# # ChangeLog for src/Actions # # Generated by Trac 1.4.4 # Apr 19, 2025, 3:24:37 PM Mon, 07 Nov 2011 12:24:02 GMT Frederik Heber [3139b2] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionTrait.cpp (moved) * src/Actions/ActionTrait.hpp (added) * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.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/HelpAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.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/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/World_calculations.hpp (modified) Renamed ActionTrait and ActionTraits. - the specialized Trait ... Mon, 07 Nov 2011 12:24:00 GMT Frederik Heber [c20b35] * src/Actions/Makefile.am (modified) Added commented-out stuff for a extra libMolecuilderActionPython.la. ... Mon, 07 Nov 2011 12:23:52 GMT Frederik Heber [949953] * src/Actions/Action_impl_python.hpp (added) * src/Actions/Action_impl_undef.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Makefile.am (modified) * src/builder_init.cpp (modified) * src/builder_init.hpp (modified) * src/cleanUp.cpp (added) * src/cleanUp.hpp (added) pyMoleCuilder now has full functionality. - For each header file ... Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [071243] * src/Actions/hello.cpp (modified) * src/Makefile.am (modified) Enhanced tiny example to resemble action structure. - Pythontest ... Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [88ba1f] * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/ValueStorage.hpp (modified) Added Action's COMMAND_stringargs() function call. - also added ... Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [ddde10] * src/Actions/Action_impl_pre.hpp (modified) FIX: In Action's COMMAND() we don't need a params instance. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [6a2dae] * src/Actions/Action_impl_header.hpp (modified) Corrected indenting in ActionTrait<>s cstor. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [05736a] * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) Simplified Action's COMMAND() definition a bit. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [d41313] * src/Actions/ActionTraits.cpp (modified) * src/Actions/ActionTraits.hpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/OptionTrait.hpp (modified) Added output operators for both ActionTraits and OptionTrait. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [dad802] * src/Actions/ActionTraits.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/OptionTrait.hpp (modified) Modified ActionTraits' and OptionTrait's cstor and dstor slightly. ... Mon, 07 Nov 2011 10:46:25 GMT Frederik Heber [83e90c] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/GlobalListOfActions.hpp (added) * src/Actions/Makefile.am (modified) New function ActionRegistry::fillRegistry() fills instead of static ... Fri, 04 Nov 2011 15:20:41 GMT Frederik Heber [693a80] * src/Actions/pyMoleCuilder.cpp (added) * src/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/CommandHelp/testsuite-python-commandhelp.at (added) * tests/regression/Python/testsuite-python.at (modified) Added pyMoleCuilder as python module with single exported function ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [a02f78] * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) FIX: Undefined preprocessor macro functions in Action_impl_....hpp. ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [807d91] * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/OptionTrait.hpp (modified) MEMFIX: Virtualized destructors of OptionTrait, ActionTraits and ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [b22179] * src/Actions/ActionTraits.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/OptionTrait.hpp (modified) FIX: Removed OptionTrait's copy constructor as there are no pointers ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [d44d7b] * src/Actions/Action.cpp (modified) Dstor of Action now unregisters itself and its Options in Action- and ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [2d31e1] * configure.ac (modified) * src/Actions/hello.cpp (modified) * src/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/run.in (added) * tests/regression/Python/testsuite-python.at (modified) Python tests are now launched via small script run.in. - this is ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [715085] * configure.ac (modified) * m4/ax_python.m4 (added) * src/Actions/hello.cpp (added) * src/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/testsuite-python.at (added) * tests/regression/testsuite.at (modified) Simple boost::python test program added. - we have a function ... Thu, 03 Nov 2011 19:44:01 GMT Frederik Heber [41a467] * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Makefile.am (modified) * src/Parser/ConfigFileBuffer.cpp (moved) * src/Parser/ConfigFileBuffer.hpp (moved) * src/Parser/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (added) * src/Parser/PcpParser_helper.hpp (added) * src/Parser/Psi3Parser.cpp (modified) * src/ThermoStatContainer.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/TextUI/TextWindow.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) LARGE: config class is now just a tiny container. - this was ... Thu, 03 Nov 2011 19:44:01 GMT Frederik Heber [47d041] * src/Actions/Action.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.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/SaveSelectedAtomsAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.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/ValueStorage.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Element/periodentafel.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.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/CommandLineParser.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/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/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Views/StreamStringView.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) HUGE: Removed all calls to Log(), eLog(), replaced by LOG() and ... Thu, 03 Nov 2011 19:44:01 GMT Frederik Heber [862b6a] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/builder_init.cpp (modified) All Actions are timed now, timings are given on exit. - Chronos is ... Thu, 03 Nov 2011 10:38:31 GMT Frederik Heber [bbff92] * LinearAlgebra/configure.ac (modified) * LinearAlgebra/doc/Doxyfile (modified) * LinearAlgebra/src/documentation/groups.dox (added) * LinearAlgebra/src/documentation/mainpage.dox (added) * LinearAlgebra/tests/CodeChecks/Makefile.am (modified) * LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (modified) * LinearAlgebra/tests/CodeChecks/testsuite-date_in_dox.at (added) * LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (modified) * LinearAlgebra/tests/CodeChecks/testsuite.at (modified) * Makefile.am (modified) * configure.ac (modified) * doc/Doxyfile (modified) * doc/userguide.xml (modified) * src/Actions/Action.hpp (modified) * src/Actions/ValueStorage.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/builder.cpp (modified) * src/documentation/code.dox (added) * src/documentation/constructs/actions.dox (added) * src/documentation/constructs/atoms.dox (added) * src/documentation/constructs/bondgraph.dox (added) * src/documentation/constructs/constructs.dox (added) * src/documentation/constructs/descriptors.dox (added) * src/documentation/constructs/fragmentation.dox (added) * src/documentation/constructs/linearalgebra.dox (added) * src/documentation/constructs/logger.dox (added) * src/documentation/constructs/molecules.dox (added) * src/documentation/constructs/observers_observables.dox (added) * src/documentation/constructs/parsers.dox (added) * src/documentation/constructs/randomnumbers.dox (added) * src/documentation/constructs/serialization.dox (added) * src/documentation/constructs/shapes.dox (added) * src/documentation/constructs/tesselation.dox (added) * src/documentation/constructs/world.dox (added) * src/documentation/copyright.dox (added) * src/documentation/faq.dox (added) * src/documentation/fileformats.dox (added) * src/documentation/future.dox (added) * src/documentation/howtos/action.dox (added) * src/documentation/howtos/howtos.dox (added) * src/documentation/install.dox (added) * src/documentation/launch.dox (added) * src/documentation/mainpage.dox (added) * src/documentation/tests/code-tests.dox (added) * src/documentation/tests/regression-tests.dox (added) * src/documentation/tests/tests.dox (added) * src/documentation/tests/unit-tests.dox (added) * src/documentation/userinterfaces/commandline.dox (added) * src/documentation/userinterfaces/graphical.dox (added) * src/documentation/userinterfaces/python.dox (added) * src/documentation/userinterfaces/textmenu.dox (added) * src/documentation/userinterfaces/userinterfaces.dox (added) * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-config_h.at (modified) * tests/CodeChecks/testsuite-date_in_dox.at (added) * tests/CodeChecks/testsuite-memdebug.at (modified) * tests/CodeChecks/testsuite.at (modified) Merge branch 'Doxygen_Documentation_Enhancement' into mergeMaster Thu, 03 Nov 2011 09:52:29 GMT Frederik Heber [7ba268] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.def (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/World.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_X.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0000.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0001.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0002.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0003.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0004.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0005.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0006.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0007.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0008.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0009.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0010.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0011.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0012.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0013.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0014.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0015.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0016.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0017.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0018.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0019.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0020.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0021.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0022.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0023.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0024.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0025.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0026.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0027.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0028.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0029.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0030.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0031.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0032.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0033.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0034.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0035.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_X.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0000.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0001.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0002.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0003.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0004.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0005.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0006.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0007.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0008.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0009.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0010.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0011.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0012.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0013.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0014.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0015.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0016.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0017.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0018.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0019.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0020.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0021.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0022.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0023.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0024.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0025.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0026.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0027.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0028.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0029.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0030.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0031.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0032.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0033.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0034.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0035.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.pdb (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.pdb (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (added) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/post/waterbox-mirrored_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/post/waterbox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/pre/water.xyz (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/post/emptybox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/post/hydrogenbox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/testsuite-analysis-dipole-correlation-empty.at (moved) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'DipoleAngularCorrelation' into mergeMaster Conflicts: ... Wed, 02 Nov 2011 01:29:33 GMT Frederik Heber [c3a70d] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) Added time-step-zero option to dipole-angular-correlation. - this ... Mon, 31 Oct 2011 17:29:04 GMT Frederik Heber [e6c470] * src/Actions/ValueStorage.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) Fixing documentation. - removed out-dated documentation. - removed ... Mon, 31 Oct 2011 17:13:52 GMT Frederik Heber [750cff] * src/Actions/Action.hpp (modified) * src/builder.cpp (modified) * src/documentation/code.dox (modified) * src/documentation/constructs/actions.dox (modified) * src/documentation/constructs/atoms.dox (added) * src/documentation/constructs/bondgraph.dox (modified) * src/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/descriptors.dox (modified) * src/documentation/constructs/fragmentation.dox (modified) * src/documentation/constructs/linearalgebra.dox (added) * src/documentation/constructs/logger.dox (added) * src/documentation/constructs/molecules.dox (added) * src/documentation/constructs/observers_observables.dox (modified) * src/documentation/constructs/parsers.dox (modified) * src/documentation/constructs/randomnumbers.dox (modified) * src/documentation/constructs/serialization.dox (modified) * src/documentation/constructs/shapes.dox (modified) * src/documentation/constructs/tesselation.dox (modified) * src/documentation/constructs/world.dox (added) * src/documentation/copyright.dox (added) * src/documentation/faq.dox (modified) * src/documentation/fileformats.dox (added) * src/documentation/howtos/action.dox (added) * src/documentation/howtos/howtos.dox (added) * src/documentation/install.dox (modified) * src/documentation/launch.dox (modified) * src/documentation/mainpage.dox (modified) * src/documentation/tests/code-tests.dox (modified) * src/documentation/tests/regression-tests.dox (modified) * src/documentation/tests/tests.dox (modified) * src/documentation/tests/unit-tests.dox (modified) * src/documentation/userinterfaces/commandline.dox (added) * src/documentation/userinterfaces/graphical.dox (added) * src/documentation/userinterfaces/textmenu.dox (added) * src/documentation/userinterfaces/userinterfaces.dox (added) HUGE: Update on documenation. - a general skeleton of the ... Mon, 31 Oct 2011 11:49:19 GMT Frederik Heber [e65878] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) Selection is now done inside DipoleAngularCorrelation. - as ... Mon, 31 Oct 2011 11:48:45 GMT Frederik Heber [99b87a] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) DipoleAngularCorrelation() can be told not to reset time to old ... Mon, 31 Oct 2011 11:48:38 GMT Frederik Heber [a860a1] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_X.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0000.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0001.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0002.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0003.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0004.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0005.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0006.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0007.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0008.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0009.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0010.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0011.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0012.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0013.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0014.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0015.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0016.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0017.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0018.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0019.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0020.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0021.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0022.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0023.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0024.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0025.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0026.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0027.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0028.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0029.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0030.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0031.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0032.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0033.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0034.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0035.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.dat (deleted) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_X.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0000.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0001.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0002.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0003.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0004.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0005.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0006.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0007.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0008.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0009.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0010.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0011.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0012.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0013.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0014.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0015.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0016.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0017.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0018.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0019.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0020.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0021.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0022.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0023.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0024.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0025.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0026.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0027.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0028.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0029.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0030.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0031.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0032.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0033.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0034.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0035.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) TESTFIX: Regression test Analysis/DipoleAngularCorrelation now also ... Mon, 31 Oct 2011 11:17:33 GMT Frederik Heber [e5ece4] * src/Actions/ValueStorage.cpp (modified) * src/Actions/ValueStorage.hpp (modified) Added operator<< to ValueStorage. - this should ease debugging in ... Mon, 31 Oct 2011 11:16:17 GMT Frederik Heber [41d023] * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (deleted) * src/Actions/ParserAction/SetParserParametersAction.cpp (added) * src/Actions/ParserAction/SetParserParametersAction.def (moved) * src/Actions/ParserAction/SetParserParametersAction.hpp (moved) * src/Parser/FormatParser_Parameters.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/SetParameters/Mpqc/post/testCLHF.in (moved) * tests/regression/Parser/SetParameters/Mpqc/pre/test.xyz (moved) * tests/regression/Parser/SetParameters/Mpqc/pre/testCLHF.in (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-basis.at (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-maxiterations.at (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-theory.at (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc.at (moved) * tests/regression/Parser/SetParameters/Psi3/pre/test.xyz (added) * tests/regression/Parser/SetParameters/Psi3/testsuite-parser-set-parameters-psi3-wavefunction.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Renamed SetMpqcParametersAction to SetParserParametersAction and ... Thu, 27 Oct 2011 16:46:20 GMT Frederik Heber [a2b0ce] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) FIX: Filenames are appended with step with fixed width of 4 digits, ... Thu, 27 Oct 2011 16:45:47 GMT Frederik Heber [cda81d] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) DipoleAngularCorrelation is now calculated per time step not over all ... Thu, 27 Oct 2011 11:07:20 GMT Frederik Heber [9e1709] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) AnalysisDipoleAngularCorrelationAction now calculates zero ... Thu, 27 Oct 2011 11:07:20 GMT Frederik Heber [bef3b9] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) Restructured code in ... Thu, 27 Oct 2011 11:06:42 GMT Frederik Heber [325687] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) DipoleAngularCorrelation() - External zero orientation vector may be ... Wed, 26 Oct 2011 15:02:53 GMT Frederik Heber [07a47e] * configure.ac (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.def (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/HydrogenSaturation_enum.hpp (added) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BreadthFirstSearchAdd.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/MoleculeLeafClass.hpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/moleculelist.cpp (modified) Replaced enable/disable-hydrogen by internal switch. - changes in ... Wed, 26 Oct 2011 15:02:46 GMT Frederik Heber [99b0dc] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order5.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order6.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order5.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order6.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order5.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order6.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order1.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order2.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order3.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order4.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order5.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order6.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) FragmentAction now has instead of path a types parameter. - new ... Wed, 26 Oct 2011 12:31:00 GMT Frederik Heber [091838] * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/FormatParser_common.cpp (modified) FormatParserStorage now explicitly needs to know which formats to ... Tue, 25 Oct 2011 15:31:54 GMT Frederik Heber [4b8630] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/World.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) World::setTime() now updates bond structure of system and related ... Tue, 25 Oct 2011 15:28:06 GMT Frederik Heber [208237b] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.def (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) Renamed DipoleAngularCorrelation(Action) -> DipoleCorrelation(Action) ... Tue, 25 Oct 2011 12:08:03 GMT Frederik 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 [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 [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 ... Thu, 20 Oct 2011 22:42:16 GMT Frederik 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: ... Thu, 20 Oct 2011 21:29:24 GMT Frederik Heber [fa9d1d] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) FIX: CreateAdjacencyAction now uses BondGraph::CreateAdjacency. Thu, 20 Oct 2011 13:20:03 GMT Frederik Heber [9317be] * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) Replaced molecule::atomVector by World::AtomComposite everywhere. Thu, 20 Oct 2011 07:04:50 GMT Frederik Heber [9c27b0] * configure.ac (modified) * 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/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Analysis/Makefile.am (added) * src/Analysis/analysis_bonds.cpp (moved) * src/Analysis/analysis_bonds.hpp (moved) * src/Analysis/analysis_correlation.cpp (moved) * src/Analysis/analysis_correlation.hpp (moved) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisBondsUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.hpp (moved) * src/Analysis/unittests/CountBondsUnitTest.cpp (moved) * src/Analysis/unittests/CountBondsUnitTest.hpp (moved) * src/Analysis/unittests/Makefile.am (added) * src/AtomicInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (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/unittests/ElementUnitTest.cpp (moved) * src/Element/unittests/ElementUnitTest.hpp (moved) * src/Element/unittests/Makefile.am (added) * src/Element/unittests/PeriodentafelUnitTest.cpp (moved) * src/Element/unittests/PeriodentafelUnitTest.hpp (moved) * src/Element/valence.db (moved) * src/Formula.cpp (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 (moved) * src/Fragmentation/datacreator.cpp (moved) * src/Fragmentation/datacreator.hpp (moved) * src/Fragmentation/defs.hpp (added) * src/Fragmentation/helpers.cpp (added) * src/Fragmentation/helpers.hpp (added) * src/Fragmentation/joiner.cpp (moved) * 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/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (moved) * src/Graph/unittests/BondGraphUnitTest.hpp (moved) * src/Graph/unittests/Makefile.am (added) * src/Helpers/Makefile.am (added) * src/Helpers/defs.hpp (modified) * src/Helpers/helpers.hpp (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/PointCloudAdaptor.hpp (modified) * src/RandomNumbers/unittests/Makefile.am (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/Tesselation/unittests/Makefile.am (added) * src/Tesselation/unittests/TesselationUnitTest.cpp (moved) * src/Tesselation/unittests/TesselationUnitTest.hpp (moved) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (moved) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (moved) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (moved) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp (moved) * src/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.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/linkedcell.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/parser.cpp (deleted) * src/parser.hpp (deleted) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaEnergies-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaEnergies-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMaxForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMaxForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMeanForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMeanForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinMeanMaxTotalForce-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaSimTime-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Forces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Makefile (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxEnergies-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxEnergies-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinEnergies-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinEnergies-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinMeanMaxTotalForce-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/SimTime-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/SimTime-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/VectorSum-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/VectorSum-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/energy-forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragmentForces-Factors.dat (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragmentKeySets.dat (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order1.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order1.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order2.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order2.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order3.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order3.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order4.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order4.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/testsuite-analyzing-heptan.at (added) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/pre/1_2-dimethoxyethane.xyz (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/pre/1_2-dimethylbenzene.xyz (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/pre/2-methylcyclohexanone.xyz (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order5.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order6.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/pre/N_N-dimethylacetamide.xyz (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at (moved) * tests/Fragmentations/Fragmenting/benzene/pre/benzene.xyz (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/pre/cholesterol.xyz (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order5.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order6.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/pre/cycloheptane.xyz (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/pre/dimethyl_bromomalonate.xyz (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at (moved) * tests/Fragmentations/Fragmenting/glucose/pre/glucose.xyz (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at (moved) * tests/Fragmentations/Fragmenting/heptan/pre/heptan.xyz (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order5.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order6.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/pre/isoleucine.xyz (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at (moved) * tests/Fragmentations/Fragmenting/neohexane/pre/neohexane.xyz (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at (moved) * tests/Fragmentations/Fragmenting/proline/pre/proline.xyz (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order1.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order2.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order3.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order4.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order5.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order6.at (moved) * tests/Fragmentations/Fragmenting/putrescine/pre/putrescine.xyz (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/pre/tartaric_acid.xyz (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at (moved) * tests/Fragmentations/Joining/heptan/post/BondFragment00/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment00/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment01/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment01/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment02/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment02/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment03/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment03/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment04/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment04/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment05/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment05/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment06/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment06/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment07/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment07/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment08/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment08/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment09/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment09/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment10/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment10/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment11/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment11/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment12/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment12/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment13/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment13/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment14/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment14/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment15/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment15/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment16/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment16/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment17/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment17/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment18/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment18/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment19/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment19/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment20/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment20/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment21/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment21/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order1.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order1.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order2.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order2.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order3.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order3.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order4.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order4.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragmentForces-Factors.dat (added) * tests/Fragmentations/Joining/heptan/pre/BondFragmentKeySets.dat (added) * tests/Fragmentations/Joining/heptan/pre/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/pcp.speed (added) * tests/Fragmentations/Joining/heptan/testsuite-joining-heptan.at (added) * tests/Fragmentations/Makefile.am (modified) * tests/Fragmentations/analyzer.in (added) * tests/Fragmentations/joiner.in (added) * tests/Fragmentations/testsuite.at (modified) * tests/Makefile.am (modified) * tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at (modified) Merge branch 'MatrixContainer_Serialization_rewrite' into stable Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber [b1ac7a] * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at (modified) Added Undo/Redo capabilities to BondLengthTableAction. - thanks to ... Mon, 17 Oct 2011 16:18:54 GMT Frederik Heber [3bdb6d] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/AtomicInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/Hbondangle.db (moved) * src/Element/Hbonddistance.db (moved) * src/Element/Makefile.am (added) * src/Element/element.cpp (moved) * src/Element/element.hpp (moved) * src/Element/elements.db (moved) * src/Element/elements_db.cpp (moved) * src/Element/elements_db.hpp (moved) * src/Element/orbitals.db (moved) * src/Element/periodentafel.cpp (moved) * src/Element/periodentafel.hpp (moved) * src/Element/valence.db (moved) * src/Formula.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ElementUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/PeriodentafelUnitTest.cpp (modified) Moved all stuff related to elements into own subfolder and has its ... Mon, 17 Oct 2011 16:18:42 GMT Frederik Heber [9b5a2c] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Analysis/Makefile.am (added) * src/Analysis/analysis_bonds.cpp (moved) * src/Analysis/analysis_bonds.hpp (moved) * src/Analysis/analysis_correlation.cpp (moved) * src/Analysis/analysis_correlation.hpp (moved) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisBondsUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.hpp (moved) * src/Analysis/unittests/CountBondsUnitTest.cpp (moved) * src/Analysis/unittests/CountBondsUnitTest.hpp (moved) * src/Analysis/unittests/Makefile.am (added) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved analysis modules into subfolder Analysis along with its unit ... Fri, 14 Oct 2011 15:15:30 GMT Frederik Heber [765f16] * 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_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/ParserTypes.cpp (added) * src/Parser/ParserTypes.def (added) * src/Parser/ParserTypes.hpp (modified) * 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/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (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/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.hpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.hpp (modified) * src/moleculelist.cpp (modified) Huge Refactoring of FormatParserStorage and all FormatParser's. ... Fri, 14 Oct 2011 15:11:19 GMT Frederik Heber [ebb87c] * src/Actions/MoleculeAction/LoadAction.cpp (modified) FIX: Added check whether suffix belongs to well-defined parser type. Fri, 14 Oct 2011 15:09:53 GMT Frederik Heber [6d0f058] * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/moleculelist.cpp (modified) Removed all FormatParserStorage::get() and ::set(). - we now call ... Fri, 14 Oct 2011 12:10:02 GMT Frederik Heber [45f835] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (modified) * tests/regression/Domain/RepeatBox/post/test-undo.xyz (added) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) Added Undo/Redo capabilities to RepeatBoxAction. - adapted ... Fri, 14 Oct 2011 12:09:30 GMT Frederik Heber [34fbb3] * src/Actions/MoleculeAction/CopyAction.cpp (modified) FIX: CopyAction did not simply use removeAtomsinMolecule(). Fri, 14 Oct 2011 10:48:21 GMT Frederik Heber [cbfb9a] * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * tests/regression/Domain/ScaleBox/post/test-undo.conf (added) * tests/regression/Domain/ScaleBox/testsuite-domain-scale-box.at (modified) Added Undo/Redo capabilities to ScaleBoxAction. - adapted ... Fri, 14 Oct 2011 10:46:54 GMT Frederik Heber [7b4a29] * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.def (modified) * tests/regression/Domain/ChangeBox/testsuite-domain-change-box.at (modified) Added Undo/Redo capabilities to ChangeBoxAction. - removed XFAIL ... Fri, 14 Oct 2011 10:44:10 GMT Frederik Heber [de7d1d] * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (modified) * tests/regression/Domain/CenterOnEdge/post/test-undo.conf (added) * tests/regression/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at (modified) Added Undo/Redo capabilities to CenterOnEdgeAction. - adapted ... Fri, 14 Oct 2011 10:41:09 GMT Frederik Heber [23526c] * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.def (modified) * tests/regression/Domain/CenterInBox/post/test-undo.conf (added) * tests/regression/Domain/CenterInBox/testsuite-domain-center-in-box.at (modified) Added Undo/Redo capabilities to CenterInBoxAction. - adapted ... Fri, 14 Oct 2011 10:37:32 GMT Frederik Heber [e670e4] * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.def (modified) * tests/regression/Domain/BoundInBox/post/test-undo.conf (added) * tests/regression/Domain/BoundInBox/post/test.conf (added) * tests/regression/Domain/BoundInBox/pre/test.conf (added) * tests/regression/Domain/BoundInBox/testsuite-domain-bound-in-box.at (added) * tests/regression/Domain/testsuite-domain.at (modified) * tests/regression/Makefile.am (modified) Added Undo/Redo capabilities to BoundInBoxAction. - also added ... Fri, 14 Oct 2011 09:43:40 GMT Frederik Heber [9cd6bf] * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (modified) * tests/regression/Domain/AddEmptyBoundary/post/test-undo.conf (added) * tests/regression/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at (modified) Added Undo/Redo capabilities to AddEmptyBoundaryAction. - adapted ... Thu, 13 Oct 2011 19:00:47 GMT Frederik Heber [d127c8] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Makefile.am (modified) * src/PointCloudAdaptor.hpp (modified) * src/Tesselation/BoundaryLineSet.cpp (moved) * src/Tesselation/BoundaryLineSet.hpp (moved) * src/Tesselation/BoundaryMaps.hpp (moved) * src/Tesselation/BoundaryPointSet.cpp (moved) * src/Tesselation/BoundaryPointSet.hpp (moved) * src/Tesselation/BoundaryPolygonSet.cpp (moved) * src/Tesselation/BoundaryPolygonSet.hpp (moved) * src/Tesselation/BoundaryTriangleSet.cpp (moved) * src/Tesselation/BoundaryTriangleSet.hpp (moved) * src/Tesselation/CandidateForTesselation.cpp (moved) * src/Tesselation/CandidateForTesselation.hpp (moved) * src/Tesselation/TesselPoint.cpp (moved) * src/Tesselation/TesselPoint.hpp (moved) * src/Tesselation/boundary.cpp (moved) * src/Tesselation/boundary.hpp (moved) * src/Tesselation/ellipsoid.cpp (moved) * src/Tesselation/ellipsoid.hpp (moved) * src/Tesselation/tesselation.cpp (moved) * src/Tesselation/tesselation.hpp (moved) * src/Tesselation/tesselationhelpers.cpp (moved) * src/Tesselation/tesselationhelpers.hpp (moved) * src/Tesselation/triangleintersectionlist.cpp (moved) * src/Tesselation/triangleintersectionlist.hpp (moved) * src/analysis_correlation.cpp (modified) * src/atom.hpp (modified) * src/builder_init.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/TesselationUnitTest.cpp (modified) * src/unittests/TesselationUnitTest.hpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified) Moved modules related to Tesselation into own source subfolder. - ... Thu, 13 Oct 2011 14:02:40 GMT Frederik Heber [61ff05] * src/Actions/CommandAction/ElementDbAction.cpp (modified) FIX: ElementDbAction uses CleanupPeriodentafel() instead of deleting ... Thu, 13 Oct 2011 13:03:40 GMT Frederik Heber [ce7fdc] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/ActionTraits.cpp (modified) * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.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/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/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/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.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/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.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/OptionTrait.hpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (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/SetWorldTimeAction.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.hpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.hpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.hpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.hpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldTime.hpp (modified) * src/World_calculations.hpp (modified) * src/builder_init.cpp (modified) HUGE: All Action-related codes resides now in namespace MoleCuilder. ... Wed, 12 Oct 2011 14:10:51 GMT Frederik Heber [220cf64] * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.def (modified) * src/Actions/CommandAction/ElementDbAction.hpp (modified) * src/unittests/PeriodentafelUnitTest.hpp (modified) * tests/regression/Options/ElementsDb/pre/test.conf (added) * tests/regression/Options/ElementsDb/testsuite-options-elements-db.at (modified) Added Undo/Redo capability to ElementDbAction. - thanks to ... Mon, 10 Oct 2011 16:58:24 GMT Frederik Heber [f08ae7] * LinearAlgebra/configure.ac (modified) * LinearAlgebra/src/LinearAlgebra/Makefile.am (modified) * LinearAlgebra/src/unittests/Makefile.am (modified) * configure.ac (modified) * m4/ax_codepatterns.m4 (modified) * m4/boost.m4 (modified) * src/Actions/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/unittests/Makefile.am (modified) Extension of usage of Tsuna's boost.m4 macro. - boost.m4 from ... Mon, 10 Oct 2011 16:58:17 GMT Frederik Heber [78d5b2] * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.def (modified) * tests/regression/Parser/Mpqc/post/empty.in (added) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-load.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-multiple-timesteps.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-multiple-timesteps.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-with-conects.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-multiple-timesteps.at (modified) Added Undo/Redo capability to LoadAction. - Added cloning of ... Mon, 10 Oct 2011 14:25:37 GMT Frederik Heber [38f991] * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) FormatParser now listens to World::AtomRemoved and ::AtomInserted ... Thu, 06 Oct 2011 16:06:10 GMT Frederik Heber [b7ff03] * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def (modified) Selection NotAtomByIdAction now gets atomId_t not const atom *. - ... Thu, 06 Oct 2011 16:06:10 GMT Frederik Heber [5a8840] * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.def (modified) Selection AtomByIdAction now gets atomId_t not const atom *. - This ... Thu, 06 Oct 2011 16:06:10 GMT Frederik Heber [12948c] * src/Actions/unittests/stubs/DummyUI.hpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (added) * src/UIElements/Query/UnsignedIntsQuery.cpp (added) * src/UIElements/TextUI/Query/TextQuery.hpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (added) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) Added new Query for std::vector of unsigned int. - this is ... Thu, 06 Oct 2011 16:06:10 GMT Frederik Heber [838cd0] * src/Actions/unittests/stubs/DummyUI.hpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.hpp (added) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (added) * src/UIElements/Query/UnsignedIntQuery.cpp (added) * src/UIElements/TextUI/Query/TextQuery.hpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (added) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) Added new Query for unsigned int. - this is preparatory to switch ... Thu, 06 Oct 2011 16:06:10 GMT Frederik Heber [5e2f80] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_bondedparticleinfo.hpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) BondedParticle no more hands out non-const ListOfBonds. - the few ... Thu, 06 Oct 2011 16:06:10 GMT Frederik Heber [db7e6d] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) BondedParticle:: register and unregister are private. - adding and ... Thu, 06 Oct 2011 09:15:04 GMT Frederik Heber [81c980b] * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (added) * src/Actions/ParserAction/SetTremoloAtomdataAction.def (added) * src/Actions/ParserAction/SetTremoloAtomdataAction.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data (added) * tests/regression/Parser/Tremolo-SetAtomdata/pre/argon.data (added) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Added new action to set the ATOMDATA in tremolo's .data output file. ... Wed, 05 Oct 2011 16:23:19 GMT Frederik Heber [f6ba43] * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.def (modified) * src/Shapes/BaseShapes.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/CreateMicelle/post/tensid.data (added) * tests/regression/Molecules/CreateMicelle/pre/tensid.data (added) * tests/regression/Molecules/CreateMicelle/pre/tensid.potentials (added) * tests/regression/Molecules/CreateMicelle/testsuite-molecules-create-micelle.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Many smaller changes to CreateMicelleAction to get it fully working ... Wed, 05 Oct 2011 09:18:21 GMT Frederik Heber [c88597] * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) Rotation of the molecule in order to bring the polar side of the ... Wed, 05 Oct 2011 09:18:21 GMT Frederik Heber [37f9d4] * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.def (modified) Changed some non-standard stuff with CreateMicelleAction. - renamed ... Wed, 05 Oct 2011 09:18:21 GMT Frederik Heber [2e352f] * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/atom.cpp (modified) * src/boundary.cpp (modified) * src/molecule.cpp (modified) Because of problems with columns in data-files, some changes were ... Wed, 05 Oct 2011 09:18:21 GMT Frederik Heber [faca99] * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/unittests/ShapeUnitTest.cpp (modified) MoleculeAction create-micelle: code updated; Baseshapes: procedure ... Wed, 05 Oct 2011 09:18:20 GMT Frederik Heber [807c0e] * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (moved) * src/Actions/MoleculeAction/CreateMicelleAction.def (added) * src/Actions/MoleculeAction/CreateMicelleAction.hpp (added) * src/Makefile.am (modified) Daniel has recently changed his mizelledata to work as an action ... Wed, 28 Sep 2011 12:48:59 GMT Frederik Heber [632a52] * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) FIX: boost::filesystem 1.47 changed output of extension(), stem(), ... Wed, 28 Sep 2011 12:48:53 GMT Frederik Heber [e5c233] * LinearAlgebra/src/LinearAlgebra/Exceptions.hpp (modified) * src/Actions/ActionExceptions.hpp (modified) * src/Actions/ValueStorage.hpp (modified) * src/Formula.hpp (modified) * src/Shapes/ShapeExceptions.hpp (modified) FIX: replaced boost/exception.hpp by boost/exception/all.hpp. Wed, 28 Sep 2011 12:40:15 GMT Frederik Heber [416f10] * src/Actions/CommandAction/HelpAction.cpp (modified) FIX: help string on domain is wrong. - CommandHelpAction() gives ... Thu, 22 Sep 2011 12:50:41 GMT Frederik Heber [718542] * 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) * tests/regression/Analysis/AngularDipoleCorrelation-DiscreteAngles/testsuite-analysis-angular-dipole-correlation-discrete-angles.at (modified) * tests/regression/Analysis/AngularDipoleCorrelation-Empty/testsuite-analysis-angular-dipole-correlation-empty.at (modified) * tests/regression/Analysis/PairCorrelation-RangeTest/testsuite-analysis-pair-correlation-range-test.at (modified) * tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified) * tests/regression/Analysis/PointCorrelation/testsuite-analysis-point-correlation.at (modified) * tests/regression/Analysis/PrincipalAxisSystem/testsuite-analysis-principal-axis-system.at (modified) * tests/regression/Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) * tests/regression/Atoms/ChangeElement/testsuite-atoms-change-element.at (modified) * tests/regression/Atoms/Remove/testsuite-atoms-remove.at (modified) * tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (modified) * tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (modified) * tests/regression/Atoms/SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at (modified) * tests/regression/Atoms/Translation/testsuite-atoms-translation.at (modified) * tests/regression/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at (modified) * tests/regression/Domain/CenterInBox/testsuite-domain-center-in-box.at (modified) * tests/regression/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at (modified) * tests/regression/Domain/ChangeBox/post/test-undo.conf (added) * tests/regression/Domain/ChangeBox/testsuite-domain-change-box.at (modified) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) * tests/regression/Domain/ScaleBox/testsuite-domain-scale-box.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (modified) * tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (modified) * tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) * tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified) * tests/regression/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-tremolo-dbond-file.at (modified) * tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) * tests/regression/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at (modified) * tests/regression/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at (modified) * tests/regression/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at (modified) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) * tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at (modified) * tests/regression/Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at (modified) * tests/regression/Molecules/SaveTemperature/testsuite-molecules-save-temperature.at (modified) * tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified) * tests/regression/Molecules/Translation/testsuite-molecules-translation.at (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) * tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at (modified) * tests/regression/Options/ElementsDb/testsuite-options-elements-db.at (modified) * tests/regression/Options/ElementsDb/testsuite-options-no-elements-db.at (modified) * tests/regression/Options/Empty/testsuite-options-empty-configs.at (modified) * tests/regression/Options/FastParsing/testsuite-options-fast-parsing.at (modified) * tests/regression/Options/Help/testsuite-options-help.at (modified) * tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at (modified) * tests/regression/Options/SetDefaultName/testsuite-options-set-default-name.at (modified) * tests/regression/Options/SetWorldTime/testsuite-options-set-world-time.at (modified) * tests/regression/Options/Verbosity/testsuite-options-verbosity.at (modified) * tests/regression/Options/Warranty/testsuite-options-warranty.at (modified) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-basis.at (modified) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-maxiterations.at (modified) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-theory.at (modified) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-empty.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-save.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-empty.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-load.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-multiple-timesteps.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-save.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-empty.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-multiple-timesteps.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-save.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-with-conects.at (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-load.at (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-save.at (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-empty.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-empty.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-multiple-timesteps.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified) * tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-select-all-atoms.at (modified) * tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-unselect-all-atoms.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-select-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-unselect-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-select-atoms-by-element.at (modified) * tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-unselect-atoms-by-element.at (modified) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-select-atom-by-id.at (modified) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-unselect-atom-by-id.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at (modified) * tests/regression/Selection/Molecules/AllMolecules/testsuite-selection-select-all-molecules.at (modified) * tests/regression/Selection/Molecules/AllMolecules/testsuite-selection-unselect-all-molecules.at (modified) * tests/regression/Selection/Molecules/ClearMolecules/testsuite-selection-clear-molecules.at (modified) * tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-select-molecules-by-formula.at (modified) * tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-unselect-molecules-by-formula.at (modified) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-select-molecules-by-name.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-unselect-molecules-by-name.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-backward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-forward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-backward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-forward.at (modified) * tests/regression/Selection/Molecules/MoleculeOfAtom/testsuite-selection-select-atoms-molecules.at (modified) * tests/regression/Selection/Molecules/MoleculeOfAtom/testsuite-selection-unselect-atoms-molecules.at (modified) * tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) Filled action's token as keyword in each test. - also all keywords ... Wed, 21 Sep 2011 20:04:30 GMT Frederik Heber [e69c87] * src/Actions/Action.cpp (modified) * src/Actions/ActionExceptions.hpp (added) * src/Actions/ActionHistory.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/boundary.cpp (modified) * src/builder_init.cpp (modified) * tests/regression/Analysis/AngularDipoleCorrelation-Empty/testsuite-analysis-angular-dipole-correlation-empty.at (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) * tests/regression/Atoms/ChangeElement/testsuite-atoms-change-element.at (modified) * tests/regression/Atoms/Remove/testsuite-atoms-remove.at (modified) * tests/regression/Atoms/RemoveCuboid/post/test-cuboid.xyz-sorted (moved) * tests/regression/Atoms/RemoveCuboid/post/test-withoutcuboid.xyz-sorted (moved) * tests/regression/Atoms/RemoveCuboid/post/test.xyz-sorted (moved) * tests/regression/Atoms/RemoveCuboid/pre/test.xyz (moved) * tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (moved) * tests/regression/Atoms/RemoveSphere/post/test-sphere.xyz-sorted (moved) * tests/regression/Atoms/RemoveSphere/post/test-withoutsphere.xyz-sorted (moved) * tests/regression/Atoms/RemoveSphere/post/test.xyz-sorted (moved) * tests/regression/Atoms/RemoveSphere/pre/test.xyz (moved) * tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (moved) * tests/regression/Atoms/Translation/testsuite-atoms-translation.at (modified) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at (modified) * tests/regression/Domain/CenterInBox/testsuite-domain-center-in-box.at (modified) * tests/regression/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at (modified) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) * tests/regression/Domain/ScaleBox/testsuite-domain-scale-box.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (added) * tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (modified) * tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at (modified) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-bond-file.at (deleted) * tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (added) * tests/regression/Molecules/BondFile/testsuite-molecules-tremolo-dbond-file.at (added) * tests/regression/Molecules/Copy/post/tensid-undo.data (added) * tests/regression/Molecules/Copy/post/test-undo.xyz (added) * tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) * tests/regression/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at (modified) * tests/regression/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at (modified) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/regression/Molecules/Translation-Periodic/post/test-undo.conf (added) * tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified) * tests/regression/Molecules/Translation/post/test-undo.conf (added) * tests/regression/Molecules/Translation/post/test2-undo.conf (added) * tests/regression/Molecules/Translation/testsuite-molecules-translation.at (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) * tests/regression/Molecules/testsuite-molecules.at (modified) * tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at (modified) * tests/regression/Options/ElementsDb/testsuite-options-elements-db.at (modified) * tests/regression/Options/FastParsing/testsuite-options-fast-parsing.at (modified) * tests/regression/Options/Help/testsuite-options-help.at (modified) * tests/regression/Options/SetDefaultName/testsuite-options-set-default-name.at (modified) * tests/regression/Options/SetWorldTime/testsuite-options-set-world-time.at (modified) * tests/regression/Options/Verbosity/testsuite-options-verbosity.at (modified) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-basis.at (added) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-maxiterations.at (added) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-theory.at (added) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc.at (modified) * tests/regression/Parser/Pcp/post/empty.conf (added) * tests/regression/Parser/Pcp/testsuite-parser-pcp-multiple-timesteps.at (added) * tests/regression/Parser/Pcp/testsuite-parser-pcp.at (modified) * tests/regression/Parser/Pdb/post/empty.pdb (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb-multiple-timesteps.at (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb-with-conects.at (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb.at (modified) * tests/regression/Parser/Tremolo/post/empty.data (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo.at (modified) * tests/regression/Parser/Xyz/post/empty.xyz (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz-multiple-timesteps.at (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz.at (modified) * tests/regression/Parser/testsuite-parser.at (modified) * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified) * tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-all-atoms.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-atoms-by-element.at (modified) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-atom-by-id.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at (modified) Splitted off Undo and Redo parts into own tests (3-step rule). - ... Thu, 21 Apr 2011 16:39:45 GMT Frederik Heber [fdcd1b] * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/Makefile.am (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Actions/unittests/stubs/DummyUI.hpp (moved) Moved DummyUI.hpp from unittests to Actions/unittests/stubs. - note ... Thu, 21 Apr 2011 16:26:04 GMT Frederik Heber [dd8990] * src/Actions/Makefile.am (modified) FIX: .def files of Actions have not been present in Makefile.am, ... Thu, 21 Apr 2011 16:25:23 GMT Frederik Heber [3001c9] * src/Actions/Makefile.am (modified) FIX: LoadAction.cpp and RemoveAction.cpp were doubly included instead ... Thu, 21 Apr 2011 16:23:50 GMT Frederik Heber [7159ed] * src/Actions/Makefile.am (modified) DISTFIX: Missing header files in Actions/Makefile.am - missing: ... Thu, 21 Apr 2011 13:51:13 GMT Frederik Heber [dac853c] * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpAction.def (modified) * tests/regression/Options/Help/testsuite-options-help.at (modified) Rewrote HelpAction. - is currently only useful to ... Thu, 21 Apr 2011 11:57:28 GMT Frederik Heber [e4b2f6] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) Added Action::help(). - Action::help() returns a string that ... Thu, 21 Apr 2011 11:57:08 GMT Frederik Heber [13799e] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) FIX: Action::getName() is now const member function. Tue, 19 Apr 2011 11:51:40 GMT Frederik Heber [3bd460a] * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.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) * tests/regression/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at (modified) * tests/regression/Domain/CenterInBox/testsuite-domain-center-in-box.at (modified) * tests/regression/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at (modified) * tests/regression/Domain/ChangeBox/testsuite-domain-change-box.at (modified) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) * tests/regression/Domain/ScaleBox/testsuite-domain-scale-box.at (modified) All Actions on domain now state the final domain size. - default ... Mon, 18 Apr 2011 15:43:58 GMT Frederik Heber [b7fbf0] * 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/MoleculeByIdAction.def (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/NotMoleculeByIdAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) FIX: select-molecule-by-id crashed when no molecules are present. - ... Mon, 18 Apr 2011 12:45:06 GMT Frederik Heber [455573] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Large Commit: SUBDIRS in src/Makefile.am replaced by include. - ... Fri, 08 Apr 2011 15:48:50 GMT Frederik Heber [bf4b9f] * LinearAlgebra/.gitignore (added) * LinearAlgebra/AUTHORS (added) * LinearAlgebra/COPYING (added) * LinearAlgebra/ChangeLog (added) * LinearAlgebra/INSTALL (added) * LinearAlgebra/LinearAlgebra-debug.pc.in (added) * LinearAlgebra/LinearAlgebra.pc.in (moved) * LinearAlgebra/Makefile.am (added) * LinearAlgebra/NEWS (added) * LinearAlgebra/README (added) * LinearAlgebra/bootstrap (added) * LinearAlgebra/build-aux/README (added) * LinearAlgebra/configure.ac (added) * LinearAlgebra/doc/Doxyfile (added) * LinearAlgebra/doc/Makefile.am (added) * LinearAlgebra/libLinearAlgebra_config.h.in (added) * LinearAlgebra/m4 (added) * LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (moved) * LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Exceptions.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Makefile.am (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.hpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Vector.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Vector.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorContent.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorInterface.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (moved) * LinearAlgebra/src/LinearAlgebra/defs.hpp (moved) * LinearAlgebra/src/LinearAlgebra/fast_functions.hpp (moved) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (moved) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.hpp (moved) * LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (moved) * LinearAlgebra/src/LinearAlgebra/vector_ops.hpp (moved) * LinearAlgebra/src/unittests/LineUnitTest.cpp (moved) * LinearAlgebra/src/unittests/LineUnitTest.hpp (moved) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (moved) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.hpp (moved) * LinearAlgebra/src/unittests/Makefile.am (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.hpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.cpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.hpp (moved) * LinearAlgebra/src/unittests/TestRunnerMain.cpp (added) * LinearAlgebra/src/unittests/UnitTestMain.cpp (added) * LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.hpp (moved) * LinearAlgebra/tests/CodeChecks/Makefile.am (added) * LinearAlgebra/tests/CodeChecks/atlocal.in (added) * LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (added) * LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (added) * LinearAlgebra/tests/CodeChecks/testsuite.at (added) * Makefile.am (modified) * bootstrap (modified) * build-aux/README (added) * config/depcomp (deleted) * config/install-sh (deleted) * config/ltmain.sh (deleted) * config/missing (deleted) * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved LinearAlgebra from folder src/ into distinct sub-package. - ... Wed, 06 Apr 2011 13:50:42 GMT Frederik Heber [3e2225f] * configure.ac (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Exceptions/CustomException.cpp (deleted) * src/Exceptions/CustomException.hpp (deleted) * src/Exceptions/Makefile.am (deleted) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Removed subdir Exceptions and libMolecuilderExceptions. - changes ... Wed, 06 Apr 2011 13:50:42 GMT Frederik Heber [336e33] * src/Actions/Action.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/ValueStorage.hpp (modified) * src/Exceptions/Makefile.am (modified) * src/Exceptions/MissingValueException.cpp (deleted) * src/Exceptions/MissingValueException.hpp (deleted) Removed MissingValueException from Exceptions. - is now ...