# # ChangeLog for src/World.cpp # # Generated by Trac 1.4.4 # Apr 3, 2025, 9:54:46 PM Tue, 06 Sep 2016 14:36:17 GMT Frederik Heber [0249ce] * src/World.cpp (modified) FIX: Pop..Action need to check whether stack is actually non-empty. ... Thu, 11 Feb 2016 08:07:11 GMT Frederik Heber [2affd1] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillVolumeAction.cpp (modified) * src/Actions/FillAction/SuspendInMoleculeAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.def (modified) * src/Actions/MoleculeAction/ChangeNameAction.def (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.def (modified) * src/Actions/MoleculeAction/SaveBondsAction.def (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.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/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/molecule.hpp (modified) Removed molecules_deprecated from World and unnecessary includes of ... Thu, 11 Feb 2016 08:06:49 GMT Frederik Heber [7f1865d] * src/World.cpp (modified) * src/World.hpp (modified) Added template functions to (un)set vector of instances in a row. Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [5cf341] * src/World.cpp (modified) * src/World.hpp (modified) Added recreateAtom() and recreateMolecule() to World. - in order to ... Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [7eec64] * src/World.cpp (modified) FIX: World needs to first destroy the molecule, then release its ids. ... Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [4965d9f] * src/World.cpp (modified) FIX: World::destroy..() did not emit SelectionChanged signal. Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [e2c2b1] * configure.ac (modified) * src/World.cpp (modified) * src/World.hpp (modified) World's ObservedContainer no longer observe. - This requires ... Tue, 13 Oct 2015 16:42:06 GMT Frederik Heber [59e7996] * src/World.cpp (modified) FIX: World needs to first destroy the atom, then release its ids. Wed, 05 Aug 2015 17:32:10 GMT Frederik Heber [f02b53] * src/World.cpp (modified) World now first releases id and then destroys the atom/molecule. - ... Wed, 05 Aug 2015 17:32:09 GMT Frederik Heber [fb95a5] * src/World.cpp (modified) * src/World.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) Added lastChanged..Id() to both World and molecule. Wed, 05 Aug 2015 17:32:07 GMT Frederik Heber [574d377] * configure.ac (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionStatusList.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Shapes/unittests/stubs/WorldSelectedMoleculesStub.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/cleanUp.cpp (modified) * src/molecule.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) Using static Observable::..NotificationsChannel() functions. - ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [143263] * src/Helpers/helpers.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Added getSelected..Ids() for both atoms and molecules. - added ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [99db9b] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.def (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.def (modified) * src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/PopAtomsAction.def (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.def (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.def (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.def (modified) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.def (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Shapes/ShapeFactory.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Replaced all World::getSelected...() to const version where possible. ... Fri, 24 Jul 2015 16:44:34 GMT Frederik Heber [795c0f] * src/Atom/AtomSet.hpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor_impl.hpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor_impl.hpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp (modified) * src/Descriptors/AtomOrderDescriptor.cpp (modified) * src/Descriptors/AtomOrderDescriptor_impl.hpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor_impl.hpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor_impl.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor_impl.hpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor_impl.hpp (modified) * src/Descriptors/DescriptorBase.hpp (modified) * src/Descriptors/DescriptorBase_impl.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) World::getAtoms() now has const versions as well. - this in turn ... Fri, 24 Jul 2015 16:44:34 GMT Frederik Heber [97445f] * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.hpp (modified) * src/Descriptors/MoleculeDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor_impl.hpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.hpp (modified) * src/Descriptors/MoleculePtrDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor_impl.hpp (modified) * src/Shapes/unittests/stubs/WorldSelectedMoleculesStub.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) World::getMolecules..() now has const versions as well. - this ... Fri, 24 Jul 2015 16:44:34 GMT Frederik Heber [270bdf] * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/World.cpp (modified) atom::getMolecule() now returns ptr to const molecule. - changed ... Thu, 23 Jul 2015 14:41:35 GMT Frederik Heber [748318] * src/World.cpp (modified) FIX: World does not sign on to molecule changes. Tue, 23 Jun 2015 06:29:02 GMT Frederik Heber [34641b] * src/World.cpp (modified) FIX: World does not to heed updates from internal MoleculeListClass. ... Tue, 10 Feb 2015 14:09:38 GMT Frederik Heber [0763ce] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/World.cpp (modified) Added BondGraph::checkBondDegree, FragmentationAction only resets ... Tue, 10 Feb 2015 14:09:10 GMT Frederik Heber [c1d837] * src/Actions/ActionSequence.hpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/PushAtomsAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) FIX: [push/pop][Atom/Molecule]Selection would store ptrs instead of ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [4f2895] * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/World.cpp (modified) FIX: World::SetTime() erased molecules twice. - once in SetTime() ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [cad383] * src/World.cpp (modified) * src/World.hpp (modified) Added push/pop[Atoms|Molecules]Selection to World. - this is mostly ... Sun, 11 Jan 2015 16:41:14 GMT Frederik Heber [a7aebd] * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/World.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) World removes empty molecules. - on destroyAtom() of molecule's ... Thu, 18 Sep 2014 18:24:53 GMT Frederik Heber [46ce1c] * src/World.cpp (modified) FIX: World::setTime() now first copies Bondgraph and then sets the ... Mon, 15 Sep 2014 15:05:28 GMT Frederik Heber [7f1b51] * 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/BondLengthTableAction.def (modified) * src/Actions/CommandAction/ElementDbAction.def (modified) * src/Actions/CommandAction/LoadSessionAction.def (modified) * src/Actions/CommandAction/StoreSessionAction.def (modified) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.def (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.def (modified) * src/Actions/GraphAction/CorrectBondDegreeAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Actions/unittests/stubs/DummyUI.hpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Specifics/Value_atom.cpp (added) * src/Parameters/Specifics/Value_atom.hpp (added) * src/Parameters/Specifics/Value_element.cpp (added) * src/Parameters/Specifics/Value_element.hpp (added) * src/Parameters/Specifics/Value_molecule.cpp (added) * src/Parameters/Specifics/Value_molecule.hpp (added) * src/Parameters/Specifics/Value_string.cpp (moved) * src/Parameters/Specifics/Value_string.hpp (moved) * src/Parameters/Validators/Ops_Validator_impl.hpp (modified) * src/Parameters/Validators/Specific/FileSuffixValidator.hpp (modified) * src/Parameters/Validators/Specific/ParserFileValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserFileValidator.hpp (modified) * src/Parameters/Validators/Validator.hpp (modified) * src/Parameters/Validators/getFlatListFromHierarchyOfValidators.hpp (added) * src/Parameters/Value.hpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/Menu.hpp (modified) * src/UIElements/Menu/Qt4/QMenu_tooltip.hpp (added) * src/UIElements/Menu/Qt4/QtMenu.hpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/QtUIFactory.hpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FilesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextUIFactory.hpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.hpp (modified) * src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp (added) * src/World.cpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Options/Warranty/testsuite-options-warranty.at (modified) Merge branch 'GUI_Fixes' into stable Mon, 08 Sep 2014 21:36:29 GMT Frederik Heber [388ddd] * src/World.cpp (modified) World::setTime() now only copies bond graph, does not re-create it. ... Thu, 28 Aug 2014 08:53:32 GMT Frederik Heber [09f615] * src/World.cpp (modified) * src/builder.cpp (modified) MEMFIX: World's homologies not deleted. - main() now uses int ... 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 [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 ... 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 14:20:38 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 14:20:35 GMT Frederik Heber [98dbee] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) World now maintains HomologyContainer instance. 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. ... Wed, 17 Apr 2013 18:56:32 GMT Frederik Heber [708277] * configure.ac (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomObserver.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.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/ShapeRegistry.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/cleanUp.cpp (modified) * src/molecule.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) FIX: Using fixed Observer in CodePatterns 1.2.6. - we now require ... Wed, 17 Apr 2013 18:56:04 GMT Frederik Heber [feb5d0] * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/DescriptorBase.hpp (modified) * src/Descriptors/MoleculeDescriptor.hpp (modified) * src/Descriptors/SelectiveConstIterator.hpp (added) * src/Descriptors/SelectiveConstIterator_impl.hpp (added) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) Added SelectiveConstIterator, allows for constant iteration over ... Mon, 18 Mar 2013 13:32:16 GMT Frederik Heber [03abd0] * src/World.cpp (modified) FIX: World::getLinkedCell() does not allow distance less than 1. - ... Wed, 13 Feb 2013 15:47:38 GMT Frederik Heber [7d82a5] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/World.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) Changed bond::ptr into boost::shared_ptr. Changes: - refactored ... Wed, 26 Sep 2012 17:24:47 GMT Frederik Heber [94d5ac6] * LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Line.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LinePoint.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Plane.cpp (modified) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Space.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Vector.cpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (modified) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (modified) * LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (modified) * LinearAlgebra/src/unittests/LineUnitTest.cpp (modified) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (modified) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (modified) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (modified) * LinearAlgebra/src/unittests/PlaneUnitTest.cpp (modified) * LinearAlgebra/src/unittests/RealSpaceMatrixUnitTest.cpp (modified) * LinearAlgebra/src/unittests/TestRunnerMain.cpp (modified) * LinearAlgebra/src/unittests/UnitTestMain.cpp (modified) * LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (modified) * LinearAlgebra/src/unittests/VectorSetUnitTest.cpp (modified) * LinearAlgebra/src/unittests/VectorUnitTest.cpp (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.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/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (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 (added) * src/Actions/CommandAction/HelpRedistributeAction.def (added) * src/Actions/CommandAction/HelpRedistributeAction.hpp (added) * 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/FillSphericalSurfaceAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (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/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/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.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/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/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.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/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.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/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/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.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/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (modified) * src/AtomIdSet.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/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/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Filling/Cluster.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/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/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/unittests/ClusterUnitTest.cpp (modified) * src/Filling/unittests/FillerUnitTest.cpp (modified) * src/Filling/unittests/IsInsideDomain_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsInsideSurface_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsValidInDomain_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsVoidNode_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/Ops_FillPredicateUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCCommandJob_MPQCData.cpp (modified) * src/Jobs/unittests/MPQCCommandJobUnitTest.cpp (modified) * src/Jobs/unittests/MPQCDataUnitTest.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/LinkedCellUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.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/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/RandomNumberValidators.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixInvertibleValidator.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixSymmetricValidator.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/ContinuousParameterTest.cpp (modified) * src/Parameters/unittests/ContinuousValueTest.cpp (modified) * src/Parameters/unittests/DiscreteParameterTest.cpp (modified) * src/Parameters/unittests/DiscreteValueTest.cpp (modified) * src/Parameters/unittests/Ops_ValidatorTest.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/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.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/TremoloParser_ElementKeys.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/ParserTremolo_ElementKeysUnitTest.cpp (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.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/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Server.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/BaseShapesUnitTest.cpp (modified) * src/Shapes/unittests/ShapeOpsUnitTest.cpp (modified) * src/Shapes/unittests/Shape_HomogeneousPointsUnitTest.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeVolumeStub.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/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.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/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/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.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/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.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/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQueryList.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.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/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.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/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/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.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.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/moleculelist.cpp (modified) * src/poolworker.cpp (modified) * src/unittests/AtomIdSetUnitTest.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/Box_BoundaryConditionsUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/MoleculeUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * src/unittests/stubs/AtomStub.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) * tests/JobMarket/mpqc.cpp (modified) FIX: As we use GSL internally, we are as of now required to use GPL ... Wed, 25 Jul 2012 14:05:16 GMT Michael Ankele [65d7ca] * src/World.cpp (modified) Fix: World::registerAtom() did not notify observers Fri, 18 May 2012 15:24:37 GMT Michael Ankele [992bd5] * src/Actions/Action.hpp (modified) * src/Parameters/ContinuousValue_impl.hpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) fixed some typoes in comments Fri, 06 Apr 2012 11:57:21 GMT Frederik Heber [69643a] * src/World.cpp (modified) * src/World.hpp (modified) World: made selection changes observable Tue, 03 Apr 2012 07:55:55 GMT Frederik Heber [ebc499] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (added) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.def (added) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.hpp (added) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (added) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.def (added) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/InvertAtoms/post/id0_missing.xyz (added) * tests/regression/Selection/Atoms/InvertAtoms/post/id0_present.xyz (added) * tests/regression/Selection/Atoms/InvertAtoms/pre/box.xyz (added) * tests/regression/Selection/Atoms/InvertAtoms/testsuite-selection-invert-atoms.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) * tests/regression/Selection/Molecules/InvertMolecules/post/mol0_missing.xyz (added) * tests/regression/Selection/Molecules/InvertMolecules/post/mol0_present.xyz (added) * tests/regression/Selection/Molecules/InvertMolecules/pre/box.xyz (added) * tests/regression/Selection/Molecules/InvertMolecules/testsuite-selection-invert-molecules.at (added) * tests/regression/Selection/Molecules/testsuite-selection-molecules.at (modified) Added InvertMoleculesAction and InvertAtomsAction. - World has two ... Wed, 22 Feb 2012 11:28:52 GMT Frederik Heber [040a5c] * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/WorldTime.hpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) WorldTime is now Observable. - this is required for the ... Fri, 17 Feb 2012 15:24:18 GMT Frederik Heber [b97a60] * src/IdPool.hpp (modified) * src/IdPool_impl.hpp (modified) * src/IdPool_policy.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) * src/documentation/constructs/world.dox (modified) * tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/post/test.xyz (modified) Modified IdPool implementation to give either unique or continuous ... Wed, 04 Jan 2012 14:28:40 GMT Frederik Heber [0aa122] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.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/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (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/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.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/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.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/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.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/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.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/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.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/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.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/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.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/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomicInfo.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/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.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/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.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/LinkedCellUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/AtomStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldStub.cpp (modified) * src/MoleculeLeafClass.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/Parameters/StringParameter.cpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.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/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/ParserXyzUnitTest.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/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/ShapeUnitTest.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/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.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/BoxCommandLineQuery.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/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/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/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.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/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.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/BoxQtQuery.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/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.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/AtomQuery.cpp (modified) * src/UIElements/Query/AtomsQuery.cpp (modified) * src/UIElements/Query/BooleanQuery.cpp (modified) * src/UIElements/Query/BoxQuery.cpp (modified) * src/UIElements/Query/DoubleQuery.cpp (modified) * src/UIElements/Query/DoublesQuery.cpp (modified) * src/UIElements/Query/ElementQuery.cpp (modified) * src/UIElements/Query/ElementsQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/FileQuery.cpp (modified) * src/UIElements/Query/IntQuery.cpp (modified) * src/UIElements/Query/IntsQuery.cpp (modified) * src/UIElements/Query/MoleculeQuery.cpp (modified) * src/UIElements/Query/MoleculesQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp (modified) * src/UIElements/Query/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.cpp (modified) * src/UIElements/Query/UnsignedIntQuery.cpp (modified) * src/UIElements/Query/UnsignedIntsQuery.cpp (modified) * src/UIElements/Query/VectorQuery.cpp (modified) * src/UIElements/Query/VectorsQuery.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/BoxTextQuery.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/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.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/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/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.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.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) Updated all source files's copyright note to current year 2012. Mon, 02 Jan 2012 13:34:29 GMT Frederik Heber [4834f4] * src/World.cpp (modified) * src/World.hpp (modified) World now has a LinkedCell_Controller and function getLinkedCell(). ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [5dfabd] * src/Atom/AtomObserver.cpp (added) * src/Atom/AtomObserver.hpp (added) * src/Atom/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) Added singleton class AtomObserver that acts as relay station to all ... Mon, 02 Jan 2012 13:00:04 GMT Frederik Heber [02ce36] * configure.ac (modified) * src/Actions/Process.hpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_observable.hpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/MoleculeListClass.hpp (modified) * src/Parser/ChangeTracker.hpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/FormatParser_common.hpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (modified) * src/UIElements/TextUI/TextStatusIndicator.hpp (modified) * 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) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.hpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.hpp (modified) * src/UIElements/Views/Qt4/QtWorldView.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/molecule.hpp (modified) We now require CodePatterns 1.2.0. - this is due to the updated ... Wed, 28 Dec 2011 15:30:06 GMT Frederik Heber [6f0841] * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.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/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.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/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Atom/AtomSet.hpp (moved) * src/Atom/AtomicInfo.cpp (moved) * src/Atom/AtomicInfo.hpp (moved) * src/Atom/Makefile.am (added) * src/Atom/TesselPoint.cpp (moved) * src/Atom/TesselPoint.hpp (moved) * src/Atom/atom.cpp (moved) * src/Atom/atom.hpp (moved) * src/Atom/atom_atominfo.cpp (moved) * src/Atom/atom_atominfo.hpp (moved) * src/Atom/atom_bondedparticle.cpp (moved) * src/Atom/atom_bondedparticle.hpp (moved) * src/Atom/atom_bondedparticleinfo.cpp (moved) * src/Atom/atom_bondedparticleinfo.hpp (moved) * src/Atom/atom_graphnode.cpp (moved) * src/Atom/atom_graphnode.hpp (moved) * src/Atom/atom_graphnodeinfo.cpp (moved) * src/Atom/atom_graphnodeinfo.hpp (moved) * src/Atom/atom_observable.cpp (moved) * src/Atom/atom_observable.hpp (moved) * src/Atom/atom_particleinfo.cpp (moved) * src/Atom/atom_particleinfo.hpp (moved) * src/Bond/bond.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/LinkedCell/PointCloudAdaptor.hpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/Makefile.am (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/TremoloParser.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/ParserXyzUnitTest.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/boundary.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Thermostat.hpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) Shifted all modules related to atoms into own subfolder src/Atom/ - ... Wed, 28 Dec 2011 15:27:49 GMT Frederik Heber [3e4fb6] * src/IdPool.hpp (added) * src/IdPool_impl.hpp (added) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/documentation/constructs/world.dox (modified) Added template class IdPool used by World to manage defragmentable id ... Wed, 28 Dec 2011 15:24:58 GMT Frederik Heber [d103d3] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.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/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (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/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.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/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.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/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.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/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.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/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.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/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.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/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.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/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/AtomicInfo.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.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/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/MoleculeLeafClass.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/Parameters/StringParameter.cpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.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/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/ParserXyzUnitTest.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/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/ShapeUnitTest.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/TesselPoint.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/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.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/BoxCommandLineQuery.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/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/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/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.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/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.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/BoxQtQuery.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/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.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/AtomQuery.cpp (modified) * src/UIElements/Query/AtomsQuery.cpp (modified) * src/UIElements/Query/BooleanQuery.cpp (modified) * src/UIElements/Query/BoxQuery.cpp (modified) * src/UIElements/Query/DoubleQuery.cpp (modified) * src/UIElements/Query/DoublesQuery.cpp (modified) * src/UIElements/Query/ElementQuery.cpp (modified) * src/UIElements/Query/ElementsQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/FileQuery.cpp (modified) * src/UIElements/Query/IntQuery.cpp (modified) * src/UIElements/Query/IntsQuery.cpp (modified) * src/UIElements/Query/MoleculeQuery.cpp (modified) * src/UIElements/Query/MoleculesQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp (modified) * src/UIElements/Query/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.cpp (modified) * src/UIElements/Query/UnsignedIntQuery.cpp (modified) * src/UIElements/Query/UnsignedIntsQuery.cpp (modified) * src/UIElements/Query/VectorQuery.cpp (modified) * src/UIElements/Query/VectorsQuery.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/BoxTextQuery.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/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.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/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/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.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/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_observable.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) Added additional check in CodeCheck's project disclaimer for current ... Mon, 07 Nov 2011 12:24:02 GMT Frederik Heber [3139b2] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionTrait.cpp (moved) * src/Actions/ActionTrait.hpp (added) * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.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.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/World_calculations.hpp (modified) Renamed ActionTrait and ActionTraits. - the specialized Trait ... Thu, 03 Nov 2011 19:44:02 GMT Frederik Heber [ab26c3] * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Makefile.am (modified) * src/Parser/PcpParser.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (moved) * src/Thermostats/ThermoStatContainer.hpp (moved) * src/Thermostats/Woodcock.cpp (modified) * src/World.cpp (modified) Moved ThermoStatContainer to folder src/Thermostats. Thu, 03 Nov 2011 09:52:29 GMT Frederik Heber [7ba268] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.def (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/World.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_X.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0000.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0001.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0002.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0003.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0004.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0005.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0006.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0007.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0008.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0009.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0010.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0011.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0012.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0013.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0014.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0015.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0016.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0017.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0018.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0019.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0020.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0021.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0022.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0023.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0024.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0025.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0026.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0027.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0028.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0029.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0030.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0031.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0032.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0033.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0034.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0035.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_X.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0000.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0001.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0002.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0003.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0004.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0005.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0006.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0007.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0008.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0009.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0010.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0011.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0012.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0013.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0014.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0015.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0016.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0017.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0018.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0019.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0020.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0021.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0022.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0023.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0024.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0025.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0026.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0027.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0028.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0029.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0030.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0031.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0032.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0033.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0034.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0035.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.pdb (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.pdb (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (added) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/post/waterbox-mirrored_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/post/waterbox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/pre/water.xyz (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/post/emptybox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/post/hydrogenbox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/testsuite-analysis-dipole-correlation-empty.at (moved) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'DipoleAngularCorrelation' into mergeMaster Conflicts: ... Tue, 25 Oct 2011 15:31:54 GMT Frederik Heber [4b8630] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/World.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) World::setTime() now updates bond structure of system and related ... Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [42127c] * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/MoleculeListClass.hpp (added) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/MainWindow.hpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/World.cpp (modified) * src/config.cpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) Extracted definition of MoleculeListClass and put into own header module. Mon, 17 Oct 2011 16:18:55 GMT Frederik Heber [4ae823] * src/Element/periodentafel.cpp (modified) * src/Element/periodentafel.hpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/World.cpp (modified) periodentafel may or may not Load internal databases in its cstor. ... Mon, 17 Oct 2011 16:18:54 GMT Frederik Heber [3bdb6d] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.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/CommandAction/ElementDbAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/AtomicInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/Hbondangle.db (moved) * src/Element/Hbonddistance.db (moved) * src/Element/Makefile.am (added) * src/Element/element.cpp (moved) * src/Element/element.hpp (moved) * src/Element/elements.db (moved) * src/Element/elements_db.cpp (moved) * src/Element/elements_db.hpp (moved) * src/Element/orbitals.db (moved) * src/Element/periodentafel.cpp (moved) * src/Element/periodentafel.hpp (moved) * src/Element/valence.db (moved) * src/Formula.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.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/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/TextWindow.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/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ElementUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/PeriodentafelUnitTest.cpp (modified) Moved all stuff related to elements into own subfolder and has its ... Thu, 13 Oct 2011 13:03:40 GMT Frederik Heber [ce7fdc] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/ActionTraits.cpp (modified) * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.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/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (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/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/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.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/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.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/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionRegistry.hpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/OptionTrait.hpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (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/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.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/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.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/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.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/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/ValueStorage.hpp (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/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.hpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.hpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.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/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.hpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldTime.hpp (modified) * src/World_calculations.hpp (modified) * src/builder_init.cpp (modified) HUGE: All Action-related codes resides now in namespace MoleCuilder. ... Mon, 10 Oct 2011 14:25:37 GMT Frederik Heber [38f991] * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) FormatParser now listens to World::AtomRemoved and ::AtomInserted ... Fri, 07 Oct 2011 10:22:17 GMT Frederik Heber [ab4a33] * src/World.cpp (modified) FIX: World::destroyAtom() now informs before atom's destruction, not ... Thu, 06 Oct 2011 16:06:10 GMT Frederik Heber [89643d] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Enabled also un selection when clicking already selected atoms. - ... Thu, 06 Oct 2011 16:06:10 GMT Frederik Heber [7188b1] * configure.ac (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeScene.cpp (deleted) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeScene.hpp (deleted) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_bondedparticleinfo.hpp (modified) * src/atom_observable.cpp (added) * src/atom_observable.hpp (added) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) Introduced atom_observables and GLWorldView observes World, ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [632508] * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Graph/BondGraph.cpp (moved) * src/Graph/BondGraph.hpp (moved) * src/Makefile.am (modified) * src/World.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisBondsUnitTest.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) Moved files bondgraph.?pp -> Graph/BondGraph.?pp. Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [f71baf] * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule_graph.cpp (modified) Made BondGraph an instance of World, removed from config. - ... Thu, 24 Feb 2011 16:26:28 GMT Frederik Heber [76163d] * src/World.cpp (modified) World::setTime() now checks whether CurrentTime changes at all. - ... Thu, 24 Feb 2011 16:06:21 GMT Frederik Heber [d297a3] * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldTime.hpp (modified) World::setTime() is single access point to modifying ... Thu, 23 Dec 2010 17:40:13 GMT Frederik Heber [ad011c] * m4/ax_codepatterns.m4 (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTraits.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/TranslateAction.cpp (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/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.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/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/SaveAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionRegistry.hpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.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/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.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/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.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/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/ValueStorage.hpp (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/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/AtomicInfo.cpp (modified) * src/BoundaryLineSet.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPolygonSet.cpp (modified) * src/BoundaryTriangleSet.cpp (modified) * src/Box.cpp (modified) * src/CandidateForTesselation.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.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/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MissingValueException.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (modified) * src/Exceptions/NotOnSurfaceException.cpp (modified) * src/Exceptions/ParseError.cpp (modified) * src/Exceptions/ShapeException.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Formula.cpp (modified) * src/Formula.hpp (modified) * src/Helpers/defs.cpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/helpers.hpp (modified) * src/LinearAlgebra/BoxVector.cpp (modified) * src/LinearAlgebra/Eigenspace.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/LineSegment.cpp (modified) * src/LinearAlgebra/LineSegmentSet.cpp (modified) * src/LinearAlgebra/LinearSystemOfEquations.cpp (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixVector_ops.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Subspace.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/VectorInterface.cpp (modified) * src/LinearAlgebra/leastsquaremin.cpp (modified) * src/LinearAlgebra/unittests/VectorUnitTest.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ChangeTracker.hpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/PointCloud.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/SubspaceFactorizer.cpp (modified) * src/TesselPoint.cpp (modified) * src/ThermoStatContainer.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/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (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/BoxCommandLineQuery.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/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/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.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/MenuDescription.hpp (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/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/QtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.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/BoxQtQuery.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/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/AtomQuery.cpp (modified) * src/UIElements/Query/AtomsQuery.cpp (modified) * src/UIElements/Query/BooleanQuery.cpp (modified) * src/UIElements/Query/BoxQuery.cpp (modified) * src/UIElements/Query/DoubleQuery.cpp (modified) * src/UIElements/Query/DoublesQuery.cpp (modified) * src/UIElements/Query/ElementQuery.cpp (modified) * src/UIElements/Query/ElementsQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/FileQuery.cpp (modified) * src/UIElements/Query/IntQuery.cpp (modified) * src/UIElements/Query/IntsQuery.cpp (modified) * src/UIElements/Query/MoleculeQuery.cpp (modified) * src/UIElements/Query/MoleculesQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/Query/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.cpp (modified) * src/UIElements/Query/VectorQuery.cpp (modified) * src/UIElements/Query/VectorsQuery.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/BoxTextQuery.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/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.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/TextStatusIndicator.hpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/GLMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.hpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.hpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.hpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/PeriodentafelUnitTest.cpp (modified) * src/unittests/SubspaceFactorizerUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) CodePatterns places all includes now in subfolder CodePatterns/. - ... Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [e4fe8d] * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Descriptors/AtomIdDescriptor.hpp (modified) * src/Descriptors/AtomShapeDescriptor.hpp (modified) * src/Descriptors/MoleculeIdDescriptor.hpp (modified) * src/Descriptors/MoleculeNameDescriptor.hpp (modified) * src/Descriptors/MoleculePtrDescriptor.hpp (modified) * src/Helpers/Makefile.am (modified) * src/Helpers/defs.cpp (moved) * src/Helpers/defs.hpp (moved) * src/Helpers/fast_functions.hpp (modified) * src/Helpers/helpers.hpp (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.hpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/Vector.hpp (modified) * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/Makefile.am (modified) * src/Patterns/Singleton.hpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.hpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/World.cpp (modified) * src/analysis_correlation.hpp (modified) * src/boundary.hpp (modified) * src/element.hpp (modified) * src/linkedcell.hpp (modified) * src/molecule_graph.cpp (modified) * src/periodentafel.hpp (modified) * src/tesselationhelpers.hpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Moved defs.?pp to subdir (and library) Helpers. - hence, include ... Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber [cca9ef] * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * src/LinearAlgebra/Vector.hpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps.hpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/atom_atominfo.hpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/BoxUnittest.hpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MatrixUnittest.hpp (modified) * src/unittests/vectorunittest.cpp (modified) Renamed Matrix to RealSpaceMatrix. - class Matrix only represents ... Sat, 30 Oct 2010 20:42:44 GMT Frederik Heber [e4afb4] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionTraits.cpp (modified) * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.def (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.def (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.def (modified) * src/Actions/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.def (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.def (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpAction.def (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.def (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/VersionAction.def (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.def (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.def (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.def (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.def (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MapOfActions.cpp (deleted) * src/Actions/MapOfActions.hpp (deleted) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.def (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.def (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.def (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.def (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.def (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.def (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/OptionRegistry.cpp (added) * src/Actions/OptionRegistry.hpp (added) * src/Actions/OptionTrait.cpp (added) * src/Actions/OptionTrait.hpp (added) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.def (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.def (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/RedoAction.cpp (added) * src/Actions/RedoAction.def (added) * src/Actions/RedoAction.hpp (added) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.def (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.def (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.def (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.def (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.def (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.def (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.def (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.def (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.def (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.def (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.def (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.def (modified) * src/Actions/UndoAction.cpp (added) * src/Actions/UndoAction.def (moved) * src/Actions/UndoAction.hpp (added) * src/Actions/ValueStorage.cpp (modified) * src/Actions/ValueStorage.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.def (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.def (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.def (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.def (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.def (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.def (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.def (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.def (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.def (modified) * src/Actions/convert5.sh (added) * src/CommandLineParser.cpp (deleted) * src/Makefile.am (modified) * src/Patterns/Registry.hpp (modified) * src/Patterns/Registry_impl.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (added) * src/UIElements/CommandLineUI/CommandLineParser.hpp (moved) * 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/BoxCommandLineQuery.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/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/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (added) * src/UIElements/CommandLineUI/TypeEnumContainer.hpp (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuDescription.hpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.hpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/World_calculations.hpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MenuDescriptionUnitTest.cpp (modified) * src/unittests/MenuDescriptionUnitTest.hpp (modified) * src/unittests/RegistryUnitTest.cpp (added) * src/unittests/RegistryUnitTest.hpp (added) * src/unittests/atomsCalculationTest.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) Huge refactoring: Introduction of Traits to Actions. This change is ... Thu, 19 Aug 2010 15:23:37 GMT Frederik Heber [654394] * src/World.cpp (modified) MEMFIX: World::numMoleculeDefragSkips and World::lastMoleculePoolSize ... Tue, 17 Aug 2010 13:14:22 GMT Frederik Heber [bcf653] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.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/TranslateAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.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/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.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/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/AtomicInfo.cpp (modified) * src/BoundaryLineSet.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPolygonSet.cpp (modified) * src/BoundaryTriangleSet.cpp (modified) * src/Box.cpp (modified) * src/CandidateForTesselation.cpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MissingValueException.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (modified) * src/Exceptions/ParseError.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Formula.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/Info.cpp (modified) * src/Helpers/Log.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/Verbose.cpp (modified) * src/Helpers/errorlogger.cpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/logger.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Matrix.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorInterface.cpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/gslvector.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Observer.cpp (modified) * src/PointCloud.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/TesselPoint.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/QT4/QTMenu.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/QT4/QTUIFactory.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/GLMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/UIElements/Views/QT4/QTWorldView.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/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/BaseShapesUnittest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/FormulaUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/MapofActionsTest.cpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/SingletonTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (modified) * src/unittests/gslmatrixunittest.cpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/memoryusageobserverunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Added copyright note to each .cpp file and an extensive one to ... Fri, 13 Aug 2010 14:08:39 GMT Frederik Heber [5f1d5b8] * src/Patterns/ObservedContainer_impl.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) BUGFIX: fixed undefined ref to ... Thu, 12 Aug 2010 16:31:02 GMT Frederik Heber [a7a087] * src/World.cpp (modified) * src/World.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) new function World::changeMoleculeId(). - copied from ... Thu, 12 Aug 2010 14:23:34 GMT Frederik Heber [fa7989] * src/World.cpp (modified) * src/atom.cpp (modified) * src/molecule.cpp (modified) FIX: World::destroyMolecule(mol *) - assert that pointer is not NULL. ... Wed, 11 Aug 2010 09:27:47 GMT Frederik Heber [bf3817] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (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/TranslateAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.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/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.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/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/BoundaryLineSet.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPolygonSet.cpp (modified) * src/BoundaryTriangleSet.cpp (modified) * src/Box.cpp (modified) * src/CandidateForTesselation.cpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MissingValueException.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (modified) * src/Exceptions/ParseError.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Formula.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/Info.cpp (modified) * src/Helpers/Log.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/Verbose.cpp (modified) * src/Helpers/errorlogger.cpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/logger.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Matrix.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorInterface.cpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/gslvector.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Observer.cpp (modified) * src/PointCloud.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/TesselPoint.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/QT4/QTMenu.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.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/GLMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/UIElements/Views/QT4/QTWorldView.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/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/FormulaUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/MapofActionsTest.cpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/SingletonTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (modified) * src/unittests/gslmatrixunittest.cpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/memoryusageobserverunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Added ifdef HAVE_CONFIG and config.h include to each and every cpp ... Fri, 06 Aug 2010 09:34:59 GMT Frederik Heber [d223d5] * Makefile.am (modified) * TestRunnerClient.cpp (added) * TestRunnerClient.h (added) * config/ltmain.sh (added) * configure.ac (modified) * libmolecuilder_config.h.in (added) * m4/gwqt4.m4 (modified) * molecuilder.pc.in (added) * src/Actions/Action.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (moved) * src/Actions/ValueStorage.hpp (moved) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (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/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/SelectiveIterator_impl.hpp (modified) * src/Exceptions/Makefile.am (added) * src/Formula.hpp (modified) * src/Helpers/Info.cpp (moved) * src/Helpers/Info.hpp (moved) * src/Helpers/Log.cpp (moved) * src/Helpers/Log.hpp (moved) * src/Helpers/Makefile.am (added) * src/Helpers/MemDebug.hpp (modified) * src/Helpers/Verbose.cpp (moved) * src/Helpers/Verbose.hpp (moved) * src/Helpers/errorlogger.cpp (moved) * src/Helpers/errorlogger.hpp (moved) * src/Helpers/helpers.cpp (moved) * src/Helpers/helpers.hpp (moved) * src/Helpers/logger.cpp (moved) * src/Helpers/logger.hpp (moved) * src/Legacy/oldmenu.cpp (modified) * src/LinearAlgebra/Line.cpp (moved) * src/LinearAlgebra/Line.hpp (moved) * src/LinearAlgebra/Makefile.am (added) * src/LinearAlgebra/Matrix.cpp (moved) * src/LinearAlgebra/Matrix.hpp (moved) * src/LinearAlgebra/MatrixContent.hpp (moved) * src/LinearAlgebra/Plane.cpp (moved) * src/LinearAlgebra/Plane.hpp (moved) * src/LinearAlgebra/Space.cpp (moved) * src/LinearAlgebra/Space.hpp (moved) * src/LinearAlgebra/Vector.cpp (moved) * src/LinearAlgebra/Vector.hpp (moved) * src/LinearAlgebra/VectorContent.hpp (moved) * src/LinearAlgebra/VectorSet.hpp (moved) * src/LinearAlgebra/gslmatrix.cpp (moved) * src/LinearAlgebra/gslmatrix.hpp (moved) * src/LinearAlgebra/gslvector.cpp (moved) * src/LinearAlgebra/gslvector.hpp (moved) * src/LinearAlgebra/linearsystemofequations.cpp (moved) * src/LinearAlgebra/linearsystemofequations.hpp (moved) * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/Makefile.am (added) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/QT4/IntQTQuery.ui (added) * src/UIElements/QT4/IntsQTQuery.ui (added) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/World.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/ShapeUnittest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.hpp (modified) * src/unittests/gslmatrixunittest.hpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.hpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector_ops.cpp (modified) Merge branch 'SharedLibraries' into stable - BUGFIX: MemDebug.cpp ... Thu, 05 Aug 2010 19:28:52 GMT Frederik Heber [57f243] * configure.ac (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/LinearAlgebra/Line.cpp (moved) * src/LinearAlgebra/Line.hpp (moved) * src/LinearAlgebra/Makefile.am (added) * src/LinearAlgebra/Matrix.cpp (moved) * src/LinearAlgebra/Matrix.hpp (moved) * src/LinearAlgebra/MatrixContent.hpp (moved) * src/LinearAlgebra/Plane.cpp (moved) * src/LinearAlgebra/Plane.hpp (moved) * src/LinearAlgebra/Space.cpp (moved) * src/LinearAlgebra/Space.hpp (moved) * src/LinearAlgebra/Vector.cpp (moved) * src/LinearAlgebra/Vector.hpp (moved) * src/LinearAlgebra/VectorContent.hpp (moved) * src/LinearAlgebra/VectorSet.hpp (moved) * src/LinearAlgebra/gslmatrix.cpp (moved) * src/LinearAlgebra/gslmatrix.hpp (moved) * src/LinearAlgebra/gslvector.cpp (moved) * src/LinearAlgebra/gslvector.hpp (moved) * src/LinearAlgebra/linearsystemofequations.cpp (moved) * src/LinearAlgebra/linearsystemofequations.hpp (moved) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/World.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/ShapeUnittest.hpp (modified) * src/unittests/gslmatrixsymmetricunittest.hpp (modified) * src/unittests/gslmatrixunittest.hpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.hpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector_ops.cpp (modified) Created libMolecuilderLinearAlgebra. - is shared. - contains the ... Thu, 05 Aug 2010 15:35:18 GMT Tillmann Crueger [6cb9c76] * src/World.cpp (modified) Changed order of destruction in World destructor Wed, 04 Aug 2010 09:34:45 GMT Tillmann Crueger [11e206] * src/World.cpp (modified) * src/defs.hpp (modified) Removed multiple definitions of some global constants from executeable Fri, 30 Jul 2010 13:07:00 GMT Tillmann Crueger [4d72e4] * src/Descriptors/AtomDescriptor.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Made the World use the new mixin for sets of atoms Wed, 28 Jul 2010 09:21:14 GMT Tillmann Crueger [677e13] * .gitignore (added) * configure.ac (modified) * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (added) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.hpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.hpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.hpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/HelpAction.hpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.hpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/CmdAction/VersionAction.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.hpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.hpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (added) * src/Actions/SelectionAction/AllAtomsAction.hpp (added) * src/Actions/SelectionAction/AllMoleculesAction.cpp (added) * src/Actions/SelectionAction/AllMoleculesAction.hpp (added) * src/Actions/SelectionAction/AtomByIdAction.cpp (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/Values.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.hpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/CommandLineParser.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (added) * src/Exceptions/IllegalTypeException.hpp (added) * src/Exceptions/MissingValueException.cpp (added) * src/Exceptions/MissingValueException.hpp (added) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/ValueStorage.cpp (added) * src/UIElements/ValueStorage.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * test_all.sh (modified) * tests/Tesselations/defs.in (modified) * tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat (modified) * tests/regression/Simple_configuration/3/post/test2.conf (deleted) * tests/regression/Simple_configuration/3/post/test2.in (deleted) * tests/regression/Simple_configuration/3/post/test2.xyz (deleted) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-filling.at (modified) * tests/regression/testsuite-fragmentation.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-tesselation.at (modified) Merge branch 'stable' into StructureRefactoring Conflicts: ... Sun, 25 Jul 2010 21:41:34 GMT Frederik Heber [e472eab] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (added) * src/Actions/SelectionAction/AllAtomsAction.hpp (added) * src/Actions/SelectionAction/AllMoleculesAction.cpp (added) * src/Actions/SelectionAction/AllMoleculesAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) Added new all/none selection actions for atoms and molecules. - new ... Sun, 25 Jul 2010 19:07:06 GMT Frederik Heber [533838] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (added) * src/CommandLineParser.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Merge branch 'SelectionActions' into ... Thu, 22 Jul 2010 22:02:54 GMT Frederik Heber [358577] * src/World.cpp (modified) Fixed used iterators in World::countSelected..() functions. Thu, 22 Jul 2010 20:28:45 GMT Frederik Heber [eacc3b] * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) converted BondFileAction to new createDialog(). - new functions ... Thu, 22 Jul 2010 14:09:53 GMT Frederik Heber [e0e156] * src/World.cpp (modified) * src/World.hpp (modified) Added World::isSelected() for selectedAtoms and selectedMolecules. Thu, 22 Jul 2010 14:08:22 GMT Tillmann Crueger [dc11c9] * src/World.cpp (modified) * src/World.hpp (modified) Made the id-pools in the World use range objects Tue, 20 Jul 2010 13:01:11 GMT Frederik Heber [be97a8] * src/Actions/ActionRegistry.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Box.cpp (added) * src/Box.hpp (added) * src/ConfigFileBuffer.cpp (modified) * src/ConfigFileBuffer.hpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (added) * src/Descriptors/AtomSelectionDescriptor.hpp (added) * src/Descriptors/AtomSelectionDescriptor_impl.hpp (added) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (added) * src/Descriptors/MoleculeSelectionDescriptor.hpp (added) * src/Descriptors/MoleculeSelectionDescriptor_impl.hpp (added) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/CustomException.hpp (modified) * src/Exceptions/NotInvertibleException.cpp (added) * src/Exceptions/NotInvertibleException.hpp (added) * src/Helpers/Assert.hpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Line.cpp (modified) * src/Line.hpp (modified) * src/Makefile.am (modified) * src/Matrix.cpp (added) * src/Matrix.hpp (added) * src/MatrixContent.hpp (added) * src/Parser/MpqcParser.hpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedContainer.hpp (added) * src/Patterns/ObservedContainer_impl.hpp (added) * src/Patterns/ObservedIterator.hpp (modified) * src/Patterns/Observer.hpp (modified) * src/Plane.hpp (modified) * src/Shapes/BaseShapes.cpp (added) * src/Shapes/BaseShapes.hpp (added) * src/Shapes/BaseShapes_impl.hpp (added) * src/Shapes/Shape.cpp (added) * src/Shapes/Shape.hpp (added) * src/Shapes/ShapeOps.cpp (added) * src/Shapes/ShapeOps.hpp (added) * src/Shapes/ShapeOps_impl.hpp (added) * src/Shapes/Shape_impl.hpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/UIElements/Views/StreamStringView.hpp (modified) * src/VectorContent.hpp (added) * src/VectorSet.cpp (deleted) * src/VectorSet.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/atom_trajectoryparticle.hpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/datacreator.hpp (modified) * src/defs.hpp (modified) * src/element.hpp (modified) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/errorlogger.hpp (modified) * src/graph.cpp (modified) * src/graph.hpp (modified) * src/gslvector.cpp (modified) * src/gslvector.hpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/logger.cpp (modified) * src/logger.hpp (modified) * src/memoryallocator.cpp (deleted) * src/memoryallocator.hpp (deleted) * src/memoryusageobserver.cpp (deleted) * src/memoryusageobserver.hpp (deleted) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.hpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MatrixUnittest.cpp (added) * src/unittests/MatrixUnittest.hpp (added) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (added) * src/unittests/ShapeUnittest.hpp (added) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) * src/verbose.cpp (modified) * src/verbose.hpp (modified) * test_all.sh (modified) * tests/Tesselations/defs.in (modified) * tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat (modified) * tests/regression/Domain/4/post/test.conf (modified) * tests/regression/testsuite-analysis.at (modified) Merge branch 'StructureRefactoring' into stable Conflicts: ... Fri, 16 Jul 2010 10:43:38 GMT Tillmann Crueger [3839e5] * src/World.cpp (modified) * src/World.hpp (modified) Added iterators over selected atoms and molecules Fri, 16 Jul 2010 10:34:12 GMT Tillmann Crueger [61d655e] * src/World.cpp (modified) * src/World.hpp (modified) Added methods for unselecting molecules and atoms Thu, 15 Jul 2010 15:30:55 GMT Tillmann Crueger [90c4280] * src/World.cpp (modified) * src/World.hpp (modified) Added several methods for selecting specific atoms in the World Wed, 14 Jul 2010 12:00:29 GMT Tillmann Crueger [5d880e] * src/World.cpp (modified) * src/World.hpp (modified) Allowed observed access to iterators on Molecules Wed, 14 Jul 2010 11:53:16 GMT Tillmann Crueger [e3d865] * src/Patterns/ObservedContainer.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Madet the internal iterators provided by the world unobserved Wed, 14 Jul 2010 10:36:29 GMT Tillmann Crueger [51be2a] * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Made iterator access to the molecules observed Sat, 10 Jul 2010 14:55:16 GMT Tillmann Crueger [b99bf3] * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Patterns/ObservedContainer.hpp (added) * src/Patterns/ObservedContainer_impl.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) Moved the observedContainer templates to the Pattern directory Thu, 08 Jul 2010 16:04:11 GMT Tillmann Crueger [127a8e] * src/World.cpp (modified) * src/World.hpp (modified) * src/defs.hpp (modified) Improved managing of Ids in the World - Improved algorithm for ... Thu, 08 Jul 2010 12:51:15 GMT Tillmann Crueger [fa0b18] * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Added Observed and Selectiv iterators over internal Structures of the ... Fri, 02 Jul 2010 13:44:23 GMT Frederik Heber [b9c847] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-tesselation.at (modified) New SetOutputFormatsAction introduced. Fixes: - World::setDomain() ...