# # ChangeLog for src/Jobs # # Generated by Trac 1.4.4 # Jan 5, 2025, 7:16:44 PM Fri, 05 May 2017 14:17:23 GMT Frederik Heber [dde50d] * ThirdParty/JobMarket/src/JobMarket/Results/FragmentResult.hpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.hpp (modified) * src/Fragmentation/KeySet.hpp (modified) * src/Fragmentation/Summation/IndexSet.hpp (modified) * src/Jobs/JobMarket/FragmentResult.hpp (modified) FIX: boost::serialization 1.58 introduced changes which breaks stand- ... Fri, 05 May 2017 14:08:59 GMT Frederik Heber [9eb71b3] * ThirdParty/CodePatterns/src/Helpers/Assert.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Chronos.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Info.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Log.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Verbose.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/errorlogger.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/logger.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Channels.cpp (modified) * ThirdParty/CodePatterns/src/Observer/GlobalObservableInfo.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Graveyard.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Notification.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Observable.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Observer.cpp (modified) * ThirdParty/CodePatterns/src/Observer/ObserverLog.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Relay.cpp (modified) * ThirdParty/CodePatterns/src/Patterns/unittests/stubs/Cacheable_threeNumbers.cpp (modified) * ThirdParty/CodePatterns/src/Patterns/unittests/stubs/ObservedValue_threeNumbers.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/ControllerCommandRegistry.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/ControllerOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/ControllerOptions_SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/FragmentController.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/FragmentController_JobIdProxy.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller_AddOn_SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller_SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller_main.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/DefaultOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentQueue.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler_ControllerListener.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler_WorkerListener.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/GlobalJobId.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/JobId.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Jobs/FragmentJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Jobs/NoOpJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Jobs/SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Listener.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/AsyncOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/CheckResultsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/GetNextJobIdOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/ReceiveResultsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/RemoveAllJobsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/RemoveAllResultsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/RemoveAllWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/SendJobsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/ShutdownOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/OperationQueue.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/OperationRegistry.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Servers/CheckAliveWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Servers/SendJobToWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Servers/ShutdownWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/SyncOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/EnrollInPoolOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/ObtainJobOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/RemoveFromPoolOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/SubmitResultOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Pool/PoolGuard.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Pool/PoolWorker.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Pool/WorkerPool.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Results/FragmentResult.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/ServerOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/SignalHandler.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/SignalOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/WorkerAddress.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/WorkerOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/atexit.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/poolworker.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/poolworker_main.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/server.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/server_main.cpp (modified) * ThirdParty/JobMarket/src/unittests/stubs/FragmentJobStub.cpp (modified) * ThirdParty/JobMarket/src/unittests/stubs/FragmentResultStub.cpp (modified) * ThirdParty/JobMarket/src/unittests/stubs/ObserverStub.cpp (modified) * ThirdParty/JobMarket/tests/CodeChecks/testsuite-memdebug.at (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Line.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinePoint.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Plane.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Space.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Vector.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (modified) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionStatusList.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (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/MirrorAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateToOriginAction.cpp (modified) * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondRemoveAction.cpp (modified) * src/Actions/BondAction/BondSetDegreeAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/DryRunAction.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/LoadSessionAction.cpp (modified) * src/Actions/CommandAction/NoDryRunAction.cpp (modified) * src/Actions/CommandAction/StoreSessionAction.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/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FillAction/FillVolumeAction.cpp (modified) * src/Actions/FillAction/SuspendInMoleculeAction.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/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (modified) * src/Actions/FragmentationAction/SaveFragmentResultsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/GraphAction/CorrectBondDegreeAction.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/UpdateMoleculesAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (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/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RemoveAction.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/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.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/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParseAtomFragmentsAction.cpp (modified) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) * src/Actions/PotentialAction/ParseParticleParametersAction.cpp (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) * src/Actions/PotentialAction/SaveAtomFragmentsAction.cpp (modified) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (modified) * src/Actions/PotentialAction/SaveParticleParametersAction.cpp (modified) * src/Actions/PotentialAction/SavePotentialsAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (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/Atoms/PopAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/PushAtomsAction.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/Molecules/PopMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.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/UndoRedoHelpers.cpp (modified) * src/Actions/Values.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/WorldAction/StepWorldTimeAction.cpp (modified) * src/Actions/toCLIString.cpp (modified) * src/Actions/toPythonString.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_SaturateDanglingBonds.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_graphnode.cpp (modified) * src/Atom/atom_graphnodeinfo.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_particleinfo.cpp (modified) * src/AtomIdSet.cpp (modified) * src/Bond/AdjacencyMatcher/AdjacencyMatcher.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/Box_BoundaryConditions.cpp (modified) * src/ControllerOptions_MPQCCommandJob.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomNameDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomOrderDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/ion.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Filling/Cluster.cpp (modified) * src/Filling/ClusterInterface.cpp (modified) * src/Filling/Filler.cpp (modified) * src/Filling/Generators/NodeGenerator.cpp (modified) * src/Filling/Inserter/Inserter.cpp (modified) * src/Filling/Inserter/RandomInserter.cpp (modified) * src/Filling/Inserter/SimpleInserter.cpp (modified) * src/Filling/Inserter/SurfaceInserter.cpp (modified) * src/Filling/Inserter/SurfaceRandomInserter.cpp (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Filling/Mesh/Mesh.cpp (modified) * src/Filling/Predicates/AnyFillPredicate.cpp (modified) * src/Filling/Predicates/FillPredicate.cpp (modified) * src/Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideSurface_FillPredicate.cpp (modified) * src/Filling/Predicates/IsValidInDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsVoidNode_FillPredicate.cpp (modified) * src/Filling/Predicates/Ops_FillPredicate.cpp (modified) * src/Filling/Preparators/BaseFillerPreparator.cpp (modified) * src/Filling/Preparators/BoxFillerPreparator.cpp (modified) * src/Filling/Preparators/ShapeSurfaceFillerPreparator.cpp (modified) * src/Filling/Preparators/ShapeVolumeFillerPreparator.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/SpecificFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToAtomFragments.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/SaturatedBond.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution_getConnections.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution_getPoints.cpp (modified) * src/Fragmentation/Exporters/unittests/stubs/SaturatedBondStub.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.cpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (modified) * src/Fragmentation/Homology/FragmentNode.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeysetStub.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/SortIndex.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/GridDownsampler.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/IndexSet.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/FragmentForces.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/SubsetMap.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/parseKeySetFile.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionArgument.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Graph/AdjacencyList.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Helpers/defs.cpp (modified) * src/Jobs/ChargeSmearer.cpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/JobMarket/FragmentJob.cpp (modified) * src/Jobs/JobMarket/FragmentResult.cpp (modified) * src/Jobs/JobMarket/JobId.cpp (modified) * src/Jobs/JobMarket/SystemCommandJob.cpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp (modified) * src/LinkedCell/LinkedCell_Model_Update.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/tripleIndex.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/MoleculeObserver.cpp (modified) * src/Parameters/Specifics/Value_atom.cpp (modified) * src/Parameters/Specifics/Value_element.cpp (modified) * src/Parameters/Specifics/Value_elements.cpp (modified) * src/Parameters/Specifics/Value_molecule.cpp (modified) * src/Parameters/Specifics/Value_string.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomDataValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomIdValidator.cpp (modified) * src/Parameters/Validators/Specific/BoundaryConditionValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxLengthValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxVectorValidator.cpp (modified) * src/Parameters/Validators/Specific/FileSuffixValidator.cpp (modified) * src/Parameters/Validators/Specific/FormulaValidator.cpp (modified) * src/Parameters/Validators/Specific/KeyValueValidator.cpp (modified) * src/Parameters/Validators/Specific/MoleculeIdValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserFileValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/PotentialTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/RandomNumberValidators.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixInvertibleValidator.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixSymmetricValidator.cpp (modified) * src/Parameters/Validators/Specific/SessionTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/ShapeNameValidator.cpp (modified) * src/Parameters/Validators/Specific/ShapeOpValidator.cpp (modified) * src/Parameters/Validators/Specific/ShapeTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorNotZeroValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorPositiveComponentsValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorZeroOneComponentsValidator.cpp (modified) * src/Parameters/unittests/stubs/ActionNameValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxLengthValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxVectorValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/TimeStepPresentValidatorStub.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Potentials/BindingModel.cpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/InternalCoordinates/CoordinatorFactory.cpp (modified) * src/Potentials/InternalCoordinates/FourBody_ImproperAngle.cpp (modified) * src/Potentials/InternalCoordinates/FourBody_TorsionAngle.cpp (modified) * src/Potentials/InternalCoordinates/OneBody_Constant.cpp (modified) * src/Potentials/InternalCoordinates/ThreeBody_Angle.cpp (modified) * src/Potentials/InternalCoordinates/TwoBody_Length.cpp (modified) * src/Potentials/PartialNucleiChargeFitter.cpp (modified) * src/Potentials/ParticleTypeCheckers.cpp (modified) * src/Potentials/Particles/Particle.cpp (modified) * src/Potentials/Particles/ParticleFactory.cpp (modified) * src/Potentials/Particles/ParticleRegistry.cpp (modified) * src/Potentials/Particles/StreamFactory_Particle.cpp (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/RegistryDeserializer_impl.hpp (modified) * src/Potentials/RegistrySerializer_Particle.cpp (modified) * src/Potentials/RegistrySerializer_impl.hpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PotentialTypes.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/StreamFactory_EmpiricalPotential.cpp (modified) * src/Potentials/TremoloPotentialFileParser.cpp (modified) * src/Potentials/TremoloPotentialTypes.cpp (modified) * src/Potentials/unittests/stubs/SerializablePotentialMock.cpp (modified) * src/Python/PythonScripting.cpp (modified) * src/Python/exit.cpp (modified) * src/Python/getBoundingBox.cpp (modified) * src/Python/getDomainVolume.cpp (modified) * src/Python/getSelectedMolarMass.cpp (modified) * src/Python/reinit.cpp (modified) * src/Python/wait.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/Server.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeFactory.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp (modified) * src/Shapes/unittests/stubs/WorldSelectedMoleculesStub.cpp (modified) * src/Shapes/unittests/stubs/moleculeStub.cpp (modified) * src/Tesselation/ApproximateShapeArea.cpp (modified) * src/Tesselation/ApproximateShapeVolume.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/TriangleMatcher/TriangleMatcher.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/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/EmptyCommandLineQuery.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/KeyValuePairCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/KeyValuePairsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.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/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/getLastPosition.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FilesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/KeyValuePairQtQuery.cpp (modified) * src/UIElements/Qt4/Query/KeyValuePairsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQueryList.cpp (modified) * src/UIElements/Qt4/Query/RealSpaceMatrixQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FilesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/KeyValuePairTextQuery.cpp (modified) * src/UIElements/TextUI/Query/KeyValuePairsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RealSpaceMatrixTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/ElementList/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QListWidgetCurveItem.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QScrollZoomer/ScrollBar.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QScrollZoomer/ScrollZoomer.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisCurveRegistry.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisData.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPageRegistry.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotCurve.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser.cpp (modified) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser_plotcurve.cpp (modified) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser_plottype.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/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtLogBox.cpp (modified) * src/UIElements/Views/Qt4/QtNumericalItem.cpp (modified) * src/UIElements/Views/Qt4/QtShapeController.cpp (modified) * src/UIElements/Views/Qt4/QtShapeList.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/controller.cpp (modified) * src/controller_AddOn_MPQCCommandJob.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/poolworker.cpp (modified) * src/unittests/stubs/AtomStub.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-memdebug.at (modified) * tests/JobMarket/mpqc.cpp (modified) Commented out MemDebug include and Memory::ignore. - MemDebug ... Wed, 15 Mar 2017 18:15:56 GMT Frederik Heber [ef7b4b] * src/Jobs/MPQCJob_Work.cpp (modified) * src/Jobs/Makefile.am (modified) * tests/regression/Fragmentation/ParseSaveFragmentResults/post/results_empty_jobmarkt_disabled.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/post/results_jobmarkt_disabled.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (modified) ENABLEFIX: disable-jobmarket is now working. - needed to add ... Thu, 09 Mar 2017 22:16:01 GMT Frederik Heber [0ee9cb3] * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Plotting/Makefile.am (modified) FIX: Removed multiple instances of libmolecuilder_config.h in ... Thu, 09 Mar 2017 09:43:23 GMT Frederik Heber [fbf005] * Makefile.am (modified) * ThirdParty/Makefile.am (modified) * ThirdParty/mpqc_open/src/bin/mpqc/Makefile.am (modified) * ThirdParty/mpqc_open/src/bin/mpqc/mpqc.cc (modified) * ThirdParty/mpqc_open/src/bin/mpqc/mpqc.h (added) * ThirdParty/mpqc_open/src/bin/mpqc/mpqc_extract.h (added) * ThirdParty/mpqc_open/src/bin/mpqc/mpqc_extract_dummy.cc (added) * ThirdParty/mpqc_open/src/bin/mpqc/mpqc_main.cc (added) * configure.ac (modified) * src/Jobs/MPQCJob_Work.cpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/mpqc_extract.cc (added) * src/Makefile.am (modified) * src/poolworker.cpp (modified) * tests/Calculations/molecuilder_mpqc.in (deleted) * tests/Calculations/molecuilder_poolworker.in (added) * tests/Calculations/testsuite-calculations-jobmarket-1_2-dimethoxyethane.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-1_2-dimethylbenzene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-2-methylcyclohexanone.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-N_N-dimethylacetamide.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-anthracene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-benzene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-cholesterol.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-coronene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-cycloheptane.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-dimethyl_bromomalonate.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-glucose.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-heptan.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-isoleucine.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-mpqc.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-naphthalene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-neohexane.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-phenanthrene.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-proline.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-putrescine.at (modified) * tests/Calculations/testsuite-calculations-jobmarket-tartaric_acid.at (modified) * tests/CodeChecks/testsuite-memdebug.at (modified) * tests/Examples/PartialChargeFitting/testsuite-examples-partialchargefitting-h2o.at (modified) * tests/Examples/Simple/testsuite-examples-simple-h2o.at (modified) * tests/Examples/molecuilder_mpqc.in (deleted) * tests/Examples/molecuilder_poolworker.in (added) * tests/integration/molecuilder_mpqc.in (deleted) * tests/integration/molecuilder_poolworker.in (added) * tests/integration/testsuite-integration-mpqc-jobs.at (modified) * tests/integration/testsuite-integration-vmg-jobs.at (modified) HUGE: Extracted libmolecuilder_mpqc that is now linked to poolworker. ... Thu, 02 Mar 2017 14:01:50 GMT Frederik Heber [cb98f1] * src/Actions/unittests/Makefile.am (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob_Work.cpp (added) * src/Jobs/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: One Definition Rule violation by mpqc. - mpqc.cc implements ... Thu, 02 Mar 2017 14:00:41 GMT Frederik Heber [79b089] * ThirdParty/Makefile.am (modified) * configure.ac (modified) * src/Jobs/Makefile.am (modified) Added vmg as another subpackage. Thu, 02 Mar 2017 07:25:41 GMT Frederik Heber [99689b] * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) FIX: Missing JobMarket_LDFLAGS in executables and unit tests. Thu, 02 Mar 2017 07:14:22 GMT Frederik Heber [4ecb2d] * LinearAlgebra/doc/am_doxygen_include.am (deleted) * LinearAlgebra/m4 (deleted) * Makefile.am (modified) * ThirdParty/LinearAlgebra/.gitignore (moved) * ThirdParty/LinearAlgebra/AUTHORS (moved) * ThirdParty/LinearAlgebra/COPYING (moved) * ThirdParty/LinearAlgebra/ChangeLog (moved) * ThirdParty/LinearAlgebra/INSTALL (moved) * ThirdParty/LinearAlgebra/LinearAlgebra-debug.pc.in (moved) * ThirdParty/LinearAlgebra/LinearAlgebra.pc.in (moved) * ThirdParty/LinearAlgebra/Makefile.am (moved) * ThirdParty/LinearAlgebra/NEWS (moved) * ThirdParty/LinearAlgebra/README (moved) * ThirdParty/LinearAlgebra/bootstrap (moved) * ThirdParty/LinearAlgebra/build-aux/README (moved) * ThirdParty/LinearAlgebra/configure.ac (moved) * ThirdParty/LinearAlgebra/doc/Doxyfile (moved) * ThirdParty/LinearAlgebra/doc/Makefile.am (moved) * ThirdParty/LinearAlgebra/doc/am_doxygen_include.am (added) * ThirdParty/LinearAlgebra/libLinearAlgebra_config.h.in (moved) * ThirdParty/LinearAlgebra/m4 (added) * ThirdParty/LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Exceptions.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Line.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Line.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinePoint.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinePoint.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegment.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegmentSet.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Makefile.am (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Plane.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Plane.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Space.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Space.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Vector.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Vector.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorContent.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorInterface.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/defs.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/fast_functions.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/leastsquaremin.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/vector_ops.hpp (moved) * ThirdParty/LinearAlgebra/src/documentation/Makefile.am (moved) * ThirdParty/LinearAlgebra/src/documentation/groups.dox (moved) * ThirdParty/LinearAlgebra/src/documentation/lines.dox (moved) * ThirdParty/LinearAlgebra/src/documentation/mainpage.dox (moved) * ThirdParty/LinearAlgebra/src/unittests/LineUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/LineUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/Makefile.am (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/PlaneUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/PlaneUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/RealSpaceMatrixUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/RealSpaceMatrixUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/TestRunnerMain.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/UnitTestMain.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorContentUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorSetUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorSetUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/Makefile.am (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/atlocal.in (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-date_in_dox.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-header-dist.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-project-disclaimer.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite.at (moved) * configure.ac (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved LinearAlgebra sub-package into ThirdParty folder. - needed to ... Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [ec1aae] * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob.hpp (modified) FIX: MPQCData now correctly checks sampled_grid to be cubic. Wed, 14 Sep 2016 18:42:53 GMT Frederik Heber [336da8] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) WindowGrid_converter's refactored a bit with ... Wed, 14 Sep 2016 18:42:52 GMT Frederik Heber [c6da5e] * src/Jobs/InterfaceVMGJob.cpp (modified) FIX: InterfaceVMGJob used box_end as end point, not as length of ... Wed, 18 May 2016 21:56:59 GMT Frederik Heber [7debff] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) VMGData additionally stores absolute residual. - we check for ... Wed, 18 May 2016 21:55:40 GMT Frederik Heber [9ff818] * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) MPQCJob and VMGJob contain reached and desired accuracy. - both set ... Tue, 13 Oct 2015 20:14:33 GMT Frederik Heber [62d092] * src/Jobs/ChargeSmearer.cpp (modified) * src/Jobs/ChargeSmearer.hpp (modified) Rewrote ChargeSmearer to use visitor pattern. - this is used for ... Tue, 13 Oct 2015 20:14:33 GMT Frederik Heber [17e4fd] * 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/Fragmentation/Interfragmenter.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/Jobs/WindowGrid_converter.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added new option DoSmearElectronicCharges to ... Tue, 13 Oct 2015 20:14:32 GMT Frederik Heber [445ce6] * src/Jobs/WindowGrid_converter.cpp (modified) Modified WindowGrid_converter::addWindowOntoGrid(): first reset, then ... Tue, 13 Oct 2015 20:14:32 GMT Frederik Heber [cceb8c] * src/Jobs/ChargeSmearer.cpp (added) * src/Jobs/ChargeSmearer.hpp (added) * src/Jobs/Makefile.am (modified) Added ChargeSmearer that is only compiled for CONDVMG. - we store ... Tue, 13 Oct 2015 20:14:16 GMT Frederik Heber [7537d1] * src/Fragmentation/Automation/ResultContainer_impl.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) Removing setting net force to zero and setting hasForce to true. Tue, 13 Oct 2015 20:13:12 GMT Frederik Heber [00d815] * src/Jobs/InterfaceVMGJob.cpp (modified) FIX: Need to divide by global number of particles, when summing ... Tue, 13 Oct 2015 20:12:54 GMT Frederik Heber [6e73f5] * src/Jobs/InterfaceVMGJob.cpp (modified) Added debugging changes to InterfaceVMGJob on force summation. Tue, 13 Oct 2015 20:12:54 GMT Frederik Heber [20bb3b] * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) MPQCData now also uses FragmentForces (instead of typedef ... Tue, 13 Oct 2015 20:12:54 GMT Frederik Heber [94db13] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (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/MPQCDataFused.hpp (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) Again changes to obtain correct longrange forces, also forces are ... Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [ce9874] * src/Jobs/InterfaceVMGJob.cpp (modified) Added extraction of long-range forces from VMGData's array f. Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [c20839] * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Plotting/Makefile.am (modified) FIX: Shared libraries's Makefile.am rules are now consistent. - ... Thu, 21 Aug 2014 06:43:46 GMT Frederik Heber [748fc7] * src/Actions/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/builder_init.cpp (modified) * src/unittests/Makefile.am (modified) libMolecuilder is now a shared library. - linking error ... Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [e9e86f] * src/Actions/unittests/Makefile.am (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) FIX: UnitTestMain placed into convenience libUnitTest. - removed ... Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [3b35e7] * LinearAlgebra/src/LinearAlgebra/Makefile.am (modified) * LinearAlgebra/src/unittests/Makefile.am (modified) * configure.ac (modified) * m4/boost.m4 (modified) * m4/qwt.m4 (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Converter/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Plotting/Makefile.am (modified) * src/unittests/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) Fixes due to update to Ubuntu 14.04. - subdir-objects is default ... Sun, 13 Jul 2014 18:05:03 GMT Frederik Heber [99692c] * src/Jobs/JobMarket/SystemCommandJob.cpp (modified) FIX: Preparation of temporary filename in SystemCommandJob now ... 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 [1d17e5] * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (added) * src/Fragmentation/Automation/MPQCCommandFragmentController.hpp (added) * src/Fragmentation/Automation/Makefile.am (modified) * src/Jobs/JobMarket/FragmentJob.hpp (modified) Added MPQCCommandFragmentController. - ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [786d28] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Lib..FragmentationAutomation and lib..Jobs now also compiled without ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [2cc7faa] * src/Jobs/Makefile.am (modified) LibJobMarket only compiled in if CONDJOBMARKET. Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [1dfe00] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) Added inclusion switch on HAVE_JOBMARKET for files depending on ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [c3de51] * 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/Makefile.am (modified) Added FragmentJob, ..Result, JobId, SystemCommandJob, and types from ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [ae68b5] * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) Fixed some boost serialization static warnings. Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [a2a2f7] * src/Actions/ActionSequence.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Box.cpp (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (modified) * src/Fragmentation/Homology/FragmentNode.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) Huge warning fix. - fixed unused variables. - fixed set but unused ... Sun, 20 Oct 2013 11:45:34 GMT Frederik Heber [b47f9c] * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) FIX: WindowGrid_converter::addWindowOntoGrid() never used ... Thu, 19 Sep 2013 20:10:24 GMT Frederik Heber [f6c19d] * src/Fragmentation/Automation/VMGDebugGridFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGDebugGridJob.hpp (modified) * src/Jobs/VMGJob.hpp (modified) InterfaceVMGDebugJob now also uses optionally open boundary (FAS ... Thu, 15 Aug 2013 08:41:17 GMT Frederik Heber [ee9018] * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) InterfaceVMGJob now may also use open boundary (FAS instead of CS). ... Thu, 15 Aug 2013 08:41:17 GMT Frederik Heber [d9d028] * src/Jobs/WindowGrid_converter.cpp (modified) * src/Jobs/WindowGrid_converter.hpp (modified) FIX: addGridOntoWindow() now working, too. - with this open ... Thu, 15 Aug 2013 08:41:17 GMT Frederik Heber [27ef5c] * src/Jobs/WindowGrid_converter.cpp (modified) * src/Jobs/WindowGrid_converter.hpp (modified) Density is now correctly written onto grid with both periodic and ... Thu, 15 Aug 2013 08:41:17 GMT Frederik Heber [e8e472b] * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) Changes in VMG interface. - discretization schemes moved from ... Thu, 15 Aug 2013 08:40:56 GMT Frederik Heber [049d4a] * src/Jobs/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) FIX: libMolecuilderUI's dependencies are now completely satisfied. ... Mon, 12 Aug 2013 11:30:33 GMT Frederik Heber [353326] * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: Changed LIBADDs and LDADDs to get rid of libtool patching. - ... 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 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 07:53:28 GMT Frederik Heber [e4721d3] * src/Jobs/InterfaceVMGJob.cpp (modified) FIX: Average forces in InterfaceVMGJob only if there actually are ... Wed, 01 May 2013 07:53:26 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. ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [fbf143] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/SetValues/unittests/Makefile.am (deleted) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp (moved) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (moved) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCData.cpp (moved) * src/Fragmentation/Summation/Containers/MPQCData.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCDataFused.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCDataMap.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCData_printKeyNames.hpp (moved) * src/Fragmentation/Summation/Containers/Makefile.am (moved) * src/Fragmentation/Summation/Containers/VMGData.cpp (moved) * src/Fragmentation/Summation/Containers/VMGData.hpp (moved) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (moved) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (moved) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (moved) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (moved) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.hpp (moved) * src/Fragmentation/Summation/Containers/extractJobIds.hpp (moved) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp (moved) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.hpp (moved) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (moved) * src/Fragmentation/Summation/Converter/DataConverter.hpp (moved) * src/Fragmentation/Summation/Converter/Makefile.am (moved) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (moved) * src/Fragmentation/Summation/SetValues/Fragment.hpp (moved) * src/Fragmentation/Summation/SetValues/Histogram.cpp (moved) * src/Fragmentation/Summation/SetValues/Histogram.hpp (moved) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (moved) * src/Fragmentation/Summation/SetValues/IndexedVectors.hpp (moved) * src/Fragmentation/Summation/SetValues/Makefile.am (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid_inline.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (added) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (moved) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) * src/Fragmentation/parseKeySetFile.cpp (moved) * src/Fragmentation/parseKeySetFile.hpp (moved) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob.hpp (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LevMartester.cpp (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/unittests/Makefile.am (modified) Placed Containers, Converter, and SetValues as subfolders into ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [8e84fe] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/SpecificFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Containers/FragmentationChargeDensity.cpp (moved) * src/Fragmentation/Containers/FragmentationChargeDensity.hpp (moved) * src/Fragmentation/Containers/FragmentationLongRangeResults.cpp (moved) * src/Fragmentation/Containers/FragmentationLongRangeResults.hpp (moved) * src/Fragmentation/Containers/FragmentationShortRangeResults.cpp (moved) * src/Fragmentation/Containers/FragmentationShortRangeResults.hpp (moved) * src/Fragmentation/Containers/MPQCData.cpp (moved) * src/Fragmentation/Containers/MPQCData.hpp (moved) * src/Fragmentation/Containers/MPQCDataFused.hpp (moved) * src/Fragmentation/Containers/MPQCDataMap.hpp (moved) * src/Fragmentation/Containers/MPQCData_printKeyNames.hpp (moved) * src/Fragmentation/Containers/Makefile.am (added) * src/Fragmentation/Containers/VMGData.cpp (moved) * src/Fragmentation/Containers/VMGData.hpp (moved) * src/Fragmentation/Containers/VMGDataFused.hpp (moved) * src/Fragmentation/Containers/VMGDataMap.hpp (moved) * src/Fragmentation/Containers/VMGData_printKeyNames.hpp (moved) * src/Fragmentation/Containers/createMatrixNrLookup.cpp (moved) * src/Fragmentation/Containers/createMatrixNrLookup.hpp (moved) * src/Fragmentation/Containers/extractJobIds.hpp (moved) * src/Fragmentation/Containers/parseKeySetFile.cpp (moved) * src/Fragmentation/Containers/parseKeySetFile.hpp (moved) * src/Fragmentation/Containers/unittests/MPQCDataUnitTest.cpp (moved) * src/Fragmentation/Containers/unittests/MPQCDataUnitTest.hpp (moved) * src/Fragmentation/Containers/unittests/Makefile.am (added) * src/Fragmentation/Converter/DataConverter.hpp (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/unittests/Makefile.am (modified) Moved ...Data and all related classes into new subfolder Containers. ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [410405] * src/Jobs/MPQCData_printKeyNames.hpp (modified) * src/Jobs/VMGData_printKeyNames.hpp (modified) FIX: ...Data_printKeyNames lacked printKeyNames include and made inline. Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [7b0494] * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Automation/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/SetValues/Makefile.am (modified) * src/Fragmentation/SetValues/SamplingGrid.cpp (moved) * src/Fragmentation/SetValues/SamplingGrid.hpp (moved) * src/Fragmentation/SetValues/SamplingGridProperties.cpp (moved) * src/Fragmentation/SetValues/SamplingGridProperties.hpp (moved) * src/Fragmentation/SetValues/SamplingGrid_inline.hpp (moved) * src/Fragmentation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (moved) * src/Fragmentation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp (moved) * src/Fragmentation/SetValues/unittests/SamplingGridUnitTest.cpp (moved) * src/Fragmentation/SetValues/unittests/SamplingGridUnitTest.hpp (moved) * src/Jobs/Grid/Makefile.am (deleted) * src/Jobs/Grid/unittests/Makefile.am (deleted) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCData.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGData.hpp (modified) * src/Jobs/VMGDebugGridJob.hpp (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved SamplingGrid... over to Fragmentation/SetValues. - adapted ... Mon, 15 Apr 2013 10:30:31 GMT Frederik Heber [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 ... Sun, 24 Feb 2013 12:59:34 GMT Frederik Heber [c91572] * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) DOCUFIX: Replaced \text by \mathrm in some formulas. Sat, 16 Feb 2013 11:32:44 GMT Frederik Heber [ef918c] * src/Jobs/Grid/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) DISTFIX: typo in header files. Fri, 15 Feb 2013 17:09:58 GMT Frederik Heber [1f1f80] * src/Jobs/Grid/SamplingGrid.cpp (modified) FIX: SamplingGrid::get..GridPoint() checks for begin, end bounds. - ... Fri, 15 Feb 2013 17:09:58 GMT Frederik Heber [313f83] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) SamplingGrid::operator*=() can now deal with incongruent windows. - ... Fri, 15 Feb 2013 17:09:58 GMT Frederik Heber [fb3485] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) Refactored copy routine out of AddOntoWindow(). - this is ... Fri, 15 Feb 2013 17:09:57 GMT Frederik Heber [c0e8fb] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGridProperties.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) Added SamplingGrid::isCongruent(). - also added unit test function. Fri, 15 Feb 2013 17:09:57 GMT Frederik Heber [56b04c] * src/Jobs/Grid/SamplingGrid.cpp (modified) FIX: SamplingGrid::getNearestLowerGridPoint(), and ::get..Upper..() ... Fri, 15 Feb 2013 17:09:57 GMT Frederik Heber [620517] * src/Jobs/Grid/Makefile.am (modified) * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGrid_inline.hpp (added) FIX: SamplingGrid::getWindowGridPoints() was broken. - or at least ... Fri, 15 Feb 2013 17:07:49 GMT Frederik Heber [b123a5] * src/Jobs/InterfaceVMGDebugGridJob.cpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (added) * src/Jobs/WindowGrid_converter.hpp (added) Shifted functions to add window onto grid into own namespace. - ... Fri, 15 Feb 2013 17:07:31 GMT Frederik Heber [8f3cdd] * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) Adapted VMGJob and its Interface to new non-zero window use. - we ... Fri, 15 Feb 2013 09:52:02 GMT Frederik Heber [64bafe0] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/Makefile.am (modified) SamplingGrid's Window start and end are now always set on a grid ... Fri, 15 Feb 2013 09:51:49 GMT Frederik Heber [c6355f] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) FIX: New non-zero window operations of SamplingGrid are now fully ... Fri, 15 Feb 2013 09:51:49 GMT Frederik Heber [de6dfb] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) Extending AddOntoWindow() by prefactor, can deal with differently ... Fri, 15 Feb 2013 09:51:49 GMT Frederik Heber [e2404f] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) New SamplingGrid::setDomainSize() and ::setWindowSize() helper functions. Fri, 15 Feb 2013 09:51:48 GMT Frederik Heber [1a00bb] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGridProperties.hpp (modified) * src/Jobs/Grid/unittests/Makefile.am (modified) * src/Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) Rewrote parts of SampingGrid such that a window of non-zero entries ... Fri, 15 Feb 2013 09:51:39 GMT Frederik Heber [98f8fe] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) SamplingGrid must have power of 2 grid size. - all number ... Thu, 14 Feb 2013 13:29:24 GMT Frederik Heber [3d9a8d] * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) * src/Jobs/Grid/SamplingGridProperties.cpp (modified) * src/Jobs/Grid/SamplingGridProperties.hpp (modified) * src/Jobs/Grid/unittests/Makefile.am (modified) * src/Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp (modified) * src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/MPQCJob_binding.hpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) SamplingGrid has no more size parameter but an end array. - this ... Thu, 14 Feb 2013 12:26:12 GMT Frederik Heber [e089fb] * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) Moved particle arrays into a new struct in VMGJob. - also the docu ... Thu, 14 Feb 2013 12:26:12 GMT Frederik Heber [1b01e9] * src/Jobs/MPQCJob_binding.hpp (added) * src/Jobs/Makefile.am (modified) * src/Server.cpp (modified) * src/poolworker.cpp (modified) FIX: Server missed forced binding to MPQCJob. - present was only to ... Wed, 13 Feb 2013 15:47:46 GMT Frederik Heber [4d4ef8] * src/Jobs/MPQCCommandJob_binding.hpp (added) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob_binding.hpp (added) * src/Jobs/VMGJob_binding.hpp (added) * src/Makefile.am (modified) * src/Server.cpp (modified) * src/poolworker.cpp (modified) FIX: Enforce binding to libMolecuilderJobs for Server and PoolWorker. ... Fri, 14 Dec 2012 17:39:52 GMT Frederik Heber [6d084a4] * src/Jobs/InterfaceVMGJob.cpp (modified) DEBUG: InterfaceVMGJob does not printGrids anymore. - output folder ... Mon, 10 Dec 2012 10:11:00 GMT Frederik Heber [cd2591] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added interpolation-degree as parameter to ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [67fec1] * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Jobs/VMGDataFused.hpp (modified) * src/Jobs/VMGDataMap.hpp (modified) * src/Jobs/VMGData_printKeyNames.hpp (modified) Changed VMGDataMap to contain entries for electron, nuclei, and total ... Mon, 10 Dec 2012 10:10:59 GMT Frederik Heber [a82602] * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) InterfaceVMGJob now also calculates nuclei interaction energy. - ... Mon, 10 Dec 2012 10:10:57 GMT Frederik Heber [447481] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/extractJobIds.hpp (added) * src/Jobs/Makefile.am (modified) Extracted template function extractJobIds() into own header file. Mon, 10 Dec 2012 10:10:57 GMT Frederik Heber [a2295a] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Summation/OrthogonalFullSummator.hpp (modified) * src/Jobs/VMGDataFused.hpp (modified) * src/Jobs/VMGDataMap.hpp (modified) * src/Jobs/VMGData_printKeyNames.hpp (modified) We now create one full potential VMGJob of each summed up grid per ... Mon, 10 Dec 2012 10:10:57 GMT Frederik Heber [238868] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.cpp (added) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (added) * src/Jobs/InterfaceVMGDebugGridJob.cpp (added) * src/Jobs/InterfaceVMGDebugGridJob.hpp (added) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob.cpp (added) * src/Jobs/VMGDebugGridJob.hpp (added) Added VMGDebugGridJob that just prints given sampled grid as VTK ... Mon, 10 Dec 2012 10:10:57 GMT Frederik Heber [4aee30] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Converter/DataConverter.hpp (modified) * src/Jobs/MPQCData.cpp (modified) * src/Jobs/MPQCData.hpp (modified) * src/Jobs/MPQCDataFused.hpp (modified) * src/Jobs/MPQCDataMap.hpp (modified) * src/Jobs/MPQCData_printKeyNames.hpp (modified) Timings of MPQCJob are now gathered for total and for the gathering ... Mon, 10 Dec 2012 10:10:56 GMT Frederik Heber [065574] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added level and near_field_cells as options to ... Mon, 10 Dec 2012 10:10:56 GMT Frederik Heber [0990e1] * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) FIX: MemDebug needs to come after VMG stuff, otherwise we run into ... Wed, 21 Nov 2012 12:46:32 GMT Frederik Heber [c5feef] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Jobs/VMGDataFused.hpp (modified) * src/Jobs/VMGDataMap.hpp (modified) Added energy_potential to fusion keys in VMGDataFused and summing up ... Wed, 21 Nov 2012 12:46:30 GMT Frederik Heber [358ddb] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalFullSummator.hpp (added) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDataFused.hpp (added) * src/Jobs/VMGDataMap.hpp (added) * src/Jobs/VMGData_printKeyNames.hpp (added) FragmentationAutomationAction now also sums up potential and obtain ... Wed, 21 Nov 2012 10:03:24 GMT Frederik Heber [184943] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/SetValues/Fragment.cpp (modified) * src/Fragmentation/SetValues/Fragment.hpp (modified) * src/Jobs/MPQCDataFused.hpp (modified) * src/Jobs/MPQCDataMap.hpp (modified) Added Fragment to MPQCData fusion maps and is used in ... Fri, 16 Nov 2012 14:13:47 GMT Frederik Heber [a1436b] * src/Jobs/InterfaceVMGJob.cpp (modified) Printing now four grids for debugging in InterfaceVMG. - also ... Fri, 16 Nov 2012 14:13:47 GMT Frederik Heber [17fcbe7] * src/Jobs/InterfaceVMGJob.cpp (modified) FIX: Correcting normalization in InterfaceVMGJob among others. - ... Fri, 16 Nov 2012 14:13:47 GMT Frederik Heber [08cc62] * src/Jobs/InterfaceVMGJob.cpp (modified) DEBUG: Modified printing of summed grid charge and grid potential. ... Fri, 16 Nov 2012 14:13:47 GMT Frederik Heber [16b4fe] * src/Jobs/InterfaceVMGJob.cpp (modified) DEBUG: Added writing grids as VTK files to InterfaceVMGJob. - ... Fri, 16 Nov 2012 14:13:47 GMT Frederik Heber [03d422a] * src/Jobs/InterfaceVMGJob.cpp (modified) Added a normalization to interpolation of charges onto particle_grid ... Fri, 16 Nov 2012 14:13:47 GMT Frederik Heber [4adef7] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) Added some debugging output to FragmentationAutomationAction. Fri, 16 Nov 2012 14:13:47 GMT Frederik Heber [2bc560] * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGData.cpp (added) * src/Jobs/VMGData.hpp (added) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) Added VMGData as container for data returned from VMGJob::Work(). Fri, 16 Nov 2012 14:13:45 GMT Frederik Heber [beb16e] * src/Fragmentation/SetValues/Histogram.cpp (modified) * src/Fragmentation/SetValues/Histogram.hpp (modified) * src/Fragmentation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/SetValues/IndexedVectors.hpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalSummation_impl.hpp (modified) * src/Fragmentation/Summation/ZeroInstance.hpp (added) * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) Added template function ZeroInstance to have zero value in ... Thu, 15 Nov 2012 15:12:54 GMT Frederik Heber [cd77fc] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCData.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) Positions and charges of nuclei are also contained in MPQCData and ... Thu, 15 Nov 2012 14:54:40 GMT Frederik Heber [e72c61] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) Added Sampling::integral(SamplingGrid&) that allows for a (charge) ... Thu, 15 Nov 2012 14:52:23 GMT Frederik Heber [a1fcc6] * src/Jobs/Grid/SamplingGrid.cpp (modified) * src/Jobs/Grid/SamplingGrid.hpp (modified) Added SamplingGrid::operator*=() for multiplying potential with ...