp (added)
	* src/Actions/CommandAction/HelpAction.cpp (added)
	* src/Actions/CommandAction/HelpAction.def (added)
	* src/Actions/CommandAction/HelpAction.hpp (added)
	* src/Actions/CommandAction/VerboseAction.cpp (added)
	* src/Actions/CommandAction/VerboseAction.def (added)
	* src/Actions/CommandAction/VerboseAction.hpp (added)
	* src/Actions/CommandAction/VersionAction.cpp (added)
	* src/Actions/CommandAction/VersionAction.def (added)
	* src/Actions/CommandAction/VersionAction.hpp (added)
	* src/Actions/ErrorAction.cpp (modified)
	* src/Actions/ErrorAction.hpp (modified)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (added)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.def (added)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.hpp (added)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.def (added)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.def (added)
	* src/Actions/FragmentationAction/FragmentationAction.hpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.def (added)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (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 (modified)
	* src/Actions/MapOfActions.hpp (modified)
	* src/Actions/MethodAction.cpp (modified)
	* src/Actions/MethodAction.hpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.cpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.def (added)
	* src/Actions/MoleculeAction/BondFileAction.hpp (modified)
	* src/Actions/MoleculeAction/ChangeNameAction.cpp (modified)
	* src/Actions/MoleculeAction/ChangeNameAction.def (added)
	* src/Actions/MoleculeAction/ChangeNameAction.hpp (modified)
	* src/Actions/MoleculeAction/CopyAction.cpp (added)
	* src/Actions/MoleculeAction/CopyAction.def (added)
	* src/Actions/MoleculeAction/CopyAction.hpp (added)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.def (added)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (added)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified)
	* src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (added)
	* src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (added)
	* src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp (added)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (added)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.def (added)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.def (added)
	* src/Actions/MoleculeAction/SaveBondsAction.hpp (modified)
	* src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveTemperatureAction.def (added)
	* src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified)
	* src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified)
	* src/Actions/MoleculeAction/SuspendInWaterAction.def (added)
	* src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified)
	* src/Actions/MoleculeAction/TranslateAction.cpp (deleted)
	* src/Actions/MoleculeAction/TranslateAction.hpp (deleted)
	* src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified)
	* src/Actions/MoleculeAction/VerletIntegrationAction.def (added)
	* src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified)
	* src/Actions/ParserAction/LoadXyzAction.cpp (modified)
	* src/Actions/ParserAction/LoadXyzAction.def (added)
	* src/Actions/ParserAction/LoadXyzAction.hpp (modified)
	* src/Actions/ParserAction/SaveXyzAction.cpp (modified)
	* src/Actions/ParserAction/SaveXyzAction.def (added)
	* src/Actions/ParserAction/SaveXyzAction.hpp (modified)
	* src/Actions/Process.cpp (modified)
	* src/Actions/SelectionAction/AllAtomsAction.cpp (modified)
	* src/Actions/SelectionAction/AllAtomsAction.def (added)
	* src/Actions/SelectionAction/AllAtomsAction.hpp (modified)
	* src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (added)
	* src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (added)
	* src/Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp (added)
	* src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (added)
	* src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (added)
	* src/Actions/SelectionAction/AllAtomsInsideSphereAction.hpp (added)
	* src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (added)
	* src/Actions/SelectionAction/AllAtomsOfMoleculeAction.def (added)
	* src/Actions/SelectionAction/AllAtomsOfMoleculeAction.hpp (added)
	* src/Actions/SelectionAction/AllMoleculesAction.cpp (modified)
	* src/Actions/SelectionAction/AllMoleculesAction.def (added)
	* src/Actions/SelectionAction/AllMoleculesAction.hpp (modified)
	* src/Actions/SelectionAction/AtomByElementAction.cpp (added)
	* src/Actions/SelectionAction/AtomByElementAction.def (added)
	* src/Actions/SelectionAction/AtomByElementAction.hpp (added)
	* src/Actions/SelectionAction/AtomByIdAction.cpp (modified)
	* src/Actions/SelectionAction/AtomByIdAction.def (added)
	* src/Actions/SelectionAction/AtomByIdAction.hpp (modified)
	* src/Actions/SelectionAction/ClearAllAtomsAction.cpp (added)
	* src/Actions/SelectionAction/ClearAllAtomsAction.def (added)
	* src/Actions/SelectionAction/ClearAllAtomsAction.hpp (added)
	* src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (added)
	* src/Actions/SelectionAction/ClearAllMoleculesAction.def (added)
	* src/Actions/SelectionAction/ClearAllMoleculesAction.hpp (added)
	* src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (added)
	* src/Actions/SelectionAction/MoleculeByFormulaAction.def (added)
	* src/Actions/SelectionAction/MoleculeByFormulaAction.hpp (added)
	* src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified)
	* src/Actions/SelectionAction/MoleculeByIdAction.def (added)
	* src/Actions/SelectionAction/MoleculeByIdAction.hpp (modified)
	* src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (added)
	* src/Actions/SelectionAction/MoleculeOfAtomAction.def (added)
	* src/Actions/SelectionAction/MoleculeOfAtomAction.hpp (added)
	* src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified)
	* src/Actions/SelectionAction/NotAllAtomsAction.def (added)
	* src/Actions/SelectionAction/NotAllAtomsAction.hpp (modified)
	* src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (added)
	* src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (added)
	* src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp (added)
	* src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (added)
	* src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (added)
	* src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.hpp (added)
	* src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (added)
	* src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (added)
	* src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.hpp (added)
	* src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified)
	* src/Actions/SelectionAction/NotAllMoleculesAction.def (added)
	* src/Actions/SelectionAction/NotAllMoleculesAction.hpp (modified)
	* src/Actions/SelectionAction/NotAtomByElementAction.cpp (added)
	* src/Actions/SelectionAction/NotAtomByElementAction.def (added)
	* src/Actions/SelectionAction/NotAtomByElementAction.hpp (added)
	* src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified)
	* src/Actions/SelectionAction/NotAtomByIdAction.def (added)
	* src/Actions/SelectionAction/NotAtomByIdAction.hpp (modified)
	* src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (added)
	* src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (added)
	* src/Actions/SelectionAction/NotMoleculeByFormulaAction.hpp (added)
	* src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified)
	* src/Actions/SelectionAction/NotMoleculeByIdAction.def (added)
	* src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (modified)
	* src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (added)
	* src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (added)
	* src/Actions/SelectionAction/NotMoleculeOfAtomAction.hpp (added)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.def (added)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.def (added)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified)
	* src/Actions/ValueStorage.cpp (added)
	* src/Actions/ValueStorage.hpp (added)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.def (added)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified)
	* src/Actions/WorldAction/BoundInBoxAction.cpp (modified)
	* src/Actions/WorldAction/BoundInBoxAction.def (added)
	* src/Actions/WorldAction/BoundInBoxAction.hpp (modified)
	* src/Actions/WorldAction/CenterInBoxAction.cpp (modified)
	* src/Actions/WorldAction/CenterInBoxAction.def (added)
	* src/Actions/WorldAction/CenterInBoxAction.hpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.def (added)
	* src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified)
	* src/Actions/WorldAction/ChangeBoxAction.cpp (modified)
	* src/Actions/WorldAction/ChangeBoxAction.def (added)
	* src/Actions/WorldAction/ChangeBoxAction.hpp (modified)
	* src/Actions/WorldAction/InputAction.cpp (modified)
	* src/Actions/WorldAction/InputAction.def (added)
	* src/Actions/WorldAction/InputAction.hpp (modified)
	* src/Actions/WorldAction/OutputAction.cpp (modified)
	* src/Actions/WorldAction/OutputAction.def (added)
	* src/Actions/WorldAction/OutputAction.hpp (modified)
	* src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (deleted)
	* src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (deleted)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.def (added)
	* src/Actions/WorldAction/RepeatBoxAction.hpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.cpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.def (added)
	* src/Actions/WorldAction/ScaleBoxAction.hpp (modified)
	* src/Actions/WorldAction/SetDefaultNameAction.cpp (modified)
	* src/Actions/WorldAction/SetDefaultNameAction.def (added)
	* src/Actions/WorldAction/SetDefaultNameAction.hpp (modified)
	* src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified)
	* src/Actions/WorldAction/SetGaussianBasisAction.def (added)
	* src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified)
	* src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified)
	* src/Actions/WorldAction/SetOutputFormatsAction.def (added)
	* src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified)
	* src/AtomSet.hpp (added)
	* src/AtomicInfo.cpp (added)
	* src/AtomicInfo.hpp (added)
	* 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/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/CandidateForTesselation.cpp (added)
	* src/CandidateForTesselation.hpp (added)
	* src/CommandLineParser.cpp (modified)
	* src/CommandLineParser.hpp (modified)
	* src/ConfigFileBuffer.cpp (modified)
	* src/Descriptors/AtomDescriptor.cpp (modified)
	* src/Descriptors/AtomDescriptor.hpp (modified)
	* src/Descriptors/AtomIdDescriptor.cpp (modified)
	* src/Descriptors/AtomSelectionDescriptor.cpp (modified)
	* src/Descriptors/AtomShapeDescriptor.cpp (modified)
	* src/Descriptors/AtomShapeDescriptor.hpp (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/MoleculePtrDescriptor.cpp (modified)
	* src/Descriptors/MoleculeSelectionDescriptor.cpp (modified)
	* src/Descriptors/SelectiveIterator_impl.hpp (modified)
	* src/Exceptions/CustomException.cpp (modified)
	* src/Exceptions/IllegalTypeException.cpp (modified)
	* src/Exceptions/LinearDependenceException.cpp (modified)
	* src/Exceptions/Makefile.am (added)
	* src/Exceptions/MathException.cpp (modified)
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	* src/Exceptions/ParseError.cpp (modified)
	* src/Exceptions/SkewException.cpp (modified)
	* src/Exceptions/ZeroVectorException.cpp (modified)
	* src/Formula.cpp (modified)
	* src/Formula.hpp (modified)
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	* src/Helpers/Makefile.am (added)
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	* src/Helpers/MemDebug.hpp (modified)
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	* src/Helpers/Verbose.hpp (moved)
	* src/Helpers/errorlogger.cpp (moved)
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	* src/Legacy/oldmenu.hpp (deleted)
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	* src/LinearAlgebra/BoxVector.hpp (added)
	* src/LinearAlgebra/Line.cpp (moved)
	* src/LinearAlgebra/Line.hpp (moved)
	* src/LinearAlgebra/LineSegment.cpp (moved)
	* src/LinearAlgebra/LineSegment.hpp (moved)
	* src/LinearAlgebra/LineSegmentSet.cpp (moved)
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	* src/LinearAlgebra/Makefile.am (added)
	* src/LinearAlgebra/Matrix.cpp (moved)
	* src/LinearAlgebra/Matrix.hpp (moved)
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	* src/LinearAlgebra/Plane.cpp (moved)
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	* src/LinearAlgebra/Space.hpp (moved)
	* src/LinearAlgebra/Vector.cpp (moved)
	* src/LinearAlgebra/Vector.hpp (moved)
	* src/LinearAlgebra/VectorContent.hpp (moved)
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	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/TremoloParser.hpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/Patterns/ObservedContainer_impl.hpp (modified)
	* src/Patterns/Observer.cpp (modified)
	* src/Patterns/Registry_impl.hpp (modified)
	* src/PointCloud.cpp (added)
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	* src/Shapes/Shape_impl.hpp (modified)
	* src/TesselPoint.cpp (added)
	* src/TesselPoint.hpp (added)
	* src/ThermoStatContainer.cpp (modified)
	* src/ThermoStatContainer.hpp (modified)
	* src/Thermostats/Berendsen.cpp (added)
	* src/Thermostats/Berendsen.hpp (added)
	* src/Thermostats/GaussianThermostat.cpp (added)
	* src/Thermostats/GaussianThermostat.hpp (added)
	* src/Thermostats/Langevin.cpp (added)
	* src/Thermostats/Langevin.hpp (added)
	* src/Thermostats/NoThermostat.cpp (added)
	* src/Thermostats/NoThermostat.hpp (added)
	* src/Thermostats/NoseHoover.cpp (added)
	* src/Thermostats/NoseHoover.hpp (added)
	* src/Thermostats/Thermostat.cpp (added)
	* src/Thermostats/Thermostat.hpp (added)
	* src/Thermostats/Woodcock.cpp (added)
	* src/Thermostats/Woodcock.hpp (added)
	* src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineWindow.hpp (modified)
	* src/UIElements/Dialog.cpp (modified)
	* src/UIElements/Dialog.hpp (modified)
	* src/UIElements/MainWindow.cpp (modified)
	* src/UIElements/Makefile.am (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/QT4/QTMenu.cpp (modified)
	* src/UIElements/Menu/SeperatorItem.cpp (modified)
	* src/UIElements/Menu/SubMenuItem.cpp (modified)
	* src/UIElements/Menu/TextMenu.cpp (modified)
	* src/UIElements/Menu/TextMenu.hpp (modified)
	* src/UIElements/QT4/IntQTQuery.ui (added)
	* src/UIElements/QT4/IntsQTQuery.ui (added)
	* src/UIElements/QT4/QTDialog.cpp (modified)
	* src/UIElements/QT4/QTDialog.hpp (modified)
	* src/UIElements/QT4/QTMainWindow.cpp (modified)
	* src/UIElements/QT4/QTUIFactory.cpp (modified)
	* src/UIElements/TextUI/TextDialog.cpp (modified)
	* src/UIElements/TextUI/TextStatusIndicator.cpp (modified)
	* src/UIElements/TextUI/TextUIFactory.cpp (modified)
	* src/UIElements/TextUI/TextWindow.cpp (modified)
	* src/UIElements/UIFactory.cpp (modified)
	* src/UIElements/ValueStorage.cpp (deleted)
	* src/UIElements/ValueStorage.hpp (deleted)
	* src/UIElements/Views/MethodStringView.cpp (modified)
	* src/UIElements/Views/QT4/GLMoleculeView.cpp (modified)
	* src/UIElements/Views/QT4/QTMoleculeView.cpp (modified)
	* src/UIElements/Views/QT4/QTStatusBar.cpp (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_bonds.hpp (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_atominfo.hpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/atom_bondedparticleinfo.cpp (modified)
	* src/atom_bondedparticleinfo.hpp (modified)
	* src/atom_graphnode.cpp (modified)
	* src/atom_graphnode.hpp (modified)
	* src/atom_graphnodeinfo.cpp (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.cpp (modified)
	* src/atom_trajectoryparticleinfo.hpp (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/config.hpp (modified)
	* src/datacreator.cpp (modified)
	* src/defs.cpp (added)
	* src/defs.hpp (modified)
	* src/element.cpp (modified)
	* src/element.hpp (modified)
	* src/elements_db.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/graph.cpp (modified)
	* src/joiner.cpp (modified)
	* src/leastsquaremin.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/molecule_template.hpp (deleted)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (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/test/ActOnAlltest.hpp (modified)
	* src/triangleintersectionlist.cpp (modified)
	* src/triangleintersectionlist.hpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/ActionSequenceTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified)
	* src/unittests/AtomDescriptorTest.cpp (modified)
	* src/unittests/AtomDescriptorTest.hpp (modified)
	* src/unittests/BoxUnittest.cpp (added)
	* src/unittests/BoxUnittest.hpp (added)
	* src/unittests/CacheableTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* src/unittests/DummyUI.hpp (added)
	* src/unittests/FormulaUnittest.cpp (modified)
	* src/unittests/LineUnittest.cpp (modified)
	* src/unittests/LineUnittest.hpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/MapofActionsTest.cpp (modified)
	* src/unittests/MatrixUnittest.cpp (modified)
	* src/unittests/MatrixUnittest.hpp (modified)
	* src/unittests/MoleculeDescriptorTest.cpp (modified)
	* src/unittests/MoleculeDescriptorTest.hpp (modified)
	* src/unittests/ObserverTest.cpp (modified)
	* src/unittests/ParserUnitTest.cpp (modified)
	* src/unittests/PlaneUnittest.cpp (modified)
	* src/unittests/PlaneUnittest.hpp (modified)
	* src/unittests/ShapeUnittest.cpp (modified)
	* src/unittests/ShapeUnittest.hpp (modified)
	* src/unittests/SingletonTest.cpp (modified)
	* src/unittests/TestRunnerMain.cpp (modified)
	* src/unittests/UnitTestMain.cpp (modified)
	* src/unittests/analysisbondsunittest.cpp (modified)
	* src/unittests/atomsCalculationTest.cpp (modified)
	* src/unittests/atomsCalculationTest.hpp (modified)
	* src/unittests/bondgraphunittest.cpp (modified)
	* src/unittests/gslmatrixsymmetricunittest.cpp (modified)
	* src/unittests/gslmatrixsymmetricunittest.hpp (modified)
	* src/unittests/gslmatrixunittest.cpp (modified)
	* src/unittests/gslmatrixunittest.hpp (modified)
	* src/unittests/gslvectorunittest.cpp (modified)
	* src/unittests/gslvectorunittest.hpp (modified)
	* src/unittests/infounittest.cpp (modified)
	* src/unittests/linearsystemofequationsunittest.cpp (modified)
	* src/unittests/linearsystemofequationsunittest.hpp (modified)
	* src/unittests/listofbondsunittest.cpp (modified)
	* src/unittests/logunittest.cpp (modified)
	* src/unittests/manipulateAtomsTest.cpp (modified)
	* src/unittests/manipulateAtomsTest.hpp (modified)
	* src/unittests/memoryallocatorunittest.cpp (modified)
	* src/unittests/memoryusageobserverunittest.cpp (modified)
	* src/unittests/periodentafelTest.cpp (modified)
	* src/unittests/periodentafelTest.hpp (modified)
	* src/unittests/stackclassunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.cpp (modified)
	* src/unittests/tesselation_boundarytriangleunittest.hpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* src/unittests/tesselation_insideoutsideunittest.hpp (modified)
	* src/unittests/tesselationunittest.cpp (modified)
	* src/unittests/tesselationunittest.hpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/unittests/vectorunittest.hpp (modified)
	* src/version.h (modified)
	* test_all.sh (modified)
	* tests/Tesselations/Makefile.am (modified)
	* tests/Tesselations/defs.in (modified)
	* tests/regression/Makefile.am (modified)
	* tests/regression/Molecules/10/post/test-rotated-xYz20.xyz (added)
	* tests/regression/Molecules/10/post/test-rotated-z180.xyz (added)
	* tests/regression/Molecules/10/post/test-rotated-z360.xyz (added)
	* tests/regression/Molecules/10/post/test-rotated-z90.xyz (added)
	* tests/regression/Molecules/10/pre/test.xyz (added)
	* tests/regression/Molecules/11/post/test-copy.xyz (added)
	* tests/regression/Molecules/11/pre/test.xyz (added)
	* tests/regression/Molecules/2/post/test.adj (modified)
	* tests/regression/Molecules/8/post/test-rotated-xYz20.xyz (added)
	* tests/regression/Molecules/8/post/test-rotated-z180.xyz (added)
	* tests/regression/Molecules/8/post/test-rotated-z360.xyz (added)
	* tests/regression/Molecules/8/post/test-rotated-z90.xyz (added)
	* tests/regression/Molecules/8/pre/test-rotated-xYz20.xyz (added)
	* tests/regression/Molecules/8/pre/test-rotated-z180.xyz (added)
	* tests/regression/Molecules/8/pre/test-rotated-z360.xyz (added)
	* tests/regression/Molecules/8/pre/test-rotated-z90.xyz (added)
	* tests/regression/Molecules/9/post/test-rotated-xYz20.xyz (added)
	* tests/regression/Molecules/9/post/test-rotated-z180.xyz (added)
	* tests/regression/Molecules/9/post/test-rotated-z360.xyz (added)
	* tests/regression/Molecules/9/post/test-rotated-z90.xyz (added)
	* tests/regression/Molecules/9/pre/test.xyz (added)
	* tests/regression/Simple_configuration/2/post/test.pdb (added)
	* tests/regression/Simple_configuration/3/post/empty.conf (moved)
	* tests/regression/Simple_configuration/5/pre/test.conf (modified)
	* tests/regression/Simple_configuration/8/post/test-cuboid.xyz-sorted (added)
	* tests/regression/Simple_configuration/8/post/test-sphere.xyz-sorted (moved)
	* tests/regression/Simple_configuration/8/post/test-withoutcuboid.xyz-sorted (added)
	* tests/regression/Simple_configuration/8/post/test-withoutsphere.xyz-sorted (added)
	* tests/regression/Simple_configuration/8/post/test.xyz-sorted (modified)
	* tests/regression/Simple_configuration/8/pre/test.conf (deleted)
	* tests/regression/Simple_configuration/8/pre/test.xyz (added)
	* tests/regression/Simple_configuration/9/post/test-shifted.xyz (added)
	* tests/regression/Simple_configuration/9/post/test.xyz (added)
	* tests/regression/Simple_configuration/9/pre/test.xyz (added)
	* tests/regression/atlocal.in (modified)
	* tests/regression/molecuilder.in (modified)
	* tests/regression/testsuite-analysis.at (modified)
	* tests/regression/testsuite-graph.at (modified)
	* tests/regression/testsuite-molecules.at (modified)
	* tests/regression/testsuite-simple_configuration.at (modified)
	* tests/regression/testsuite-standard_options.at (modified)
	* tests/regression/testsuite.at (modified)

	Merge branch 'StructureRefactoring' into Shapes

	Conflicts:
	        ...


Thu, 05 Aug 2010 19:28:52 GMT Frederik Heber <heber@…> [57f243]
	* configure.ac (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/Actions/AtomAction/AddAction.cpp (modified)
	* src/Actions/AtomAction/AddAction.hpp (modified)
	* src/Actions/AtomAction/ChangeElementAction.cpp (modified)
	* src/Actions/MapOfActions.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified)
	* src/Actions/MoleculeAction/TranslateAction.cpp (modified)
	* src/Actions/MoleculeAction/TranslateAction.hpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified)
	* src/Actions/WorldAction/ChangeBoxAction.cpp (modified)
	* src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified)
	* src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.hpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.cpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.hpp (modified)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/Legacy/oldmenu.cpp (modified)
	* src/LinearAlgebra/Line.cpp (moved)
	* src/LinearAlgebra/Line.hpp (moved)
	* src/LinearAlgebra/Makefile.am (added)
	* src/LinearAlgebra/Matrix.cpp (moved)
	* src/LinearAlgebra/Matrix.hpp (moved)
	* src/LinearAlgebra/MatrixContent.hpp (moved)
	* src/LinearAlgebra/Plane.cpp (moved)
	* src/LinearAlgebra/Plane.hpp (moved)
	* src/LinearAlgebra/Space.cpp (moved)
	* src/LinearAlgebra/Space.hpp (moved)
	* src/LinearAlgebra/Vector.cpp (moved)
	* src/LinearAlgebra/Vector.hpp (moved)
	* src/LinearAlgebra/VectorContent.hpp (moved)
	* src/LinearAlgebra/VectorSet.hpp (moved)
	* src/LinearAlgebra/gslmatrix.cpp (moved)
	* src/LinearAlgebra/gslmatrix.hpp (moved)
	* src/LinearAlgebra/gslvector.cpp (moved)
	* src/LinearAlgebra/gslvector.hpp (moved)
	* src/LinearAlgebra/linearsystemofequations.cpp (moved)
	* src/LinearAlgebra/linearsystemofequations.hpp (moved)
	* src/Makefile.am (modified)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Shapes/BaseShapes.cpp (modified)
	* src/Shapes/ShapeOps_impl.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified)
	* src/UIElements/Dialog.cpp (modified)
	* src/UIElements/Dialog.hpp (modified)
	* src/UIElements/QT4/QTDialog.cpp (modified)
	* src/UIElements/TextUI/TextDialog.cpp (modified)
	* src/World.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/atom_trajectoryparticleinfo.hpp (modified)
	* src/bondgraph.cpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/leastsquaremin.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/test/ActOnAlltest.hpp (modified)
	* src/triangleintersectionlist.cpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (modified)
	* src/unittests/BoxUnittest.cpp (modified)
	* src/unittests/LineUnittest.cpp (modified)
	* src/unittests/LineUnittest.hpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/MatrixUnittest.cpp (modified)
	* src/unittests/PlaneUnittest.cpp (modified)
	* src/unittests/PlaneUnittest.hpp (modified)
	* src/unittests/ShapeUnittest.cpp (modified)
	* src/unittests/ShapeUnittest.hpp (modified)
	* src/unittests/gslmatrixsymmetricunittest.hpp (modified)
	* src/unittests/gslmatrixunittest.hpp (modified)
	* src/unittests/gslvectorunittest.hpp (modified)
	* src/unittests/linearsystemofequationsunittest.cpp (modified)
	* src/unittests/linearsystemofequationsunittest.hpp (modified)
	* src/unittests/vectorunittest.cpp (modified)
	* src/unittests/vectorunittest.hpp (modified)
	* src/vector_ops.cpp (modified)

	Created libMolecuilderLinearAlgebra.

	- is shared.
	- contains the ...


Fri, 30 Jul 2010 12:28:14 GMT Tillmann Crueger <crueger@…> [e1ab97]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	Added a function that allows fast creation of a cuboid box by giving ...


Thu, 29 Jul 2010 13:56:45 GMT Tillmann Crueger <crueger@…> [29ac78]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	Added a method that produces the bounding planes for a Box


Thu, 29 Jul 2010 13:56:45 GMT Tillmann Crueger <crueger@…> [77374e]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	Added BoundaryConditions to the Box class


Wed, 28 Jul 2010 09:35:44 GMT Tillmann Crueger <crueger@…> [400170]
	* .gitignore (added)
	* configure.ac (modified)
	* src/Actions/Action.cpp (modified)
	* src/Actions/Action.hpp (modified)
	* src/Actions/ActionHistory.cpp (modified)
	* src/Actions/ActionHistory.hpp (modified)
	* src/Actions/ActionSequence.cpp (modified)
	* src/Actions/ActionSequence.hpp (modified)
	* src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified)
	* src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified)
	* src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified)
	* src/Actions/AnalysisAction/PointCorrelationAction.cpp (added)
	* src/Actions/AnalysisAction/PointCorrelationAction.hpp (added)
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified)
	* src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (added)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (added)
	* src/Actions/AtomAction/AddAction.cpp (modified)
	* src/Actions/AtomAction/AddAction.hpp (modified)
	* src/Actions/AtomAction/ChangeElementAction.cpp (modified)
	* src/Actions/AtomAction/ChangeElementAction.hpp (modified)
	* src/Actions/AtomAction/RemoveAction.cpp (modified)
	* src/Actions/AtomAction/RemoveAction.hpp (modified)
	* src/Actions/Calculation.hpp (modified)
	* src/Actions/Calculation_impl.hpp (modified)
	* src/Actions/CmdAction/BondLengthTableAction.cpp (modified)
	* src/Actions/CmdAction/BondLengthTableAction.hpp (modified)
	* src/Actions/CmdAction/ElementDbAction.cpp (modified)
	* src/Actions/CmdAction/ElementDbAction.hpp (modified)
	* src/Actions/CmdAction/FastParsingAction.cpp (modified)
	* src/Actions/CmdAction/FastParsingAction.hpp (modified)
	* src/Actions/CmdAction/HelpAction.cpp (modified)
	* src/Actions/CmdAction/HelpAction.hpp (modified)
	* src/Actions/CmdAction/VerboseAction.cpp (modified)
	* src/Actions/CmdAction/VerboseAction.hpp (modified)
	* src/Actions/CmdAction/VersionAction.cpp (modified)
	* src/Actions/CmdAction/VersionAction.hpp (modified)
	* src/Actions/ErrorAction.cpp (modified)
	* src/Actions/ErrorAction.hpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.hpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (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 (modified)
	* src/Actions/MapOfActions.hpp (modified)
	* src/Actions/MethodAction.cpp (modified)
	* src/Actions/MethodAction.hpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.cpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.hpp (modified)
	* src/Actions/MoleculeAction/ChangeNameAction.cpp (modified)
	* src/Actions/MoleculeAction/ChangeNameAction.hpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.hpp (modified)
	* src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified)
	* src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified)
	* src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified)
	* src/Actions/MoleculeAction/TranslateAction.cpp (modified)
	* src/Actions/MoleculeAction/TranslateAction.hpp (modified)
	* src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified)
	* src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified)
	* src/Actions/ParserAction/LoadXyzAction.cpp (modified)
	* src/Actions/ParserAction/LoadXyzAction.hpp (modified)
	* src/Actions/ParserAction/SaveXyzAction.cpp (modified)
	* src/Actions/ParserAction/SaveXyzAction.hpp (modified)
	* src/Actions/SelectionAction/AllAtomsAction.cpp (added)
	* src/Actions/SelectionAction/AllAtomsAction.hpp (added)
	* src/Actions/SelectionAction/AllMoleculesAction.cpp (added)
	* src/Actions/SelectionAction/AllMoleculesAction.hpp (added)
	* src/Actions/SelectionAction/AtomByIdAction.cpp (added)
	* src/Actions/SelectionAction/AtomByIdAction.hpp (added)
	* src/Actions/SelectionAction/MoleculeByIdAction.cpp (added)
	* src/Actions/SelectionAction/MoleculeByIdAction.hpp (added)
	* src/Actions/SelectionAction/NotAllAtomsAction.cpp (added)
	* src/Actions/SelectionAction/NotAllAtomsAction.hpp (added)
	* src/Actions/SelectionAction/NotAllMoleculesAction.cpp (added)
	* src/Actions/SelectionAction/NotAllMoleculesAction.hpp (added)
	* src/Actions/SelectionAction/NotAtomByIdAction.cpp (added)
	* src/Actions/SelectionAction/NotAtomByIdAction.hpp (added)
	* src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (added)
	* src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (added)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified)
	* src/Actions/Values.hpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified)
	* src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified)
	* src/Actions/WorldAction/BoundInBoxAction.cpp (modified)
	* src/Actions/WorldAction/BoundInBoxAction.hpp (modified)
	* src/Actions/WorldAction/CenterInBoxAction.cpp (modified)
	* src/Actions/WorldAction/CenterInBoxAction.hpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified)
	* src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified)
	* src/Actions/WorldAction/ChangeBoxAction.cpp (modified)
	* src/Actions/WorldAction/ChangeBoxAction.hpp (modified)
	* src/Actions/WorldAction/InputAction.cpp (modified)
	* src/Actions/WorldAction/InputAction.hpp (modified)
	* src/Actions/WorldAction/OutputAction.cpp (modified)
	* src/Actions/WorldAction/OutputAction.hpp (modified)
	* src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified)
	* src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.hpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.cpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.hpp (modified)
	* src/Actions/WorldAction/SetDefaultNameAction.cpp (modified)
	* src/Actions/WorldAction/SetDefaultNameAction.hpp (modified)
	* src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified)
	* src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified)
	* src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified)
	* src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/CommandLineParser.cpp (modified)
	* src/Exceptions/IllegalTypeException.cpp (added)
	* src/Exceptions/IllegalTypeException.hpp (added)
	* src/Exceptions/MissingValueException.cpp (added)
	* src/Exceptions/MissingValueException.hpp (added)
	* src/Makefile.am (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/Makefile.am (modified)
	* src/UIElements/Menu/TextMenu.cpp (modified)
	* src/UIElements/Menu/TextMenu.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/UIElements/ValueStorage.cpp (added)
	* src/UIElements/ValueStorage.hpp (added)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)
	* src/unittests/ActionSequenceTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified)
	* test_all.sh (modified)
	* tests/Tesselations/defs.in (modified)
	* tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat (modified)
	* tests/regression/Simple_configuration/3/post/test2.conf (deleted)
	* tests/regression/Simple_configuration/3/post/test2.in (deleted)
	* tests/regression/Simple_configuration/3/post/test2.xyz (deleted)
	* tests/regression/testsuite-analysis.at (modified)
	* tests/regression/testsuite-filling.at (modified)
	* tests/regression/testsuite-fragmentation.at (modified)
	* tests/regression/testsuite-molecules.at (modified)
	* tests/regression/testsuite-simple_configuration.at (modified)
	* tests/regression/testsuite-tesselation.at (modified)

	Merge branch 'StructureRefactoring' into Shapes


Sun, 25 Jul 2010 15:07:07 GMT Frederik Heber <heber@…> [0ff6b5]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	Box::isInside() function added to check whether a given vector is ...


Thu, 15 Jul 2010 13:50:54 GMT Tillmann Crueger <crueger@…> [c538d1]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	Added a method that allows producing a Shape from a box


Fri, 02 Jul 2010 09:36:29 GMT Tillmann Crueger <crueger@…> [7ac4af]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	Added an optimized version of the Box::explode() method for n=1


Fri, 02 Jul 2010 09:28:10 GMT Tillmann Crueger <crueger@…> [a630fd]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	Made the Box::explode() method take an aditional parameters ...


Fri, 02 Jul 2010 09:12:10 GMT Tillmann Crueger <crueger@…> [abd8f7]
	* src/Box.hpp (modified)

	Added comments for Box class


Thu, 01 Jul 2010 13:44:39 GMT Tillmann Crueger <crueger@…> [014475]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/VectorSet.hpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Made all places use the periodicDistance() and ...


Thu, 01 Jul 2010 12:44:37 GMT Tillmann Crueger <crueger@…> [12cf773]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/VectorSet.hpp (modified)

	Added a define that makes the definition of VectorSets simpler


Wed, 30 Jun 2010 16:46:53 GMT Tillmann Crueger <crueger@…> [527de2]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	Added a function that allows to find the closest periodic point in a
	Box


Wed, 30 Jun 2010 16:17:24 GMT Tillmann Crueger <crueger@…> [89e820]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	Added a function that allows an expansion of a Point into its 27 ...


Wed, 30 Jun 2010 15:39:55 GMT Tillmann Crueger <crueger@…> [f429d7]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Move Vector::WrapPeriodically to Box class


Wed, 30 Jun 2010 15:16:10 GMT Tillmann Crueger <crueger@…> [3dcb1f]
	* src/Actions/WorldAction/ChangeBoxAction.cpp (modified)
	* src/Actions/WorldAction/ScaleBoxAction.cpp (modified)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/unittests/LineUnittest.cpp (modified)
	* src/unittests/PlaneUnittest.cpp (modified)
	* src/unittests/linearsystemofequationsunittest.cpp (modified)
	* src/vector.hpp (modified)
	* src/vector_ops.cpp (modified)

	Added two functions to Box class to translate Vectors from Box-Space ...


Wed, 30 Jun 2010 10:21:12 GMT Tillmann Crueger <crueger@…> [7579a4b]
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)

	Added Copy constructor and Assignment operator to Box class


Wed, 30 Jun 2010 09:42:58 GMT Tillmann Crueger <crueger@…> [83c09a]
	* src/Box.cpp (added)
	* src/Box.hpp (added)
	* src/Makefile.am (modified)

	Added a basic Box class to store cell_size as well as inverse of ...