# # ChangeLog for / # # Generated by Trac 1.6 # May 25, 2025, 8:12:12 PM Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [97c2550] * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomObserver.hpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (added) * src/Atom/unittests/AtomObserverUnitTest.hpp (added) * src/Atom/unittests/Makefile.am (added) * src/Atom/unittests/stubs/ObserverStub.cpp (added) * src/Atom/unittests/stubs/ObserverStub.hpp (added) * src/unittests/Makefile.am (modified) Added unit test for AtomObserver. - added position and element ... 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 13:00:05 GMT Frederik Heber [2614e2a] * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model.hpp (modified) * src/LinkedCell/unittests/stubs/LinkedCell_ModelStub.cpp (modified) LinkedCell_Model now inherits Observer. - implemented facade for ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [fe8253] * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Controller.hpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.hpp (modified) Added first reasonable heuristic, and added required implementation ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [9a5649] * src/LinkedCell/unittests/Makefile.am (modified) * src/LinkedCell/unittests/stubs/LinkedCellStub.cpp (added) * src/LinkedCell/unittests/stubs/LinkedCell_ModelStub.cpp (added) * src/LinkedCell/unittests/stubs/LinkedCell_ViewStub.cpp (added) LinkedCell_ControllerUnitTest only depends on stubs now. - i.e. we ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [fea945] * src/LinkedCell/LinkedCell_Controller.cpp (added) * src/LinkedCell/LinkedCell_Controller.hpp (added) * src/LinkedCell/Makefile.am (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (added) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.hpp (added) * src/LinkedCell/unittests/Makefile.am (modified) Added simple implementation for LinkedCell_Controller. - ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [6b91e64] * src/LinkedCell/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Added convenience library for files of new LinkedCell implementation. ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [c379f9] * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/defs.hpp (added) Extracted defines for unit tests and placed into extra header file ... Mon, 02 Jan 2012 13:00:04 GMT Frederik Heber [5344e4] * src/LinkedCell/LinkedCell.hpp (modified) * src/LinkedCell/LinkedCell_View.cpp (added) * src/LinkedCell/LinkedCell_View.hpp (added) * src/LinkedCell/types.hpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (added) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.hpp (added) * src/LinkedCell/unittests/Makefile.am (modified) Added implementation of linked cell view part with high-level ... Mon, 02 Jan 2012 13:00:04 GMT Frederik Heber [d82961] * src/LinkedCell/LinkedCell_Model.cpp (added) * src/LinkedCell/LinkedCell_Model.hpp (added) * src/LinkedCell/LinkedCell_Model_inline.hpp (added) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (added) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.hpp (added) * src/LinkedCell/unittests/Makefile.am (modified) Added implementation of linked cell model part using LinkedCell. - ... 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 15:30:07 GMT Frederik Heber [b3fb31] * src/LinkedCell/types.hpp (modified) Added MAX_LINKEDCELLNODES enum to types.hpp. Wed, 28 Dec 2011 15:30:07 GMT Frederik Heber [71d81a] * src/Box.cpp (modified) FIX: Box::Box did not initialize Conditions_t with RealSpaceMatrix ... Wed, 28 Dec 2011 15:30:07 GMT Frederik Heber [95422c] * src/LinkedCell/types.hpp (modified) FIX: LinkedCell/types.hpp now uses NDIM instead of 3. Wed, 28 Dec 2011 15:30:07 GMT Frederik Heber [794bc8] * configure.ac (modified) * src/LinkedCell/LinkedCell.cpp (added) * src/LinkedCell/LinkedCell.hpp (added) * src/LinkedCell/types.hpp (added) * src/LinkedCell/unittests/LinkedCellUnitTest.cpp (added) * src/LinkedCell/unittests/LinkedCellUnitTest.hpp (added) * src/LinkedCell/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Added LinkedCell as commodity class around LinkedList. - LinkedList ... Wed, 28 Dec 2011 15:30:06 GMT Frederik Heber [df9cbd] * src/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/linkedcell.dox (added) Added documentation on how refactored linked cell structure is ... 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 15:30:06 GMT Frederik Heber [91f592] * src/LinkedCell/Makefile.am (added) * src/LinkedCell/unittests/Makefile.am (added) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (moved) * src/LinkedCell/unittests/linkedcellUnitTest.hpp (moved) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/unittests/Makefile.am (modified) Added own convenience library for LinkedCell construct. Wed, 28 Dec 2011 15:30:06 GMT Frederik Heber [aa6c75] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) Removed some unnecessary LinkedCell.hpp include's. Wed, 28 Dec 2011 15:30:06 GMT Frederik Heber [53c7fc] * 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/SurfaceCorrelationAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/LinkedCell/IPointCloud.hpp (moved) * src/LinkedCell/PointCloudAdaptor.hpp (moved) * src/LinkedCell/linkedcell.cpp (moved) * src/LinkedCell/linkedcell.hpp (moved) * src/Makefile.am (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/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.hpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) Moved linkedcell.[ch]pp and related files to folder src/LinkedCell. ... 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 15:27:15 GMT Frederik Heber [401f90] * configure.ac (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Tesselation/BoundaryMaps.hpp (modified) * src/Tesselation/boundary.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * tests/regression/Molecules/BondFile/post/test.pdb (modified) * tests/regression/Tesselation/BigNonConvex/post/NonConvexEnvelope.dat (modified) Merge branch 'Removing_molecule_atomSet' into ... Wed, 28 Dec 2011 15:25:49 GMT Frederik Heber [adb5cda] * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/molecule.hpp (modified) Removed typedef molecule::atomSet and some commented-out, deprecated ... Wed, 28 Dec 2011 15:25:49 GMT Frederik Heber [afa9d8] * tests/regression/Molecules/BondFile/post/test.pdb (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (modified) * tests/regression/Tesselation/BigNonConvex/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) TESTFIX: Fixed regression tests Molecules/BondFile and ... Wed, 28 Dec 2011 15:25:49 GMT Frederik Heber [59fff1] * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Tesselation/BoundaryMaps.hpp (modified) * src/Tesselation/boundary.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) Replaced the molecule::const_iterator by a true const version of the ... Wed, 28 Dec 2011 15:25:48 GMT Frederik Heber [30c753] * configure.ac (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) Removed atomSet atoms in class molecule and replaced by a ... Wed, 28 Dec 2011 15:24:59 GMT Frederik Heber [f9b967] * src/Parser/TremoloParser.cpp (modified) FIX: Removed unique()'ing usedFields call in each FormatParser< ... Wed, 28 Dec 2011 15:24:59 GMT Frederik Heber [89a31d] * src/Parser/TremoloParser.cpp (modified) Enhanced verbosity of FormatParser< tremolo >::readAtomDataLine(). Wed, 28 Dec 2011 15:24:58 GMT Frederik Heber [f99714] * LinearAlgebra/configure.ac (modified) * configure.ac (modified) FIX: Finally correctly implemented all --enable-... switches in ... Wed, 28 Dec 2011 15:24:58 GMT Frederik Heber [f23303] * src/Parser/TremoloParser.cpp (modified) Small fixes to FormatParser< tremolo >::parseKnownTypes() to give ... 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 ... Wed, 28 Dec 2011 15:24:58 GMT Frederik Heber [908dc7] * src/molecule_geometry.cpp (modified) FIX: molecule::CenterInBox() made noise on std::cout, banned to LOG. Wed, 28 Dec 2011 15:24:58 GMT Frederik Heber [abae35] * 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/Menu/MenuInterface.cpp (modified) * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (added) * tests/CodeChecks/testsuite.at (modified) Added CodeCheck on presence of project disclaimer in all .cpp files. ... Wed, 28 Dec 2011 15:24:58 GMT Frederik Heber [6108fd] * src/Element/unittests/Makefile.am (modified) FIX: Added missing CodePatterns libs to Element's unit tests. Wed, 28 Dec 2011 15:24:57 GMT Frederik Heber [bab4f9] * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) FIX: Setting up and purging ActionRegistry instance in ... Wed, 28 Dec 2011 15:24:57 GMT Frederik Heber [7bace8] * LinearAlgebra/src/unittests/Makefile.am (modified) FIX: LinearAlgebra's testrunner was not linked against boost ... Wed, 28 Dec 2011 15:24:57 GMT Frederik Heber [db1a72] * LinearAlgebra/configure.ac (modified) * configure.ac (modified) FIX: Corrected check for gsl's blas requirement. Wed, 28 Dec 2011 15:24:57 GMT Frederik Heber [c015b3] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * tests/Makefile.am (modified) * tests/Python/AllActions/getPossibleOptions.sh (moved) * tests/Python/AllActions/listcmds.py (moved) * tests/Python/AllActions/missing.dat (moved) * tests/Python/AllActions/moltest.py (moved) * tests/Python/AllActions/moltest_check.py (moved) * tests/Python/AllActions/options.dat (moved) * tests/Python/AllActions/testsuite-python-allactions.at (added) * tests/Python/AllActions/testsuite-python-options_dat.at (added) * tests/Python/BoxMaker/post/out.data (moved) * tests/Python/BoxMaker/post/out.xyz (moved) * tests/Python/BoxMaker/pre/argon.data (moved) * tests/Python/BoxMaker/pre/argon.potentials (moved) * tests/Python/BoxMaker/pre/argon.tremolo (moved) * tests/Python/BoxMaker/testsuite-python-boxmaker.at (added) * tests/Python/CommandHelp/testsuite-python-commandhelp.at (moved) * tests/Python/Makefile.am (added) * tests/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (moved) * tests/Python/atlocal.in (added) * tests/Python/run.in (moved) * tests/Python/testsuite.at (added) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/testsuite-python-allactions.at (deleted) * tests/regression/Python/AllActions/testsuite-python-options_dat.at (deleted) * tests/regression/Python/BoxMaker/testsuite-python-boxmaker.at (deleted) * tests/regression/Python/testsuite-python.at (deleted) * tests/regression/testsuite.at (modified) * utils/Makefile.am (modified) Added enable-switches for Qt-based GUI and python module and scripts. ... Wed, 28 Dec 2011 15:24:56 GMT Frederik Heber [f3b8a5] * LinearAlgebra/configure.ac (modified) * configure.ac (modified) Changed enable switches in configure.ac. - with-valgrind is ... Wed, 28 Dec 2011 15:24:56 GMT Frederik Heber [e06010] * Makefile.am (modified) * m4/ax_python.m4 (modified) FIX: Added missing ax_python.m4, added support for 2.7. - added ... Wed, 28 Dec 2011 15:24:24 GMT Frederik Heber [b136f6] * src/unittests/LinkedCellUnitTest.cpp (modified) FIX: Added Assert_Do to linkedcellUnitTest. Wed, 28 Dec 2011 15:24:24 GMT Frederik Heber [68c923] * LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (modified) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Box.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/IPointCloud.hpp (modified) * src/Parser/ChangeTracker.hpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) Lots of small compiler warning fixes. Issues: - non-virtual ... Wed, 28 Dec 2011 15:24:23 GMT Frederik Heber [de29ad6] * LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/Graph/BondGraph.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) Some optimization to speed up Subgraph dissections. - Replaced ... Thu, 10 Nov 2011 16:05:43 GMT Frederik Heber [bde4a6] * configure.ac (modified) Set version to 1.2.0 - Molecuilder library is now 6:0:0. - ... Thu, 10 Nov 2011 16:05:39 GMT Frederik Heber [936a02] * data/bondtables/bondtable.dat (added) * data/databases/Hbondangle.db (moved) * data/databases/Hbonddistance.db (moved) * data/databases/elements.db (moved) * data/databases/orbitals.db (moved) * data/databases/valence.db (moved) * data/molecules/ATPase.pdb (added) * data/molecules/AntifreezeProtein.pdb (added) * data/molecules/bpti.pdb (added) * data/molecules/oxirane.pdb (added) * data/molecules/portlandite.pdb (added) * data/molecules/propene.pdb (added) * data/molecules/testosterone.pdb (added) * data/molecules/tmv_periodic_segment.pdb (added) * data/molecules/tmv_periodic_tube.pdb (added) * data/molecules/water.pdb (added) * src/Makefile.am (modified) * src/documentation/data.dox (added) * src/documentation/mainpage.dox (modified) Creating data dir for bondtables, databases, and molecules. - Moved ... Thu, 10 Nov 2011 11:23:54 GMT Frederik Heber [1a041f] * src/documentation/debug.dox (added) DOCU: added documentation on how to debug the code. Thu, 10 Nov 2011 11:23:49 GMT Frederik Heber [04e1fb] * configure.ac (modified) * utils/Makefile.am (modified) * utils/python_wrapper.in (added) Added rules to utils/Makefile.am such that python script can be ... Thu, 10 Nov 2011 10:21:23 GMT Frederik Heber [938ffd] * Makefile.am (modified) * configure.ac (modified) * utils/Makefile.am (added) Added Makefile to utils to install python scripts. Thu, 10 Nov 2011 10:21:23 GMT Frederik Heber [0d571d7] * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) DISTCHECKFIX: Forgot to set write permissions for new ec.data test ... Thu, 10 Nov 2011 10:21:23 GMT Frederik Heber [a55be1] * tests/regression/Makefile.am (modified) DISTCHECKFIX: testsuite does not depends on run scripts. - ... Tue, 08 Nov 2011 11:45:15 GMT Frederik Heber [12facf] * src/Actions/hello.cpp (deleted) * src/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/Pythontest/testsuite-python-pythontest.at (deleted) * tests/regression/Python/testsuite-python.at (modified) Removed now obsolete Pythontest including regression test. - as ... Tue, 08 Nov 2011 11:45:15 GMT Frederik Heber [dd0f1b] * tests/CodeChecks/testsuite-config_h.at (modified) DISTCHECKFIX: Added AllActionPython.hpp and AllActionHeaders.hpp to ... Tue, 08 Nov 2011 11:45:15 GMT Frederik Heber [48d3c0] * src/Actions/Makefile.am (modified) * src/Makefile.am (modified) DISTCHECKFIX: Added some missing header files in src/Actions. - ... Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [4269ca] * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) FIX: Some Qt includes were not style-consistent. Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [5dfeeb] * LinearAlgebra/doc/Makefile.am (modified) * doc/Makefile.am (modified) DISTCHECKFIX: Added forgotten Doxyfile to EXTRA_DIST. Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [24da48] * src/Actions/Makefile.am (modified) DISTCHECKFIX: Added missing ActionTraits.hpp to src/Actions/Makefile.am. Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [c1ab1f] * src/Actions/Makefile.am (modified) DISTCHECKFIX: Added all Reaction...hpp to src/Actions/Makefile.am. Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [ed3000] * Makefile.am (modified) DISTCHECKFIX: Removed bnv_have_qt.m4 from EXTRA_DIST. Mon, 07 Nov 2011 18:34:05 GMT Frederik Heber [e85bf2] * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-globallistofactions_hpp.at (added) * tests/CodeChecks/testsuite.at (modified) Added code check test whether every .def's Action is listed in ... Mon, 07 Nov 2011 18:33:50 GMT Frederik Heber [5ab796] * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/moltest_check.py (added) * tests/regression/Python/AllActions/options.dat (modified) * tests/regression/Python/AllActions/testsuite-python-options_dat.at (added) * tests/regression/Python/testsuite-python.at (modified) Added regression test on whether all options in the python module are ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [f894fe] * utils/boxmaker.py.in (modified) Changed GetSourceMolareMass() and GetSourceBBabs() of boxmaker.py. ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [f89b45] * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (added) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.def (added) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/pyMoleCuilder.cpp (modified) * tests/regression/Analysis/CalculateBoundingBox/testsuite-analysis-calculate-bounding-box.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/listcmds.py (added) * tests/regression/Python/AllActions/moltest.py (modified) * tests/regression/Python/AllActions/options.dat (modified) * tests/regression/Python/AllActions/testsuite-python-allactions.at (modified) Added Reaction CalculateBoundingBoxAction. - calculate bounding box ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [55f299] * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (added) * src/Actions/AnalysisAction/CalculateMolarMassAction.def (added) * src/Actions/AnalysisAction/CalculateMolarMassAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Analysis/CalculateMolarMass/pre/argon.xyz (added) * tests/regression/Analysis/CalculateMolarMass/pre/water.xyz (added) * tests/regression/Analysis/CalculateMolarMass/testsuite-analysis-calculate-molar-mass.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/options.dat (modified) Added Reaction CalculateMolarMassAction. - calculate molar mass ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [6c61a9] * tests/regression/Makefile.am (modified) * tests/regression/Python/BoxMaker/post/out.data (added) * tests/regression/Python/BoxMaker/post/out.xyz (added) * tests/regression/Python/BoxMaker/pre/argon.data (added) * tests/regression/Python/BoxMaker/pre/argon.potentials (added) * tests/regression/Python/BoxMaker/pre/argon.tremolo (added) * tests/regression/Python/BoxMaker/testsuite-python-boxmaker.at (added) * tests/regression/Python/testsuite-python.at (modified) Added regression test for boxmaker.py. Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [2aa9ef] * utils/boxmaker.py.in (modified) UpdateSource function of boxmaker.py is not an external call to ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [dfef3f] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/cleanUp.cpp (modified) FIX: empty states Action::success and ::failure are now managed by ... Mon, 07 Nov 2011 16:13:17 GMT Frederik Heber [d628da] * src/Actions/Action_impl_python.hpp (modified) Added docstring also to python exported functions without any ... Mon, 07 Nov 2011 16:13:17 GMT Frederik Heber [567357] * src/Actions/pyMoleCuilder.cpp (modified) * src/cleanUp.cpp (modified) * src/cleanUp.hpp (modified) FIX: cleanUp() replaced by module_reinit() and .._exit() in ... Mon, 07 Nov 2011 16:13:01 GMT Frederik Heber [b5d38d] * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/builder_init.hpp (modified) * src/cleanUp.cpp (modified) * src/cleanUp.hpp (modified) Moved dumpMemory() and saveAll() from module builder_init to cleanUp. Mon, 07 Nov 2011 16:12:25 GMT Frederik Heber [bcfb77] * configure.ac (modified) * utils/boxmaker.py.in (moved) Added correct shebang to boxmaker.py. - also configure fills in ... Mon, 07 Nov 2011 16:12:25 GMT Frederik Heber [239cc5] * utils/boxmaker.py (modified) Didn't save the file -.-" Mon, 07 Nov 2011 16:12:25 GMT Frederik Heber [bfbb62] * utils/boxmaker.py (modified) Final version 1.0 - Added shebang line - Added short file ... Mon, 07 Nov 2011 16:12:25 GMT Frederik Heber [c0c85f] * utils/boxmaker.py (modified) Restructured Code - temp_source.xyz is created only once - boolean ... Mon, 07 Nov 2011 16:12:25 GMT Frederik Heber [b82ede] * utils/HOWTO-boxmaker (added) Very basic documentation on how to use boxmaker Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [0ad49c] * utils/boxmaker.py (modified) Update: Automatic mass calculation Also: - Shortcut for every option Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [39cbae] * utils/boxmaker.py (modified) Update: Unit handling - temp might have a dimension now - Leading ... Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [751d7f1] * utils/boxmaker.py (modified) Update: Shortcuts for common Parameters Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [32bc47] * utils/boxmaker.py (modified) Update: autorotate Not tested yet, but it seems like it does ... Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [0c83d8] * utils/boxmaker.py (modified) Less ugly advanced version - Class (struct) based global options - ... Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [5735ba] * utils/boxmaker.py (added) Ugly base version of boxmaker.py TODO: - stability fixes - ... Mon, 07 Nov 2011 12:24:07 GMT Frederik Heber [54088a] * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.def (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.hpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Analysis/CalculateCellVolume/testsuite-analysis-calculate-cell-volume.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (added) * tests/regression/Python/testsuite-python.at (modified) Added first Reaction named CalculateCellVolumeAction. - this sets ... Mon, 07 Nov 2011 12:24:06 GMT Frederik Heber [6aa485] * src/Actions/Action_impl_python.hpp (modified) * src/Actions/Action_impl_undef.hpp (modified) Actions exported to Python may contain a returntype. - returntype ... Mon, 07 Nov 2011 12:24:06 GMT Frederik Heber [1540859] * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (added) * src/Actions/AnalysisAction/CalculateCellVolumeAction.def (added) * src/Actions/AnalysisAction/CalculateCellVolumeAction.hpp (added) * src/Actions/Reaction.hpp (added) * src/Actions/Reaction_impl.hpp (added) * src/Actions/Reaction_impl_header.hpp (added) * src/Actions/Reaction_impl_pre.hpp (added) Added Reaction as Action with a return value. - this is derived ... Mon, 07 Nov 2011 12:24:05 GMT Frederik Heber [874597] * src/Actions/Action_impl_python.hpp (modified) FIX: some defines were forgotten to be undefined in ... Mon, 07 Nov 2011 12:24:05 GMT Frederik Heber [9d613f] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * tests/regression/Domain/RepeatBox/post/ec.data (added) * tests/regression/Domain/RepeatBox/pre/ec.data (added) * tests/regression/Domain/RepeatBox/pre/ec.potentials (added) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) FIX: RepeatBoxAction did not use CopyMolecule() but copied by hand. ... Mon, 07 Nov 2011 12:24:05 GMT Frederik Heber [f27fa7] * tests/regression/Python/AllActions/testsuite-python-allactions.at (modified) TESTFIX: Added test whether calling not present command truely fails. ... Mon, 07 Nov 2011 12:24:04 GMT Frederik Heber [cbb32d] * tests/regression/Python/AllActions/moltest.py (modified) * tests/regression/Python/AllActions/testsuite-python-allactions.at (modified) Small cosmetical changes to moltest.py. - We now use Popen to call ... Mon, 07 Nov 2011 12:24:03 GMT Frederik Heber [3493da] * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/getPossibleOptions.sh (added) * tests/regression/Python/AllActions/missing.dat (added) * tests/regression/Python/AllActions/options.dat (added) * tests/regression/Python/AllActions/testsuite-python-allactions.at (added) * tests/regression/Python/testsuite-python.at (modified) Gathered default values for each action and wrote regression test ... Mon, 07 Nov 2011 12:24:03 GMT Frederik Heber [6ca7b9] * tests/regression/Python/AllActions/moltest.py (added) Wrote python script to gather all functions in a pyMoleCuilder module ... 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 ... Mon, 07 Nov 2011 12:24:00 GMT Frederik Heber [c20b35] * src/Actions/Makefile.am (modified) Added commented-out stuff for a extra libMolecuilderActionPython.la. ... Mon, 07 Nov 2011 12:23:52 GMT Frederik Heber [949953] * src/Actions/Action_impl_python.hpp (added) * src/Actions/Action_impl_undef.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Makefile.am (modified) * src/builder_init.cpp (modified) * src/builder_init.hpp (modified) * src/cleanUp.cpp (added) * src/cleanUp.hpp (added) pyMoleCuilder now has full functionality. - For each header file ... Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [071243] * src/Actions/hello.cpp (modified) * src/Makefile.am (modified) Enhanced tiny example to resemble action structure. - Pythontest ... Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [88ba1f] * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/ValueStorage.hpp (modified) Added Action's COMMAND_stringargs() function call. - also added ... Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [ddde10] * src/Actions/Action_impl_pre.hpp (modified) FIX: In Action's COMMAND() we don't need a params instance. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [6a2dae] * src/Actions/Action_impl_header.hpp (modified) Corrected indenting in ActionTrait<>s cstor. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [05736a] * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) Simplified Action's COMMAND() definition a bit. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [d41313] * src/Actions/ActionTraits.cpp (modified) * src/Actions/ActionTraits.hpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/OptionTrait.hpp (modified) Added output operators for both ActionTraits and OptionTrait. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [dad802] * src/Actions/ActionTraits.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/OptionTrait.hpp (modified) Modified ActionTraits' and OptionTrait's cstor and dstor slightly. ... Mon, 07 Nov 2011 10:46:25 GMT Frederik Heber [83e90c] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/GlobalListOfActions.hpp (added) * src/Actions/Makefile.am (modified) New function ActionRegistry::fillRegistry() fills instead of static ...