# # ChangeLog for src # # Generated by Trac 1.6 # May 23, 2025, 11:42:01 PM 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 ... Fri, 04 Nov 2011 15:20:22 GMT Frederik Heber [46bba0] * src/Analysis/Makefile.am (modified) * src/Element/Makefile.am (modified) * src/Helpers/Makefile.am (modified) FIX: Removed versioning info from some convenience libraries. Fri, 04 Nov 2011 15:20:22 GMT Frederik Heber [42c9e2] * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.hpp (modified) FIX: getKeys() and getValues() are now simply internal functions of ... Fri, 04 Nov 2011 15:20:21 GMT Frederik Heber [13c969] * src/atom_atominfo.cpp (modified) FIX: atominfo::getType() does not care whether element exists. - ... Fri, 04 Nov 2011 15:20:21 GMT Frederik Heber [e5cec4] * configure.ac (modified) * m4/bnv_have_qt.m4 (deleted) * src/UIElements/Makefile.am (modified) Removed macro bnv_have_qt, replaced by pkg-config info. - ... Fri, 04 Nov 2011 15:19:53 GMT Frederik Heber [4faa30] * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) FIX: EmptyQtQuery forgot to initialise thisLayout. Fri, 04 Nov 2011 15:19:32 GMT Frederik Heber [3b5fca] * src/Makefile.am (modified) FIX: joiner, analzer and units lacked appropriate ..._LDFLAGS. - ... Fri, 04 Nov 2011 15:19:31 GMT Frederik Heber [6bdba0] * LinearAlgebra/doc/Makefile.am (modified) * LinearAlgebra/src/documentation/Makefile.am (added) * doc/Makefile.am (modified) * src/documentation/Makefile.am (added) DISTCHECKFIX: all .dox files are now given as EXTRA_DIST. - ... Fri, 04 Nov 2011 15:19:11 GMT Frederik Heber [d24953] * src/Makefile.am (modified) * tests/CodeChecks/testsuite-config_h.at (modified) * tests/CodeChecks/testsuite-memdebug.at (modified) DISTCHECKFIX: target unity.cpp has no MemDebug.hpp or config.h. - ... Fri, 04 Nov 2011 08:07:54 GMT Frederik Heber [262ecc] * m4/boost.m4 (modified) * src/Fragmentation/Makefile.am (modified) * src/Makefile.am (modified) DISTCHECKFIX: Forgotten .hpp files included. Thu, 03 Nov 2011 19:44:02 GMT Frederik Heber [c2808e] * src/Parser/ChangeTracker.cpp (modified) * src/Parser/XyzParser.cpp (modified) FormatParser< xyz >::save() now uses numeric_limits. Thu, 03 Nov 2011 19:44:02 GMT Frederik Heber [ab26c3] * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Makefile.am (modified) * src/Parser/PcpParser.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (moved) * src/Thermostats/ThermoStatContainer.hpp (moved) * src/Thermostats/Woodcock.cpp (modified) * src/World.cpp (modified) Moved ThermoStatContainer to folder src/Thermostats. 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 10:35:53 GMT Frederik Heber [f11c23] * src/documentation/code.dox (modified) * src/documentation/future.dox (added) Added documentation on how to understand the code and its (maybe) ... 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) * 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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 01:29:40 GMT Frederik Heber [5837dd] * src/Analysis/analysis_correlation.cpp (modified) Cosmetical fix to PairCorrelation(). 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 ... Wed, 02 Nov 2011 01:28:20 GMT Frederik Heber [870b4b] * src/Analysis/analysis_correlation.cpp (modified) Added rejected molecule counting to DipoleAngularCorrelation(). Tue, 01 Nov 2011 20:45:48 GMT Frederik Heber [a28cc4] * src/documentation/userinterfaces/python.dox (added) * src/documentation/userinterfaces/userinterfaces.dox (modified) DOCU: Added python as fourth user interface. Tue, 01 Nov 2011 20:45:14 GMT Frederik Heber [35a889] * src/documentation/userinterfaces/commandline.dox (modified) * src/documentation/userinterfaces/graphical.dox (modified) * src/documentation/userinterfaces/textmenu.dox (modified) * src/documentation/userinterfaces/userinterfaces.dox (modified) DOCUFIX: Prefixes all three userinterface labels with userinterfaces-. Tue, 01 Nov 2011 19:56:15 GMT Frederik Heber [bc3411] * src/documentation/constructs/serialization.dox (modified) DOCU: Added some important notes in usual mistakes to serialization.dox. 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 11:48:46 GMT Frederik Heber [505d05] * src/Analysis/analysis_correlation.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_X.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0000.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0001.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0002.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0003.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0004.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0005.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0006.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0007.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0008.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0009.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0010.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0011.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0012.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0013.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0014.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0015.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0016.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0017.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0018.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0019.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0020.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0021.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0022.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0023.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0024.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0025.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0026.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0027.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0028.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0029.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0030.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0031.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0032.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0033.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0034.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0035.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) DipoleAngularCorrelation: output now contains name _and position_ of ... Mon, 31 Oct 2011 11:48:46 GMT Frederik Heber [72105a] * src/Analysis/analysis_correlation.cpp (modified) Verbosity fix: DipoleAngularCorrelation() - info given when ... 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 ... Fri, 28 Oct 2011 15:05:03 GMT Frederik Heber [19bc74] * src/documentation/code.dox (added) * src/documentation/constructs/actions.dox (moved) * 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/observers_observables.dox (moved) * src/documentation/constructs/parsers.dox (added) * src/documentation/constructs/randomnumbers.dox (added) * src/documentation/constructs/serialization.dox (moved) * src/documentation/constructs/shapes.dox (added) * src/documentation/constructs/tesselation.dox (added) * src/documentation/faq.dox (modified) * src/documentation/groups.dox (deleted) * src/documentation/install.dox (added) * src/documentation/launch.dox (added) * src/documentation/mainpage.dox (modified) * 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) Explained most of the tests. 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 12:43:16 GMT Frederik Heber [babcc1] * src/Fragmentation/Fragmentation.cpp (modified) * src/MoleculeListClass.hpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/moleculelist.cpp (modified) MoleculeListClass::OutputConfigForListOfFragments() now uses ... 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 15:33:14 GMT Frederik Heber [0a7fad] * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) Refactored part of code in DipoleAngularCorrelation into new method ... Tue, 25 Oct 2011 15:33:14 GMT Frederik Heber [1cc661] * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) Refactored part of DipoleAngularCorrelation into method ... Tue, 25 Oct 2011 15:33:14 GMT Frederik Heber [be0c61] * src/Analysis/analysis_correlation.cpp (modified) FIX: DipoleAngularCorrelation() - ZeroVector is now map over atoms, ... 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 15:28:27 GMT Frederik Heber [4fc828] * src/Analysis/analysis_correlation.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_X.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.pdb (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.pdb (added) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) DipoleAngularCorrelation working with multi-timestep PDBs with CONECT ... 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 [851be8] * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/AdaptivityMap.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) Moved functions that deal with adaptivity from fragmentation_helpers ... Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [730d7a] * src/Fragmentation/AdaptivityMap.cpp (added) * src/Fragmentation/AdaptivityMap.hpp (added) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) New class AdaptivityMap and moved some functions from ... Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [75363b] * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySet.hpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) Extracted functions from fragmentation_helpers and placed them in ... Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [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 [f7fd17] * src/molecule.hpp (modified) FIX: Removed remnant definition of molecule::StoreForcesFile(). - ... 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 [ba94c5] * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) * src/Makefile.am (modified) * src/graph.cpp (deleted) * src/graph.hpp (deleted) * src/molecule.cpp (modified) * src/molecule.hpp (modified) Removed modules graph.[ch]pp. - typedef of KeyStack is placed in ... Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [dadc74] * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/Graph.cpp (added) * src/Fragmentation/Graph.hpp (added) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/UniqueFragments.hpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) * src/graph.cpp (modified) * src/graph.hpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) Extracted Graph (map of KeySets) into own class from graph.hpp. - ... Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [f0674a] * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/KeySet.cpp (added) * src/Fragmentation/KeySet.hpp (added) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/graph.cpp (modified) * src/graph.hpp (modified) * src/moleculelist.cpp (modified) Extracted KeySet from graph.hpp and made into distinct class. - ... Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [246e13] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Fragmentation.cpp (moved) * src/Fragmentation/Fragmentation.hpp (added) * src/Fragmentation/Makefile.am (modified) * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) Placed FragmentMolecule, FragmentBOSSANOVA and subfunctions into own ... Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [212c179] * src/Fragmentation/BondsPerShortestPath.cpp (added) * src/Fragmentation/BondsPerShortestPath.hpp (added) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/UniqueFragments.hpp (modified) * src/molecule_fragmentation.cpp (modified) Placed all functions related to BondsPerSPList into own class ... Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [d0b375b] * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/UniqueFragments.hpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) Removed ShortestPathList. - there have been references in the code ... Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [f67817f] * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/PowerSetGenerator.cpp (added) * src/Fragmentation/PowerSetGenerator.hpp (added) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) Extracted power set generation into own class PowerSetGenerator. Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [23fb72] * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/UniqueFragments.hpp (modified) * src/molecule_fragmentation.cpp (modified) Encapsulated UniqueFragments::Root with getter/setter. Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [f6d1d0] * src/Fragmentation/UniqueFragments.hpp (modified) Made some member variable of UniqueFragments private. Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [a03d25] * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/UniqueFragments.cpp (added) * src/Fragmentation/UniqueFragments.hpp (added) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) * src/graph.cpp (modified) * src/graph.hpp (modified) * src/molecule_fragmentation.cpp (modified) Placed all routines working on UniqueFragments struct inside this ... Tue, 25 Oct 2011 12:08:02 GMT Frederik Heber [d9a032] * src/Fragmentation/Makefile.am (modified) * src/Makefile.am (modified) Initiated own conveniance library for folder src/Fragmentation. - ... Tue, 25 Oct 2011 12:08:02 GMT Frederik Heber [ba1823] * src/Fragmentation/fragmentation_helpers.cpp (added) * src/Fragmentation/fragmentation_helpers.hpp (added) * src/Makefile.am (modified) * src/molecule_fragmentation.cpp (modified) Moved all helpers fragmentation functions into folder src/Fragmentation. Tue, 25 Oct 2011 12:08:02 GMT Frederik Heber [708798] * src/Graph/Makefile.am (modified) FIX: removed -version-info from libMolecuilderGraph. - it's just a ... Tue, 25 Oct 2011 12:08:02 GMT Frederik Heber [ec87e4] * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.hpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (added) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp (added) * src/Graph/unittests/Makefile.am (modified) * src/molecule_fragmentation.cpp (modified) Rewrite of CheckAgainstAdjacencyFile. - we now construct two ... 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 13:20:09 GMT Frederik Heber [539f32] * src/Graph/BondGraph.cpp (modified) Enhanced BondGraph::CreateAdjacency() a bit. 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 12:39:01 GMT Frederik Heber [025048] * src/Box.cpp (modified) * src/Box.hpp (modified) Enhanced Box::periodicDistanceSquared() by an internal_explode(). - ... 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) * 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* 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) * 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(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 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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 ... Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber [829761] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) New function BondGraph::CleanupBondLengthTable(). - allows for ... Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber [1ac24b] * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.hpp (modified) Added unit test function SerializationTest to BondGraphUnitTest. Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber [f007a1] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) Added serialization capability to class BondGraph. - note that we ... Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber [9b6663] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.hpp (modified) Added operator==() to BondGraph. - also added new unit test ... Tue, 18 Oct 2011 15:48:57 GMT Frederik Heber [2d5fee] * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) Added unit test functions SerializationTest for KeySetsContainer and ... Tue, 18 Oct 2011 15:42:54 GMT Frederik Heber [942906] * configure.ac (modified) * src/Fragmentation/KeySetsContainer.hpp (modified) * src/Fragmentation/MatrixContainer.hpp (modified) Added serialize() template functions to MatrixContainer and ... Tue, 18 Oct 2011 08:32:28 GMT Frederik Heber [752bb4] * src/Parser/Psi3Parser.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) Added regression test Parser/Psi3. - this is heavily inspired from ... Tue, 18 Oct 2011 08:23:11 GMT Frederik Heber [d640ea] * src/Parser/Psi3Parser.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) Implemented Psi3Parser::save(). - also we now have working unit ... Tue, 18 Oct 2011 08:23:11 GMT Frederik Heber [9011c1] * src/atom.cpp (modified) * src/atom.hpp (modified) Added atom::OutputPsi3Line() to output a Psi3 conforming geometry line. Tue, 18 Oct 2011 08:22:49 GMT Frederik Heber [120a86] * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) TESTFIX: Added check whether streams are empty to ... Tue, 18 Oct 2011 08:07:56 GMT Frederik Heber [1b145f] * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/KeySetsContainer.hpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/MatrixContainer.hpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.hpp (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.hpp (modified) Added operator==() to KeySetsContainer and MatrixContainer. - also ... Tue, 18 Oct 2011 08:07:37 GMT Frederik Heber [9758f7] * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/KeySetsContainer.hpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/MatrixContainer.hpp (modified) Removed C arrays in KeySetsContainer and MatrixContainer. - ... Mon, 17 Oct 2011 20:17:51 GMT Frederik Heber [a9b86d] * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Fragmentation/EnergyMatrix.cpp (added) * src/Fragmentation/EnergyMatrix.hpp (added) * src/Fragmentation/ForceMatrix.cpp (added) * src/Fragmentation/ForceMatrix.hpp (added) * src/Fragmentation/HessianMatrix.cpp (added) * src/Fragmentation/HessianMatrix.hpp (added) * src/Fragmentation/KeySetsContainer.cpp (added) * src/Fragmentation/KeySetsContainer.hpp (added) * src/Fragmentation/Makefile.am (added) * src/Fragmentation/MatrixContainer.cpp (added) * src/Fragmentation/MatrixContainer.hpp (added) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/defs.hpp (added) * src/Fragmentation/helpers.cpp (added) * src/Fragmentation/helpers.hpp (added) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/parser.cpp (deleted) * src/Fragmentation/parser.hpp (deleted) * src/Graph/BondGraph.cpp (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) Split up modules parser.[ch]pp into one module per class. - fixed ... Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber [c17091] * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) Added convenience function Psi3Parser_Parameters::getReferenceName(). Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber [a67cf0] * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) Renamed Psi3Parser_Parameters::multipParam to ::multiplicityParam. Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber [032f31] * src/Parser/Psi3Parser.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) Implemented Psi3Parser::load(). - also we now have working unit ... Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber [7f570c] * configure.ac (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_Parameters.hpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) Moved operator<<() and operator>>() from Mpqc/Psi3Parser_Parameters ... Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber [f758dd] * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) ParserPsi3UnitTest::ParameterSetterTest() is working. Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber [154a45] * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.hpp (modified) ParserPsi3UnitTest::ParameterCloneTest() is working. Mon, 17 Oct 2011 16:56:36 GMT Frederik Heber [1bef07] * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/Makefile.am (modified) * src/Parser/ParserTypes.def (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/unittests/Makefile.am (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (added) * src/Parser/unittests/ParserPsi3UnitTest.hpp (added) Added first working version of a Psi3Parser. - is so far mostly ... Mon, 17 Oct 2011 16:56:36 GMT Frederik Heber [ee50c1] * src/Parser/FormatParser_Parameters.cpp (added) * src/Parser/FormatParser_Parameters.hpp (modified) * 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/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.hpp (modified) Complete rewrite of MpqcParser_Parameters to incorporate new ... Mon, 17 Oct 2011 16:56:31 GMT Frederik Heber [89a67f] * src/Parser/Parameters/StringParameter.cpp (added) * src/Parser/Parameters/StringParameter.hpp (added) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (added) * src/Parser/Parameters/unittests/StringParameterUnitTest.hpp (added) Added StringParameter as ContinuousParameter as string do not ... Mon, 17 Oct 2011 16:52:28 GMT Frederik Heber [c0da07] * src/Parser/Parameters/ContinuousParameter.hpp (modified) * src/Parser/Parameters/ContinuousParameter_impl.hpp (modified) * src/Parser/Parameters/DiscreteParameter.hpp (modified) * src/Parser/Parameters/DiscreteParameter_impl.hpp (modified) Added constructor that set value to ContinuousParameter and ...