#
# ChangeLog for src/Fragmentation
#
# Generated by Trac 1.6
# May 23, 2025, 11:58:53 PM

Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [730d7a]
	* src/Fragmentation/AdaptivityMap.cpp (added)
	* src/Fragmentation/AdaptivityMap.hpp (added)
	* src/Fragmentation/Fragmentation.cpp (modified)
	* src/Fragmentation/Graph.cpp (modified)
	* src/Fragmentation/Graph.hpp (modified)
	* src/Fragmentation/Makefile.am (modified)
	* src/Fragmentation/fragmentation_helpers.cpp (modified)
	* src/Fragmentation/fragmentation_helpers.hpp (modified)

	New class AdaptivityMap and moved some functions from ...


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [75363b]
	* src/Fragmentation/Fragmentation.cpp (modified)
	* src/Fragmentation/Graph.cpp (modified)
	* src/Fragmentation/Graph.hpp (modified)
	* src/Fragmentation/KeySet.cpp (modified)
	* src/Fragmentation/KeySet.hpp (modified)
	* src/Fragmentation/fragmentation_helpers.cpp (modified)
	* src/Fragmentation/fragmentation_helpers.hpp (modified)

	Extracted functions from fragmentation_helpers and placed them in ...


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [42127c]
	* src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/LoadAction.cpp (modified)
	* src/Actions/WorldAction/InputAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Analysis/analysis_bonds.cpp (modified)
	* src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* src/Analysis/unittests/CountBondsUnitTest.cpp (modified)
	* src/Fragmentation/Fragmentation.cpp (modified)
	* src/Graph/ConnectedSubgraph.cpp (modified)
	* src/Graph/DepthFirstSearchAnalysis.cpp (modified)
	* src/MoleculeListClass.hpp (added)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/Psi3Parser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/XyzParser.cpp (modified)
	* src/Tesselation/boundary.cpp (modified)
	* src/UIElements/MainWindow.hpp (modified)
	* src/UIElements/TextUI/TextWindow.cpp (modified)
	* src/UIElements/Views/Qt4/QtWorldView.cpp (modified)
	* src/World.cpp (modified)
	* src/config.cpp (modified)
	* src/molecule.hpp (modified)
	* src/moleculelist.cpp (modified)

	Extracted definition of MoleculeListClass and put into own header
	module.


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [d3abb1]
	* src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified)
	* src/Fragmentation/Fragmentation.cpp (modified)
	* src/Graph/DepthFirstSearchAnalysis.cpp (modified)
	* src/Makefile.am (modified)
	* src/MoleculeLeafClass.cpp (added)
	* src/MoleculeLeafClass.hpp (added)
	* src/molecule.hpp (modified)
	* src/moleculelist.cpp (modified)

	Extracted MoleculeLeafClass into own module.

	- removed some ...


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [ba94c5]
	* src/Fragmentation/Fragmentation.cpp (modified)
	* src/Fragmentation/Fragmentation.hpp (modified)
	* src/Fragmentation/UniqueFragments.cpp (modified)
	* src/Fragmentation/fragmentation_helpers.cpp (modified)
	* src/Fragmentation/fragmentation_helpers.hpp (modified)
	* src/Makefile.am (modified)
	* src/graph.cpp (deleted)
	* src/graph.hpp (deleted)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)

	Removed modules graph.[ch]pp.

	- typedef of KeyStack is placed in ...


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [dadc74]
	* src/Fragmentation/BondsPerShortestPath.hpp (modified)
	* src/Fragmentation/Fragmentation.cpp (modified)
	* src/Fragmentation/Fragmentation.hpp (modified)
	* src/Fragmentation/Graph.cpp (added)
	* src/Fragmentation/Graph.hpp (added)
	* src/Fragmentation/Makefile.am (modified)
	* src/Fragmentation/PowerSetGenerator.hpp (modified)
	* src/Fragmentation/UniqueFragments.cpp (modified)
	* src/Fragmentation/UniqueFragments.hpp (modified)
	* src/Fragmentation/fragmentation_helpers.cpp (modified)
	* src/Fragmentation/fragmentation_helpers.hpp (modified)
	* src/graph.cpp (modified)
	* src/graph.hpp (modified)
	* src/molecule.hpp (modified)
	* src/moleculelist.cpp (modified)

	Extracted Graph (map of KeySets) into own class from graph.hpp.

	- ...


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [f0674a]
	* src/Fragmentation/BondsPerShortestPath.cpp (modified)
	* src/Fragmentation/Fragmentation.cpp (modified)
	* src/Fragmentation/Fragmentation.hpp (modified)
	* src/Fragmentation/KeySet.cpp (added)
	* src/Fragmentation/KeySet.hpp (added)
	* src/Fragmentation/Makefile.am (modified)
	* src/Fragmentation/PowerSetGenerator.cpp (modified)
	* src/Fragmentation/UniqueFragments.cpp (modified)
	* src/Fragmentation/fragmentation_helpers.cpp (modified)
	* src/graph.cpp (modified)
	* src/graph.hpp (modified)
	* src/moleculelist.cpp (modified)

	Extracted KeySet from graph.hpp and made into distinct class.

	- ...


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [246e13]
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Fragmentation/Fragmentation.cpp (moved)
	* src/Fragmentation/Fragmentation.hpp (added)
	* src/Fragmentation/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Placed FragmentMolecule, FragmentBOSSANOVA and subfunctions into own ...


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [212c179]
	* src/Fragmentation/BondsPerShortestPath.cpp (added)
	* src/Fragmentation/BondsPerShortestPath.hpp (added)
	* src/Fragmentation/Makefile.am (modified)
	* src/Fragmentation/PowerSetGenerator.cpp (modified)
	* src/Fragmentation/PowerSetGenerator.hpp (modified)
	* src/Fragmentation/UniqueFragments.cpp (modified)
	* src/Fragmentation/UniqueFragments.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)

	Placed all functions related to BondsPerSPList into own class ...


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [d0b375b]
	* src/Fragmentation/UniqueFragments.cpp (modified)
	* src/Fragmentation/UniqueFragments.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)

	Removed ShortestPathList.

	- there have been references in the code ...


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [f67817f]
	* src/Fragmentation/Makefile.am (modified)
	* src/Fragmentation/PowerSetGenerator.cpp (added)
	* src/Fragmentation/PowerSetGenerator.hpp (added)
	* src/Fragmentation/fragmentation_helpers.cpp (modified)
	* src/Fragmentation/fragmentation_helpers.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)

	Extracted power set generation into own class PowerSetGenerator.


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [23fb72]
	* src/Fragmentation/UniqueFragments.cpp (modified)
	* src/Fragmentation/UniqueFragments.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)

	Encapsulated UniqueFragments::Root with getter/setter.


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [f6d1d0]
	* src/Fragmentation/UniqueFragments.hpp (modified)

	Made some member variable of UniqueFragments private.


Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber <heber@…> [a03d25]
	* src/Fragmentation/Makefile.am (modified)
	* src/Fragmentation/UniqueFragments.cpp (added)
	* src/Fragmentation/UniqueFragments.hpp (added)
	* src/Fragmentation/fragmentation_helpers.cpp (modified)
	* src/Fragmentation/fragmentation_helpers.hpp (modified)
	* src/graph.cpp (modified)
	* src/graph.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)

	Placed all routines working on UniqueFragments struct inside this ...


Tue, 25 Oct 2011 12:08:02 GMT Frederik Heber <heber@…> [d9a032]
	* src/Fragmentation/Makefile.am (modified)
	* src/Makefile.am (modified)

	Initiated own conveniance library for folder src/Fragmentation.

	- ...


Tue, 25 Oct 2011 12:08:02 GMT Frederik Heber <heber@…> [ba1823]
	* src/Fragmentation/fragmentation_helpers.cpp (added)
	* src/Fragmentation/fragmentation_helpers.hpp (added)
	* src/Makefile.am (modified)
	* src/molecule_fragmentation.cpp (modified)

	Moved all helpers fragmentation functions into folder
	src/Fragmentation.


Tue, 18 Oct 2011 15:48:57 GMT Frederik Heber <heber@…> [2d5fee]
	* src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified)
	* src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified)

	Added unit test functions SerializationTest for KeySetsContainer and ...


Tue, 18 Oct 2011 15:42:54 GMT Frederik Heber <heber@…> [942906]
	* configure.ac (modified)
	* src/Fragmentation/KeySetsContainer.hpp (modified)
	* src/Fragmentation/MatrixContainer.hpp (modified)

	Added serialize() template functions to MatrixContainer and ...


Tue, 18 Oct 2011 08:07:56 GMT Frederik Heber <heber@…> [1b145f]
	* src/Fragmentation/KeySetsContainer.cpp (modified)
	* src/Fragmentation/KeySetsContainer.hpp (modified)
	* src/Fragmentation/MatrixContainer.cpp (modified)
	* src/Fragmentation/MatrixContainer.hpp (modified)
	* src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified)
	* src/Fragmentation/unittests/KeySetsContainerUnitTest.hpp (modified)
	* src/Fragmentation/unittests/Makefile.am (modified)
	* src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified)
	* src/Fragmentation/unittests/MatrixContainerUnitTest.hpp (modified)

	Added operator==() to KeySetsContainer and MatrixContainer.

	- also ...


Tue, 18 Oct 2011 08:07:37 GMT Frederik Heber <heber@…> [9758f7]
	* src/Fragmentation/EnergyMatrix.cpp (modified)
	* src/Fragmentation/ForceMatrix.cpp (modified)
	* src/Fragmentation/HessianMatrix.cpp (modified)
	* src/Fragmentation/KeySetsContainer.cpp (modified)
	* src/Fragmentation/KeySetsContainer.hpp (modified)
	* src/Fragmentation/MatrixContainer.cpp (modified)
	* src/Fragmentation/MatrixContainer.hpp (modified)

	Removed C arrays in KeySetsContainer and MatrixContainer.

	- ...


Mon, 17 Oct 2011 20:17:51 GMT Frederik Heber <heber@…> [a9b86d]
	* src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified)
	* src/Dynamics/MinimiseConstrainedPotential.cpp (modified)
	* src/Dynamics/VerletForceIntegration.hpp (modified)
	* src/Fragmentation/EnergyMatrix.cpp (added)
	* src/Fragmentation/EnergyMatrix.hpp (added)
	* src/Fragmentation/ForceMatrix.cpp (added)
	* src/Fragmentation/ForceMatrix.hpp (added)
	* src/Fragmentation/HessianMatrix.cpp (added)
	* src/Fragmentation/HessianMatrix.hpp (added)
	* src/Fragmentation/KeySetsContainer.cpp (added)
	* src/Fragmentation/KeySetsContainer.hpp (added)
	* src/Fragmentation/Makefile.am (added)
	* src/Fragmentation/MatrixContainer.cpp (added)
	* src/Fragmentation/MatrixContainer.hpp (added)
	* src/Fragmentation/analyzer.cpp (modified)
	* src/Fragmentation/datacreator.cpp (modified)
	* src/Fragmentation/defs.hpp (added)
	* src/Fragmentation/helpers.cpp (added)
	* src/Fragmentation/helpers.hpp (added)
	* src/Fragmentation/joiner.cpp (modified)
	* src/Fragmentation/parser.cpp (deleted)
	* src/Fragmentation/parser.hpp (deleted)
	* src/Graph/BondGraph.cpp (modified)
	* src/Makefile.am (modified)
	* src/UIElements/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom_atominfo.cpp (modified)

	Split up modules parser.[ch]pp into one module per class.

	- fixed ...


Mon, 17 Oct 2011 16:18:56 GMT Frederik Heber <heber@…> [5f61dde]
	* src/Fragmentation/parser.cpp (modified)
	* src/Fragmentation/parser.hpp (modified)

	Removed usage of namespace std in module parser.[ch]pp.


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

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


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

	Added unittests to Fragmentation subfolder.

	- added empty tests for ...


Thu, 13 Oct 2011 19:00:47 GMT Frederik Heber <heber@…> [bc28b0]
	* src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified)
	* src/Dynamics/MinimiseConstrainedPotential.cpp (modified)
	* src/Dynamics/VerletForceIntegration.hpp (modified)
	* src/Fragmentation/analyzer.cpp (moved)
	* src/Fragmentation/datacreator.cpp (moved)
	* src/Fragmentation/datacreator.hpp (moved)
	* src/Fragmentation/joiner.cpp (moved)
	* src/Fragmentation/parser.cpp (moved)
	* src/Fragmentation/parser.hpp (moved)
	* src/Graph/BondGraph.cpp (modified)
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom_atominfo.cpp (modified)

	Moved modules associated with fragmentation into source subfolder ...