# # ChangeLog for src # # Generated by Trac 1.6 # May 24, 2025, 8:33:16 AM Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [9b56f34] * src/Actions/ActionSequence.cpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/toCLIString.cpp (added) * src/Actions/toCLIString.hpp (added) ActionParameters need special format when given to CLI. - ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [bad589] * src/Actions/ActionQueue.cpp (modified) * src/Actions/CommandAction/StoreSessionAction.cpp (added) * src/Actions/CommandAction/StoreSessionAction.def (added) * src/Actions/CommandAction/StoreSessionAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/Session/post/test.sh (added) * tests/regression/Options/Session/testsuite-options-store-session.at (added) * tests/regression/Options/testsuite-options.at (modified) Added StoreSessionAction to store the current session to file. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [46b181] * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) * src/Actions/Reaction_impl_header.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) Added Action::outputAsCLI() and ActionQueue::outputAsCLI(). - ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [76096d] * src/Element/periodentafel.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/boundary.cpp (modified) FIX: Several fixes found through CppCheck. - strncpy does not ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [f54cda] * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) Action::call() is private, replaced by ActionQueue::queueAction(). Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [c5177f] * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) FIX: Reaction's hasResult() and getResult() are const member functions. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [05c989] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) Actions are now called through ActionQueue. - Action::call() is ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [126867] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/OptionRegistry.hpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/World.cpp (modified) Actions no longer register themselves, ActionQueue::addAction() ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [d649b7] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/getLastPosition.cpp (added) * src/UIElements/Menu/getLastPosition.hpp (added) Added functor getLastPosition, extracted from ActionRegistry. - ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [6367dd] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) ActionHistory now is part of ActionQueue. - TESTFIX: changes to ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [b5b01e] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionParameters.hpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/ActionState.hpp (added) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondRemoveAction.cpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpRedistributeAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.hpp (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Shapes/AllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotAllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotShapeByNameAction.cpp (modified) * src/Actions/SelectionAction/Shapes/ShapeByNameAction.cpp (modified) * src/Actions/ShapeAction/CombineShapesAction.cpp (modified) * src/Actions/ShapeAction/CreateShapeAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/RotateShapeAction.cpp (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (modified) * src/Actions/ShapeAction/TranslateShapeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) ActionState extracted into own header file, rename Action::state_ptr ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [f92ef3] * src/Actions/Action.hpp (modified) * src/Actions/ActionParameters.hpp (added) * src/Actions/Makefile.am (modified) Extracted ActionParameters into own header file. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [ed3944] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) ActionQueue contains now ptr to ActionRegistry to allow forward ref ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [d67e6c] * src/Fragmentation/defs.hpp (modified) FIX: Changed inclusion guards of Fragmentation/defs.hpp to allow for ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [671a47] * src/Helpers/defs.hpp (modified) FIX: Converted Helpers/defs.hpp with dos2unix. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [40ec38] * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) FIX: AnalysisBondsUnitTest did not check numbers numerically. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [0c8056] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Action_impl_python.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/HelpRedistributeAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/World.cpp (modified) Actions now get ptr to ActionRegistry in cstor. - this is the last ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [a6ceab] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) FIX: ActionRegistry's function now get ref to token string. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [690741] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.hpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.hpp (modified) * src/cleanUp.cpp (modified) Added getListOfActions() and getActionsTrait() to completely wrap ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [1d3563] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) Main functions of ActionRegistry are now tunneled through ActionQueue. Thu, 19 Sep 2013 20:23:51 GMT Frederik Heber [628577] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (added) * src/Actions/ActionQueue.hpp (added) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/PythonScripting.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/cleanUp.cpp (modified) Introduced ActionQueue which contains internal ActionRegistry. - ... Thu, 19 Sep 2013 20:22:55 GMT Frederik Heber [732507] * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/SpecificFragmentController.cpp (modified) * src/Fragmentation/Automation/SpecificFragmentController.hpp (modified) * src/Fragmentation/Automation/SpecificFragmentController_ResultContainer_impl.hpp (added) * src/Fragmentation/Automation/SpecificFragmentController_impl.hpp (deleted) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) SpecificFragmentController now contains template ResultContainer. - ... Thu, 19 Sep 2013 20:21:37 GMT Frederik Heber [1e5f84] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) FragmentationAutomationAction does long-range jobs now depending on ... 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 15:16:39 GMT Frederik Heber [938e62] * src/UIElements/Makefile.am (modified) FIX: libMolecuilderPotentials.la is always compiled, we just remove ... Mon, 12 Aug 2013 11:30:33 GMT Frederik Heber [f5724f] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (moved) * src/Actions/PotentialAction/FitParticleChargesAction.def (moved) * src/Actions/PotentialAction/FitParticleChargesAction.hpp (moved) * src/Actions/PotentialAction/FitPotentialAction.cpp (moved) * src/Actions/PotentialAction/FitPotentialAction.def (moved) * src/Actions/PotentialAction/FitPotentialAction.hpp (moved) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (moved) * src/Actions/PotentialAction/ParseHomologiesAction.def (moved) * src/Actions/PotentialAction/ParseHomologiesAction.hpp (moved) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (moved) * src/Actions/PotentialAction/SaveHomologiesAction.def (moved) * src/Actions/PotentialAction/SaveHomologiesAction.hpp (moved) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/FitParticleCharges/pre/homology_grid.dat (moved) * tests/regression/Potential/FitParticleCharges/pre/water.pdb (moved) * tests/regression/Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at (moved) * tests/regression/Potential/FitPotential/pre/angle_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/harmonic_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/improper_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/length_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/lj_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/torsion_homology.dat (moved) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (moved) * tests/regression/Potential/testsuite-potential.at (added) * tests/regression/testsuite.at (modified) Moved all FragmentationActions related to potentials into own menu ... Mon, 12 Aug 2013 11:30:33 GMT Frederik Heber [353326] * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: Changed LIBADDs and LDADDs to get rid of libtool patching. - ... Mon, 12 Aug 2013 11:30:33 GMT Frederik Heber [474c62] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FIX: Typo in FragmentationAction. Mon, 12 Aug 2013 11:30:33 GMT Frederik Heber [57ba6f] * src/Parameters/Value.hpp (modified) FIX: Value's ConvertTo< std::vector > did convert empty strings to ... Mon, 12 Aug 2013 11:30:31 GMT Frederik Heber [321470] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) FIX: Fragmentation's OrderAtSite was written per molecule and with ... Fri, 09 Aug 2013 14:26:27 GMT Frederik Heber [3e93bd4] * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) FIX: SetOutputFormatsAction fails on unknown parser type. Fri, 09 Aug 2013 14:26:27 GMT Frederik Heber [abb641] * src/Graph/AdjacencyList.cpp (modified) FIX: AdjacencyList missed atoms without bonds. - this caused an ... Fri, 09 Aug 2013 14:26:27 GMT Frederik Heber [d067e35] * src/World.cpp (modified) FIX: World asserted greater not greater equal LC distance. Fri, 09 Aug 2013 14:26:27 GMT Frederik Heber [d7e931] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (added) * src/UIElements/Views/Qt4/QtTimeLine.hpp (added) Added Timeline slider to QtMainWindow. - this allows quick setting ... Fri, 09 Aug 2013 14:26:27 GMT Frederik Heber [89b992] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) GLWorldView now listens to World::TimeChanged() and updates view. - ... Fri, 09 Aug 2013 14:20:38 GMT Frederik Heber [2a8731] * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) World now has channel TimeChanged. - FIX: SetWorldTimeAction uses ... Fri, 09 Aug 2013 14:20:38 GMT Frederik Heber [cd9a59] * src/Atom/AtomObserver.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_observable.hpp (modified) Added TrajectoryChanged channel to atom_observable. - this lets us ... Fri, 09 Aug 2013 14:20:38 GMT Frederik Heber [13c5c1] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * tests/Python/AllActions/options.dat (modified) FragmentationAction uses Interfragmenter to add non-bonded fragments. Fri, 09 Aug 2013 14:20:38 GMT Frederik Heber [0331ee] * src/Fragmentation/Graph.hpp (modified) * src/Fragmentation/Interfragmenter.cpp (added) * src/Fragmentation/Interfragmenter.hpp (added) * src/Fragmentation/Makefile.am (modified) Added functor to add non-bonded union of fragments. - this is done ... Fri, 09 Aug 2013 14:20:38 GMT Frederik Heber [c1353f5] * src/AtomIdSet.cpp (modified) * src/AtomIdSet.hpp (modified) Added AtomIdSet cstor that converts from a KeySet. - as this ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [ff90e3] * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/PotentialTypes.def (modified) Renamed potential token harmonic to harmonic_bond. Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [791a12] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (added) * src/Potentials/Specifics/FourBodyPotential_Improper.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp (added) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) * tests/regression/Fragmentation/FitPotential/pre/improper_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added improper potential based on torsion potential with flipped ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [a74a96] * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (modified) Made function_theta of FourBodyPotential_Torsion virtual. - also ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [e2037e] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (added) * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp (added) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) * tests/regression/Fragmentation/FitPotential/pre/torsion_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added FourBodyPotential_Torsion. - also added regression test to ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [484e2a] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (moved) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (moved) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.cpp (moved) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.hpp (moved) Renamed PairPotential_Angle -> ThreeBodyPotential_Angle and also ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [1413f4] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (added) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp (added) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.hpp (added) * tests/regression/Fragmentation/FitPotential/pre/lj_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added LennardJones pair potential. - this is for later fitting ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [4792ab] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added set-threshold option to FitPotentialAction. - TESTFIX: ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [af4318] * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/GenericValidators.hpp (modified) * src/Parameters/Validators/GenericValidators_impl.hpp (added) Implemented GenericValidators. Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [c4a323] * src/Actions/FragmentationAction/FitParticleChargesAction.cpp (added) * src/Actions/FragmentationAction/FitParticleChargesAction.def (added) * src/Actions/FragmentationAction/FitParticleChargesAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Fragmentation/FitParticleCharges/pre/homology_grid.dat (added) * tests/regression/Fragmentation/FitParticleCharges/pre/water.pdb (added) * tests/regression/Fragmentation/FitParticleCharges/testsuite-fragmentation-fit-particle-charges.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added FitParticleChargesAction for fitting partial nuclei charges to ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [e355b31] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Added both_sampled_potential to VMGData, analogous to ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [bf1d1b] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * tests/Python/AllActions/options.dat (modified) HomologyContainer now stores full struct as value to HomologyGraph ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [ff09f3] * src/Potentials/Makefile.am (modified) * src/Potentials/Particles/Particle.cpp (added) * src/Potentials/Particles/Particle.hpp (added) * src/Potentials/Particles/ParticleRegistry.cpp (added) * src/Potentials/Particles/ParticleRegistry.hpp (added) Added Particle and ParticleRegistry class. - Paricle class contains ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [f60d95] * src/Potentials/PartialNucleiChargeFitter.cpp (modified) * src/Potentials/PartialNucleiChargeFitter.hpp (modified) PartialNucleiChargeFitter writes potential, solution, and residuum to ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [58fcbe5] * src/Potentials/Makefile.am (modified) * src/Potentials/PartialNucleiChargeFitter.cpp (added) * src/Potentials/PartialNucleiChargeFitter.hpp (added) * src/Potentials/unittests/Makefile.am (modified) * src/Potentials/unittests/PartialNucleiChargeFitterUnitTest.cpp (added) * src/Potentials/unittests/PartialNucleiChargeFitterUnitTest.hpp (added) Added functor for fitting partial nuclear charges. - is simply via ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [3f64ee] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) Extracted SamplingGrid::getDiscreteWindowIndices() from ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [b5f548] * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties_inline.hpp (added) * src/Fragmentation/Summation/SetValues/SamplingGrid_inline.hpp (modified) FIX: Shifted all helper functions from SamplingGrid to ..Properties. ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [af2c7ec] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) TrainingData now generates internal list of all arguments. - ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [31a2be] * src/FunctionApproximation/Extractors.cpp (modified) FIX: Extractors::filterArgumentsByParticleTypes() did wrongly break ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [a633f6] * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) Added splitUpArgumentsByModelsFilter() to CompoundPotential. - this ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [51e0e3] * configure.ac (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) Added two filter functions to Extractors. - renamed ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [0f5d38] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/helpers.hpp (modified) Added getSpecificFilter() and getSpecificArgumentCount() to ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [f0025d] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Renamed getFragmentSpecificExtractor() -> getSpecificExtractor(). Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [d449a9] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * src/Actions/FragmentationAction/ParseHomologiesAction.cpp (added) * src/Actions/FragmentationAction/ParseHomologiesAction.def (added) * src/Actions/FragmentationAction/ParseHomologiesAction.hpp (added) * src/Actions/FragmentationAction/SaveHomologiesAction.cpp (added) * src/Actions/FragmentationAction/SaveHomologiesAction.def (added) * src/Actions/FragmentationAction/SaveHomologiesAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Split off parsing and saving of homologies into new Actions. Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [1e1098] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (added) * src/UIElements/Views/Qt4/QtHomologyList.hpp (added) Added table of all present HomologyGraph keys to QtMainWindow. Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [98dbee] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) World now maintains HomologyContainer instance. Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [bcc24f] * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) Made HomologyContainer observable. - added clear() and getNextKey() ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [a8bc27a] * src/Fragmentation/Homology/HomologyContainer.hpp (modified) FIX: HomologyContainer::getHomologousGraphs() is actually const ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [0afe00] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) Extracted printNodes() and printEdges from HomologyGraph's output ... Fri, 09 Aug 2013 14:20:18 GMT Frederik Heber [39986b] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (added) * src/Actions/FragmentationAction/MolecularDynamicsAction.def (added) * src/Actions/FragmentationAction/MolecularDynamicsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) Added new MakroAction MolecularDynamicsAction. - this resides ... Thu, 11 Jul 2013 21:44:01 GMT Frederik Heber [9c1324] * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (added) * src/Actions/MakroAction_impl_pre.hpp (added) Equipped MakroAction with some boost::preprocessor magic, ... Thu, 11 Jul 2013 21:43:31 GMT Frederik Heber [bcb593] * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Molecules/VerletIntegration/post/test.conf (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) FIX: VerletIntegrationAction now assumes forces have just been ... Tue, 09 Jul 2013 06:21:28 GMT Frederik Heber [11f0fa] * src/Atom/atom.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.hpp (modified) FIX: Newly created atoms must have trajectories reaching out till ... Tue, 09 Jul 2013 06:21:28 GMT Frederik Heber [f73351] * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * tests/regression/Atoms/Add/post/empty.conf (modified) * tests/regression/Domain/ChangeBox/post/test-undo.conf (modified) * tests/regression/Domain/ChangeBox/post/test.conf (modified) FIX: Some Thermostats would cause NaN on zero temperature. - ... Tue, 09 Jul 2013 06:21:05 GMT Frederik Heber [e5ebaf] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Forces obtained from fragmentation summation are now set. - i.e. ... Mon, 08 Jul 2013 14:22:04 GMT Frederik Heber [62164d] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) Writing final parameters to potential-file. Mon, 08 Jul 2013 14:22:04 GMT Frederik Heber [a315e8] * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/Specific/EmptyStringValidator.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Potential type is given via extra option not "fit-potential". - ... Mon, 08 Jul 2013 14:22:04 GMT Frederik Heber [a504946] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * tests/Python/AllActions/options.dat (modified) Training data can now be written to optional file. Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [49dcf7] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) Added catching of SerializablePotentialException in FitPotentialAction. Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [baccf6] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) FitPotentialAction now uses new CompoundPotential to fit. - ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [7c1091] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) Extended CompoundPotential for multiple occurences of argument ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [c5e63a] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialDeserializer.cpp (added) * src/Potentials/PotentialDeserializer.hpp (added) * src/Potentials/PotentialSerializer.cpp (added) * src/Potentials/PotentialSerializer.hpp (added) * src/Potentials/SerializablePotential.cpp (modified) Added De(serializer) functors for instanting potentials from stream info. Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [3723f0] * src/Potentials/SerializablePotential.cpp (modified) FIX: SerializablePotential prints no comma following empty ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [6d9073] * src/Potentials/SerializablePotential.cpp (modified) FIX: SerializablePotential::stream_from() wrongly used ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [b3b31e] * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) Added PotentialFactory::createInstance() that uses default cstors. ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [a82d33] * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) FIX: Default cstor of specific potentials did not allocate parameter ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [713888] * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/SerializablePotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Made PotentialFactory friend of all specific potentials and added ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [acc9b1] * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PotentialTypes.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) FIX: Added new copyright lines to files in src/Potentials, too. Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [b15ae7] * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) Removed energy_offset from ManyBodyPotential_Tersoff. Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [1e242a] * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Removed energy_offset from PairPotential_Angle. - regression test ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [065a16] * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) Removed energy_offset from PairPotential_Harmonic. Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [919c8a] * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Removed energy_offset from PairPotential_Morse. - regression test ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [1e565c] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/SaturationPotential.cpp (deleted) * src/Potentials/Specifics/SaturationPotential.hpp (deleted) Removed SaturationPotential. - SaturationPotential can be seen as a ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [7e5b94] * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) CompoundPotential now combines ConstantPotential and ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [cf4905] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added concatenateArguments to Extractors. Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [8203ce8] * src/FunctionApproximation/Extractors.cpp (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (added) * src/Potentials/Specifics/ConstantPotential.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp (added) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) Added ConstantPotential to fit a non-zero offset in potential energy. ...