# # ChangeLog for src/Fragmentation # # Generated by Trac 1.4.4 # Apr 21, 2025, 9:40:28 AM Thu, 18 Sep 2014 18:24:51 GMT Frederik Heber [8cc22f] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/TesselPoint.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/molecule_geometry.cpp (modified) Changed how trajectories are stored, not as vecor but as map. - ... Wed, 17 Sep 2014 19:44:31 GMT Frederik Heber [2a6d8c] * src/Fragmentation/Exporters/SaturationDistanceMaximizer.hpp (modified) DOCUFIX: Doyxygen formula was broken in SaturationDistanceMaximizer. Thu, 28 Aug 2014 08:53:42 GMT Frederik Heber [185e6f] * src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp (modified) MEMFIX: SaturationDistanceMaximizer::operator() did not delete Advocate. Thu, 28 Aug 2014 08:53:32 GMT Frederik Heber [707a2b] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) FIX: FitPotentialAction's getFirstGraphwithSpecifiedElements() access ... Thu, 21 Aug 2014 06:43:48 GMT Frederik Heber [07ecc5] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) FIX: FragmentationAutomationAction did not fail correctly with ... Thu, 21 Aug 2014 06:43:46 GMT Frederik Heber [748fc7] * src/Actions/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/builder_init.cpp (modified) * src/unittests/Makefile.am (modified) libMolecuilder is now a shared library. - linking error ... Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [e9e86f] * src/Actions/unittests/Makefile.am (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) FIX: UnitTestMain placed into convenience libUnitTest. - removed ... Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [09806a] * src/Fragmentation/Interfragmenter.cpp (modified) FIX: Interfragmenter had iter collision. Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [fe77df] * src/Fragmentation/Automation/SpecificFragmentController_ReceiveResultContainer_impl.hpp (modified) FIX: ReceiveResultContainer could not find functions from base class. Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [3b35e7] * LinearAlgebra/src/LinearAlgebra/Makefile.am (modified) * LinearAlgebra/src/unittests/Makefile.am (modified) * configure.ac (modified) * m4/boost.m4 (modified) * m4/qwt.m4 (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Converter/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Plotting/Makefile.am (modified) * src/unittests/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) Fixes due to update to Ubuntu 14.04. - subdir-objects is default ... Wed, 20 Aug 2014 12:58:30 GMT Frederik Heber [45cdce6] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.hpp (modified) MPQCCommandFragmentController supports FragmentationAutomationAction ... Wed, 20 Aug 2014 12:58:30 GMT Frederik Heber [f14972] * src/Fragmentation/Fragmentation.cpp (modified) FIX: CheckOrderAtSite() called PrintAtomMask() with wrong AtomCount. Sat, 16 Aug 2014 15:52:30 GMT Frederik Heber [5d5550] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) FragmentationAction now compiles global saturation positions information. Sat, 16 Aug 2014 15:52:30 GMT Frederik Heber [a1d1dd] * src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp (added) * src/Fragmentation/Exporters/SaturationDistanceMaximizer.hpp (added) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.cpp (added) * src/Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.hpp (added) * src/Fragmentation/Exporters/unittests/stubs/SaturatedBondStub.cpp (added) * src/Fragmentation/Makefile.am (modified) Added SaturationDistanceMaximizer to determine best alphas for ... Sat, 16 Aug 2014 15:52:30 GMT Frederik Heber [bac32f] * src/Fragmentation/Exporters/SaturatedBond.cpp (added) * src/Fragmentation/Exporters/SaturatedBond.hpp (added) * src/Fragmentation/Makefile.am (modified) Added SaturatedBond as container for a "dangling bond" and its ... Sat, 16 Aug 2014 15:52:30 GMT Frederik Heber [98a293b] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.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/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) SaturatedFragment can deal with a global saturation position map. - ... Thu, 14 Aug 2014 14:49:51 GMT Frederik Heber [de2cbf] * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) Added SaturateFragment()::saturateAtom() replacing all cut bonds at ... Thu, 14 Aug 2014 14:49:51 GMT Frederik Heber [9d3264] * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) Refactored SaturatedFragment::saturate() using list of cut bonds. - ... Thu, 14 Aug 2014 14:49:51 GMT Frederik Heber [3fbdca] * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if ... Thu, 14 Aug 2014 14:49:51 GMT Frederik Heber [06804b] * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (deleted) * src/Graph/BreadthFirstSearchAdd.hpp (deleted) * src/Graph/Makefile.am (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) Removed molecule::AddHydrogenReplacement() and BreadthFirstSearchAdd. ... Mon, 14 Jul 2014 11:15:18 GMT Frederik Heber [a61dbb] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * tests/regression/Fragmentation/FragmentationAutomation/pre/test.conf (added) * tests/regression/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) In CommandLineUI actions are skipped after failing action. - ... Sun, 13 Jul 2014 18:04:51 GMT Frederik Heber [d6a7b9] * configure.ac (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.hpp (modified) * src/Jobs/JobMarket/SystemCommandJob.cpp (modified) * src/Jobs/JobMarket/SystemCommandJob.hpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) Specifying executable and suffix in SystemCommandJob with ... Sun, 13 Jul 2014 07:41:15 GMT Frederik Heber [18ed8c] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/Makefile.am (modified) * src/Jobs/Makefile.am (modified) All HAVE_VMG also check for HAVE_JOBMARKET. - right now VMG is not ... Sun, 13 Jul 2014 07:41:14 GMT Frederik Heber [2e584e] * configure.ac (modified) * src/Fragmentation/analyzer.cpp (deleted) * src/Fragmentation/datacreator.cpp (deleted) * src/Fragmentation/datacreator.hpp (deleted) * src/Fragmentation/joiner.cpp (deleted) * src/Makefile.am (modified) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaEnergies-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaEnergies-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaForces-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMaxForces-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMaxForces-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMeanForces-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMeanForces-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinForces-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinForces-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinMeanMaxTotalForce-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaSimTime-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Fragment.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Fragment.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-FragmentOrder.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-FragmentOrder.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/Forces-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/Makefile (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxEnergies-FragmentOrder.dat 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tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragmentForces-Factors.dat (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragmentKeySets.dat (deleted) * tests/Fragmentations/Joining/heptan/pre/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/testsuite-joining-heptan.at (deleted) * tests/Fragmentations/Makefile.am (modified) * tests/Fragmentations/analyzer.in (deleted) * tests/Fragmentations/joiner.in (deleted) * tests/Fragmentations/testsuite.at (modified) Removed (very) old joiner and analyzer programs. - they are not ... Sun, 13 Jul 2014 07:41:14 GMT Frederik Heber [1d17e5] * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (added) * src/Fragmentation/Automation/MPQCCommandFragmentController.hpp (added) * src/Fragmentation/Automation/Makefile.am (modified) * src/Jobs/JobMarket/FragmentJob.hpp (modified) Added MPQCCommandFragmentController. - ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [786d28] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Lib..FragmentationAutomation and lib..Jobs now also compiled without ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [1dfe00] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) Added inclusion switch on HAVE_JOBMARKET for files depending on ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [a498c1] * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/ResultContainer.hpp (added) * src/Fragmentation/Automation/ResultContainer_impl.hpp (added) * src/Fragmentation/Automation/SpecificFragmentController.hpp (modified) * src/Fragmentation/Automation/SpecificFragmentController_ReceiveResultContainer_impl.hpp (modified) Extracted ResultContainer from ReceiveResultContainer. Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [d4eaf1] * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/SpecificFragmentController.hpp (modified) * src/Fragmentation/Automation/SpecificFragmentController_ReceiveResultContainer_impl.hpp (moved) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) Renamed ResultContainer -> ReceivedResultContainer. - this belongs ... Tue, 20 May 2014 09:14:56 GMT Frederik Heber [caece4] * src/Fragmentation/Fragmentation.cpp (modified) * src/documentation/code.dox (modified) * src/documentation/constructs/actions.dox (modified) * src/documentation/constructs/atoms.dox (modified) * src/documentation/constructs/bondgraph.dox (modified) * src/documentation/constructs/filling.dox (modified) * src/documentation/constructs/fragmentation.dox (modified) * src/documentation/constructs/potentials.dox (modified) * src/documentation/constructs/serialization.dox (modified) * src/documentation/constructs/shaperegistry.dox (modified) * src/documentation/constructs/shapes.dox (modified) * src/documentation/constructs/tesselation.dox (modified) * src/documentation/constructs/validators.dox (modified) * src/documentation/copyright.dox (modified) * src/documentation/fileformats.dox (modified) * src/documentation/future.dox (modified) * src/documentation/install.dox (modified) * src/documentation/launch.dox (modified) * src/documentation/mainpage.dox (modified) * src/documentation/tests/code-tests.dox (modified) * src/documentation/tests/regression-tests.dox (modified) * src/documentation/userinterfaces/commandline.dox (modified) * src/documentation/userinterfaces/graphical.dox (modified) * src/documentation/userinterfaces/python.dox (modified) * src/documentation/userinterfaces/textmenu.dox (modified) Enhanced documentation significantly. - went through all of the ... Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [d9f2b3] * src/Fragmentation/Automation/SpecificFragmentController.cpp (modified) * src/Fragmentation/Automation/SpecificFragmentController.hpp (modified) * src/Fragmentation/Automation/SpecificFragmentController_ResultContainer_impl.hpp (modified) SpecificFragmentController has a ref to an updatehandler to call in ... Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [d76d65] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (modified) FIX: MPQCDataFragmentMap_t can be summed up in ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [ae68b5] * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) Fixed some boost serialization static warnings. Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [a2a2f7] * src/Actions/ActionSequence.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Box.cpp (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (modified) * src/Fragmentation/Homology/FragmentNode.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) Huge warning fix. - fixed unused variables. - fixed set but unused ... Mon, 03 Mar 2014 14:06:36 GMT Frederik Heber [eddab7] * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) FIX: getSummedShortRangeResults() usage of typename incompatible with ... Sun, 20 Oct 2013 11:45:34 GMT Frederik Heber [e0cf82] * src/Fragmentation/Automation/SpecificFragmentController.cpp (modified) Cut down verbosity of SpecificFragmentController with ... Thu, 17 Oct 2013 07:24:42 GMT Frederik Heber [d29b31] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_LongRangeEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_LongRangeEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults_OBC.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults_PBC.dat (modified) Longrange energy is now also calculated for level 1. - level 1 sum ... Thu, 17 Oct 2013 07:24:25 GMT Frederik Heber [c8d13f5] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (modified) * src/Fragmentation/Summation/IndexSet.hpp (modified) * src/Fragmentation/Summation/writeIndexedTable.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_IndexedEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_IndexedEnergy.dat (modified) Summed up results are now handed-over to FragmentationResultContainer ... Thu, 17 Oct 2013 07:24:25 GMT Frederik Heber [47cee7] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/HeaderPrinter.hpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/ValuePrinter.hpp (modified) * src/Fragmentation/Summation/writeIndexedTable.hpp (added) * src/Fragmentation/Summation/writeTable.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_IndexedEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_IndexedEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Writing out energy file with value and contribution per index set - ... Thu, 17 Oct 2013 07:24:06 GMT Frederik Heber [675cd6] * src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/AllLevelSummator.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/Summation_impl.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) (Orthogonal)Summator are notified via out-of-range matrixnr to omit ... Thu, 17 Oct 2013 07:24:06 GMT Frederik Heber [58952a] * src/Fragmentation/Summation/SetValue.hpp (modified) * src/Fragmentation/Summation/ZeroInstance.hpp (modified) SetValue treats ZeroInstance as value special. - ZeroInstance in ... Thu, 17 Oct 2013 07:14:21 GMT Frederik Heber [955051] * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.hpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.hpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties_inline.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.cpp (added) * src/Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.hpp (added) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (modified) Added (in)equality operators to all SetValues. - only Fragment and ... Mon, 14 Oct 2013 23:42:04 GMT Frederik Heber [e0ae58d] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (modified) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.hpp (modified) createMatrixNrLookup now requires a ValueMask. - adapted all ... Mon, 14 Oct 2013 23:42:04 GMT Frederik Heber [7d507c] * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) FIX: Histogram::superposeOtherHistogram() could not deal with empty ... Mon, 14 Oct 2013 23:42:04 GMT Frederik Heber [adb51ab] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Helpers/defs.cpp (modified) * src/Helpers/defs.hpp (modified) FragmentationAction stores cycles to file and in ... Mon, 14 Oct 2013 23:42:03 GMT Frederik Heber [fe0cb8] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added option DoCyclesFull to FragmentationAction. - FIX: ... Sat, 05 Oct 2013 09:33:18 GMT Frederik Heber [4e6a60] * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Potentials/InternalCoordinates/Coordinator.hpp (modified) * src/Potentials/InternalCoordinates/CoordinatorFactory.cpp (modified) * src/Potentials/InternalCoordinates/CoordinatorFactory.hpp (added) * src/Potentials/Makefile.am (modified) Added CoordinatorFactory that returns the correct Coordinator for a ... Sat, 05 Oct 2013 09:32:45 GMT Frederik Heber [d20ded] * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.cpp (added) * src/UIElements/Views/Qt4/QtFragmentList.hpp (added) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FragmentResultContainer is Observable and displayed by ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [76096d] * src/Element/periodentafel.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/boundary.cpp (modified) FIX: Several fixes found through CppCheck. - strncpy does not ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [d67e6c] * src/Fragmentation/defs.hpp (modified) FIX: Changed inclusion guards of Fragmentation/defs.hpp to allow for ... Thu, 19 Sep 2013 20:22:55 GMT Frederik Heber [732507] * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/SpecificFragmentController.cpp (modified) * src/Fragmentation/Automation/SpecificFragmentController.hpp (modified) * src/Fragmentation/Automation/SpecificFragmentController_ResultContainer_impl.hpp (added) * src/Fragmentation/Automation/SpecificFragmentController_impl.hpp (deleted) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) SpecificFragmentController now contains template ResultContainer. - ... Thu, 19 Sep 2013 20:10:24 GMT Frederik Heber [f6c19d] * src/Fragmentation/Automation/VMGDebugGridFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGDebugGridJob.hpp (modified) * src/Jobs/VMGJob.hpp (modified) InterfaceVMGDebugJob now also uses optionally open boundary (FAS ... Thu, 15 Aug 2013 08:41:17 GMT Frederik Heber [ee9018] * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) InterfaceVMGJob now may also use open boundary (FAS instead of CS). ... Mon, 12 Aug 2013 11:30:33 GMT Frederik Heber [353326] * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: Changed LIBADDs and LDADDs to get rid of libtool patching. - ... Mon, 12 Aug 2013 11:30:31 GMT Frederik Heber [321470] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) FIX: Fragmentation's OrderAtSite was written per molecule and with ... Fri, 09 Aug 2013 14:20:38 GMT Frederik Heber [0331ee] * src/Fragmentation/Graph.hpp (modified) * src/Fragmentation/Interfragmenter.cpp (added) * src/Fragmentation/Interfragmenter.hpp (added) * src/Fragmentation/Makefile.am (modified) Added functor to add non-bonded union of fragments. - this is done ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [e355b31] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Added both_sampled_potential to VMGData, analogous to ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [bf1d1b] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * tests/Python/AllActions/options.dat (modified) HomologyContainer now stores full struct as value to HomologyGraph ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [3f64ee] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) Extracted SamplingGrid::getDiscreteWindowIndices() from ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [b5f548] * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties_inline.hpp (added) * src/Fragmentation/Summation/SetValues/SamplingGrid_inline.hpp (modified) FIX: Shifted all helper functions from SamplingGrid to ..Properties. ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [bcc24f] * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) Made HomologyContainer observable. - added clear() and getNextKey() ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [a8bc27a] * src/Fragmentation/Homology/HomologyContainer.hpp (modified) FIX: HomologyContainer::getHomologousGraphs() is actually const ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [0afe00] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) Extracted printNodes() and printEdges from HomologyGraph's output ... Tue, 09 Jul 2013 06:21:28 GMT Frederik Heber [11f0fa] * src/Atom/atom.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.hpp (modified) FIX: Newly created atoms must have trajectories reaching out till ... Tue, 09 Jul 2013 06:21:05 GMT Frederik Heber [e5ebaf] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Forces obtained from fragmentation summation are now set. - i.e. ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [7c1091] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) Extended CompoundPotential for multiple occurences of argument ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [154e88] * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp (modified) * src/Potentials/CompoundPotential.cpp (added) * src/Potentials/CompoundPotential.hpp (added) * src/Potentials/Makefile.am (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (added) * src/Potentials/unittests/CompoundPotentialUnitTest.hpp (added) * src/Potentials/unittests/Makefile.am (modified) Added CompoundPotential as container for multiple FunctionModels. - ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [a953c4] * configure.ac (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) Using priorizing of jobs. - we now require JobMarket 1.1.4. - ... Mon, 08 Jul 2013 14:22:00 GMT Frederik Heber [4b8ab7] * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) FIX: Histogram did not use the pair-wise operator<<(). - his ... Wed, 12 Jun 2013 10:11:59 GMT Frederik Heber [5aaa43] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (modified) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/parseKeySetFile.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/Parameters/Validators/Specific/PotentialTypeValidator.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/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) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/cleanUp.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) * tests/regression/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Graph/CreateAdjacency/testsuite-graph-create-adjacency.at (modified) * tests/regression/Graph/DestroyAdjacency/testsuite-graph-destroy-adjacency.at (modified) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) * tests/regression/testsuite.at (modified) FIX: Fixed new copyright line since start of 2013 in CodeChecks test. ... Mon, 06 May 2013 21:33:49 GMT Frederik Heber [87d6bd] * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Fragmentation/Mask.hpp (modified) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (modified) * src/Parameters/Validators/DiscreteValidator.hpp (modified) * src/Parameters/Validators/RangeValidator.hpp (modified) * src/Parameters/Validators/RangeValidator_impl.hpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/UIElements/Dialog.hpp (modified) FIX: Fixing several clang errors such that we may safely use the ... Fri, 03 May 2013 11:58:26 GMT Frederik Heber [661d2d] * src/Fragmentation/Summation/Makefile.am (modified) FIX: Replaced BOOST_LDFLAGS by flags specific to boost serialization ... Fri, 03 May 2013 09:46:46 GMT Frederik Heber [f7ce2b] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) FIX: HomologyGraph::operator<<() did print last comma, too. Fri, 03 May 2013 09:46:45 GMT Frederik Heber [e2925fd] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Eigenhistogram.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Eigenvalues.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Energy.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Forces.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_LongRangeEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Times.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_VMGEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Eigenhistogram.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Eigenvalues.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Energy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Forces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Times.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentShortRangeResults.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Split long-range calculations into two parts to overcome ... Fri, 03 May 2013 09:46:45 GMT Frederik Heber [5281ff] * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (modified) REFACTOR: extracted initLookups() in FragmentationLongRangeResults ... 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 [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 ... 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 ... 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 [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 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. - ...