# # ChangeLog for src/Fragmentation # # Generated by Trac 1.6 # May 24, 2025, 8:40:37 AM 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 11:56:08 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 [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. - ... 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 12:42:36 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 ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber [e920d3d] * src/Fragmentation/Homology/FragmentNode.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/LevMartester.cpp (modified) Added getFirstGraphwithTimesSpecificElement(). - this allows to ... Sun, 24 Feb 2013 12:59:34 GMT Frederik Heber [c91572] * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) DOCUFIX: Replaced \text by \mathrm in some formulas. Sun, 24 Feb 2013 12:59:18 GMT Frederik Heber [d760bb] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (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) REFACTOR: PowerSetGenerator now creates all orders in one go, not ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [4a77be7] * src/Fragmentation/SetValues/Fragment.hpp (modified) Added charge_t to Fragment. Thu, 14 Feb 2013 13:29:24 GMT Frederik Heber [3d9a8d] * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGridProperties.cpp (modified) * src/Jobs/Grid/SamplingGridProperties.hpp (modified) * src/Jobs/Grid/unittests/Makefile.am (modified) * src/Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/MPQCJob_binding.hpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) SamplingGrid has no more size parameter but an end array. - this ... Wed, 13 Feb 2013 16:38:23 GMT Frederik Heber [312c0d] * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (added) FIX: HomologyContainerUnitTest does not require libMolecuilderUI ... Wed, 13 Feb 2013 15:47:38 GMT Frederik Heber [7d82a5] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/World.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) Changed bond::ptr into boost::shared_ptr. Changes: - refactored ... Thu, 17 Jan 2013 22:59:15 GMT Frederik Heber [88c8ec] * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/BondInfo.hpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BreadthFirstSearchAdd.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.hpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) REFACTOR: Replaced all "bond *" appearances by bond::ptr. - this is ... Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber [bf12d1] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/writeTable.hpp (modified) FIX: WriteTable might fail because of size_t difference. - ... Sun, 16 Dec 2012 19:47:28 GMT Frederik Heber [fe0355] * src/Fragmentation/Homology/HomologyGraph_getFromKeysetStub.cpp (moved) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Split HomologyGraph_getFromKeyset module off from ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [28e203] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) FIX: nodes_t and edges_t in HomologyGraph must be a map. - there ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [d058e6] * src/Fragmentation/Homology/HomologyContainer.hpp (modified) Exposed const begin,end of container in HomologyContainer to allow ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [79398d] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) Extended map in FragmentResults to a pair of ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [2dd305] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) Split FragmentResults functionality in cstor into cstor and ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [bfbd4a] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) Storing KeySet file with global ids now. - We now parse in key set ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [e71325] * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/AdaptivityMap.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) FIX: All functions in Fragmentation and related now use const string ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [17c03f] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/parseKeySetFile.cpp (added) * src/Fragmentation/Automation/parseKeySetFile.hpp (added) Extracted parseKeySetFile from FragmentationResults, ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [372c912] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (modified) Extended HomologyGraph to also be constructable from IndexSet ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [b8f0b25] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (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) * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) Extended FragmentResults and FragmentationChargeDensity to contain ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [69e065] * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) Added getContributionForIndexSet() and ...Value...() to ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber [07266b] * src/Fragmentation/Summation/SetValueMap.hpp (modified) Added SetValueMap::getConstValue() for getting const reference to ... Fri, 14 Dec 2012 14:29:54 GMT Frederik Heber [e85169] * src/Fragmentation/BondsPerShortestPath.cpp (modified) FIX: Prevented errors message occured due to clearing BondsPerSPList. ... Thu, 13 Dec 2012 10:12:51 GMT Frederik Heber [79ac03] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/AdaptivityMap.hpp (modified) * src/Fragmentation/AtomMask.hpp (added) * src/Fragmentation/Exporters/ExportGraph.cpp (added) * src/Fragmentation/Exporters/ExportGraph.hpp (added) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (added) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (added) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (added) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (added) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (added) * src/Fragmentation/Homology/FragmentEdge.hpp (added) * src/Fragmentation/Homology/FragmentNode.cpp (added) * src/Fragmentation/Homology/FragmentNode.hpp (added) * src/Fragmentation/Homology/HomologyContainer.cpp (added) * src/Fragmentation/Homology/HomologyContainer.hpp (added) * src/Fragmentation/Homology/HomologyGraph.cpp (added) * src/Fragmentation/Homology/HomologyGraph.hpp (added) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/Makefile.am (added) * src/Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (added) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Mask.hpp (added) * src/Fragmentation/MoleculeMask.hpp (added) * src/Fragmentation/SortIndex.cpp (added) * src/Fragmentation/SortIndex.hpp (added) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) * src/Graph/AdjacencyList.cpp (added) * src/Graph/AdjacencyList.hpp (added) * src/Graph/CheckAgainstAdjacencyFile.cpp (deleted) * src/Graph/CheckAgainstAdjacencyFile.hpp (deleted) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.hpp (modified) * src/Graph/ListOfLocalAtoms.hpp (added) * src/Graph/Makefile.am (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (added) * src/Graph/unittests/AdjacencyListUnitTest.hpp (added) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (deleted) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp (deleted) * src/Graph/unittests/Makefile.am (modified) * src/MoleculeLeafClass.cpp (modified) * src/MoleculeLeafClass.hpp (modified) * src/MoleculeListClass.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/Makefile.am (modified) * tests/CodeChecks/testsuite-header-dist.at (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) * tests/regression/Molecules/SaveAdjacency/post/test.adj (modified) Merge branch 'Fragmentation_Homology' into Candidate_v1.3.7 ... Thu, 13 Dec 2012 10:05:42 GMT Frederik Heber [a576eb] * src/Fragmentation/SetValues/Fragment.cpp (modified) * src/Fragmentation/SetValues/Fragment.hpp (modified) * src/Fragmentation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/SetValues/unittests/FragmentUnitTest.hpp (modified) * src/Fragmentation/SetValues/unittests/Makefile.am (modified) Added serialization capability to Fragment. - also added unit test ... Thu, 13 Dec 2012 09:32:50 GMT Frederik Heber [12a24c] * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) Added serialization to HomologyContainer and completed ... Thu, 13 Dec 2012 09:32:50 GMT Frederik Heber [67db80] * src/Fragmentation/Homology/FragmentEdge.cpp (modified) * src/Fragmentation/Homology/FragmentEdge.hpp (modified) * src/Fragmentation/Homology/FragmentNode.cpp (modified) * src/Fragmentation/Homology/FragmentNode.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) Added serialization capabilities to FragmentEdge, FragmentNode, and ... Mon, 10 Dec 2012 10:11:00 GMT Frederik Heber [cd2591] * 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/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added interpolation-degree as parameter to ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [67fec1] * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Jobs/VMGDataFused.hpp (modified) * src/Jobs/VMGDataMap.hpp (modified) * src/Jobs/VMGData_printKeyNames.hpp (modified) Changed VMGDataMap to contain entries for electron, nuclei, and total ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [5a5196] * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) FIX: Now we OrthogonalSumPerLevel potential * charge per fragment. ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [d4f31f] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) FIX: FragmentResults now sums up long-range correction only for level ... Mon, 10 Dec 2012 10:10:58 GMT Frederik Heber [19c50e] * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.hpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalFullSummator.hpp (deleted) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/SortedVector.hpp (modified) * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/Summation/SubsetMap.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/unittests/SubsetMapUnitTest.cpp (modified) * src/Fragmentation/Summation/unittests/SubsetMapUnitTest.hpp (modified) IndexSetContainer now treats super set specially. - The super set ... Mon, 10 Dec 2012 10:10:58 GMT Frederik Heber [27594e] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.cpp (added) * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (added) * src/Fragmentation/Automation/Makefile.am (modified) Added FragmentationChargeDensity to contain summed up charge density. Mon, 10 Dec 2012 10:10:58 GMT Frederik Heber [376a3b] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (added) * src/Fragmentation/Automation/FragmentationResults.hpp (added) * src/Fragmentation/Automation/Makefile.am (modified) Added FragmentationResults as a container to hold final fragmentation ... Mon, 10 Dec 2012 10:10:58 GMT Frederik Heber [a3112d] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) (Orthogonal)SumUpPerLevel now is template for the data structure, ... Mon, 10 Dec 2012 10:10:58 GMT Frederik Heber [184615] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/createMatrixNrLookup.cpp (added) * src/Fragmentation/Automation/createMatrixNrLookup.hpp (added) Extracted createMatrixNrLookup() into own header file. Mon, 10 Dec 2012 10:10:57 GMT Frederik Heber [447481] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/extractJobIds.hpp (added) * src/Jobs/Makefile.am (modified) Extracted template function extractJobIds() into own header file. Mon, 10 Dec 2012 10:10:57 GMT Frederik Heber [a2295a] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Summation/OrthogonalFullSummator.hpp (modified) * src/Jobs/VMGDataFused.hpp (modified) * src/Jobs/VMGDataMap.hpp (modified) * src/Jobs/VMGData_printKeyNames.hpp (modified) We now create one full potential VMGJob of each summed up grid per ... Mon, 10 Dec 2012 10:10:57 GMT Frederik Heber [238868] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.cpp (added) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (added) * src/Jobs/InterfaceVMGDebugGridJob.cpp (added) * src/Jobs/InterfaceVMGDebugGridJob.hpp (added) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob.cpp (added) * src/Jobs/VMGDebugGridJob.hpp (added) Added VMGDebugGridJob that just prints given sampled grid as VTK ... Mon, 10 Dec 2012 10:10:57 GMT Frederik Heber [4aee30] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Converter/DataConverter.hpp (modified) * src/Jobs/MPQCData.cpp (modified) * src/Jobs/MPQCData.hpp (modified) * src/Jobs/MPQCDataFused.hpp (modified) * src/Jobs/MPQCDataMap.hpp (modified) * src/Jobs/MPQCData_printKeyNames.hpp (modified) Timings of MPQCJob are now gathered for total and for the gathering ... Mon, 10 Dec 2012 10:10:56 GMT Frederik Heber [de84ef] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) FIX: Poisson problem is now calculated in atomic length units. - as ... Mon, 10 Dec 2012 10:10:56 GMT Frederik Heber [065574] * 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/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added level and near_field_cells as options to ... Mon, 10 Dec 2012 10:10:56 GMT Frederik Heber [c44322] * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) Using operator<<(SamplingGrid&) to give debug info in ... Mon, 10 Dec 2012 10:10:19 GMT Frederik Heber [ffe057] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (added) * src/Fragmentation/Automation/MPQCFragmentController.hpp (added) * src/Fragmentation/Automation/Makefile.am (added) * src/Fragmentation/Automation/SpecificFragmentController.cpp (added) * src/Fragmentation/Automation/SpecificFragmentController.hpp (added) * src/Fragmentation/Automation/SpecificFragmentController_impl.hpp (added) * src/Fragmentation/Automation/VMGFragmentController.cpp (added) * src/Fragmentation/Automation/VMGFragmentController.hpp (added) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Added SpecificFragmentController and subclasses that contain ... Mon, 03 Dec 2012 09:50:02 GMT Frederik Heber [e15ffe] * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) Added HomologyContainer::operator<<(). Mon, 03 Dec 2012 09:50:02 GMT Frederik Heber [54a561] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) Added output operator to HomologyGraph. Mon, 03 Dec 2012 09:50:02 GMT Frederik Heber [77b350] * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (added) * src/Fragmentation/Makefile.am (modified) HomologyGraph may now be created from a given KeySet referring to ... Mon, 03 Dec 2012 09:50:02 GMT Frederik Heber [7b6b21f] * src/Fragmentation/Homology/HomologyGraph.cpp (added) * src/Fragmentation/Homology/HomologyGraph.hpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) Added HomologyGraph that contains combined information on edges and ... Mon, 03 Dec 2012 09:50:01 GMT Frederik Heber [8387e0] * src/Fragmentation/Homology/FragmentEdge.cpp (added) * src/Fragmentation/Homology/FragmentEdge.hpp (added) * src/Fragmentation/Homology/FragmentNode.cpp (added) * src/Fragmentation/Homology/FragmentNode.hpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) Added FragmentNode and FragmentEdge to contain all information for ... Mon, 03 Dec 2012 09:50:01 GMT Frederik Heber [4694df] * src/Fragmentation/Homology/HomologyContainer.cpp (added) * src/Fragmentation/Homology/HomologyContainer.hpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/Makefile.am (added) * src/Fragmentation/Makefile.am (modified) * src/unittests/Makefile.am (modified) Added class HomologyContainer and unit test. - is basically a ... Mon, 03 Dec 2012 09:50:01 GMT Frederik Heber [3aa8a5] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Graph/AdjacencyList.cpp (modified) * src/Graph/AdjacencyList.hpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.hpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) * tests/regression/Molecules/SaveAdjacency/post/test.adj (modified) REFACTOR: AdjacencyList now just contains a single internal map. - ... Mon, 03 Dec 2012 09:50:01 GMT Frederik Heber [0fad93] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Graph/AdjacencyList.cpp (moved) * src/Graph/AdjacencyList.hpp (moved) * src/Graph/Makefile.am (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (moved) * src/Graph/unittests/AdjacencyListUnitTest.hpp (moved) * src/Graph/unittests/Makefile.am (modified) Renamed CheckAgainstAdjacencyFile -> AdjacencyList. - operator() is ... Mon, 03 Dec 2012 09:50:01 GMT Frederik Heber [91207d] * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) AtomMask is now fully used, only marked atoms end up in fragments. ... Mon, 03 Dec 2012 09:50:01 GMT Frederik Heber [2ab6b6] * src/Fragmentation/Fragmentation.cpp (modified) FIX: Fragmentation::TranslateIndicesToGlobalIDs() now returns truely ... Mon, 03 Dec 2012 09:50:01 GMT Frederik Heber [b4f72c] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) * src/Fragmentation/SortIndex.cpp (modified) * src/Fragmentation/SortIndex.hpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) ExportGraph_ToFiles now does not require molecule reference anymore. ... Mon, 03 Dec 2012 09:50:00 GMT Frederik Heber [dcbb5d] * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/SortIndex.cpp (added) * src/Fragmentation/SortIndex.hpp (added) * src/MoleculeListClass.hpp (modified) * src/moleculelist.cpp (modified) REFACTOR: Replaced SortIndex by a distinct class to allow replacement. Mon, 03 Dec 2012 09:49:59 GMT Frederik Heber [ca8bea] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * 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/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) * src/Fragmentation/Makefile.am (modified) * src/molecule.cpp (modified) ExportGraph_ToFiles performs now the storing of the generated Graph ... Mon, 03 Dec 2012 09:49:30 GMT Frederik Heber [de0af2] * src/Fragmentation/Exporters/ExportGraph.cpp (added) * src/Fragmentation/Exporters/ExportGraph.hpp (added) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (added) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (added) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (added) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (added) * tests/CodeChecks/testsuite-header-dist.at (modified) Added some initial files for exporting a fragmented system to ... Mon, 03 Dec 2012 09:49:30 GMT Frederik Heber [339910] * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/MoleculeLeafClass.hpp (modified) Fragmentation now operates on a single molecule. - ... Mon, 03 Dec 2012 09:49:30 GMT Frederik Heber [b9401e] * src/Fragmentation/Fragmentation.cpp (modified) Removed Correcting bond degree in Fragmentation::FragmentMolecule(). Mon, 03 Dec 2012 09:49:30 GMT Frederik Heber [9511c7] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) CheckAgainstAdjacencyFile is now instantiated in FragmentationAction ... Mon, 03 Dec 2012 09:49:30 GMT Frederik Heber [06f41f3] * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.hpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp (modified) CheckAgainstAdjacencyFile now works on given vector of atomids. - ... Mon, 03 Dec 2012 09:49:06 GMT Frederik Heber [b78dfd] * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) Added helper getGlobalIdsFromLocalIds. - for ... Mon, 03 Dec 2012 09:49:06 GMT Frederik Heber [bf42a0] * src/Fragmentation/fragmentation_helpers.hpp (modified) FIX: Renamed double inclusion preventer of fragmentation_helpers. - ... Mon, 03 Dec 2012 09:49:06 GMT Frederik Heber [3501d2] * src/Fragmentation/Fragmentation.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.hpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) REFACTOR: CheckAgainstAdjacencyFile now gets File in cstor. - we ... Mon, 03 Dec 2012 09:49:06 GMT Frederik Heber [2a0eb0] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/AtomMask.hpp (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) FragmentationAction now works on selected atoms, split into ... Mon, 03 Dec 2012 09:49:06 GMT Frederik Heber [34e74fd] * src/Fragmentation/Fragmentation.cpp (modified) FIX: Fragmentation::GuesstimateFragmentCount() now uses saturation in ... Mon, 03 Dec 2012 09:49:05 GMT Frederik Heber [e554d0] * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/MoleculeListClass.hpp (modified) * src/moleculelist.cpp (modified) Removed SortIndex as (unused) parameter in ... Mon, 03 Dec 2012 09:48:50 GMT Frederik Heber [d4d7a1] * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/MoleculeListClass.hpp (modified) * src/moleculelist.cpp (modified) SortIndex is now a map. - SortIndex is used for giving forces in ... Tue, 27 Nov 2012 08:35:34 GMT Frederik Heber [3dd32f] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/OrthogonalFullSummator.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) MatrixNrLookup ist now used const throughout templated functors. - ... Tue, 27 Nov 2012 08:35:34 GMT Frederik Heber [c9f9bb] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Converter/DataConverter.hpp (modified) * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/OrthogonalFullSummator.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/UIElements/Makefile.am (modified) Combining FragmentResult's id and ...Data in ... Tue, 27 Nov 2012 08:35:34 GMT Frederik Heber [0398bd] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Converter/DataConverter.hpp (added) * src/Fragmentation/Converter/Makefile.am (added) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (added) * src/Fragmentation/Summation/SumUpPerLevel.hpp (added) * src/Makefile.am (modified) Moved ConvertDataTo and ..SumUpPerLevel into distinct header files. Tue, 27 Nov 2012 08:35:34 GMT Frederik Heber [302345] * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) FIX: (Orthogonal)Summator would not create correct indices for ... Tue, 27 Nov 2012 08:35:33 GMT Frederik Heber [7f8525] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/SetValues/Histogram.cpp (modified) Changed overall debug levels in output of FragmentationAutomationAction. Wed, 21 Nov 2012 12:46:30 GMT Frederik Heber [358ddb] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalFullSummator.hpp (added) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDataFused.hpp (added) * src/Jobs/VMGDataMap.hpp (added) * src/Jobs/VMGData_printKeyNames.hpp (added) FragmentationAutomationAction now also sums up potential and obtain ... Wed, 21 Nov 2012 10:03:24 GMT Frederik Heber [f3bc5f] * src/Fragmentation/SetValues/Fragment.cpp (modified) * src/Fragmentation/SetValues/Fragment.hpp (modified) * src/Fragmentation/SetValues/unittests/FragmentUnitTest.cpp (added) * src/Fragmentation/SetValues/unittests/FragmentUnitTest.hpp (added) * src/Fragmentation/SetValues/unittests/Makefile.am (modified) Added extensive unit tests and some more functions to Fragment. Wed, 21 Nov 2012 10:03:24 GMT Frederik Heber [184943] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/SetValues/Fragment.cpp (modified) * src/Fragmentation/SetValues/Fragment.hpp (modified) * src/Jobs/MPQCDataFused.hpp (modified) * src/Jobs/MPQCDataMap.hpp (modified) Added Fragment to MPQCData fusion maps and is used in ... Wed, 21 Nov 2012 10:03:24 GMT Frederik Heber [c74fdb] * src/Fragmentation/SetValues/Fragment.cpp (added) * src/Fragmentation/SetValues/Fragment.hpp (added) * src/Fragmentation/SetValues/Makefile.am (modified) Added new SetValue Fragment for summing up nuclei positions and ... Fri, 16 Nov 2012 14:13:46 GMT Frederik Heber [27afbf] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/ValuePrinter.hpp (modified) * src/Fragmentation/Summation/writeTable.hpp (added) FragmentationAutomationAction now prints table of results for energy, ... Fri, 16 Nov 2012 14:13:46 GMT Frederik Heber [c42a43] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/ValuePrinter.hpp (added) Added ValuePrinter with templated operator() for mpl::for_each to ... Fri, 16 Nov 2012 14:13:46 GMT Frederik Heber [20b3df] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/HeaderPrinter.hpp (added) * src/Fragmentation/Summation/Makefile.am (modified) Added HeaderPrinter with templated operator() for mpl::for_each to ... Fri, 16 Nov 2012 14:13:45 GMT Frederik Heber [beb16e] * src/Fragmentation/SetValues/Histogram.cpp (modified) * src/Fragmentation/SetValues/Histogram.hpp (modified) * src/Fragmentation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/SetValues/IndexedVectors.hpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalSummation_impl.hpp (modified) * src/Fragmentation/Summation/ZeroInstance.hpp (added) * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) Added template function ZeroInstance to have zero value in ... Fri, 16 Nov 2012 14:13:45 GMT Frederik Heber [3102010] * src/Fragmentation/Summation/OrthogonalSummation.hpp (modified) * src/Fragmentation/Summation/Summation.hpp (modified) Getter (Orthogonal)Summation::getSetVales() added. - this is ... Fri, 16 Nov 2012 14:13:45 GMT Frederik Heber [ff9963] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (moved) * src/Fragmentation/Summation/AllLevelSummator.hpp (moved) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalSummation.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummation_impl.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/Summation.hpp (modified) * src/Fragmentation/Summation/Summation_impl.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) * src/Fragmentation/Summation/unittests/OrthogonalSummationUnitTest.cpp (modified) * src/Fragmentation/Summation/unittests/SummationUnitTest.cpp (modified) (Orthogonal)Summation now goes level-wise. - print(Orthogonal)Sum ... Fri, 16 Nov 2012 14:13:45 GMT Frederik Heber [8a0e78] * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.hpp (modified) * src/Fragmentation/Summation/unittests/IndexSetContainerUnitTest.cpp (modified) * src/Fragmentation/Summation/unittests/IndexSetContainerUnitTest.hpp (modified) Added IndexSetContainer::countSetsTillLevel() to count sets up to ... Fri, 16 Nov 2012 14:13:45 GMT Frederik Heber [a96b02] * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) (Orthogonal)Summator now have internal instance Summation. - added ... Fri, 16 Nov 2012 14:13:44 GMT Frederik Heber [d199cc] * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/Summation/SubsetMap.hpp (modified) Added new function SubsetMap::getMaximumSetLevel(). - just gives ... Fri, 16 Nov 2012 14:13:44 GMT Frederik Heber [db11d4] * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/Summation/SubsetMap.hpp (modified) * src/Fragmentation/Summation/unittests/SubsetMapUnitTest.cpp (modified) * src/Fragmentation/Summation/unittests/SubsetMapUnitTest.hpp (modified) Added SubsetMap::getMaximumSubsetLevel() to know up to which level to ... Fri, 16 Nov 2012 14:13:43 GMT Frederik Heber [a67a04] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/SetValues/IndexedVectors.hpp (modified) * src/Fragmentation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) * src/Fragmentation/SetValues/unittests/IndexedVectorsUnitTest.hpp (modified) IndexedVector's cstor ignores -1 as indices. - this is to allow for ...