# # ChangeLog for src # # Generated by Trac 1.6 # May 24, 2025, 10:21:26 AM Fri, 03 May 2013 09:44:43 GMT Frederik Heber [781408] * src/Fragmentation/Summation/IndexSet.hpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.hpp (modified) FIX: Added inline comparators for IndexSet::ptr, fixed ... Wed, 01 May 2013 07:53:28 GMT Frederik Heber [e4721d3] * src/Jobs/InterfaceVMGJob.cpp (modified) FIX: Average forces in InterfaceVMGJob only if there actually are ... Wed, 01 May 2013 07:53:28 GMT Frederik Heber [10f0cb] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) VERBOSE: Increased verbosity level for grid printing. - grid values ... Wed, 01 May 2013 07:53:26 GMT Frederik Heber [b6b21a] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added option DoPrintDebug to FragmentationAutomationAction. - this ... Wed, 01 May 2013 07:52:55 GMT Frederik Heber [6ff62c] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenhistogram.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenvalues.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Energy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Forces.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentResults.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Added DoValenceOnly has new option to FragmentationAutomationAction. ... Thu, 18 Apr 2013 16:23:48 GMT Frederik Heber [53c579] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) Removed fragment as parameter from ... Thu, 18 Apr 2013 16:23:26 GMT Frederik Heber [4f04ab8] * configure.ac (modified) * m4/boost.m4 (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) Using boost::graph to obtain maximum matching for bond degree ... Wed, 17 Apr 2013 18:56:55 GMT Frederik Heber [326000] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) BondGraph::CorrectBondDegree() now allows for incrementing only on a ... Wed, 17 Apr 2013 18:56:54 GMT Frederik Heber [378fc6b] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_observable.hpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) Refactored CorrectBondDegree() and resetBondDegree() out of ... Wed, 17 Apr 2013 18:56:54 GMT Frederik Heber [4b62d3] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) GLMoleculeObject_bond sets width of cylinder according to BondDegree. Wed, 17 Apr 2013 18:56:54 GMT Frederik Heber [2d5137] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp (modified) GLMoleculeObject may set scale independently for each component. - ... Wed, 17 Apr 2013 18:56:54 GMT Frederik Heber [1f693d] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Bond/bond_observable.hpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) Wrapped Bond::BondDegree in getter. - This is preparatory for a new ... Wed, 17 Apr 2013 18:56:53 GMT Frederik Heber [88ada9] * src/Atom/atom_bondedparticle.cpp (modified) Enhanced BondedParticle::CorrectBondDegree() to first fill up ... Wed, 17 Apr 2013 18:56:52 GMT Frederik Heber [c8bbf2] * src/UIElements/Qt4/QtMainWindow.cpp (modified) FIX: Added update() after show() in QtMainWindow. Wed, 17 Apr 2013 18:56:52 GMT Frederik Heber [70db8f] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) FIX: Significantly simplified observer use in GLMoleculeObject_bond. ... Wed, 17 Apr 2013 18:56:33 GMT Frederik Heber [411202d] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) FIX: Lowered verbosity of RepeatBoxAction. Wed, 17 Apr 2013 18:56:32 GMT Frederik Heber [ba6b5c] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: Assert wrong way round in GLWorldScene::removeShape(). Wed, 17 Apr 2013 18:56:32 GMT Frederik Heber [691318] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) FIX: GLMoleculeObject_shape did tesselate with fixed radius. - this ... Wed, 17 Apr 2013 18:56:32 GMT Frederik Heber [708277] * configure.ac (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomObserver.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/cleanUp.cpp (modified) * src/molecule.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) FIX: Using fixed Observer in CodePatterns 1.2.6. - we now require ... Wed, 17 Apr 2013 18:56:31 GMT Frederik Heber [79d0b9] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FIX: Fragmentation requires a bond graph with correct degrees. - ... Wed, 17 Apr 2013 18:56:06 GMT Frederik Heber [1d2d01e] * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Controller.hpp (modified) Fixing minimum sensible length for LinkedCell_Controller. - we did ... Wed, 17 Apr 2013 18:56:05 GMT Frederik Heber [0773bd] * src/Tesselation/CandidateForTesselation.cpp (modified) * utils/developer/tcl/README (added) * utils/developer/tcl/animatesphere.tcl (added) * utils/developer/tcl/showsurface.tcl (added) * utils/developer/tcl/surfacing.tcl (added) Added Tcl scripts used for visualizing faulty rolling spheres or the ... Wed, 17 Apr 2013 18:56:04 GMT Frederik Heber [feb5d0] * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/DescriptorBase.hpp (modified) * src/Descriptors/MoleculeDescriptor.hpp (modified) * src/Descriptors/SelectiveConstIterator.hpp (added) * src/Descriptors/SelectiveConstIterator_impl.hpp (added) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) Added SelectiveConstIterator, allows for constant iteration over ... Wed, 17 Apr 2013 18:56:04 GMT Frederik Heber [2448f8] * src/documentation/userinterfaces/python.dox (modified) DOCU: Explained autostart file usage molecuilder.py in python.dox. Wed, 17 Apr 2013 18:56:03 GMT Frederik Heber [08a09ed] * src/Shapes/ShapeOps.cpp (modified) Implemented getSurfaceArea() and getVolume() for Stretch_imp and ... Wed, 17 Apr 2013 18:56:03 GMT Frederik Heber [69f38a] * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) FileQtQuery now has filter with all config, all data, and any files. Wed, 17 Apr 2013 18:55:54 GMT Frederik Heber [30f2815] * src/Parser/MpqcParser.cpp (modified) * tests/regression/Parser/Mpqc/pre/testCLHF_n.in (added) * tests/regression/Parser/Mpqc/pre/testCLHF_n_ascend_ids.in (added) * tests/regression/Parser/Mpqc/pre/testCLHF_n_mixed_ids.in (added) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) MpqcParser now also understands "_n_ atoms geometry" lines. - ... Tue, 16 Apr 2013 06:30:39 GMT Frederik Heber [214240] * src/Actions/Makefile.am (modified) * src/Analysis/Makefile.am (modified) * src/Atom/Makefile.am (modified) * src/Element/Makefile.am (modified) * src/Filling/Makefile.am (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/Makefile.am (modified) * src/Fragmentation/Summation/Converter/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/FunctionApproximation/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Helpers/Makefile.am (modified) * src/LinkedCell/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Potentials/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/UIElements/Makefile.am (modified) FIX: Most of the includedirs were wrongly set. - each just needs to ... Mon, 15 Apr 2013 18:13:46 GMT Frederik Heber [a3fc46] * src/Fragmentation/Summation/Containers/MPQCData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummation_impl.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/Summation_impl.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) FIX: Fixed printKeyName inclusions a bit. - they are now inline ... Mon, 15 Apr 2013 18:13:46 GMT Frederik Heber [1b5a40] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/OrthogonalSummation_impl.hpp (modified) * src/Fragmentation/Summation/SetValue.hpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/Summation/Summation_impl.hpp (modified) VERBOSE: Changed verbosity of Summation process to make a lot less ... Mon, 15 Apr 2013 18:13:36 GMT Frederik Heber [eb32b6] * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenvalues.dat (modified) Eigenvalue summation uses two sets: added and subtracted values. - ... Mon, 15 Apr 2013 18:13:36 GMT Frederik Heber [5c867e] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (added) * src/Fragmentation/Summation/SetValues/Eigenvalues.hpp (added) * src/Fragmentation/Summation/SetValues/Histogram.hpp (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenhistogram.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenvalues.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Added new SetValue Eigenvalues to just add up the set of eigenvalues. ... Mon, 15 Apr 2013 18:13:36 GMT Frederik Heber [e95c8b] * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenvalues.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Re-added printing of eigenvalues as histogram. - TEST: added check ... Mon, 15 Apr 2013 18:13:36 GMT Frederik Heber [658485] * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) Switched off automatic bin width calculation in Histogram. Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [55e1bc] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Energy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Forces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Times.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentResults.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) FragmentationResultContainer is serializable. - ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [a3427f] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (added) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (added) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.hpp (added) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (added) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (added) * src/Fragmentation/Summation/Containers/Makefile.am (modified) Split FragmentationAutomationAction into calculation and analysis. ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [fbf143] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/SetValues/unittests/Makefile.am (deleted) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp (moved) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (moved) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCData.cpp (moved) * src/Fragmentation/Summation/Containers/MPQCData.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCDataFused.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCDataMap.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCData_printKeyNames.hpp (moved) * src/Fragmentation/Summation/Containers/Makefile.am (moved) * src/Fragmentation/Summation/Containers/VMGData.cpp (moved) * src/Fragmentation/Summation/Containers/VMGData.hpp (moved) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (moved) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (moved) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (moved) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (moved) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.hpp (moved) * src/Fragmentation/Summation/Containers/extractJobIds.hpp (moved) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp (moved) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.hpp (moved) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (moved) * src/Fragmentation/Summation/Converter/DataConverter.hpp (moved) * src/Fragmentation/Summation/Converter/Makefile.am (moved) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (moved) * src/Fragmentation/Summation/SetValues/Fragment.hpp (moved) * src/Fragmentation/Summation/SetValues/Histogram.cpp (moved) * src/Fragmentation/Summation/SetValues/Histogram.hpp (moved) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (moved) * src/Fragmentation/Summation/SetValues/IndexedVectors.hpp (moved) * src/Fragmentation/Summation/SetValues/Makefile.am (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid_inline.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (added) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (moved) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) * src/Fragmentation/parseKeySetFile.cpp (moved) * src/Fragmentation/parseKeySetFile.hpp (moved) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob.hpp (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LevMartester.cpp (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/unittests/Makefile.am (modified) Placed Containers, Converter, and SetValues as subfolders into ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [8e84fe] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/SpecificFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Containers/FragmentationChargeDensity.cpp (moved) * src/Fragmentation/Containers/FragmentationChargeDensity.hpp (moved) * src/Fragmentation/Containers/FragmentationLongRangeResults.cpp (moved) * src/Fragmentation/Containers/FragmentationLongRangeResults.hpp (moved) * src/Fragmentation/Containers/FragmentationShortRangeResults.cpp (moved) * src/Fragmentation/Containers/FragmentationShortRangeResults.hpp (moved) * src/Fragmentation/Containers/MPQCData.cpp (moved) * src/Fragmentation/Containers/MPQCData.hpp (moved) * src/Fragmentation/Containers/MPQCDataFused.hpp (moved) * src/Fragmentation/Containers/MPQCDataMap.hpp (moved) * src/Fragmentation/Containers/MPQCData_printKeyNames.hpp (moved) * src/Fragmentation/Containers/Makefile.am (added) * src/Fragmentation/Containers/VMGData.cpp (moved) * src/Fragmentation/Containers/VMGData.hpp (moved) * src/Fragmentation/Containers/VMGDataFused.hpp (moved) * src/Fragmentation/Containers/VMGDataMap.hpp (moved) * src/Fragmentation/Containers/VMGData_printKeyNames.hpp (moved) * src/Fragmentation/Containers/createMatrixNrLookup.cpp (moved) * src/Fragmentation/Containers/createMatrixNrLookup.hpp (moved) * src/Fragmentation/Containers/extractJobIds.hpp (moved) * src/Fragmentation/Containers/parseKeySetFile.cpp (moved) * src/Fragmentation/Containers/parseKeySetFile.hpp (moved) * src/Fragmentation/Containers/unittests/MPQCDataUnitTest.cpp (moved) * src/Fragmentation/Containers/unittests/MPQCDataUnitTest.hpp (moved) * src/Fragmentation/Containers/unittests/Makefile.am (added) * src/Fragmentation/Converter/DataConverter.hpp (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/unittests/Makefile.am (modified) Moved ...Data and all related classes into new subfolder Containers. ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [410405] * src/Jobs/MPQCData_printKeyNames.hpp (modified) * src/Jobs/VMGData_printKeyNames.hpp (modified) FIX: ...Data_printKeyNames lacked printKeyNames include and made inline. Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [7b0494] * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Automation/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/SetValues/Makefile.am (modified) * src/Fragmentation/SetValues/SamplingGrid.cpp (moved) * src/Fragmentation/SetValues/SamplingGrid.hpp (moved) * src/Fragmentation/SetValues/SamplingGridProperties.cpp (moved) * src/Fragmentation/SetValues/SamplingGridProperties.hpp (moved) * src/Fragmentation/SetValues/SamplingGrid_inline.hpp (moved) * src/Fragmentation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (moved) * src/Fragmentation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp (moved) * src/Fragmentation/SetValues/unittests/SamplingGridUnitTest.cpp (moved) * src/Fragmentation/SetValues/unittests/SamplingGridUnitTest.hpp (moved) * src/Jobs/Grid/Makefile.am (deleted) * src/Jobs/Grid/unittests/Makefile.am (deleted) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCData.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGData.hpp (modified) * src/Jobs/VMGDebugGridJob.hpp (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved SamplingGrid... over to Fragmentation/SetValues. - adapted ... Mon, 15 Apr 2013 10:30:31 GMT Frederik Heber [0cd8cf] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationLongRangeResults.cpp (moved) * src/Fragmentation/Automation/FragmentationLongRangeResults.hpp (moved) * src/Fragmentation/Automation/FragmentationShortRangeResults.cpp (added) * src/Fragmentation/Automation/FragmentationShortRangeResults.hpp (added) * src/Fragmentation/Automation/Makefile.am (modified) Split FragmentationResults into ..ShortRange.. and ..LongRange... - ... Mon, 15 Apr 2013 10:30:31 GMT Frederik Heber [503acc1] * configure.ac (modified) * m4/boost.m4 (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Jobs/MPQCData.cpp (modified) * src/Jobs/MPQCData.hpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob.hpp (modified) MPQCJob and MPQCData now have bool to decide whether to sample ... Mon, 15 Apr 2013 10:28:25 GMT Frederik Heber [bae7bc] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (added) * src/Actions/FragmentationAction/ParseFragmentJobsAction.def (added) * src/Actions/FragmentationAction/ParseFragmentJobsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) Outsourced parsing of fragment files into ParseFragmentJobsAction ... Mon, 15 Apr 2013 10:28:25 GMT Frederik Heber [4f44ae] * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.hpp (modified) Added ForceMatrix::parseIndices() from indices of KeySetsContainer. Mon, 15 Apr 2013 10:28:22 GMT Frederik Heber [ac9ca4] * configure.ac (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (added) * src/Fragmentation/Automation/FragmentJobQueue.hpp (added) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/KeySetsContainer.hpp (modified) * src/Fragmentation/Makefile.am (modified) FragmentAction creates FragmentJobs if no output-types are given. - ... Sun, 14 Apr 2013 21:41:07 GMT Frederik Heber [dd0c8f] * 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/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/FilesCommandLineQuery.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/RealSpaceMatrixCommandLineQuery.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) Removed all error messages on missing values in CommandLineUI. - ... Sun, 14 Apr 2013 18:35:28 GMT Frederik Heber [c1a221] * src/Fragmentation/Summation/SubsetMap.cpp (modified) FIX: SubsetMap::getMaximumSetLevel() did not catch empty Lookup ... Sun, 14 Apr 2013 18:35:28 GMT Frederik Heber [78ca37] * src/Fragmentation/fragmentation_helpers.cpp (modified) FIX: printAtomMask() becomes very expensive for large molecules. - ... Sun, 14 Apr 2013 18:35:27 GMT Frederik Heber [c6ab91] * src/molecule.cpp (modified) * src/molecule.hpp (modified) Wrote faster molecule::FindAtom(). - due to local id nature in ... Sun, 14 Apr 2013 18:35:27 GMT Frederik Heber [356ae4] * src/molecule.cpp (modified) FIX: molecule::AddAtom() inserted indirectly two times. - ... Mon, 08 Apr 2013 11:56:18 GMT Frederik Heber [a1d035] * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) Converted TouchedList from int* to std::vector in ... Mon, 08 Apr 2013 11:56:18 GMT Frederik Heber [569e42] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FragmentationAction does not reinsert first graph anymore but copies it. Mon, 08 Apr 2013 11:56:18 GMT Frederik Heber [8ac66b4] * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Graph/BondGraph.cpp (modified) VERBOSE: Lots of changes to verbosity of fragmentation process. Mon, 08 Apr 2013 11:56:18 GMT Frederik Heber [830b3e] * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) VERBOSE: Changed Parser's verbosity level for stating "Saving changes." Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [7cdf58] * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) ExportGraph_ToFiles now uses one-by-one procedure to store fragments. ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [c39675] * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) Added saturate() to SaturatedFragment. - basically, this is ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [6cabaac] * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) Extended ExportGraph to spill our molecular fragments one by one. - ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [7d5fcd] * src/Fragmentation/Exporters/SaturatedFragment.cpp (added) * src/Fragmentation/Exporters/SaturatedFragment.hpp (added) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (added) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.hpp (added) * src/Fragmentation/Makefile.am (modified) Added SaturatedFragment as a wrapper to KeySet with saturation hydrogens. Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [c3df23] * src/Fragmentation/Exporters/HydrogenPool.cpp (added) * src/Fragmentation/Exporters/HydrogenPool.hpp (added) * src/Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.cpp (added) * src/Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.hpp (added) * src/Fragmentation/Exporters/unittests/Makefile.am (added) * src/Fragmentation/Makefile.am (modified) * src/unittests/Makefile.am (modified) Added HydrogenPool for controlling a set of saturation hydrogens. Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [3b0d2a] * src/cleanUp.cpp (modified) Added more timing output to cleanUp(). - final printTiming() is now ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [8652a30] * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) * src/Fragmentation/Makefile.am (modified) Moved some functions from ExportGraph_ToFiles into ExportGraph. - ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [22b786] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.def (modified) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (added) * src/Actions/GraphAction/UpdateMoleculesAction.def (added) * src/Actions/GraphAction/UpdateMoleculesAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) Made SubgraphDissection a MakroAction and added ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [560cbf] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (added) * src/Actions/GraphAction/DestroyAdjacencyAction.def (added) * src/Actions/GraphAction/DestroyAdjacencyAction.hpp (added) * src/Actions/Makefile.am (modified) * tests/regression/Graph/DestroyAdjacency/pre/ethane.pdb (added) * tests/regression/Graph/DestroyAdjacency/testsuite-graph-destroy-adjacency.at (added) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Makefile.am (modified) Added a DestroyAdjacencyAction with undo/redo. - also added ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [055ad7] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.def (modified) * tests/regression/Graph/CreateAdjacency/post/ethane-half.pdb (added) * tests/regression/Graph/CreateAdjacency/post/ethane.pdb (added) * tests/regression/Graph/CreateAdjacency/pre/ethane.xyz (added) * tests/regression/Graph/CreateAdjacency/testsuite-graph-create-adjacency.at (added) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Makefile.am (modified) Added Undo/Redo functionality to CreateAdjacencyAction. - also ... Fri, 22 Mar 2013 00:04:17 GMT Frederik Heber [ddeed2] * configure.ac (modified) * src/cleanUp.cpp (modified) Using enhanced precision of CodePatterns' Chronos. - we now require ... Fri, 22 Mar 2013 00:04:17 GMT Frederik Heber [d948b4] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) atom_bondedparticle::addBond() returns no longer const bond::ptr. - ... Fri, 22 Mar 2013 00:04:17 GMT Frederik Heber [31021ab] * LinearAlgebra/configure.ac (modified) * LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (modified) * LinearAlgebra/src/unittests/VectorSetUnitTest.cpp (modified) * LinearAlgebra/src/unittests/VectorSetUnitTest.hpp (modified) * src/Box.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) Optimized Bondgraph detection. - VectorSet::minDistance() now ... Fri, 22 Mar 2013 00:04:17 GMT Frederik Heber [cf1183] * src/LinkedCell/LinkedCell_Controller.cpp (modified) FIX: LinkedCell_Controller::updateModels() tried toString()'ing NULL. Fri, 22 Mar 2013 00:04:16 GMT Frederik Heber [4f54b3] * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) FIX: AllAtomsInsideVolumeAction stored state with additional ... Fri, 22 Mar 2013 00:03:38 GMT Frederik Heber [5589e7e] * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (added) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def (added) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/StoreSaturatedFragment/post/BondFragment0.xyz (added) * tests/regression/Fragmentation/StoreSaturatedFragment/pre/C6-0.Sheet.Aligned.xyz (added) * tests/regression/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added StoreSaturatedFragmentAction to save a set of atoms satured ... Mon, 18 Mar 2013 14:46:12 GMT Frederik Heber [d5b90b] * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * tests/regression/Parser/Xyz/post/HugeCoordinates.xyz (added) * tests/regression/Parser/Xyz/pre/HugeCoordinates.xyz (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) FIX: XyzParser had lacking precision beyond coordinates of 100000. ... Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [15463a] * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) Extended LinkedCell_Controller::getBestModel() to take box into ... Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [335011] * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) VERBOSE: Trimmed down verbosity when creating a bond graph and on ... Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [3b0cfc] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) FIX: Coloring of bond halves was wrong way around. Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [03abd0] * src/World.cpp (modified) FIX: World::getLinkedCell() does not allow distance less than 1. - ... Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [1f5e97] * src/Parser/PdbParser.cpp (modified) FIX: PdbParser::saveLine() did not restrict some id values. - ... Mon, 18 Mar 2013 13:31:46 GMT Frederik Heber [105b72] * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.hpp (modified) FIX: PdbParser skipped when coordinate exceeded 9999.999. - the ... Sun, 17 Mar 2013 18:27:37 GMT Frederik Heber [e9bdef] * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0001.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0003.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0007.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0008.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0013.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0018.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0027.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0028.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0030.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0033.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0035.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0001.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0003.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.0013.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0018.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.0030.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0033.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0035.dat (modified) TESTFIX: Analysis' DipoleAngularCorrelation() and BinData() suffered ... Mon, 11 Mar 2013 22:31:46 GMT Frederik Heber [8c9049] * src/documentation/constructs/qt-gui.dox (modified) * src/documentation/constructs/shaperegistry.dox (modified) DOCU: Updates for qt-gui and shaperegistry documentation. Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [5c3ad5] * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) Modified SaturationPotential to allow fitting to e.g. HCC as well. ... Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [64bdfd] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) Changed Extractor's combineArguments() to neglect same arguments. - ... Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [035c0d] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) Removed typedef charges_t from FunctionModel, using ... Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [da2d5c] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) Removed parameter charges from getFragmentSpecificExtractor(). Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [3d2559] * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/SerializablePotential.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) Added virtual stream_to/from functions to SerializablePotential. - ... Wed, 27 Feb 2013 12:43:09 GMT Frederik Heber [dbcc47] * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) Arguments for PairPotential_Angle were used in wrong order. Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [863456] * src/Fragmentation/Fragmentation.cpp (modified) Small changes to printAtomMask(). Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [5a4955] * src/Fragmentation/Fragmentation.cpp (modified) We remove all single-index fragments in FragmentMolecule(). - this ... Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [276ac6] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) FIX: ExportGraph_ToFiles needs to know about hydrogen treatment to ... Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [a82127] * src/Potentials/Specifics/SaturationPotential.cpp (modified) FIX: SaturationPotential takes both angles in each triple. - ... Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [4ff79c] * src/LevMartester.cpp (modified) LevMartester casts FunctionModel to SerializablePotential if possible ... Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [77552d] * src/LevMartester.cpp (modified) FIX: LevMartester gives which distance in written table refers to ... Wed, 27 Feb 2013 12:42:37 GMT Frederik Heber [46fcc0] * src/LevMartester.cpp (modified) LevMartester has new option fragment such that fragment to use as ... Wed, 27 Feb 2013 12:42:36 GMT Frederik Heber [39a07a] * src/Fragmentation/Homology/HomologyContainer.hpp (modified) HomologyContainer now gives iterator on its keys, i.e. stored ... Wed, 27 Feb 2013 12:42:36 GMT Frederik Heber [9291d04] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (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 (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * tests/Python/AllActions/options.dat (modified) Split saturation with hydrogen of treatment of hydrogen. - now ... Wed, 27 Feb 2013 12:42:36 GMT Frederik Heber [c7c615] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FIX: FragmentationAction gave wrong number of molecules. Wed, 27 Feb 2013 12:39:33 GMT Frederik Heber [c16cce] * src/LevMartester.cpp (modified) Training fragments are sorted by error to fit value into a map. - ... Wed, 27 Feb 2013 12:39:33 GMT Frederik Heber [3e236e] * src/LevMartester.cpp (modified) LevMartester now fits potentials given on the command-line. - ... Wed, 27 Feb 2013 12:39:33 GMT Frederik Heber [d76ce74] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (added) * src/Potentials/PotentialFactory.hpp (added) Added PotentialFactory for creating potentials. Wed, 27 Feb 2013 12:39:15 GMT Frederik Heber [05f437] * src/LevMartester.cpp (modified) LevMartester now contains three generalized fits to Angle, Morse, and ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [e36ba2] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) FunctionModel extended by triplefunction setter, does nothing by ...