# # ChangeLog for / # # Generated by Trac 1.6 # May 28, 2025, 7:03:59 AM Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [d33bb8] * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) Added Tesselation::IsPointBelowSurroundingPolygon(). - ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [f1ae15] * src/Tesselation/tesselation.cpp (modified) FIX: Filling of non-convex polygon with only minimal angles did not ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [c2c786] * src/Tesselation/tesselation.cpp (modified) FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [6d5280] * LinearAlgebra/src/LinearAlgebra/Line.cpp (modified) FIX: Reduced verbosity noise from Line::getIntersection(). - ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [b8d215] * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) Changed some verbosities in Tesselation code. - modifications in ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [dfe054] * src/Tesselation/tesselationhelpers.cpp (modified) DOCUFIX: Corrected formula for general tetrahedron in docu. - also ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [75d42a] * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [c2f306] * src/Tesselation/tesselation.cpp (modified) FIX: RemoveTesselationLine() needs to erase line from OpenLines if ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [bb86bd] * src/Tesselation/tesselation.cpp (modified) FIX: AddTesselationLine() would only work in initial tesselation ... Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [613790] * src/Tesselation/tesselation.cpp (modified) FIX: Changed all performCriticalExit() into ASSERT() in tesselation. Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [cead3f] * doc/userguide/userguide.xml (modified) * utils/developer/raster3d/header.r3d (added) FIX: Raster3D needs header.r3d, which had been missing so far. Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [cfb9c5] * src/Actions/ActionQueue.cpp (modified) FIX: Setting ActionQueue::_lastchangedaction without heeding whether ... Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [1b6cec] * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when ... Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [7d320c] * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) MEMFIX: Static coordinator instances of specificv potentials need to ... Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [4da4de] * configure.ac (modified) * m4/boost.m4 (modified) FIX: Added Boost::MultiIndexContainer check for MemDebug. - this ... Sun, 19 Oct 2014 17:12:37 GMT Frederik Heber [3b1798] * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.hpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FIX: QtHomologyList's plot widget was too high (and fixed). - also ... Sun, 19 Oct 2014 17:12:11 GMT Frederik Heber [5c8807] * doc/userguide/userguide.xml (modified) * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.def (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.hpp (added) * src/Actions/AtomAction/TranslateToOriginAction.cpp (added) * src/Actions/AtomAction/TranslateToOriginAction.def (added) * src/Actions/AtomAction/TranslateToOriginAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted-weighted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/pre/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9 ... Sun, 19 Oct 2014 17:10:16 GMT Frederik Heber [b119a0] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/TesselPoint.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/World.cpp (modified) * src/molecule_geometry.cpp (modified) Merge branch 'DynamicMolecules' into Candidate_v1.4.9 Sun, 19 Oct 2014 17:09:30 GMT Frederik Heber [9e1bfb] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.hpp (added) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (added) * src/Actions/PotentialAction/ParsePotentialsAction.def (added) * src/Actions/PotentialAction/ParsePotentialsAction.hpp (added) * src/Actions/PotentialAction/SavePotentialsAction.cpp (added) * src/Actions/PotentialAction/SavePotentialsAction.def (added) * src/Actions/PotentialAction/SavePotentialsAction.hpp (added) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialTrainer.cpp (added) * src/Potentials/PotentialTrainer.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9 Sun, 19 Oct 2014 17:08:51 GMT Frederik Heber [0ea063] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Actions/PotentialAction/SavePotentialsAction.cpp (added) * src/Actions/PotentialAction/SavePotentialsAction.def (added) * src/Actions/PotentialAction/SavePotentialsAction.hpp (added) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/PotentialTrainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Extracted SavePotentialsAction. - PotentialTrainer::StorePotentials ... Sun, 19 Oct 2014 17:08:50 GMT Frederik Heber [f1eabd] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (added) * src/Actions/PotentialAction/ParsePotentialsAction.def (added) * src/Actions/PotentialAction/ParsePotentialsAction.hpp (added) * tests/Python/AllActions/options.dat (modified) Extracted ParsePotentialsAction from FitCompoundPotentialAction. Sun, 19 Oct 2014 17:08:36 GMT Frederik Heber [98d166] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.hpp (added) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialTrainer.cpp (added) * src/Potentials/PotentialTrainer.hpp (added) Split FitPotentialAction into two actions. - FitPotentialAction ... Fri, 19 Sep 2014 07:10:04 GMT Frederik Heber [2ed3bf] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/MirrorAction.cpp (added) * src/Actions/AtomAction/MirrorAction.def (added) * src/Actions/AtomAction/MirrorAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Atoms/Mirror/post/test-mirrored.xyz (added) * tests/regression/Atoms/Mirror/post/test.xyz (added) * tests/regression/Atoms/Mirror/pre/test.xyz (added) * tests/regression/Atoms/Mirror/testsuite-atoms-mirror.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'MirrorAtoms' into Candidate_v1.4.9 Fri, 19 Sep 2014 07:09:53 GMT Frederik Heber [7acbfc] * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) Merge branch 'ActionFixes' into Candidate_v1.4.9 Thu, 18 Sep 2014 23:32:23 GMT Frederik Heber [bbf6dc] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/MirrorAction.cpp (added) * src/Actions/AtomAction/MirrorAction.def (added) * src/Actions/AtomAction/MirrorAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Atoms/Mirror/post/test-mirrored.xyz (added) * tests/regression/Atoms/Mirror/post/test.xyz (added) * tests/regression/Atoms/Mirror/pre/test.xyz (added) * tests/regression/Atoms/Mirror/testsuite-atoms-mirror.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added AtomMirrorAction. - also added regression tests. 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 ... Thu, 18 Sep 2014 18:24:51 GMT Frederik Heber [8cc22f] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/TesselPoint.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/molecule_geometry.cpp (modified) Changed how trajectories are stored, not as vecor but as map. - ... Thu, 18 Sep 2014 17:23:14 GMT Frederik Heber [c7fe90] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/TranslateToOriginAction.cpp (added) * src/Actions/AtomAction/TranslateToOriginAction.def (added) * src/Actions/AtomAction/TranslateToOriginAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted-weighted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/pre/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added TranslateToOriginAction. - also added regression test. Thu, 18 Sep 2014 17:19:38 GMT Frederik Heber [f4b626a] * doc/userguide/userguide.xml (modified) * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.def (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) Added AverageMoleculeForceAction for measuring average force acting ... Wed, 17 Sep 2014 22:30:50 GMT Frederik Heber [7a7b34] * src/Atom/atom.cpp (modified) FIX: atom's copy cstor does not need to copy positions, ... again. Wed, 17 Sep 2014 22:30:29 GMT Frederik Heber [054d47] * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) FIX: (Not)AtomByIdAction would fail with assert if not atoms are ... Wed, 17 Sep 2014 21:30:38 GMT Frederik Heber [9bce96] * doc/userguide/userguide.xml (modified) DOCU: Fixed all missing links in userguide. - each section now has ... Wed, 17 Sep 2014 21:29:44 GMT Frederik Heber [f73e06] * doc/userguide/userguide.xml (modified) * tests/CodeChecks/testsuite-action_present_in_userguide.at (modified) DOCU: Added all missing Actions to userguide. - removed XFAIL from ... Wed, 17 Sep 2014 19:44:31 GMT Frederik Heber [c62e27] * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-action_present_in_userguide.at (added) * tests/CodeChecks/testsuite.at (modified) Added CodeChecks test that every action appears in the userguide. - ... Wed, 17 Sep 2014 19:44:31 GMT Frederik Heber [2a6d8c] * src/Fragmentation/Exporters/SaturationDistanceMaximizer.hpp (modified) DOCUFIX: Doyxygen formula was broken in SaturationDistanceMaximizer. Wed, 17 Sep 2014 19:44:31 GMT Frederik Heber [ced7f0] * src/Actions/CommandAction/VersionAction.cpp (modified) VersionAction also prints to log, not only to status. Wed, 17 Sep 2014 17:03:30 GMT Frederik Heber [7f6a2f] * configure.ac (modified) Set version to 1.4.8. - MoleCuilder library is now 14:1:0. - ... Tue, 16 Sep 2014 06:21:20 GMT Frederik Heber [06b5df] * src/Actions/ActionQueue.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) FIX: CommandLineParser causes idling thread when parsing goes wrong. ... Mon, 15 Sep 2014 21:46:01 GMT Frederik Heber [7e1a88] * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) MEMFIX: Thrown ParserException causes mem leak in LoadAction - also ... 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, 15 Sep 2014 14:28:50 GMT Frederik Heber [b73545] * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (modified) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * 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/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Potentials/PartialNucleiChargeFitter.cpp (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/PotentialRegistry.hpp (modified) * src/Potentials/SerializablePotential.hpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * src/cleanUp.cpp (modified) * src/documentation/tests/tests.dox (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified) Merge branch 'MemFixes' into stable Conflicts: ... Mon, 15 Sep 2014 14:22:29 GMT Frederik Heber [55736b] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.def (modified) * src/Actions/FillAction/FillVolumeAction.cpp (added) * src/Actions/FillAction/FillVolumeAction.def (added) * src/Actions/FillAction/FillVolumeAction.hpp (added) * src/Actions/FillAction/SuspendInMoleculeAction.cpp (added) * src/Actions/FillAction/SuspendInMoleculeAction.def (added) * src/Actions/FillAction/SuspendInMoleculeAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (deleted) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (deleted) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.hpp (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (deleted) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (deleted) * src/Actions/MoleculeAction/SuspendInWaterAction.def (deleted) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (deleted) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Filling/Inserter/SurfaceRandomInserter.cpp (added) * src/Filling/Inserter/SurfaceRandomInserter.hpp (added) * src/Filling/Makefile.am (modified) * src/Filling/Mesh/MeshAdaptor.hpp (modified) * src/Filling/Preparators/BaseFillerPreparator.cpp (added) * src/Filling/Preparators/BaseFillerPreparator.hpp (added) * src/Filling/Preparators/BoxFillerPreparator.cpp (added) * src/Filling/Preparators/BoxFillerPreparator.hpp (added) * src/Filling/Preparators/ShapeSurfaceFillerPreparator.cpp (added) * src/Filling/Preparators/ShapeSurfaceFillerPreparator.hpp (added) * src/Filling/Preparators/ShapeVolumeFillerPreparator.cpp (added) * src/Filling/Preparators/ShapeVolumeFillerPreparator.hpp (added) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/boundary.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) * src/documentation/constructs/filling.dox (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/moleculelist.cpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Analysis/DipoleCorrelation-Empty/testsuite-analysis-dipole-correlation-empty.at (modified) * tests/regression/Filling/FillSurface/post/tensid-undo.data (moved) * tests/regression/Filling/FillSurface/post/tensid.data (moved) * tests/regression/Filling/FillSurface/post/water_cube.xyz (added) * tests/regression/Filling/FillSurface/post/water_cylinder.xyz (added) * tests/regression/Filling/FillSurface/post/water_sphere.xyz (added) * tests/regression/Filling/FillSurface/post/water_undo.xyz (added) * tests/regression/Filling/FillSurface/pre/tensid.data (moved) * tests/regression/Filling/FillSurface/pre/tensid.potentials (moved) * tests/regression/Filling/FillSurface/pre/water.xyz (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-cube.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-cylinder.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-everywhere.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-micelle.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-nowhere.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-sphere.at (added) * tests/regression/Filling/FillVoidWithMolecule/post/propane.xyz (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/test.conf (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/test.xyz (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.potentials (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/test.conf (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/water.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (deleted) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (deleted) * tests/regression/Filling/FillVolume/post/water_cylinder.xyz (added) * tests/regression/Filling/FillVolume/post/water_undo.xyz (added) * tests/regression/Filling/FillVolume/pre/water.xyz (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-cube.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-cylinder.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-everywhere.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-nowhere.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-sphere.at (added) * tests/regression/Filling/FillWithMolecule/post/propane.xyz (deleted) * tests/regression/Filling/FillWithMolecule/post/test.conf (deleted) * tests/regression/Filling/FillWithMolecule/pre/test.conf (deleted) * tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (deleted) * tests/regression/Filling/RegularGrid/post/solved_double_sles.data (modified) * tests/regression/Filling/RegularGrid/post/solved_single_sles.data (modified) * tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid-with-surface.at (moved) * tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid.at (moved) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (deleted) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at (modified) Merge branch 'Cleanup_old_code' into stable Mon, 15 Sep 2014 11:52:56 GMT Frederik Heber [5524ae9] * src/documentation/tests/tests.dox (modified) DOCU: Update on test policy with respect to now working valgrind tests. Mon, 15 Sep 2014 11:52:56 GMT Frederik Heber [8d4eaa] * src/Actions/CommandAction/ElementDbAction.cpp (modified) MEMFIX: ElementDbAction would loose memory when parsing command-line ... Mon, 15 Sep 2014 11:52:39 GMT Frederik Heber [11d433] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) MEMFIX: ActionQueue was not stopped() when argument parsing failed. ... Sun, 14 Sep 2014 16:22:48 GMT Frederik Heber [8859b5] * src/Actions/ActionQueue.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.hpp (modified) * src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp (added) Added QtFavoriteActions to QtToolBar to spawn placeholder icons of ... Fri, 12 Sep 2014 08:00:16 GMT Frederik Heber [29b52b] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) Made ActionQueue observable. - has channel ActionQueued. - this is ... Fri, 12 Sep 2014 07:57:18 GMT Frederik Heber [9bdcc9] * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FIX: QtHomologyList lacked use of FunctionModel::filter_t to split up ... Thu, 11 Sep 2014 07:30:53 GMT Frederik Heber [0ac3e3] * src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FIX: QSeisPlotPage takes up all remaining space in QtHomologyList. ... Thu, 11 Sep 2014 07:20:26 GMT Frederik Heber [f8bccc] * 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/Value.hpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) FIX: QtQueryList now works with pointers, FileQtQuery gives name of ... Wed, 10 Sep 2014 19:10:27 GMT Frederik Heber [5a9f4c] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) Removed lots of commented-out code from GLWorldView. Wed, 10 Sep 2014 19:10:26 GMT Frederik Heber [2b7375] * src/Tesselation/boundary.cpp (modified) * src/Tesselation/boundary.hpp (modified) Removed PrepareClustersInWater(). Wed, 10 Sep 2014 19:10:26 GMT Frederik Heber [aa55d0] * src/Actions/FillAction/SuspendInMoleculeAction.cpp (added) * src/Actions/FillAction/SuspendInMoleculeAction.def (added) * src/Actions/FillAction/SuspendInMoleculeAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (deleted) * src/Actions/MoleculeAction/SuspendInWaterAction.def (deleted) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (deleted) * tests/Python/AllActions/options.dat (modified) * tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at (modified) Moved and renamed SuspendInWaterAction from Molecule.. to ... Wed, 10 Sep 2014 19:10:26 GMT Frederik Heber [2528d8] * src/Tesselation/boundary.cpp (modified) * src/Tesselation/boundary.hpp (modified) Removed FillBoxWithMolecule(), FillVoidWithMolecule, and helper ... Wed, 10 Sep 2014 19:10:26 GMT Frederik Heber [16c7dd] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (deleted) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (deleted) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.hpp (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (deleted) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Analysis/DipoleCorrelation-Empty/testsuite-analysis-dipole-correlation-empty.at (modified) * tests/regression/Filling/FillVoidWithMolecule/post/propane.xyz (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/test.conf (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/test.xyz (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.potentials (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/test.conf (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/water.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (deleted) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (deleted) * tests/regression/Filling/FillWithMolecule/post/propane.xyz (deleted) * tests/regression/Filling/FillWithMolecule/post/test.conf (deleted) * tests/regression/Filling/FillWithMolecule/pre/test.conf (deleted) * tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (deleted) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) Removed FillVoidWithMolecule and FillWithMolecule actions. - these ... Wed, 10 Sep 2014 19:00:56 GMT Frederik Heber [df9f20] * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.def (modified) * src/Filling/Inserter/SurfaceRandomInserter.cpp (added) * src/Filling/Inserter/SurfaceRandomInserter.hpp (added) * src/Filling/Makefile.am (modified) * src/Filling/Preparators/ShapeSurfaceFillerPreparator.cpp (added) * src/Filling/Preparators/ShapeSurfaceFillerPreparator.hpp (added) * tests/regression/Filling/FillSurface/post/tensid-undo.data (moved) * tests/regression/Filling/FillSurface/post/tensid.data (moved) * tests/regression/Filling/FillSurface/post/water_cube.xyz (added) * tests/regression/Filling/FillSurface/post/water_cylinder.xyz (added) * tests/regression/Filling/FillSurface/post/water_sphere.xyz (added) * tests/regression/Filling/FillSurface/post/water_undo.xyz (added) * tests/regression/Filling/FillSurface/pre/tensid.data (moved) * tests/regression/Filling/FillSurface/pre/tensid.potentials (moved) * tests/regression/Filling/FillSurface/pre/water.xyz (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-cube.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-cylinder.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-everywhere.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-micelle.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-nowhere.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-sphere.at (added) * tests/regression/Filling/SphericalSurface/testsuite-fill-spherical-surface.at (deleted) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) Refactored FillSurfaceAction to also use FillerPreparators. - added ... Wed, 10 Sep 2014 18:59:16 GMT Frederik Heber [6801f4] * src/Actions/FillAction/FillVolumeAction.cpp (added) * src/Actions/FillAction/FillVolumeAction.def (added) * src/Actions/FillAction/FillVolumeAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Filling/Makefile.am (modified) * src/Filling/Mesh/MeshAdaptor.hpp (modified) * src/Filling/Preparators/ShapeVolumeFillerPreparator.cpp (added) * src/Filling/Preparators/ShapeVolumeFillerPreparator.hpp (added) * tests/regression/Filling/FillVolume/post/water_cylinder.xyz (added) * tests/regression/Filling/FillVolume/post/water_undo.xyz (added) * tests/regression/Filling/FillVolume/pre/water.xyz (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-cube.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-cylinder.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-everywhere.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-nowhere.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-sphere.at (added) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) Added FillVolumeAction for filling a Shape's volume. - added ... Wed, 10 Sep 2014 07:55:15 GMT Frederik Heber [36f45c] * tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid-with-surface.at (moved) * tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid.at (moved) * tests/regression/Filling/SphericalSurface/testsuite-fill-spherical-surface.at (moved) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) FIX: Renamed testsuite-molecules-fill-.. -> testsuite-fill-.. in ... Wed, 10 Sep 2014 07:55:12 GMT Frederik Heber [cae614] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Filling/Makefile.am (modified) * src/Filling/Preparators/BaseFillerPreparator.cpp (added) * src/Filling/Preparators/BaseFillerPreparator.hpp (added) * src/Filling/Preparators/BoxFillerPreparator.cpp (added) * src/Filling/Preparators/BoxFillerPreparator.hpp (added) * src/documentation/constructs/filling.dox (modified) Extracted filler preparing functionality from FillRegularGridAction. ... Wed, 10 Sep 2014 07:45:55 GMT Frederik Heber [a090e3] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * tests/regression/Filling/RegularGrid/post/solved_double_sles.data (modified) * tests/regression/Filling/RegularGrid/post/solved_single_sles.data (modified) FIX: FillRegularGridAction requires filler molecule at origin. - ... Tue, 09 Sep 2014 22:27:26 GMT Frederik Heber [0741f4d] * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) FIX: new item is just to some default values in QtMoleculeList, ... Tue, 09 Sep 2014 22:27:26 GMT Frederik Heber [86c013] * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/Qt4/QMenu_tooltip.hpp (added) * src/UIElements/Menu/Qt4/QtMenu.hpp (modified) * src/UIElements/Views/Qt4/QtToolBar.cpp (modified) QMenu extended for tooltips, but not working yet. - somehow no ... Tue, 09 Sep 2014 22:27:26 GMT Frederik Heber [163110] * src/Actions/Action.cpp (modified) * src/Actions/unittests/stubs/DummyUI.hpp (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/Menu/Menu.cpp (modified) * src/UIElements/Menu/Menu.hpp (modified) * src/UIElements/Menu/Qt4/QtMenu.hpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (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/FilesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (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/QtToolBar.cpp (modified) In QTUI Dialog window now has a meaningful title. - Dialog cstor ... Tue, 09 Sep 2014 22:27:26 GMT Frederik Heber [152e5c] * src/Actions/Action_impl_pre.hpp (modified) FIX: Querys now have own description as tooltip, not Action's. Tue, 09 Sep 2014 22:19:15 GMT Frederik Heber [0fe135] * src/UIElements/Dialog.cpp (modified) * tests/regression/Options/Warranty/testsuite-options-warranty.at (modified) In QTUI empty dialogs no longer have to be confirmed. - this was ... Tue, 09 Sep 2014 22:09:57 GMT Frederik Heber [95cfac] * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/CommandAction/ElementDbAction.def (modified) * src/Actions/CommandAction/LoadSessionAction.def (modified) * src/Actions/CommandAction/StoreSessionAction.def (modified) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.def (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) Added FileSuffixValidator to all Actions where missing but ... Tue, 09 Sep 2014 19:42:32 GMT Frederik Heber [833b15] * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/moleculelist.cpp (modified) FIX: Changes to function signatures in molecule_geometry. - no more ... Tue, 09 Sep 2014 18:26:21 GMT Frederik Heber [2d701e] * src/molecule_geometry.cpp (modified) FIX: molecule::Translate() used in CenterInBox(), CenterEdge(), ... Mon, 08 Sep 2014 21:37:32 GMT Frederik Heber [dae158] * src/Parameters/Makefile.am (modified) * 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/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) FileQtQuery retrieves valid suffixes from validators. - added ... Mon, 08 Sep 2014 21:36:29 GMT Frederik Heber [ce4126] * 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/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) FIX: Added update mechanism to GLWorldScene when WorldTime changes. ... Mon, 08 Sep 2014 21:36:29 GMT Frederik Heber [8592c9] * src/Tesselation/tesselation.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) FIX: GLMoleculeObject_shape might use empty point list for ... Mon, 08 Sep 2014 21:36:29 GMT Frederik Heber [42ffb5] * src/Graph/BondGraph.hpp (modified) FIX: BondGraph::cleanAdjacencyList() killed bonds of time steps ... Mon, 08 Sep 2014 21:36:29 GMT Frederik Heber [dc798d] * src/Actions/GraphAction/CorrectBondDegreeAction.cpp (modified) FIX: Removed some misleading output of CorrectBondDegreeAction. 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. ... Mon, 08 Sep 2014 21:36:29 GMT Frederik Heber [553c54] * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.def (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.def (modified) * tests/Python/AllActions/options.dat (modified) Added option keep-bondgraph to MolecularDynamicsAction and ... Mon, 01 Sep 2014 15:22:20 GMT Frederik Heber [40bb9e] * src/molecule_geometry.cpp (modified) FIX: molecule::Translate() uses AtomSet directly. Thu, 28 Aug 2014 08:53:42 GMT Frederik Heber [052c10] * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/tesselation.cpp (modified) MEMFIX: Tesselation::operator() did not free linkedlist. Thu, 28 Aug 2014 08:53:42 GMT Frederik Heber [7ee21d] * 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/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) MEMFIX: Many analysis_correlation function allocated return map ... Thu, 28 Aug 2014 08:53:42 GMT Frederik Heber [6b3e5e] * src/Potentials/PartialNucleiChargeFitter.cpp (modified) MEMFIX: PartialNucleiChargeFitter lost memory. - operator() and ... Thu, 28 Aug 2014 08:53:42 GMT Frederik Heber [96c7d2] * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/PotentialRegistry.hpp (modified) * src/Potentials/SerializablePotential.hpp (modified) * src/cleanUp.cpp (modified) MEMFIX: PotentialRegistry's dstor forgot cleanup(). - also we purge ... Thu, 28 Aug 2014 08:53:42 GMT Frederik Heber [185e6f] * src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp (modified) MEMFIX: SaturationDistanceMaximizer::operator() did not delete Advocate. Thu, 28 Aug 2014 08:53:32 GMT Frederik Heber [b0b2d2] * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (modified) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) MEMFIX: RealSpaceMatrix's and MatrixContent's serialization leaked ... Thu, 28 Aug 2014 08:53:32 GMT Frederik Heber [7f1a1a] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) MEMFIX: ActionQueue would loose memory when action failed. - we ... Thu, 28 Aug 2014 08:53:32 GMT Frederik Heber [3d70e3] * src/Parser/PdbParser.cpp (modified) MEMFIX: Mismatched delete in PdbParser::Save(). 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, 28 Aug 2014 08:53:32 GMT Frederik Heber [62c378a] * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified) FIX: Made checks in random number engine and distribution regression ... Thu, 28 Aug 2014 08:53:32 GMT Frederik Heber [520029] * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) FIX: regression test add atoms outside boundary had given boundary ... Thu, 28 Aug 2014 08:53:32 GMT Frederik Heber [25aa5a] * src/Box.cpp (modified) * src/Box.hpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) FIX: Box::setM() did not use const ref as argument. Thu, 28 Aug 2014 08:53:32 GMT Frederik Heber [707a2b] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) FIX: FitPotentialAction's getFirstGraphwithSpecifiedElements() access ... Thu, 28 Aug 2014 08:53:32 GMT Frederik Heber [8946a0] * src/Actions/Process.cpp (modified) FIX: Process' dstor would always stop() even if not start()ed. - ... Thu, 21 Aug 2014 06:59:43 GMT Frederik Heber [29b35e] * configure.ac (modified) Set version to 1.4.7. - MoleCuilder library is now 14:0:0. - ... Thu, 21 Aug 2014 06:59:33 GMT Frederik Heber [a91710] * LinearAlgebra/src/LinearAlgebra/Makefile.am (modified) * LinearAlgebra/src/unittests/Makefile.am (modified) * configure.ac (modified) * m4/boost.m4 (modified) * m4/qwt.m4 (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/Action_impl_python.hpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/unittests/Makefile.am (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/SpecificFragmentController_ReceiveResultContainer_impl.hpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Summation/Containers/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Converter/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/UIElements/Views/Qt4/Plotting/Makefile.am (modified) * src/builder_init.cpp (modified) * src/documentation/install.dox (modified) * src/unittests/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) Merge branch 'Fixes_Ubuntu14_04' into stable Thu, 21 Aug 2014 06:59:06 GMT Frederik Heber [0c72e2] * src/documentation/install.dox (modified) DOCU: Updated documentation on Ubuntu 14.04. Thu, 21 Aug 2014 06:43:48 GMT Frederik Heber [07ecc5] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) FIX: FragmentationAutomationAction did not fail correctly with ... Thu, 21 Aug 2014 06:43:46 GMT Frederik Heber [748fc7] * src/Actions/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/builder_init.cpp (modified) * src/unittests/Makefile.am (modified) libMolecuilder is now a shared library. - linking error ... Wed, 20 Aug 2014 13:10:38 GMT Frederik Heber [4c9101] * configure.ac (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * src/UIElements/Views/Qt4/QDebugStream.hpp (modified) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at (modified) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at (modified) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at (modified) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at (modified) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at (modified) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order1.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order2.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order3.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order4.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order5.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order6.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order1.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order2.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order3.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order4.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order5.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order6.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order1.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order2.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order3.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order4.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order5.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order6.at (modified) Merge branch 'VariousFixes' into stable Wed, 20 Aug 2014 13:10:07 GMT Frederik Heber [fc3aff] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/AtomAction/RemoveAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (added) * src/Actions/FragmentationAction/StructuralOptimizationAction.def (added) * src/Actions/FragmentationAction/StructuralOptimizationAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (added) * src/Actions/MoleculeAction/ForceAnnealingAction.def (added) * src/Actions/MoleculeAction/ForceAnnealingAction.hpp (added) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/AtomicInfo.hpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/TesselPoint.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Dynamics/AtomicForceManipulator.hpp (added) * src/Dynamics/ForceAnnealing.hpp (added) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Makefile.am (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-testsuite-in-makefile.at (added) * tests/CodeChecks/testsuite.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo.conf (added) * tests/regression/Molecules/ForceAnnealing/post/test.conf (added) * tests/regression/Molecules/ForceAnnealing/pre/test.conf (added) * tests/regression/Molecules/ForceAnnealing/pre/test.forces (added) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (added) * tests/regression/Molecules/VerletIntegration/post/test-undo.conf (added) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) * tests/regression/Molecules/testsuite-molecules.at (modified) Merge branch 'StructuralOptimization' into stable Wed, 20 Aug 2014 13:09:40 GMT Frederik Heber [ee4f2d] * LinearAlgebra/src/LinearAlgebra/Makefile.am (modified) * LinearAlgebra/src/LinearAlgebra/Plane.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Vector.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Vector.hpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) * Makefile.am (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/CorrectBondDegreeAction.cpp (added) * src/Actions/GraphAction/CorrectBondDegreeAction.def (added) * src/Actions/GraphAction/CorrectBondDegreeAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Element/elements_db.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) * src/Fragmentation/Exporters/SaturatedBond.cpp (added) * src/Fragmentation/Exporters/SaturatedBond.hpp (added) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) * src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp (added) * src/Fragmentation/Exporters/SaturationDistanceMaximizer.hpp (added) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.cpp (added) * src/Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.hpp (added) * src/Fragmentation/Exporters/unittests/stubs/SaturatedBondStub.cpp (added) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (deleted) * src/Graph/BreadthFirstSearchAdd.hpp (deleted) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Tesselation/Makefile.am (added) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * tests/Calculations/testsuite-calculations-1_2-dimethoxyethane.at (modified) * tests/Calculations/testsuite-calculations-1_2-dimethylbenzene.at (modified) * tests/Calculations/testsuite-calculations-2-methylcyclohexanone.at (modified) * tests/Calculations/testsuite-calculations-N_N-dimethylacetamide.at (modified) * tests/Calculations/testsuite-calculations-anthracene.at (modified) * tests/Calculations/testsuite-calculations-benzene.at (modified) * tests/Calculations/testsuite-calculations-cholesterol.at (modified) * tests/Calculations/testsuite-calculations-coronene.at (modified) * tests/Calculations/testsuite-calculations-cycloheptane.at (modified) * tests/Calculations/testsuite-calculations-dimethyl_bromomalonate.at (modified) * tests/Calculations/testsuite-calculations-glucose.at (modified) * tests/Calculations/testsuite-calculations-heptan.at (modified) * tests/Calculations/testsuite-calculations-isoleucine.at (modified) * tests/Calculations/testsuite-calculations-naphthalene.at (modified) * tests/Calculations/testsuite-calculations-neohexane.at (modified) * tests/Calculations/testsuite-calculations-phenanthrene.at (modified) * tests/Calculations/testsuite-calculations-proline.at (modified) * tests/Calculations/testsuite-calculations-putrescine.at (modified) * tests/Calculations/testsuite-calculations-tartaric_acid.at (modified) * tests/Fragmentations/testsuite.at (modified) * tests/Makefile.am (modified) Merge branch 'EnhancingHydrogenSaturation' into stable Wed, 20 Aug 2014 12:59:22 GMT Frederik Heber [2cb77c] * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at (modified) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at (modified) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at (modified) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at (modified) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at (modified) * tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order1.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order2.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order3.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order4.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order5.at (modified) * tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order6.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order1.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order2.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order3.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order4.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order5.at (modified) * tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order6.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order1.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order2.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order3.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order4.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order5.at (modified) * tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order6.at (modified) FIX: Fragmentations tests used -I and not --correct-bonddegree in ... Wed, 20 Aug 2014 12:59:22 GMT Frederik Heber [83cc3e] * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) FIX: CyclicStructureAnalysis did not robustly detect all cycles. - ...