# # ChangeLog for src/Actions/FragmentationAction # # Generated by Trac 1.4.4 # Mar 19, 2025, 11:04:18 AM Tue, 10 Feb 2015 14:09:38 GMT Frederik Heber [ca09be] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/ResultContainer_impl.hpp (modified) * src/Fragmentation/Automation/SpecificFragmentController_ReceiveResultContainer_impl.hpp (modified) FIX: FragmentationAutomationAction checks FragmentControllers' ... Tue, 10 Feb 2015 14:09:38 GMT Frederik Heber [0763ce] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/World.cpp (modified) Added BondGraph::checkBondDegree, FragmentationAction only resets ... Tue, 10 Feb 2015 14:09:38 GMT Frederik Heber [cd5aa0] * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) Added correct-bonddegree to MolDyn and StructOpt Actions. - this is ... Tue, 10 Feb 2015 14:09:10 GMT Frederik Heber [329cf3] * src/Actions/ActionSequence.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) FIX: All MakroActions now have prototype_actions and copy from that. ... Tue, 09 Sep 2014 22:09:57 GMT Frederik Heber [95cfac] * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/CommandAction/ElementDbAction.def (modified) * src/Actions/CommandAction/LoadSessionAction.def (modified) * src/Actions/CommandAction/StoreSessionAction.def (modified) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.def (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) Added FileSuffixValidator to all Actions where missing but ... Mon, 08 Sep 2014 21:36:29 GMT Frederik Heber [553c54] * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.def (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.def (modified) * tests/Python/AllActions/options.dat (modified) Added option keep-bondgraph to MolecularDynamicsAction and ... 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 ... 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 [e5f61ba] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (added) * src/Actions/FragmentationAction/StructuralOptimizationAction.def (added) * src/Actions/FragmentationAction/StructuralOptimizationAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) Added MakroAction StructureOptimizationAction. - performs similarly ... 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 [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. - ... Mon, 14 Jul 2014 11:16:23 GMT Frederik Heber [d8821e] * Makefile.am (modified) * configure.ac (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Element/Makefile.am (modified) * src/Element/element.hpp (modified) * src/Element/ion.cpp (added) * src/Element/ion.hpp (added) * src/Element/periodentafel.cpp (modified) * src/Element/periodentafel.hpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/IonUnitTest.cpp (added) * src/Element/unittests/IonUnitTest.hpp (added) * src/Element/unittests/Makefile.am (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (added) * src/Fragmentation/Automation/MPQCCommandFragmentController.hpp (added) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * 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 (added) * src/Fragmentation/Automation/SpecificFragmentController_ResultContainer_impl.hpp (deleted) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/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/Fragmentation/analyzer.cpp (deleted) * src/Fragmentation/datacreator.cpp (deleted) * src/Fragmentation/datacreator.hpp (deleted) * src/Fragmentation/joiner.cpp (deleted) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/Jobs/JobMarket/FragmentJob.cpp (added) * src/Jobs/JobMarket/FragmentJob.hpp (added) * src/Jobs/JobMarket/FragmentResult.cpp (added) * src/Jobs/JobMarket/FragmentResult.hpp (added) * src/Jobs/JobMarket/JobId.cpp (added) * src/Jobs/JobMarket/JobId.hpp (added) * src/Jobs/JobMarket/SystemCommandJob.cpp (added) * src/Jobs/JobMarket/SystemCommandJob.hpp (added) * src/Jobs/JobMarket/types.hpp (added) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Makefile.am (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.cpp (modified) * src/Potentials/helpers.hpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) * src/Potentials/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/cleanUp.cpp (modified) * src/documentation/constructs/potentials.dox (modified) * tests/Calculations/Makefile.am (added) * tests/Calculations/atlocal.in (added) * tests/Calculations/molecuilder.in (moved) * tests/Calculations/testsuite-calculations-1_2-dimethoxyethane.at (added) * tests/Calculations/testsuite-calculations-1_2-dimethylbenzene.at (added) * tests/Calculations/testsuite-calculations-2-methylcyclohexanone.at (added) * tests/Calculations/testsuite-calculations-N_N-dimethylacetamide.at (added) * tests/Calculations/testsuite-calculations-anthracene.at (added) * tests/Calculations/testsuite-calculations-benzene.at (added) * tests/Calculations/testsuite-calculations-cholesterol.at (added) * tests/Calculations/testsuite-calculations-coronene.at (added) * tests/Calculations/testsuite-calculations-cycloheptane.at (added) * tests/Calculations/testsuite-calculations-dimethyl_bromomalonate.at (added) * tests/Calculations/testsuite-calculations-glucose.at (added) * tests/Calculations/testsuite-calculations-heptan.at (added) * tests/Calculations/testsuite-calculations-isoleucine.at (added) * tests/Calculations/testsuite-calculations-mpqc.at (added) * tests/Calculations/testsuite-calculations-naphthalene.at (added) * tests/Calculations/testsuite-calculations-neohexane.at (added) * tests/Calculations/testsuite-calculations-phenanthrene.at (added) * tests/Calculations/testsuite-calculations-proline.at (added) * tests/Calculations/testsuite-calculations-putrescine.at (added) * tests/Calculations/testsuite-calculations-tartaric_acid.at (added) * tests/Calculations/testsuite.at (added) * 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 (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxEnergies-FragmentOrder.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Fragment.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Fragment.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-FragmentOrder.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-FragmentOrder.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Fragment.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Fragment.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-FragmentOrder.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-FragmentOrder.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MinEnergies-FragmentOrder.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MinEnergies-FragmentOrder.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Fragment.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Fragment.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-FragmentOrder.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-FragmentOrder.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/MinMeanMaxTotalForce-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/SimTime-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/SimTime-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/VectorSum-Order.dat (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/VectorSum-Order.pyx (deleted) * tests/Fragmentations/Analyzing/heptan/post/plots/energy-forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragmentForces-Factors.dat (deleted) * tests/Fragmentations/Analyzing/heptan/pre/BondFragmentKeySets.dat (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order1.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order1.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order2.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order2.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order3.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order3.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order4.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order4.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.energy.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.energyfragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.forcefragment.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.forces.all (deleted) * tests/Fragmentations/Analyzing/heptan/pre/pcp.speed (deleted) * tests/Fragmentations/Analyzing/heptan/testsuite-analyzing-heptan.at (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment00/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment00/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment01/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment01/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment02/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment02/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment03/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment03/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment04/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment04/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment05/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment05/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment06/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment06/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment07/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment07/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment08/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment08/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment09/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment09/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment10/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment10/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment11/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment11/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment12/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment12/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment13/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment13/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment14/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment14/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment15/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment15/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment16/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment16/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment17/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment17/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment18/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment18/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment19/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment19/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment20/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment20/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment21/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/BondFragment21/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/pcp.Order1.energy.all (deleted) * tests/Fragmentations/Joining/heptan/post/pcp.Order1.forces.all (deleted) * tests/Fragmentations/Joining/heptan/post/pcp.Order2.energy.all (deleted) * tests/Fragmentations/Joining/heptan/post/pcp.Order2.forces.all (deleted) * tests/Fragmentations/Joining/heptan/post/pcp.Order3.energy.all (deleted) * tests/Fragmentations/Joining/heptan/post/pcp.Order3.forces.all (deleted) * tests/Fragmentations/Joining/heptan/post/pcp.Order4.energy.all (deleted) * tests/Fragmentations/Joining/heptan/post/pcp.Order4.forces.all (deleted) * tests/Fragmentations/Joining/heptan/post/pcp.energyfragment.all (deleted) * tests/Fragmentations/Joining/heptan/post/pcp.forcefragment.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.energy.all (deleted) * 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/joiner.in (deleted) * tests/Fragmentations/testsuite.at (modified) * tests/Makefile.am (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) Merge branch 'Fragmentation_Automation_wo_JobMarket' into stable ... 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 [bf0ff3] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) Using MPQCCommandFragmentController in FragmentationAutomationAction. ... 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 21:32:03 GMT Frederik Heber [26b4d62] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondRemoveAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/LoadSessionAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.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/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotShapeByNameAction.cpp (modified) * src/Actions/SelectionAction/Shapes/ShapeByNameAction.cpp (modified) * src/Actions/ShapeAction/CombineShapesAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) All Actions now give correct failure status via STATUS() macro. Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [c09f94] * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) Transformed FragmentationAutomationAction into a Process. - Removed ... Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [5eaa23] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.def (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) Added sensible default values to MolecularDynamics sequence of Actions. 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 [9bac15] * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) FIX: MolecularDynamicsAction needs to clear fragment results after ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [f47e00b] * src/Actions/FragmentationAction/MolecularDynamicsAction.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.def (modified) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * tests/regression/Options/Session/post/complextest.py (modified) * tests/regression/Options/Session/post/complextest.sh (modified) FIX: SubgraphDissectionAction is now a MakroAction, fixed store- ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [237f93] * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) FIX: MolecularDynamicsAction now prepares normally not inside ... 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 [16893f] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.cpp (added) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.def (added) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) Added ClearFragmentationResultsAction. - As we retain summed ... 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 [f58e56] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) Extracted cycle contribution calculation into distinct function. Thu, 17 Oct 2013 07:24:06 GMT Frederik Heber [0588e9] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FragmentMolecule/pre/benzene.pdb (added) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) AnalyseFragmentationResultsAction now also calculates and prints ... 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 [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: ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [b5b01e] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionParameters.hpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/ActionState.hpp (added) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondRemoveAction.cpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpRedistributeAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.hpp (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Shapes/AllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotAllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotShapeByNameAction.cpp (modified) * src/Actions/SelectionAction/Shapes/ShapeByNameAction.cpp (modified) * src/Actions/ShapeAction/CombineShapesAction.cpp (modified) * src/Actions/ShapeAction/CreateShapeAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/RotateShapeAction.cpp (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (modified) * src/Actions/ShapeAction/TranslateShapeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) ActionState extracted into own header file, rename Action::state_ptr ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [1d3563] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) Main functions of ActionRegistry are now tunneled through ActionQueue. Thu, 19 Sep 2013 20:23:51 GMT Frederik Heber [628577] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (added) * src/Actions/ActionQueue.hpp (added) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/PythonScripting.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/cleanUp.cpp (modified) Introduced ActionQueue which contains internal ActionRegistry. - ... Thu, 19 Sep 2013 20:21:37 GMT Frederik Heber [1e5f84] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) FragmentationAutomationAction does long-range jobs now depending on ... Mon, 12 Aug 2013 11:30:33 GMT Frederik Heber [f5724f] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (moved) * src/Actions/PotentialAction/FitParticleChargesAction.def (moved) * src/Actions/PotentialAction/FitParticleChargesAction.hpp (moved) * src/Actions/PotentialAction/FitPotentialAction.cpp (moved) * src/Actions/PotentialAction/FitPotentialAction.def (moved) * src/Actions/PotentialAction/FitPotentialAction.hpp (moved) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (moved) * src/Actions/PotentialAction/ParseHomologiesAction.def (moved) * src/Actions/PotentialAction/ParseHomologiesAction.hpp (moved) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (moved) * src/Actions/PotentialAction/SaveHomologiesAction.def (moved) * src/Actions/PotentialAction/SaveHomologiesAction.hpp (moved) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/FitParticleCharges/pre/homology_grid.dat (moved) * tests/regression/Potential/FitParticleCharges/pre/water.pdb (moved) * tests/regression/Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at (moved) * tests/regression/Potential/FitPotential/pre/angle_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/harmonic_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/improper_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/length_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/lj_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/torsion_homology.dat (moved) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (moved) * tests/regression/Potential/testsuite-potential.at (added) * tests/regression/testsuite.at (modified) Moved all FragmentationActions related to potentials into own menu ... Mon, 12 Aug 2013 11:30:33 GMT Frederik Heber [474c62] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FIX: Typo in FragmentationAction. 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 [13c5c1] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * tests/Python/AllActions/options.dat (modified) FragmentationAction uses Interfragmenter to add non-bonded fragments. Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [4792ab] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added set-threshold option to FitPotentialAction. - TESTFIX: ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [c4a323] * src/Actions/FragmentationAction/FitParticleChargesAction.cpp (added) * src/Actions/FragmentationAction/FitParticleChargesAction.def (added) * src/Actions/FragmentationAction/FitParticleChargesAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Fragmentation/FitParticleCharges/pre/homology_grid.dat (added) * tests/regression/Fragmentation/FitParticleCharges/pre/water.pdb (added) * tests/regression/Fragmentation/FitParticleCharges/testsuite-fragmentation-fit-particle-charges.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added FitParticleChargesAction for fitting partial nuclei charges to ... 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 [af2c7ec] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) TrainingData now generates internal list of all arguments. - ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [f0025d] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Renamed getFragmentSpecificExtractor() -> getSpecificExtractor(). Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [d449a9] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * src/Actions/FragmentationAction/ParseHomologiesAction.cpp (added) * src/Actions/FragmentationAction/ParseHomologiesAction.def (added) * src/Actions/FragmentationAction/ParseHomologiesAction.hpp (added) * src/Actions/FragmentationAction/SaveHomologiesAction.cpp (added) * src/Actions/FragmentationAction/SaveHomologiesAction.def (added) * src/Actions/FragmentationAction/SaveHomologiesAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Split off parsing and saving of homologies into new Actions. Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [98dbee] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) World now maintains HomologyContainer instance. Fri, 09 Aug 2013 14:20:18 GMT Frederik Heber [39986b] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (added) * src/Actions/FragmentationAction/MolecularDynamicsAction.def (added) * src/Actions/FragmentationAction/MolecularDynamicsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) Added new MakroAction MolecularDynamicsAction. - this resides ... 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 14:22:04 GMT Frederik Heber [62164d] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) Writing final parameters to potential-file. Mon, 08 Jul 2013 14:22:04 GMT Frederik Heber [a315e8] * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/Specific/EmptyStringValidator.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Potential type is given via extra option not "fit-potential". - ... Mon, 08 Jul 2013 14:22:04 GMT Frederik Heber [a504946] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * tests/Python/AllActions/options.dat (modified) Training data can now be written to optional file. Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [49dcf7] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) Added catching of SerializablePotentialException in FitPotentialAction. Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [baccf6] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) FitPotentialAction now uses new CompoundPotential to fit. - ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [3536a5f] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) FIX: Tiny fix to FitPotentialAction with static_casts. 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. ... Fri, 03 May 2013 11:58:26 GMT Frederik Heber [48d20d] * configure.ac (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (added) * src/Actions/FragmentationAction/FitPotentialAction.def (added) * src/Actions/FragmentationAction/FitPotentialAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/LevMartester.cpp (deleted) * src/Makefile.am (modified) * src/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/potentials.dox (modified) * src/documentation/install.dox (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/pre/angle_homology.dat (added) * tests/regression/Fragmentation/FitPotential/pre/length_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/testsuite.at (modified) Added new action FitPotentialAction to fit empirical potentials. - ... 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 ... 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 18:56:31 GMT Frederik Heber [79d0b9] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FIX: Fragmentation requires a bond graph with correct degrees. - ... 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 [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 18:13:22 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 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 10:28:22 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. - ... Mon, 08 Apr 2013 11:56:18 GMT Frederik Heber [569e42] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FragmentationAction does not reinsert first graph anymore but copies it. Fri, 22 Mar 2013 00:03:38 GMT Frederik Heber [5589e7e] * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (added) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def (added) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/StoreSaturatedFragment/post/BondFragment0.xyz (added) * tests/regression/Fragmentation/StoreSaturatedFragment/pre/C6-0.Sheet.Aligned.xyz (added) * tests/regression/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added StoreSaturatedFragmentAction to save a set of atoms satured ... 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 [9291d04] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.def (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/HydrogenSaturation_enum.hpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * tests/Python/AllActions/options.dat (modified) Split saturation with hydrogen of treatment of hydrogen. - now ... Wed, 27 Feb 2013 12:42:36 GMT Frederik Heber [c7c615] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FIX: FragmentationAction gave wrong number of molecules. Wed, 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. - ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber [91a565] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) DEBUG: Added some debugging output for constructed HomologyGraphs in ... 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 [d1ba0d] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/moleculelist.cpp (modified) FIX: Forces-Factors are now written with global ids, ... 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 [766767] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) appendToHomologyFile() now constructs the HomologyGraph and its ... 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 17:39:40 GMT Frederik Heber [240c3e] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * tests/Python/AllActions/options.dat (modified) FragmentationAutomationAction now uses a file containing a serialized ... 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 ... Mon, 10 Dec 2012 10:11:00 GMT Frederik Heber [db6f7d] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * tests/JobMarket/pre/heptan.xyz (added) * tests/JobMarket/testsuite-jobmarket-molecuilderrun.at (modified) FIX: We must not assert but check whether full molecule is loaded in ... 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 [82cbe4] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) Writing additional VMGEnergy table to file. 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 [4f056e] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) Refactored controller usage in FragmentationAutomationAction: Made ... 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 [86cfac5] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) Resulting tables in FragmentationAutomationAction are now written to ... 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.